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  • Ocean dynamics  (51)
  • Genomics  (47)
  • American Meteorological Society  (51)
  • Oxford University Press  (47)
  • Annual Reviews
  • 1
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    Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations (2015)
    Oxford University Press
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    Publication Date: 2015-09-19
    Description: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
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    Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging (2015)
    Oxford University Press
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    Publication Date: 2015-08-29
    Description: Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage of this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled design (same individual at different time points) would overcome this problem but is often limited by the relatively small numbers of available paired samples and the statistics being used. To overcome these limitations, we have developed a new vector-based approach, termed three-component analysis, which incorporates temporal distance, signal intensity and variance into one single score for gene ranking and is combined with gene set enrichment analysis. We tested our method on a unique age-based sample set of human skin fibroblasts and combined genome-wide transcription, DNA methylation and histone methylation (H3K4me3 and H3K27me3) data. Importantly, our method can now for the first time demonstrate a clear age-dependent decrease in expression of genes coding for proteins involved in translation and ribosome function. Using analogies with data from lower organisms, we propose a model where age-dependent down-regulation of protein translation-related components contributes to extend human lifespan.
    Keywords: Genomics
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  • 3
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    Accurate read-based metagenome characterization using a hierarchical suite of unique signatures (2015)
    Oxford University Press
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    Publication Date: 2015-05-29
    Description: A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines G enomic O rigins T hrough T axonomic CHA llenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.
    Keywords: Genomics
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  • 4
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    An accurate clone-based haplotyping method by overlapping pool sequencing (2016)
    Oxford University Press
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    Publication Date: 2016-07-09
    Description: Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate.
    Keywords: Genomics
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  • 5
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    Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes: molecular insight into sex-specific processes and translational repression (2016)
    Oxford University Press
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    Publication Date: 2016-07-28
    Description: Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilization in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here, we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organization and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilization; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these ‘repressed transcripts’ have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies.
    Keywords: Genomics
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  • 6
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    Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse (2013)
    Oxford University Press
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    Publication Date: 2013-06-08
    Description: DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging owing to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of cytosine–guanine dinucleotide islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared with adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development.
    Keywords: Genomics
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  • 7
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    Multiplex sequencing of pooled mitochondrial genomes--a crucial step toward biodiversity analysis using mito-metagenomics (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species 〉15 kb and the remaining 〉10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.
    Keywords: Genomics
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  • 8
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    Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Chromatin modifiers and histone modifications are components of a chromatin-signaling network involved in transcription and its regulation. The interactions between chromatin modifiers and histone modifications are often unknown, are based on the analysis of few genes or are studied in vitro . Here, we apply computational methods to recover interactions between chromatin modifiers and histone modifications from genome-wide ChIP-Seq data. These interactions provide a high-confidence backbone of the chromatin-signaling network. Many recovered interactions have literature support; others provide hypotheses about yet unknown interactions. We experimentally verified two of these predicted interactions, leading to a link between H4K20me1 and members of the Polycomb Repressive Complexes 1 and 2. Our results suggest that our computationally derived interactions are likely to lead to novel biological insights required to establish the connectivity of the chromatin-signaling network involved in transcription and its regulation.
    Keywords: Genomics
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  • 9
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    Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform (2015)
    Oxford University Press
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    Publication Date: 2015-04-02
    Description: With read lengths of currently up to 2 x 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.
    Keywords: Genomics
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  • 10
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    iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data (2015)
    Oxford University Press
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    Publication Date: 2015-04-02
    Description: RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se , other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, iRNA-seq , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.
    Keywords: Genomics
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  • 11
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    Identification of large-scale genomic variation in cancer genomes using in silico reference models (2016)
    Oxford University Press
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    Publication Date: 2016-01-09
    Description: Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.
    Keywords: Genomics
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  • 12
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    Haploinsufficiency predictions without study bias (2015)
    Oxford University Press
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    Publication Date: 2015-08-29
    Description: Any given human individual carries multiple genetic variants that disrupt protein-coding genes, through structural variation, as well as nucleotide variants and indels. Predicting the phenotypic consequences of a gene disruption remains a significant challenge. Current approaches employ information from a range of biological networks to predict which human genes are haploinsufficient (meaning two copies are required for normal function) or essential (meaning at least one copy is required for viability). Using recently available study gene sets, we show that these approaches are strongly biased towards providing accurate predictions for well-studied genes. By contrast, we derive a haploinsufficiency score from a combination of unbiased large-scale high-throughput datasets, including gene co-expression and genetic variation in over 6000 human exomes. Our approach provides a haploinsufficiency prediction for over twice as many genes currently unassociated with papers listed in Pubmed as three commonly-used approaches, and outperforms these approaches for predicting haploinsufficiency for less-studied genes. We also show that fine-tuning the predictor on a set of well-studied ‘gold standard’ haploinsufficient genes does not improve the prediction for less-studied genes. This new score can readily be used to prioritize gene disruptions resulting from any genetic variant, including copy number variants, indels and single-nucleotide variants.
    Keywords: Genomics
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  • 13
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    Robust meta-analysis of gene expression using the elastic net (2015)
    Oxford University Press
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    Publication Date: 2015-07-12
    Description: Meta-analysis of gene expression has enabled numerous insights into biological systems, but current methods have several limitations. We developed a method to perform a meta-analysis using the elastic net, a powerful and versatile approach for classification and regression. To demonstrate the utility of our method, we conducted a meta-analysis of lung cancer gene expression based on publicly available data. Using 629 samples from five data sets, we trained a multinomial classifier to distinguish between four lung cancer subtypes. Our meta-analysis-derived classifier included 58 genes and achieved 91% accuracy on leave-one-study-out cross-validation and on three independent data sets. Our method makes meta-analysis of gene expression more systematic and expands the range of questions that a meta-analysis can be used to address. As the amount of publicly available gene expression data continues to grow, our method will be an effective tool to help distill these data into knowledge.
    Keywords: Genomics
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  • 14
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    Jointly characterizing epigenetic dynamics across multiple human cell types (2016)
    Oxford University Press
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    Publication Date: 2016-08-20
    Description: Advanced sequencing technologies have generated a plethora of data for many chromatin marks in multiple tissues and cell types, yet there is lack of a generalized tool for optimal utility of those data. A major challenge is to quantitatively model the epigenetic dynamics across both the genome and many cell types for understanding their impacts on differential gene regulation and disease. We introduce IDEAS, an i ntegrative and d iscriminative e pigenome a nnotation s ystem, for jointly characterizing epigenetic landscapes in many cell types and detecting differential regulatory regions. A key distinction between our method and existing state-of-the-art algorithms is that IDEAS integrates epigenomes of many cell types simultaneously in a way that preserves the position-dependent and cell type-specific information at fine scales, thereby greatly improving segmentation accuracy and producing comparable annotations across cell types.
    Keywords: Genomics
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  • 15
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    Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli (2016)
    Oxford University Press
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    Publication Date: 2016-09-03
    Description: A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 x 10 –4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 x 10 –5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS 1 , IS 2 , IS 5 and IS 186 . Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS 186 target-sites, 5'-GGGG(N6/N7)CCCC-3'. We also detected 48 long deletions not involving IS elements.
    Keywords: Genomics
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  • 16
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    Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles (2015)
    Oxford University Press
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    Publication Date: 2015-04-21
    Description: Extensive and multi-dimensional data sets generated from recent cancer omics profiling projects have presented new challenges and opportunities for unraveling the complexity of cancer genome landscapes. In particular, distinguishing the unique complement of genes that drive tumorigenesis in each patient from a sea of passenger mutations is necessary for translating the full benefit of cancer genome sequencing into the clinic. We address this need by presenting a data integration framework (OncoIMPACT) to nominate patient-specific driver genes based on their phenotypic impact. Extensive in silico and in vitro validation helped establish OncoIMPACT's robustness, improved precision over competing approaches and verifiable patient and cell line specific predictions (2/2 and 6/7 true positives and negatives, respectively). In particular, we computationally predicted and experimentally validated the gene TRIM24 as a putative novel amplified driver in a melanoma patient. Applying OncoIMPACT to more than 1000 tumor samples, we generated patient-specific driver gene lists in five different cancer types to identify modes of synergistic action. We also provide the first demonstration that computationally derived driver mutation signatures can be overall superior to single gene and gene expression based signatures in enabling patient stratification and prognostication. Source code and executables for OncoIMPACT are freely available from http://sourceforge.net/projects/oncoimpact .
    Keywords: Genomics
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  • 17
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    ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion (2015)
    Oxford University Press
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    Publication Date: 2015-05-20
    Description: Analysis of rewired upstream subnetworks impacting downstream differential gene expression aids the delineation of evolving molecular mechanisms. Cumulative statistics based on conventional differential correlation are limited for subnetwork rewiring analysis since rewiring is not necessarily equivalent to change in correlation coefficients. Here we present a computational method ChiNet to quantify subnetwork rewiring by statistical heterogeneity that enables detection of potential genotype changes causing altered transcription regulation in evolving organisms. Given a differentially expressed downstream gene set, ChiNet backtracks a rewired upstream subnetwork from a super-network including gene interactions known to occur under various molecular contexts. We benchmarked ChiNet for its high accuracy in distinguishing rewired artificial subnetworks, in silico yeast transcription-metabolic subnetworks, and rewired transcription subnetworks for Candida albicans versus Saccharomyces cerevisiae , against two differential-correlation based subnetwork rewiring approaches. Then, using transcriptome data from tolerant S. cerevisiae strain NRRL Y-50049 and a wild-type intolerant strain, ChiNet identified 44 metabolic pathways affected by rewired transcription subnetworks anchored to major adaptively activated transcription factor genes YAP1 , RPN4 , SFP1 and ROX1 , in response to toxic chemical challenges involved in lignocellulose-to-biofuels conversion. These findings support the use of ChiNet in rewiring analysis of subnetworks where differential interaction patterns resulting from divergent nonlinear dynamics abound.
    Keywords: Genomics
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  • 18
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    Assembly constraints drive co-evolution among ribosomal constituents (2015)
    Oxford University Press
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    Publication Date: 2015-06-24
    Description: Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein–RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein–rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a ‘proof of concept’ that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites.
    Keywords: Genomics
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  • 19
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    Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins (2015)
    Oxford University Press
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    Publication Date: 2015-02-18
    Description: The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates’ recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins , implemented in Python and C and supported on Linux and Mac OS X.
    Keywords: Genomics
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  • 20
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    BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers (2015)
    Oxford University Press
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    Publication Date: 2015-02-18
    Description: Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for ‘targeted’ resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a ‘kmer’ strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings.
    Keywords: Genomics
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  • 21
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    miRVaS: a tool to predict the impact of genetic variants on miRNAs (2016)
    Oxford University Press
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    Publication Date: 2016-02-20
    Description: Genetic variants in or near miRNA genes can have profound effects on miRNA expression and targeting. As user-friendly software for the impact prediction of miRNA variants on a large scale is still lacking, we created a tool called miRVaS. miRVaS automates this prediction by annotating the location of the variant relative to functional regions within the miRNA hairpin (seed, mature, loop, hairpin arm, flanks) and by annotating all predicted structural changes within the miRNA due to the variant. In addition, the tool defines the most important region that is predicted to have structural changes and calculates a conservation score that is indicative of the reliability of the structure prediction. The output is presented in a tab-separated file, which enables fast screening, and in an html file, which allows visual comparison between wild-type and variant structures. All separate images are provided for downstream use. Finally, we tested two different approaches on a small test set of published functionally validated genetic variants for their capacity to predict the impact of variants on miRNA expression.
    Keywords: Genomics
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  • 22
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    NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision (2016)
    Oxford University Press
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    Publication Date: 2016-02-20
    Description: Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts ( trans -spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (‘NCLscan’), which utilized a stepwise alignment strategy to almost completely eliminate false calls (〉98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans -spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans -spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
    Keywords: Genomics
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    Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data (2015)
    Oxford University Press
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    Publication Date: 2015-12-02
    Description: Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.
    Keywords: Genomics
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    HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-07
    Description: Identity by descent (IBD) can be reliably detected for long shared DNA segments, which are found in related individuals. However, many studies contain cohorts of unrelated individuals that share only short IBD segments. New sequencing technologies facilitate identification of short IBD segments through rare variants, which convey more information on IBD than common variants. Current IBD detection methods, however, are not designed to use rare variants for the detection of short IBD segments. Short IBD segments reveal genetic structures at high resolution. Therefore, they can help to improve imputation and phasing, to increase genotyping accuracy for low-coverage sequencing and to increase the power of association studies. Since short IBD segments are further assumed to be old, they can shed light on the evolutionary history of humans. We propose HapFABIA, a computational method that applies biclustering to identify very short IBD segments characterized by rare variants. HapFABIA is designed to detect short IBD segments in genotype data that were obtained from next-generation sequencing, but can also be applied to DNA microarray data. Especially in next-generation sequencing data, HapFABIA exploits rare variants for IBD detection. HapFABIA significantly outperformed competing algorithms at detecting short IBD segments on artificial and simulated data with rare variants. HapFABIA identified 160 588 different short IBD segments characterized by rare variants with a median length of 23 kb (mean 24 kb) in data for chromosome 1 of the 1000 Genomes Project. These short IBD segments contain 752 000 single nucleotide variants (SNVs), which account for 39% of the rare variants and 23.5% of all variants. The vast majority—152 000 IBD segments—are shared by Africans, while only 19 000 and 11 000 are shared by Europeans and Asians, respectively. IBD segments that match the Denisova or the Neandertal genome are found significantly more often in Asians and Europeans but also, in some cases exclusively, in Africans. The lengths of IBD segments and their sharing between continental populations indicate that many short IBD segments from chromosome 1 existed before humans migrated out of Africa. Thus, rare variants that tag these short IBD segments predate human migration from Africa. The software package HapFABIA is available from Bioconductor. All data sets, result files and programs for data simulation, preprocessing and evaluation are supplied at http://www.bioinf.jku.at/research/short-IBD .
    Keywords: Genomics
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    Comprehensive analysis of the functional microRNA-mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression (2013)
    Oxford University Press
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    Publication Date: 2013-12-07
    Description: Glioma is the most common and fatal primary brain tumour with poor prognosis; however, the functional roles of miRNAs in glioma malignant progression are insufficiently understood. Here, we used an integrated approach to identify miRNA functional targets during glioma malignant progression by combining the paired expression profiles of miRNAs and mRNAs across 160 Chinese glioma patients, and further constructed the functional miRNA–mRNA regulatory network. As a result, most tumour-suppressive miRNAs in glioma progression were newly discovered, whose functions were widely involved in gliomagenesis. Moreover, three miRNA signatures, with different combinations of hub miRNAs (regulations≥30) were constructed, which could independently predict the survival of patients with all gliomas, high-grade glioma and glioblastoma. Our network-based method increased the ability to identify the prognostic biomarkers, when compared with the traditional method and random conditions. Hsa-miR-524-5p and hsa-miR-628-5p, shared by these three signatures, acted as protective factors and their expression decreased gradually during glioma progression. Functional analysis of these miRNA signatures highlighted their critical roles in cell cycle and cell proliferation in glioblastoma malignant progression, especially hsa-miR-524-5p and hsa-miR-628-5p exhibited dominant regulatory activities. Therefore, network-based biomarkers are expected to be more effective and provide deep insights into the molecular mechanism of glioma malignant progression.
    Keywords: Genomics
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    Interaction-based discovery of functionally important genes in cancers (2014)
    Oxford University Press
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    Publication Date: 2014-02-11
    Description: A major challenge in cancer genomics is uncovering genes with an active role in tumorigenesis from a potentially large pool of mutated genes across patient samples. Here we focus on the interactions that proteins make with nucleic acids, small molecules, ions and peptides, and show that residues within proteins that are involved in these interactions are more frequently affected by mutations observed in large-scale cancer genomic data than are other residues. We leverage this observation to predict genes that play a functionally important role in cancers by introducing a computational pipeline ( http://canbind.princeton.edu ) for mapping large-scale cancer exome data across patients onto protein structures, and automatically extracting proteins with an enriched number of mutations affecting their nucleic acid, small molecule, ion or peptide binding sites. Using this computational approach, we show that many previously known genes implicated in cancers are enriched in mutations within the binding sites of their encoded proteins. By focusing on functionally relevant portions of proteins—specifically those known to be involved in molecular interactions—our approach is particularly well suited to detect infrequent mutations that may nonetheless be important in cancer, and should aid in expanding our functional understanding of the genomic landscape of cancer.
    Keywords: Genomics
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    Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis (2014)
    Oxford University Press
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    Publication Date: 2014-04-03
    Description: Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea ( Arabidopsis petraea subsp. umbrosa ), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica . The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated ( r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental responses.
    Keywords: Genomics
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    EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization (2015)
    Oxford University Press
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    Publication Date: 2015-03-14
    Description: Methods to interpret personal genome sequences are increasingly required. Here, we report a novel framework (EvoTol) to identify disease-causing genes using patient sequence data from within protein coding-regions. EvoTol quantifies a gene's intolerance to mutation using evolutionary conservation of protein sequences and can incorporate tissue-specific gene expression data. We apply this framework to the analysis of whole-exome sequence data in epilepsy and congenital heart disease, and demonstrate EvoTol's ability to identify known disease-causing genes is unmatched by competing methods. Application of EvoTol to the human interactome revealed networks enriched for genes intolerant to protein sequence variation, informing novel polygenic contributions to human disease.
    Keywords: Genomics
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    Base-resolution methylation patterns accurately predict transcription factor bindings in vivo (2015)
    Oxford University Press
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    Publication Date: 2015-03-14
    Description: Detecting in vivo transcription factor (TF) binding is important for understanding gene regulatory circuitries. ChIP-seq is a powerful technique to empirically define TF binding in vivo . However, the multitude of distinct TFs makes genome-wide profiling for them all labor-intensive and costly. Algorithms for in silico prediction of TF binding have been developed, based mostly on histone modification or DNase I hypersensitivity data in conjunction with DNA motif and other genomic features. However, technical limitations of these methods prevent them from being applied broadly, especially in clinical settings. We conducted a comprehensive survey involving multiple cell lines, TFs, and methylation types and found that there are intimate relationships between TF binding and methylation level changes around the binding sites. Exploiting the connection between DNA methylation and TF binding, we proposed a novel supervised learning approach to predict TF–DNA interaction using data from base-resolution whole-genome methylation sequencing experiments. We devised beta-binomial models to characterize methylation data around TF binding sites and the background. Along with other static genomic features, we adopted a random forest framework to predict TF–DNA interaction. After conducting comprehensive tests, we saw that the proposed method accurately predicts TF binding and performs favorably versus competing methods.
    Keywords: Genomics
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    Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs (2012)
    Oxford University Press
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    Publication Date: 2012-10-10
    Description: Enriching target sequences in sequencing libraries via capture hybridization to bait/probes is an efficient means of leveraging the capabilities of next-generation sequencing for obtaining sequence data from target regions of interest. However, homologous sequences from non-target regions may also be enriched by such methods. Here we investigate the fidelity of capture enrichment for complete mitochondrial DNA (mtDNA) genome sequencing by analyzing sequence data for nuclear copies of mtDNA (NUMTs). Using capture-enriched sequencing data from a mitochondria-free cell line and the parental cell line, and from samples previously sequenced from long-range PCR products, we demonstrate that NUMT alleles are indeed present in capture-enriched sequence data, but at low enough levels to not influence calling the authentic mtDNA genome sequence. However, distinguishing NUMT alleles from true low-level mutations (e.g. heteroplasmy) is more challenging. We develop here a computational method to distinguish NUMT alleles from heteroplasmies, using sequence data from artificial mixtures to optimize the method.
    Keywords: Genomics
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    FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs (2012)
    Oxford University Press
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    Publication Date: 2012-10-10
    Description: Single nucleotide polymorphisms (SNPs) are increasingly used to tag genetic loci associated with phenotypes such as risk of complex diseases. Technically, this is done genome-wide without prior restriction or knowledge of biological feasibility in scans referred to as genome-wide association studies (GWAS). Depending on the linkage disequilibrium (LD) structure at a particular locus, such tagSNPs may be surrogates for many thousands of other SNPs, and it is difficult to distinguish those that may play a functional role in the phenotype from those simply genetically linked. Because a large proportion of tagSNPs have been identified within non-coding regions of the genome, distinguishing functional from non-functional SNPs has been an even greater challenge. A strategy was recently proposed that prioritizes surrogate SNPs based on non-coding chromatin and epigenomic mapping techniques that have become feasible with the advent of massively parallel sequencing. Here, we introduce an R/Bioconductor software package that enables the identification of candidate functional SNPs by integrating information from tagSNP locations, lists of linked SNPs from the 1000 genomes project and locations of chromatin features which may have functional significance. Availability: FunciSNP is available from Bioconductor (bioconductor.org).
    Keywords: Genomics
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    A phylogenomics approach for selecting robust sets of phylogenetic markers (2014)
    Oxford University Press
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    Publication Date: 2014-04-15
    Description: Reconstructing the evolutionary relationships of species is a major goal in biology. Despite the increasing number of completely sequenced genomes, a large number of phylogenetic projects rely on targeted sequencing and analysis of a relatively small sample of marker genes. The selection of these phylogenetic markers should ideally be based on accurate predictions of their combined, rather than individual, potential to accurately resolve the phylogeny of interest. Here we present and validate a new phylogenomics strategy to efficiently select a minimal set of stable markers able to reconstruct the underlying species phylogeny. In contrast to previous approaches, our methodology does not only rely on the ability of individual genes to reconstruct a known phylogeny, but it also explores the combined power of sets of concatenated genes to accurately infer phylogenetic relationships of species not previously analyzed. We applied our approach to two broad sets of cyanobacterial and ascomycetous fungal species, and provide two minimal sets of six and four genes, respectively, necessary to fully resolve the target phylogenies. This approach paves the way for the informed selection of phylogenetic markers in the effort of reconstructing the tree of life.
    Keywords: Genomics
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    Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system (2016)
    Oxford University Press
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    Publication Date: 2016-05-20
    Description: Visualization of chromosomal dynamics is important for understanding many fundamental intra-nuclear processes. Efficient and reliable live-cell multicolor labeling of chromosomal loci can realize this goal. However, the current methods are constrained mainly by insufficient labeling throughput, efficiency, flexibility as well as photostability. Here we have developed a new approach to realize dual-color chromosomal loci imaging based on a modified single-guide RNA (sgRNA) of the CRISPR/Cas9 system. The modification of sgRNA was optimized by structure-guided engineering of the original sgRNA, consisting of RNA aptamer insertions that bind fluorescent protein-tagged effectors. By labeling and tracking telomeres, centromeres and genomic loci, we demonstrate that the new approach is easy to implement and enables robust dual-color imaging of genomic elements. Importantly, our data also indicate that the fast exchange rate of RNA aptamer binding effectors makes our sgRNA-based labeling method much more tolerant to photobleaching than the Cas9-based labeling method. This is crucial for continuous, long-term tracking of chromosomal dynamics. Lastly, as our method is complementary to other live-cell genomic labeling systems, it is therefore possible to combine them into a plentiful palette for the study of native chromatin organization and genome ultrastructure dynamics in living cells.
    Keywords: Genomics
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    A robust PCR primer design platform applied to the detection of Acidobacteria Group 1 in soil (2012)
    Oxford University Press
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    Publication Date: 2012-06-28
    Description: Environmental biosurveillance and microbial ecology studies use PCR-based assays to detect and quantify microbial taxa and gene sequences within a complex background of microorganisms. However, the fragmentary nature and growing quantity of DNA-sequence data make group-specific assay design challenging. We solved this problem by developing a software platform that enables PCR-assay design at an unprecedented scale. As a demonstration, we developed quantitative PCR assays for a globally widespread, ecologically important bacterial group in soil, Acidobacteria Group 1. A total of 33 684 Acidobacteria 16S rRNA gene sequences were used for assay design. Following 1 week of computation on a 376-core cluster, 83 assays were obtained. We validated the specificity of the top three assays, collectively predicted to detect 42% of the Acidobacteria Group 1 sequences, by PCR amplification and sequencing of DNA from soil. Based on previous analyses of 16S rRNA gene sequencing, Acidobacteria Group 1 species were expected to decrease in response to elevated atmospheric CO 2 . Quantitative PCR results, using the Acidobacteria Group 1-specific PCR assays, confirmed the expected decrease and provided higher statistical confidence than the 16S rRNA gene-sequencing data. These results demonstrate a powerful capacity to address previously intractable assay design challenges.
    Keywords: Genomics
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    Shape-based alignment of genomic landscapes in multi-scale resolution (2012)
    Oxford University Press
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    Publication Date: 2012-08-08
    Description: Due to dramatic advances in DNA technology, quantitative measures of annotation data can now be obtained in continuous coordinates across the entire genome, allowing various heterogeneous ‘genomic landscapes’ to emerge. Although much effort has been devoted to comparing DNA sequences, not much attention has been given to comparing these large quantities of data comprehensively. In this article, we introduce a method for rapidly detecting local regions that show high correlations between genomic landscapes. We overcame the size problem for genome-wide data by converting the data into series of symbols and then carrying out sequence alignment. We also decomposed the oscillation of the landscape data into different frequency bands before analysis, since the real genomic landscape is a mixture of embedded and confounded biological processes working at different scales in the cell nucleus. To verify the usefulness and generality of our method, we applied our approach to well investigated landscapes from the human genome, including several histone modifications. Furthermore, by applying our method to over 20 genomic landscapes in human and 12 in mouse, we found that DNA replication timing and the density of Alu insertions are highly correlated genome-wide in both species, even though the Alu elements have amplified independently in the two genomes. To our knowledge, this is the first method to align genomic landscapes at multiple scales according to their shape.
    Keywords: Genomics
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    Turning gold into 'junk': transposable elements utilize central proteins of cellular networks (2013)
    Oxford University Press
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    Publication Date: 2013-03-13
    Description: The numerous discovered cases of domesticated transposable element (TE) proteins led to the recognition that TEs are a significant source of evolutionary innovation. However, much less is known about the reverse process, whether and to what degree the evolution of TEs is influenced by the genome of their hosts. We addressed this issue by searching for cases of incorporation of host genes into the sequence of TEs and examined the systems-level properties of these genes using the Saccharomyces cerevisiae and Drosophila melanogaster genomes. We identified 51 cases where the evolutionary scenario was the incorporation of a host gene fragment into a TE consensus sequence, and we show that both the yeast and fly homologues of the incorporated protein sequences have central positions in the cellular networks. An analysis of selective pressure (Ka/Ks ratio) detected significant selection in 37% of the cases. Recent research on retrovirus-host interactions shows that virus proteins preferentially target hubs of the host interaction networks enabling them to take over the host cell using only a few proteins. We propose that TEs face a similar evolutionary pressure to evolve proteins with high interacting capacities and take some of the necessary protein domains directly from their hosts.
    Keywords: Genomics
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    Elimination of unaltered DNA in mixed clinical samples via nuclease-assisted minor-allele enrichment (2016)
    Oxford University Press
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    Publication Date: 2016-11-01
    Description: Presence of excess unaltered, wild-type (WT) DNA providing no information of biological or clinical value often masks rare alterations containing diagnostic or therapeutic clues in cancer, prenatal diagnosis, infectious diseases or organ transplantation. With the surge of high-throughput technologies there is a growing demand for removing unaltered DNA over large pools-of-sequences. Here we present nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO), a single-step approach with broad genome coverage that can remove WT-DNA from numerous sequences simultaneously, prior to genomic analysis. NaME-PrO employs a double-strand-DNA-specific nuclease and overlapping oligonucleotide-probes interrogating WT-DNA targets and guiding nuclease digestion to these sites. Mutation-containing DNA creates probe-DNA mismatches that inhibit digestion, thus subsequent DNA-amplification magnifies DNA-alterations at all selected targets. We demonstrate several-hundred-fold mutation enrichment in diverse human samples on multiple clinically relevant targets including tumor samples and circulating DNA in 50-plex reactions. Enrichment enables routine mutation detection at 0.01% abundance while by adjusting conditions it is possible to sequence mutations down to 0.00003% abundance, or to scan tumor-suppressor genes for rare mutations. NaME-PrO introduces a simple and highly parallel process to remove un-informative DNA sequences and unmask clinically and biologically useful alterations.
    Keywords: Genomics
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    Recurrent transcriptional clusters in the genome of mouse pluripotent stem cells (2012)
    Oxford University Press
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    Publication Date: 2012-10-24
    Description: A number of studies have shown that transcriptome analysis in terms of chromosomal location can reveal regions of non-random transcriptional activity within the genome. Genomic clusters of differentially expressed genes can identify genomic patterns of structural organization, underlying copy number variations or long-range epigenetic regulation such as X-chromosome inactivation. Here we apply an integrative bioinformatics analysis to a collection of 315 freely available mouse pluripotent stem cell samples to discover transcriptional clusters in the genome. We show that over half of the analysed samples (56.83%) carry whole or partial-chromosome spanning clusters which recur in genomic regions previously implicated in chromosomal imbalances. Strikingly, we found that the presence of such large-clusters is linked to the differential expression of a limited number of genes, common to all samples carrying clusters irrespectively of the chromosome where the cluster is found. We have used these genes to train and test classification models that can predict samples that carry large-scale clusters on any chromosome with over 90% accuracy. Our findings suggest that there is a common downstream activation in these cells that affects a limited number of nodes. We propose that this effect is linked to selective advantage and identify potential driver genes.
    Keywords: Genomics
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    HapZipper: sharing HapMap populations just got easier (2012)
    Oxford University Press
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    Publication Date: 2012-11-04
    Description: The rapidly growing amount of genomic sequence data being generated and made publicly available necessitate the development of new data storage and archiving methods. The vast amount of data being shared and manipulated also create new challenges for network resources. Thus, developing advanced data compression techniques is becoming an integral part of data production and analysis. The HapMap project is one of the largest public resources of human single-nucleotide polymorphisms (SNPs), characterizing over 3 million SNPs genotyped in over 1000 individuals. The standard format and biological properties of HapMap data suggest that a dedicated genetic compression method can outperform generic compression tools. We propose a compression methodology for genetic data by introducing H ap Z ipper , a lossless compression tool tailored to compress HapMap data beyond benchmarks defined by generic tools such as gzip , bzip2 and lzma . We demonstrate the usefulness of H ap Z ipper by compressing HapMap 3 populations to 〈5% of their original sizes. H ap Z ipper is freely downloadable from https://bitbucket.org/pchanda/hapzipper/downloads/HapZipper.tar.bz2 .
    Keywords: Genomics
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    Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features (2012)
    Oxford University Press
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    Publication Date: 2012-11-04
    Description: Spliced alignment plays a central role in the precise identification of eukaryotic gene structures. Even though many spliced alignment programs have been developed, recent rapid progress in DNA sequencing technologies demands further improvements in software tools. Benchmarking algorithms under various conditions is an indispensable task for the development of better software; however, there is a dire lack of appropriate datasets usable for benchmarking spliced alignment programs. In this study, we have constructed two types of datasets: simulated sequence datasets and actual cross-species datasets. The datasets are designed to correspond to various real situations, i.e. divergent eukaryotic species, different types of reference sequences, and the wide divergence between query and target sequences. In addition, we have developed an extended version of our program Spaln , which incorporates two additional features to the scoring scheme of the original version, and examined this extended version, Spaln2, together with the original Spaln and other representative aligners based on our benchmark datasets. Although the effects of the modifications are not individually striking, Spaln2 is consistently most accurate and reasonably fast in most practical cases, especially for plants and fungi and for increasingly divergent pairs of target and query sequences.
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    Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways (2013)
    Oxford University Press
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    Publication Date: 2013-05-04
    Description: Various ‘omics’ technologies, including microarrays and gas chromatography mass spectrometry, can be used to identify hundreds of interesting genes, proteins and metabolites, such as differential genes, proteins and metabolites associated with diseases. Identifying metabolic pathways has become an invaluable aid to understanding the genes and metabolites associated with studying conditions. However, the classical methods used to identify pathways fail to accurately consider joint power of interesting gene/metabolite and the key regions impacted by them within metabolic pathways. In this study, we propose a powerful analytical method referred to as Subpathway-GM for the identification of metabolic subpathways. This provides a more accurate level of pathway analysis by integrating information from genes and metabolites, and their positions and cascade regions within the given pathway. We analyzed two colorectal cancer and one metastatic prostate cancer data sets and demonstrated that Subpathway-GM was able to identify disease-relevant subpathways whose corresponding entire pathways might be ignored using classical entire pathway identification methods. Further analysis indicated that the power of a joint genes/metabolites and subpathway strategy based on their topologies may play a key role in reliably recalling disease-relevant subpathways and finding novel subpathways.
    Keywords: Genomics
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    Combination of fluorescence color and melting temperature as a two-dimensional label for homogeneous multiplex PCR detection (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-14
    Description: Multiplex analytical systems that allow detection of multiple nucleic acid targets in one assay can provide rapid characterization of a sample while still saving cost and resources. However, few systems have proven to offer a solution for mid-plex (e.g. 10- to 50-plex) analysis that is high throughput and cost effective. Here we describe the combined use of fluorescence color and melting temperature (T m ) as a virtual 2D label that enables homogenous detection of one order of magnitude more targets than current strategies on real-time polymerase chain reaction platform. The target was first hybridized with a pair of ligation oligonucleotides, one of which harbored an artificial sequence that had a unique T m when hybridized with a reporter fluorogenic probe. The ligated products were then amplified by a universal primer pair and denatured by a melting curve analysis procedure. The targets were identified by their respective T m values in the corresponding fluorescence detection channels. The proof-of-principle of this approach was validated by genotyping 15 high-risk human papillomaviruses and 48 human single-nucleotide polymorphisms. The robustness of this method was demonstrated by analyzing a large number of clinical samples in both cases. The combined merits of multiplexity, flexibility and simplicity should make this approach suitable for a variety of applications.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Analysis of the epigenetic status of telomeres by using ChIP-seq data (2012)
    Oxford University Press
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    Publication Date: 2012-11-25
    Description: The chromatin structure of eukaryotic telomeres plays an essential role in telomere functions. However, their study might be impaired by the presence of interstitial telomeric sequences (ITSs), which have a widespread distribution in different model systems. We have developed a simple approach to study the chromatin structure of Arabidopsis telomeres independently of ITSs by analyzing ChIP-seq data. This approach could be used to study the chromatin structure of telomeres in some other eukaryotes. The analysis of ChIP-seq experiments revealed that Arabidopsis telomeres have higher density of histone H3 than centromeres, which might reflects their short nucleosomal organization. These experiments also revealed that Arabidopsis telomeres have lower levels of heterochromatic marks than centromeres (H3K9 Me2 and H3K27 Me ), higher levels of some euchromatic marks (H3K4 Me2 and H3K9Ac) and similar or lower levels of other euchromatic marks (H3K4 Me3 , H3K36 Me2 , H3K36 Me3 and H3K18Ac). Interestingly, the ChIP-seq experiments also revealed that Arabidopsis telomeres exhibit high levels of H3K27 Me3 , a repressive mark that associates with many euchromatic genes. The epigenetic profile of Arabidopsis telomeres is closely related to the previously defined chromatin state 2. This chromatin state is found in 23% of Arabidopsis genes, many of which are repressed or lowly expressed. At least, in part, this scenario is similar in rice.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Allele-specific copy-number discovery from whole-genome and whole-exome sequencing (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-18
    Description: Copy-number variants (CNVs) are a major form of genetic variation and a risk factor for various human diseases, so it is crucial to accurately detect and characterize them. It is conceivable that allele-specific reads from high-throughput sequencing data could be leveraged to both enhance CNV detection and produce allele-specific copy number (ASCN) calls. Although statistical methods have been developed to detect CNVs using whole-genome sequence (WGS) and/or whole-exome sequence (WES) data, information from allele-specific read counts has not yet been adequately exploited. In this paper, we develop an integrated method, called AS-GENSENG, which incorporates allele-specific read counts in CNV detection and estimates ASCN using either WGS or WES data. To evaluate the performance of AS-GENSENG, we conducted extensive simulations, generated empirical data using existing WGS and WES data sets and validated predicted CNVs using an independent methodology. We conclude that AS-GENSENG not only predicts accurate ASCN calls but also improves the accuracy of total copy number calls, owing to its unique ability to exploit information from both total and allele-specific read counts while accounting for various experimental biases in sequence data. Our novel, user-friendly and computationally efficient method and a complete analytic protocol is freely available at https://sourceforge.net/projects/asgenseng/ .
    Keywords: Genomics
    Print ISSN: 0305-1048
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    Topics: Biology
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    Microbial species delineation using whole genome sequences (2015)
    Oxford University Press
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    Publication Date: 2015-08-18
    Description: Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required.
    Keywords: Genomics
    Print ISSN: 0305-1048
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    Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics (2015)
    Oxford University Press
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    Publication Date: 2015-08-18
    Description: Classically or alternatively activated macrophages (M1 and M2, respectively) play distinct and important roles for microbiocidal activity, regulation of inflammation and tissue homeostasis. Despite this, their transcriptional regulatory dynamics are poorly understood. Using promoter-level expression profiling by non-biased deepCAGE we have studied the transcriptional dynamics of classically and alternatively activated macrophages. Transcription factor (TF) binding motif activity analysis revealed four motifs, NFKB1_REL_RELA, IRF1,2, IRF7 and TBP that are commonly activated but have distinct activity dynamics in M1 and M2 activation. We observe matching changes in the expression profiles of the corresponding TFs and show that only a restricted set of TFs change expression. There is an overall drastic and transient up-regulation in M1 and a weaker and more sustainable up-regulation in M2. Novel TFs, such as Thap6, Maff , (M1) and Hivep1, Nfil3, Prdm1 , (M2) among others, were suggested to be involved in the activation processes. Additionally, 52 (M1) and 67 (M2) novel differentially expressed genes and, for the first time, several differentially expressed long non-coding RNA (lncRNA) transcriptome markers were identified. In conclusion, the finding of novel motifs, TFs and protein-coding and lncRNA genes is an important step forward to fully understand the transcriptional machinery of macrophage activation.
    Keywords: Genomics
    Print ISSN: 0305-1048
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    RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2 (2016)
    Oxford University Press
    Details
    Publication Date: 2016-12-01
    Description: The RAG1/RAG2 endonuclease initiates V(D)J recombination at antigen receptor loci but also binds to thousands of places outside of these loci. RAG2 localizes directly to lysine 4 trimethylated histone 3 (H3K4me3) through a plant homeodomain (PHD) finger. The relative contribution of RAG2-dependent and RAG1-intrinsic mechanisms in determining RAG1 binding patterns is not known. Through analysis of deep RAG1 ChIP-seq data, we provide a quantitative description of the forces underlying genome-wide targeting of RAG1. Surprisingly, sequence-specific DNA binding contributes minimally to RAG1 targeting outside of antigen receptor loci. Instead, RAG1 binding is driven by two distinct modes of interaction with chromatin: the first is driven by H3K4me3, promoter-focused and dependent on the RAG2 PHD, and the second is defined by H3K27Ac, enhancer-focused and dependent on ‘non-core’ portions of RAG1. Based on this and additional chromatin and genomic features, we formulated a predictive model of RAG1 targeting to the genome. RAG1 binding sites predicted by our model correlate well with observed patterns of RAG1-mediated breaks in human pro-B acute lymphoblastic leukemia. Overall, this study provides an integrative model for RAG1 genome-wide binding and off-target activity and reveals a novel role for the RAG1 non-core region in RAG1 targeting.
    Keywords: Genomics
    Print ISSN: 0305-1048
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    Topics: Biology
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    Mesoscale eddy-internal wave coupling. Part I : symmetry, wave capture, and results from the Mid-Ocean Dynamics Experiment (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2008. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 38 (2008): 2556-2574, doi:10.1175/2008JPO3666.1.
    Description: Vertical profiles of horizontal velocity obtained during the Mid-Ocean Dynamics Experiment (MODE) provided the first published estimates of the high vertical wavenumber structure of horizontal velocity. The data were interpreted as being representative of the background internal wave field, and thus, despite some evidence of excess downward energy propagation associated with coherent near-inertial features that was interpreted in terms of atmospheric generation, these data provided the basis for a revision to the Garrett and Munk spectral model. These data are reinterpreted through the lens of 30 years of research. Rather than representing the background wave field, atmospheric generation, or even near-inertial wave trapping, the coherent high wavenumber features are characteristic of internal wave capture in a mesoscale strain field. Wave capture represents a generalization of critical layer events for flows lacking the spatial symmetry inherent in a parallel shear flow or isolated vortex.
    Description: Salary support for this analysis was provided by Woods Hole Oceanographic Institution bridge support funds.
    Keywords: Eddies ; Ocean dynamics ; Internal waves ; Ocean variability
    Repository Name: Woods Hole Open Access Server
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    Dynamics in the deep Canada Basin, Arctic Ocean, inferred by thermistor chain time series (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 37 (2007): 1066–1076, doi:10.1175/JPO3032.1.
    Description: A 50-day time series of high-resolution temperature in the deepest layers of the Canada Basin in the Arctic Ocean indicates that the deep Canada Basin is a dynamically active environment, not the quiet, stable basin often assumed. Vertical motions at the near-inertial (tidal) frequency have amplitudes of 10– 20 m. These vertical displacements are surprisingly large considering the downward near-inertial internal wave energy flux typically observed in the Canada Basin. In addition to motion in the internal-wave frequency band, the measurements indicate distinctive subinertial temperature fluctuations, possibly due to intrusions of new water masses.
    Keywords: Arctic ; Ocean dynamics ; Ship observations
    Repository Name: Woods Hole Open Access Server
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    On the effective capacity of the dense-water reservoir for the Nordic Seas overflow : some effects of topography and wind stress (2013)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 418–431, doi:10.1175/JPO-D-12-087.1.
    Description: The overflow of the dense water mass across the Greenland–Scotland Ridge (GSR) from the Nordic Seas drives the Atlantic meridional overturning circulation (AMOC). The Nordic Seas is a large basin with an enormous reservoir capacity. The volume of the dense water above the GSR sill depth in the Nordic Seas, according to previous estimates, is sufficient to supply decades of overflow transport. This large capacity buffers overflow’s responses to atmospheric variations and prevents an abrupt shutdown of the AMOC. In this study, the authors use a numerical and an analytical model to show that the effective reservoir capacity of the Nordic Seas is actually much smaller than what was estimated previously. Basin-scale oceanic circulation is nearly geostrophic and its streamlines are basically the same as the isobaths. The vast majority of the dense water is stored inside closed geostrophic contours in the deep basin and thus is not freely available to the overflow. The positive wind stress curl in the Nordic Seas forces a convergence of the dense water toward the deep basin and makes the interior water even more removed from the overflow-feeding boundary current. Eddies generated by the baroclinic instability help transport the interior water mass to the boundary current. But in absence of a robust renewal of deep water, the boundary current weakens rapidly and the eddy-generating mechanism becomes less effective. This study indicates that the Nordic Seas has a relatively small capacity as a dense water reservoir and thus the overflow transport is sensitive to climate changes.
    Description: This study has been supported by National Science Foundation (OCE0927017,ARC1107412).
    Description: 2013-08-01
    Keywords: Bottom currents ; Drainage flow ; Meridional overturning circulation ; Ocean dynamics ; Potential vorticity ; Topographic effects
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    On eddy viscosity, energy cascades, and the horizontal resolution of gridded satellite altimeter products (2013)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 283–300, doi:10.1175/JPO-D-11-0240.1.
    Description: Motivated by the recent interest in ocean energetics, the widespread use of horizontal eddy viscosity in models, and the promise of high horizontal resolution data from the planned wide-swath satellite altimeter, this paper explores the impacts of horizontal eddy viscosity and horizontal grid resolution on geostrophic turbulence, with a particular focus on spectral kinetic energy fluxes Π(K) computed in the isotropic wavenumber (K) domain. The paper utilizes idealized two-layer quasigeostrophic (QG) models, realistic high-resolution ocean general circulation models, and present-generation gridded satellite altimeter data. Adding horizontal eddy viscosity to the QG model results in a forward cascade at smaller scales, in apparent agreement with results from present-generation altimetry. Eddy viscosity is taken to roughly represent coupling of mesoscale eddies to internal waves or to submesoscale eddies. Filtering the output of either the QG or realistic models before computing Π(K) also greatly increases the forward cascade. Such filtering mimics the smoothing inherent in the construction of present-generation gridded altimeter data. It is therefore difficult to say whether the forward cascades seen in present-generation altimeter data are due to real physics (represented here by eddy viscosity) or to insufficient horizontal resolution. The inverse cascade at larger scales remains in the models even after filtering, suggesting that its existence in the models and in altimeter data is robust. However, the magnitude of the inverse cascade is affected by filtering, suggesting that the wide-swath altimeter will allow a more accurate determination of the inverse cascade at larger scales as well as providing important constraints on smaller-scale dynamics.
    Description: BKA received support from Office of Naval Research Grant N00014-11-1-0487, National Science Foundation (NSF) Grants OCE-0924481 and OCE- 09607820, and University of Michigan startup funds. KLP acknowledges support from Woods Hole Oceanographic Institution bridge support funds. RBS acknowledges support from NSF grants OCE-0960834 and OCE-0851457, a contract with the National Oceanography Centre, Southampton, and a NASA subcontract to Boston University. JFS and JGR were supported by the projects ‘‘Global and remote littoral forcing in global ocean models’’ and ‘‘Agesotrophic vorticity dynamics of the ocean,’’ respectively, both sponsored by the Office of Naval Research under program element 601153N.
    Description: 2013-08-01
    Keywords: Eddies ; Nonlinear dynamics ; Ocean dynamics ; Satellite observations ; Ocean models
    Repository Name: Woods Hole Open Access Server
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    Multidecadal Indian Ocean variability linked to the Pacific and implications for preconditioning Indian Ocean dipole events (2017)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 30 (2017): 1739-1751, doi:10.1175/JCLI-D-16-0200.1.
    Description: The Indian Ocean has sustained robust surface warming in recent decades, but the role of multidecadal variability remains unclear. Using ocean model hindcasts, characteristics of low-frequency Indian Ocean temperature variations are explored. Simulated upper-ocean temperature changes across the Indian Ocean in the hindcast are consistent with those recorded in observational products and ocean reanalyses. Indian Ocean temperatures exhibit strong warming trends since the 1950s limited to the surface and south of 30°S, while extensive subsurface cooling occurs over much of the tropical Indian Ocean. Previous work focused on diagnosing causes of these long-term trends in the Indian Ocean over the second half of the twentieth century. Instead, the temporal evolution of Indian Ocean subsurface heat content is shown here to reveal distinct multidecadal variations associated with the Pacific decadal oscillation, and the long-term trends are thus interpreted to result from aliasing of the low-frequency variability. Transmission of the multidecadal signal occurs via an oceanic pathway through the Indonesian Throughflow and is manifest across the Indian Ocean centered along 12°S as westward-propagating Rossby waves modulating thermocline and subsurface heat content variations. Resulting low-frequency changes in the eastern Indian Ocean thermocline depth are associated with decadal variations in the frequency of Indian Ocean dipole (IOD) events, with positive IOD events unusually common in the 1960s and 1990s with a relatively shallow thermocline. In contrast, the deeper thermocline depth in the 1970s and 1980s is associated with frequent negative IOD and rare positive IOD events. Changes in Pacific wind forcing in recent decades and associated rapid increases in Indian Ocean subsurface heat content can thus affect the basin’s leading mode of variability, with implications for regional climate and vulnerable societies in surrounding countries.
    Description: This research was supported by a Research Fellowship by the Alexander von Humboldt Foundation, as well as the Ocean Climate Change Institute and the Investment in Science Fund at WHOI.
    Description: 2017-08-15
    Keywords: Indian Ocean ; Ocean dynamics ; Climate variability ; Multidecadal variability ; Pacific decadal oscillation
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    Circulation induced by isolated dense water formation over closed topographic contours (2017)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 2251-2265, doi:10.1175/JPO-D-17-0042.1.
    Description: The problem of localized dense water formation over a sloping bottom is considered for the general case in which the topography forms a closed contour. This class of problems is motivated by topography around islands or shallow shoals in which convection resulting from brine rejection or surface heat loss reaches the bottom. The focus of this study is on the large-scale circulation that is forced far from the region of surface forcing. The authors find that a cyclonic current is generated around the topography, in the opposite sense to the propagation of the dense water plume. In physical terms, this current results from the propagation of low sea surface height from the region of dense water formation anticyclonically along the topographic contours back to the formation region. This pressure gradient is then balanced by a cyclonic geostrophic flow. This basic structure is well predicted by a linear quasigeostrophic theory, a primitive equation model, and in rotating tank experiments. For sufficiently strong forcing, the anticyclonic circulation of the dense plume meets this cyclonic circulation to produce a sharp front and offshore advection of dense water at the bottom and buoyant water at the surface. This nonlinear limit is demonstrated in both the primitive equation model and in the tank experiments.
    Description: MAS was supported by the National Science Foundation under Grant OCE-1534618. Support for CC was given by the WHOI Ocean Climate Change Institute Proposal 27071273.
    Description: 2018-03-20
    Keywords: Bottom currents ; Buoyancy ; Ocean dynamics ; Density currents
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    Ocean eddy dynamics in a coupled ocean-atmosphere model (2010)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 37 (2007): 1103-1121, doi:10.1175/jpo3041.1.
    Description: The role of mesoscale oceanic eddies is analyzed in a quasigeostrophic coupled ocean–atmosphere model operating at a large Reynolds number. The model dynamics are characterized by decadal variability that involves nonlinear adjustment of the ocean to coherent north–south shifts of the atmosphere. The oceanic eddy effects are diagnosed by the dynamical decomposition method adapted for nonstationary external forcing. The main effects of the eddies are an enhancement of the oceanic eastward jet separating the subpolar and subtropical gyres and a weakening of the gyres. The flow-enhancing effect is due to nonlinear rectification driven by fluctuations of the eddy forcing. This is a nonlocal process involving generation of the eddies by the flow instabilities in the western boundary current and the upstream part of the eastward jet. The eddies are advected by the mean current to the east, where they backscatter into the rectified enhancement of the eastward jet. The gyre-weakening effect, which is due to the time-mean buoyancy component of the eddy forcing, is a result of the baroclinic instability of the westward return currents. The diagnosed eddy forcing is parameterized in a non-eddy-resolving ocean model, as a nonstationary random process, in which the corresponding parameters are derived from the control coupled simulation. The key parameter of the random process—its variance—is related to the large-scale flow baroclinicity index. It is shown that the coupled model with the non-eddy-resolving ocean component and the parameterized eddies correctly simulates climatology and low-frequency variability of the control eddy-resolving coupled solution.
    Description: Funding for this work came from NSF Grants OCE 02-221066 and OCE 03-44094. Additional funding for PB was provided by the U.K. Royal Society Fellowship and by WHOI Grants 27100056 and 52990035.
    Keywords: Ocean dynamics ; Ocean models ; Eddies ; Jets ; Coupled models
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    Effect of sea surface temperature-wind stress coupling on baroclinic instability in the ocean (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 37 (2007): 1092–1097, doi:10.1175/JPO3045.1.
    Description: The impact of the observed relationship between sea surface temperature and surface wind stress on baroclinic instability in the ocean is explored using linear theory and a nonlinear model. A simple parameterization of the influence of sea surface temperature on wind stress is used to derive a surface boundary condition for the vertical velocity at the base of the oceanic Ekman layer. This boundary condition is applied to the classic linear, quasigeostrophic stability problem for a uniformly sheared flow originally studied by Eady in the 1940s. The results demonstrate that for a wind directed from warm water toward cold water, the coupling acts to enhance the growth rate, and increase the wavelength, of the most unstable wave. Winds in the opposite sense reduce the growth rate and decrease the wavelength of the most unstable wave. For representative coupling strengths, the change in growth rate can be as large as ±O(50%). This effect is largest for shallow, strongly stratified, low-latitude flows.
    Description: This work was supported by the Office of Naval Research Grant N00014-05-1-0300.
    Keywords: Wind stress ; Instability ; Sea surface temperature ; Baroclinic flows ; Ocean dynamics
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    Time-dependent response to cooling in a beta-plane basin (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2006. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 36 (2006): 2185-2198, doi:10.1175/JPO2967.1.
    Description: The time-dependent response of an ocean basin to the imposition of cooling (or heating) is examined in the context of a quasigeostrophic, two-layer model on the beta plane. The focus is on the structure and magnitude of the vertical motion and its response to both a switch-on forcing and a periodic forcing. The model employed is a time-dependent version of an earlier model used to discuss the intensification of sinking in the region of the western boundary current. The height of the interface of the two-layer model serves as an analog of temperature, and the vertical velocity at the interface consists of a cross-isopycnal velocity modeled in terms of a relaxation to a prescribed interface height, an adiabatic representation of eddy thickness fluxes parameterized as lateral diffusion of thickness, and the local vertical motion of the interface itself. The presence of time dependence adds additional dynamical features to the problem, in particular the emergence of low-frequency, weakly damped Rossby basin modes. If the buoyancy forcing is zonally uniform the basin responds to a switch-on of the forcing by coming into steady-state equilibrium after the passage of a single baroclinic Rossby wave. If the forcing is nonuniform in the zonal direction, a sequence of Rossby basin modes is excited and their decay is required before the basin achieves a steady state. For reasonable parameter values the boundary layers, in which both horizontal and vertical circulations are closed, are quasi-steady and respond to the instantaneous state of the interior. As in the steady problem the flow is sensitive to small nonquasigeostrophic mass fluxes across the perimeter of the basin. These fluxes generally excite basin modes as well. The basin modes will also be weakly excited if the beta-plane approximation is relaxed. The response to periodic forcing is also examined, and the sensitivity of the response to the structure of the forcing is similar to the switch-on problem.
    Description: This research was supported in part by NSF Grant OCE-9901654,
    Keywords: Vertical motion ; Ocean dynamics ; Buoyancy ; Ocean models
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    An equatorial ocean bottleneck in global climate models (2012)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 25 (2012): 343–349, doi:10.1175/JCLI-D-11-00059.1.
    Description: The Equatorial Undercurrent (EUC) is a major component of the tropical Pacific Ocean circulation. EUC velocity in most global climate models is sluggish relative to observations. Insufficient ocean resolution slows the EUC in the eastern Pacific where nonlinear terms should dominate the zonal momentum balance. A slow EUC in the east creates a bottleneck for the EUC to the west. However, this bottleneck does not impair other major components of the tropical circulation, including upwelling and poleward transport. In most models, upwelling velocity and poleward transport divergence fall within directly estimated uncertainties. Both of these transports play a critical role in a theory for how the tropical Pacific may change under increased radiative forcing, that is, the ocean dynamical thermostat mechanism. These findings suggest that, in the mean, global climate models may not underrepresent the role of equatorial ocean circulation, nor perhaps bias the balance between competing mechanisms for how the tropical Pacific might change in the future. Implications for model improvement under higher resolution are also discussed.
    Description: KBK gratefully acknowledges the J. Lamar Worzel Assistant Scientist Fund. GCJ is supported by NOAA’s Office of Oceanic and Atmospheric Research. RM gratefully acknowledges the generous support and hospitality of the Divecha Centre for Climate Change and CAOS at IISc, Bangalore, and partial support by NASA PO grants.
    Description: 2012-07-01
    Keywords: Tropics ; Ocean circulation ; Ocean dynamics ; Climate models ; Coupled models ; Ocean models
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    Horizontal density structure and restratification of the Arctic Ocean surface layer (2012)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 42 (2012): 659–668, doi:10.1175/JPO-D-11-0125.1.
    Description: Ice-tethered profiler (ITP) measurements from the Arctic Ocean’s Canada Basin indicate an ocean surface layer beneath sea ice with significant horizontal density structure on scales of hundreds of kilometers to the order 1 km submesoscale. The observed horizontal gradients in density are dynamically important in that they are associated with restratification of the surface ocean when dense water flows under light water. Such restratification is prevalent in wintertime and competes with convective mixing upon buoyancy forcing (e.g., ice growth and brine rejection) and shear-driven mixing when the ice moves relative to the ocean. Frontal structure and estimates of the balanced Richardson number point to the likelihood of dynamical restratification by isopycnal tilt and submesoscale baroclinic instability. Based on the evidence here, it is likely that submesoscale processes play an important role in setting surface-layer properties and lateral density variability in the Arctic Ocean.
    Description: Funding was provided by the National Science Foundation Office of Polar Programs Arctic Sciences Section under Awards ARC-0519899, ARC-0856479, and ARC-0806306. Support was also provided by the Woods Hole Oceanographic Institution Arctic Research Initiative.
    Description: 2012-10-01
    Keywords: Arctic ; Ocean dynamics
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    Strengthening of the Pacific Equatorial Undercurrent in the SODA reanalysis : mechanisms, ocean dynamics, and implications (2014)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 27 (2014): 2405–2416, doi:10.1175/JCLI-D-13-00359.1.
    Description: Several recent studies utilizing global climate models predict that the Pacific Equatorial Undercurrent (EUC) will strengthen over the twenty-first century. Here, historical changes in the tropical Pacific are investigated using the Simple Ocean Data Assimilation (SODA) reanalysis toward understanding the dynamics and mechanisms that may dictate such a change. Although SODA does not assimilate velocity observations, the seasonal-to-interannual variability of the EUC estimated by SODA corresponds well with moored observations over a ~20-yr common period. Long-term trends in SODA indicate that the EUC core velocity has increased by 16% century−1 and as much as 47% century−1 at fixed locations since the mid-1800s. Diagnosis of the zonal momentum budget in the equatorial Pacific reveals two distinct seasonal mechanisms that explain the EUC strengthening. The first is characterized by strengthening of the western Pacific trade winds and hence oceanic zonal pressure gradient during boreal spring. The second entails weakening of eastern Pacific trade winds during boreal summer, which weakens the surface current and reduces EUC deceleration through vertical friction. EUC strengthening has important ecological implications as upwelling affects the thermal and biogeochemical environment. Furthermore, given the potential large-scale influence of EUC strength and depth on the heat budget in the eastern Pacific, the seasonal strengthening of the EUC may help reconcile paradoxical observations of Walker circulation slowdown and zonal SST gradient strengthening. Such a process would represent a new dynamical “thermostat” on CO2-forced warming of the tropical Pacific Ocean, emphasizing the importance of ocean dynamics and seasonality in understanding climate change projections.
    Description: EJDis supported by NSFGrantsOCE-1031971 and OCE-1233282. KBK is supported by NSF Grant OCE-1233282.
    Description: 2014-09-15
    Keywords: Tropics ; Currents ; Ocean dynamics ; Atmosphere-ocean interaction ; Climate variability ; Reanalysis data
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    The Equatorial Undercurrent and TAO sampling bias from a decade at SEA (2014)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 21 (2014): 2015–2025, doi:10.1175/JTECH-D-13-00262.1.
    Description: The NOAA Tropical Atmosphere Ocean (TAO) moored array has, for three decades, been a valuable resource for monitoring and forecasting El Niño–Southern Oscillation and understanding physical oceanographic as well as coupled processes in the tropical Pacific influencing global climate. Acoustic Doppler current profiler (ADCP) measurements by TAO moorings provide benchmarks for evaluating numerical simulations of subsurface circulation including the Equatorial Undercurrent (EUC). Meanwhile, the Sea Education Association (SEA) has been collecting data during repeat cruises to the central equatorial Pacific Ocean (160°–126°W) throughout the past decade that provide useful cross validation and quantitative insight into the potential for stationary observing platforms such as TAO to incur sampling biases related to the strength of the EUC. This paper describes some essential sampling characteristics of the SEA dataset, compares SEA and TAO velocity measurements in the vicinity of the EUC, shares new insight into EUC characteristics and behavior only observable in repeat cross-equatorial sections, and estimates the sampling bias incurred by equatorial TAO moorings in their estimates of the velocity and transport of the EUC. The SEA high-resolution ADCP dataset compares well with concurrent TAO measurements (RMSE = 0.05 m s−1; R2 = 0.98), suggests that the EUC core meanders sinusoidally about the equator between ±0.4° latitude, and reveals a mean sampling bias of equatorial measurements (e.g., TAO) of the EUC’s zonal velocity of −0.14 ± 0.03 m s−1 as well as a ~10% underestimation of EUC volume transport. A bias-corrected monthly record and climatology of EUC strength at 140°W for 1990–2010 is presented.
    Description: The authors thank the NSF Physical Oceanography program (OCE-1233282) and the WHOI Academic Programs Office for funding.
    Description: 2015-03-01
    Keywords: Pacific Ocean ; Tropics ; Currents ; Ocean dynamics ; Buoy observations ; Sampling
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    Spreading of Denmark Strait overflow water in the western subpolar North Atlantic : insights from eddy-resolving simulations with a passive tracer (2016)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2913–2932, doi:10.1175/JPO-D-14-0179.1.
    Description: The oceanic deep circulation is shared between concentrated deep western boundary currents (DWBCs) and broader interior pathways, a process that is sensitive to seafloor topography. This study investigates the spreading and deepening of Denmark Strait overflow water (DSOW) in the western subpolar North Atlantic using two ° eddy-resolving Atlantic simulations, including a passive tracer injected into the DSOW. The deepest layers of DSOW transit from a narrow DWBC in the southern Irminger Sea into widespread westward flow across the central Labrador Sea, which remerges along the Labrador coast. This abyssal circulation, in contrast to the upper levels of overflow water that remain as a boundary current, blankets the deep Labrador Sea with DSOW. Farther downstream after being steered around the abrupt topography of Orphan Knoll, DSOW again leaves the boundary, forming cyclonic recirculation cells in the deep Newfoundland basin. The deep recirculation, mostly driven by the meandering pathway of the upper North Atlantic Current, leads to accumulation of tracer offshore of Orphan Knoll, precisely where a local maximum of chlorofluorocarbon (CFC) inventory is observed. At Flemish Cap, eddy fluxes carry ~20% of the tracer transport from the boundary current into the interior. Potential vorticity is conserved as the flow of DSOW broadens at the transition from steep to less steep continental rise into the Labrador Sea, while around the abrupt topography of Orphan Knoll, potential vorticity is not conserved and the DSOW deepens significantly.
    Description: This work is supported by ONR Award N00014-09-1-0587, the NSF Physical Oceanography Program, and NASA Ocean Surface Topography Science Team Program.
    Description: 2016-06-01
    Keywords: Circulation/ Dynamics ; Abyssal circulation ; Boundary currents ; Ocean circulation ; Ocean dynamics ; Potential vorticity ; Topographic effects
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    A note on interior pathways in the meridional overturning circulation (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 643-646, doi:10.1175/JPO-D-17-0240.1.
    Description: A simple oceanic model is presented for source–sink flow on the β plane to discuss the pathways from source to sink when transport boundary layers have large enough Reynolds numbers to be inertial in their dynamics. A representation of the flow as a Fofonoff gyre, suggested by prior work on inertial boundary layers and eddy-driven circulations in two-dimensional turbulent flows, indicates that even when the source and sink are aligned along the same western boundary the flow must intrude deep into the interior before exiting at the sink. The existence of interior pathways for the flow is thus an intrinsic property of an inertial circulation and is not dependent on particular geographical basin geometry.
    Description: 2018-09-12
    Keywords: Abyssal circulation ; Bottom currents ; Nonlinear dynamics ; Ocean circulation ; Ocean dynamics ; Potential vorticity
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    Large changes in sea ice triggered by small changes in Atlantic water temperature (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 31 (2018): 4847-4863, doi:10.1175/JCLI-D-17-0802.1.
    Description: The sensitivity of sea ice to the temperature of inflowing Atlantic water across the Greenland–Scotland Ridge is investigated using an eddy-resolving configuration of the Massachusetts Institute of Technology General Circulation Model with idealized topography. During the last glacial period, when climate on Greenland is known to have been extremely unstable, sea ice is thought to have covered the Nordic seas. The dramatic excursions in climate during this period, seen as large abrupt warming events on Greenland and known as Dansgaard–Oeschger (DO) events, are proposed to have been caused by a rapid retreat of Nordic seas sea ice. Here, we show that a full sea ice cover and Arctic-like stratification can exist in the Nordic seas given a sufficiently cold Atlantic inflow and corresponding low transport of heat across the Greenland–Scotland Ridge. Once sea ice is established, continued sea ice formation and melt efficiently freshens the surface ocean and makes the deeper layers more saline. This creates a strong salinity stratification in the Nordic seas, similar to today’s Arctic Ocean, with a cold fresh surface layer protecting the overlying sea ice from the warm Atlantic water below. There is a nonlinear response in Nordic seas sea ice to Atlantic water temperature with simulated large abrupt changes in sea ice given small changes in inflowing temperature. This suggests that the DO events were more likely to have occurred during periods of reduced warm Atlantic water inflow to the Nordic seas.
    Description: The research was supported by the Centre for Climate Dynamics at the Bjerknes Centre for Climate Research. The research leading to these results is part of the ice2ice project funded by the European Research Council under the European Community Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 610055.
    Keywords: Ocean ; Arctic ; Sea ice ; Ocean dynamics ; Paleoclimate ; General circulation models
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    Long-term performance of Aanderaa optodes and Sea-Bird SBE-43 dissolved-oxygen sensors bottom mounted at 32 m in Massachusetts Bay (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 24 (2007): 1924-1935, doi:10.1175/JTECH2078.1.
    Description: A field evaluation of two new dissolved-oxygen sensing technologies, the Aanderaa Instruments AS optode model 3830 and the Sea-Bird Electronics, Inc., model SBE43, was carried out at about 32-m water depth in western Massachusetts Bay. The optode is an optical sensor that measures fluorescence quenching by oxygen molecules, while the SBE43 is a Clark polarographic membrane sensor. Optodes were continuously deployed on bottom tripod frames by exchanging sensors every 4 months over a 19-month period. A Sea-Bird SBE43 was added during one 4-month deployment. These moored observations compared well with oxygen measurements from profiles collected during monthly shipboard surveys conducted by the Massachusetts Water Resources Authority. The mean correlation coefficient between the moored measurements and shipboard survey data was 〉0.9, the mean difference was 0.06 mL L−1, and the standard deviation of the difference was 0.15 mL L−1. The correlation coefficient between the optode and the SBE43 was 〉0.9 and the mean difference was 0.07 mL L−1. Optode measurements degraded when fouling was severe enough to block oxygen molecules from entering the sensing foil over a significant portion of the sensing window. Drift observed in two optodes beginning at about 225 and 390 days of deployment is attributed to degradation of the sensing foil. Flushing is necessary to equilibrate the Sea-Bird sensor. Power consumption by the SBE43 and required pump was 19.2 mWh per sample, and the optode consumed 0.9 mWh per sample, both within expected values based on manufacturers’ specifications.
    Description: This work was funded by the MWRA and USGS.
    Keywords: Instrumentation ; Sensors ; Ocean dynamics ; Ship observations ; In situ observations
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    Interaction of Ekman layers and islands (2013)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 1028–1041, doi:10.1175/JPO-D-12-0159.1.
    Description: The circulation induced by the interaction of surface Ekman transport with an island is considered using both numerical models and linear theory. The basic response is similar to that found for the interaction of Ekman layers and an infinite boundary, namely downwelling (upwelling) in narrow boundary layers and deformation-scale baroclinic boundary layers with associated strong geostrophic flows. The presence of the island boundary, however, allows the pressure signal to propagate around the island so that the regions of upwelling and downwelling are dynamically connected. In the absence of stratification the island acts as an effective barrier to the Ekman transport. The presence of stratification supports baroclinic boundary currents that provide an advective pathway from one side of the island to the other. The resulting steady circulation is quite complex. Near the island, both geostrophic and ageostrophic velocity components are typically large. The density anomaly is maximum below the surface and, for positive wind stress, exhibits an anticyclonic phase rotation with depth (direction of Kelvin wave propagation) such that anomalously warm water can lie below regions of Ekman upwelling. The horizontal and vertical velocities exhibit similar phase changes with depth. The addition of a sloping bottom can act to shield the deep return flow from interacting with the island and providing mass transport into/out of the surface Ekman layer. In these cases, the required transport is provided by a pair of recirculation gyres that connect the narrow upwelling/downwelling boundary layers on the eastern and western sides of the island, thus directly connecting the Ekman transport across the island.
    Description: This study was supported by the National Science Foundation under Grants OCE-0826656 and OCE-0959381 (MAS), and OCE-0925061 (JP).
    Description: 2013-11-01
    Keywords: Coastal flows ; Ekman pumping/transport ; Ocean dynamics
    Repository Name: Woods Hole Open Access Server
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    An inertial model of the interaction of Ekman layers and planetary islands (2014)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 1398–1406, doi:10.1175/JPO-D-13-028.1.
    Description: An adiabatic, inertial, and quasigeostrophic model is used to discuss the interaction of surface Ekman transport with an island. The theory extends the recent work of Spall and Pedlosky to include an analytical and nonlinear model for the interaction. The presence of an island that interrupts a uniform Ekman layer transport raises interesting questions about the resulting circulation. The consequential upwelling around the island can lead to a local intake of fluid from the geostrophic region beneath the Ekman layer or to a more complex flow around the island in which the fluid entering the Ekman layer on one portion of the island's perimeter is replaced by a flow along the island's boundary from a downwelling region located elsewhere on the island. This becomes especially pertinent when the flow is quasigeostrophic and adiabatic. The oncoming geostrophic flow that balances the offshore Ekman flux is largely diverted around the island, and the Ekman flux is fed by a transfer of fluid from the western to the eastern side of the island. As opposed to the linear, dissipative model described earlier, this transfer takes place even in the absence of a topographic skirt around the island. The principal effect of topography in the inertial model is to introduce an asymmetry between the circulation on the northern and southern sides of the island. The quasigeostrophic model allows a simple solution to the model problem with topography and yet the resulting three-dimensional circulation is surprisingly complex with streamlines connecting each side of the island.
    Description: This research was supported in part by NSF Grant OCE Grant 0925061.
    Keywords: Baroclinic flows ; Large-scale motions ; Nonlinear dynamics ; Ocean circulation ; Ocean dynamics ; Topographic effects
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    On the crossover of boundary currents in an idealized model of the Red Sea (2015)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 1410–1425, doi:10.1175/JPO-D-14-0192.1.
    Description: The west-to-east crossover of boundary currents has been seen in mean circulation schemes from several past models of the Red Sea. This study investigates the mechanisms that produce and control the crossover in an idealized, eddy-resolving numerical model of the Red Sea. The authors also review the observational evidence and derive an analytical estimate for the crossover latitude. The surface buoyancy loss increases northward in the idealized model, and the resultant mean circulation consists of an anticyclonic gyre in the south and a cyclonic gyre in the north. In the midbasin, the northward surface flow crosses from the western boundary to the eastern boundary. Numerical experiments with different parameters indicate that the crossover latitude of the boundary currents changes with f0, β, and the meridional gradient of surface buoyancy forcing. In the analytical estimate, which is based on quasigeostrophic, β-plane dynamics, the crossover is predicted to lie at the latitude where the net potential vorticity advection (including an eddy component) is zero. Various terms in the potential vorticity budget can be estimated using a buoyancy budget, a thermal wind balance, and a parameterization of baroclinic instability.
    Description: This work is supported by Award USA 00002, KSA 00011, and KSA 00011/02 made by King Abdullah University of Science and Technology (KAUST), by National Science Foundation Grants OCE0927017, OCE1154641, and OCE85464100, and by the Woods Hole Oceanographic Institution Academic Program Office.
    Description: 2015-11-01
    Keywords: Circulation/ Dynamics ; Boundary currents ; Buoyancy ; Ocean circulation ; Ocean dynamics
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    Influences of time-dependent precipitation on water mass transformation, heat fluxes, and deep convection in marginal seas (2015)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 1822–1842, doi:10.1175/JPO-D-14-0147.1.
    Description: Influences of time-dependent precipitation on water mass transformation and heat budgets in an idealized marginal sea are examined using theoretical and numerical models. The equations proposed by Spall in 2012 are extended to cases with time-dependent precipitation whose form is either a step function or a sinusoidal function. The theory predicts the differences in temperature and salinity between the convective water and the boundary current as well as the magnitudes of heat fluxes into the marginal sea and across the sea surface. Moreover, the theory reveals that there are three inherent time scales: relaxation time scales for temperature and salinity and a precipitation time scale. The relaxation time scales are determined by a steady solution of the theoretical model with steady precipitation. The relaxation time scale for temperature is always smaller than that for salinity as a result of not only the difference in the form of fluxes at the surface but also the variation in the eddy transport from the boundary current. These three time scales and the precipitation amplitude determine the strength of the ocean response to changes in precipitation and the phase relation between precipitation, changes in salinity and temperature, and changes in heat fluxes. It is demonstrated that the theoretical predictions agree qualitatively well with results from the eddy-resolving numerical model. This demonstrates the fundamental role of mesoscale eddies in the ocean response to time-dependent forcing and provides a framework with which to assess the extent to which observed variability in marginal sea convection and water mass transformation are consistent with an external forcing by variations in precipitation.
    Description: This work was initiated at the 2013 WHOI Geophysical Fluid Dynamics Summer Program, which was supported by the National Science Foundation and the Office of Naval Research. This work was also supported by Grant-in-Aid for Research Fellow (25·8466) of the Ministry of Education, Culture, Sports and Technology (MEXT), Japan, the Program for Leading Graduate Schools, MEXT, Japan (YY), and by the National Science Foundation Grant OCE-1232389 (MAS).
    Description: 2016-01-01
    Keywords: Circulation/ Dynamics ; Boundary currents ; Deep convection ; Eddies ; Ocean dynamics ; Atm/Ocean Structure/ Phenomena ; Precipitation
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    The interaction of an eastward-flowing current and an island : sub- and supercritical flow (2015)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2806–2819, doi:10.1175/JPO-D-15-0061.1.
    Description: An eastward-flowing current of a homogeneous fluid with velocity U, contained in a channel of width L, impinges on an island of width of O(L), and the resulting interaction and dynamics are studied for values of the supercriticality parameter, b = βL2/U, both larger and smaller than π2. The former case is subcritical with respect to Rossby waves, and the latter is supercritical. The nature of the flow field depends strongly on b, and in particular, the nature of the flow around the island and the proportion of the flow passing to the north or south of the island are sensitive to b and to the position of the island in the channel. The problem is studied analytically in a relatively simple, nonlinear quasigeostrophic and adiabatic framework and numerically with a shallow-water model that allows a qualitative extension of the results to the equator. Although the issues involved are motivated by the interaction of the Equatorial Undercurrent and the Galapagos Islands, the analysis presented here focuses on the fundamental issue of the distinctive nature of the flow as a function of Rossby wave criticality.
    Description: Supported by the National Science Foundation Grant OCE-0959381.
    Description: 2016-05-01
    Keywords: Circulation/ Dynamics ; Ocean circulation ; Ocean dynamics ; Waves, oceanic
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    Impact of two plumes’ interaction on submarine melting of tidewater glaciers : a laboratory study (2016)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 361–367, doi:10.1175/JPO-D-15-0171.1.
    Description: Idealized laboratory experiments investigate the glacier–ocean boundary dynamics near a vertical glacier in a two-layer stratified fluid. Discharge of meltwater runoff at the base of the glacier (subglacial discharge) enhances submarine melting. In the laboratory, the effect of multiple sources of subglacial discharge is simulated by introducing freshwater at freezing temperature from two point sources at the base of an ice block representing the glacier. The buoyant plumes of cold meltwater and subglacial discharge water entrain warm ambient water, rise vertically, and interact within a layer of depth H2 if the distance between the sources x0 is smaller than H2α/0.35, where α is the entrainment constant. The plume water detaches from the glacier face at the interface between the two layers and/or at the free surface, as confirmed by previous numerical studies and field observations. A plume model is used to explain the observed nonmonotonic dependence of submarine melting on the sources’ separation. The distance between the two sources influences the entrainment of warm water in the plumes and consequently the amount of submarine melting and the final location of the meltwater within the water column. Two interacting plumes located very close together are observed to melt approximately half as much as two independent plumes. The inclusion, or parameterization, of the dynamics regulating multiple plumes’ interaction is therefore necessary for a correct estimate of submarine melting. Hence, the distribution and number of sources of subglacial discharge may play an important role in glacial melt rates and fjord stratification and circulation.
    Description: Support to C.C. was given by the NSF Project OCE-1130008 and OCE-1434041. V.M.G. received support from the “Gori” Fellowship.
    Description: 2016-07-01
    Keywords: Geographic location/entity ; Glaciers ; Circulation/ Dynamics ; Buoyancy ; Entrainment ; Ocean dynamics ; Small scale processes ; Models and modeling ; Laboratory/physical models
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    Shelf–open ocean exchange forced by wind jets (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 163-174, doi:10.1175/JPO-D-17-0161.1.
    Description: The general problem of exchange from a shallow shelf across sharp topography to the deep ocean forced by narrow, cross-shelf wind jets is studied using quasigeostrophic theory and an idealized primitive equation numerical model. Interest is motivated by katabatic winds that emanate from narrow fjords in southeast Greenland, although similar topographically constrained wind jets are found throughout the world’s oceans. Because there is no net vorticity input by the wind, the circulation is largely confined to the region near the forcing. Circulation over the shelf is limited by bottom friction for weakly stratified flows, but stratification allows for much stronger upper-layer flows that are regulated by weak coupling to the lower layer. Over the sloping topography, the topographic beta effect limits the deep flow, while, for sufficient stratification, the upper-layer flow can cross the topography to connect the shelf to the open ocean. This can be an effective transport mechanism even for short, strong wind events because damping of the upper-layer flow is weak. A variety of transients are generated for an abrupt onset of winds, including short topography Rossby waves, long topographic Rossby waves, and inertial waves. Using parameters representative of southeast Greenland, katabatic wind events will force an offshore transport of O(0.4) Sv (1 Sv ≡ 106 m3 s−1) that, when considered for 2 days, will result in an offshore flux of O(5 × 1010) m3.
    Description: MAS was supported by the National Science Foundation under Grant OCE-1533170.
    Description: 2018-07-18
    Keywords: Coastal flows ; Downslope winds ; Ocean dynamics
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    On the weakly nonlinear Ekman layer : thickness and flux (2010)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2008. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 38 (2008): 1334-1339, doi:10.1175/2007JPO3830.1.
    Description: The first-order effects of nonlinearity on the thickness and frictionally driven flux in the Ekman layer are described for the case of an Ekman layer on a solid, flat plate driven by an overlying geostrophic flow as well as the Ekman layer on a free surface driven by a wind stress in the presence of a deep geostrophic current. In both examples, the fluid is homogeneous. Particular attention is paid to the effect of nonlinearity in determining the thickness of the Ekman layer in both cases. An analytical expression for the Ekman layer thickness as a function of Rossby number is given when the Rossby number is small. The result is obtained by insisting that the perturbation expansion of the Ekman problem in powers of the Rossby number remains uniformly valid. There are two competing physical effects. The relative vorticity of the geostrophic currents tends to reduce the width of the layer, but the vertical velocity induced in the layer can fatten or thin the layer depending on the sign of the vertical velocity. The regularized expansion is shown to give, to lowest order, expressions for the flux in agreement with earlier calculations.
    Description: This research was supported in part by NSF Grant OCE-0451086.
    Keywords: Ekman pumping/transport ; Nonlinear dynamics ; Dynamics ; Ocean dynamics
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    A model of multiple zonal jets in the oceans : dynamical and kinematical analysis (2010)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2009. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 39 (2009): 2711-2734, doi:10.1175/2009JPO4093.1.
    Description: Multiple alternating zonal jets observed in the ocean are studied with an idealized quasigeostrophic zonal-channel model, with the supercritical, zonal background flow imposed. Both eastward and westward background flows with vertical shear are considered. The underlying nonlinear dynamics is illuminated with analysis of the vertical-mode interactions and time-mean eddy fluxes. Interactions between the vertical modes are systematically studied. The barotropic component of the jets is maintained by both barotropic–barotropic and baroclinic–baroclinic time-mean interactions; thus, the barotropic component of the jets cannot be accurately simulated with a randomly forced barotropic model. The roles of the vertical-mode interactions in driving the baroclinic component of the jets are also characterized. Not only the first but also the second baroclinic mode is found to be important for maintaining the baroclinic component of the jets, whereas the barotropic component of the jets is maintained mostly by the barotropic and first baroclinic modes. The properties of the eddy forcing were systematically studied. It is shown that the baroclinic component of the jets is maintained by Reynolds stress forcing and resisted by form stress forcing only in the eastward background flow. In the westward background flow, the jets are maintained by form stress forcing and resisted by Reynolds stress forcing. The meridional scaling and kinematical properties of the jets are studied as well as the roles of meridional boundaries. The Rhines scaling for meridional spacing of the jets is not generally confirmed, and it is also shown that there are multiple stable equilibria with different numbers of the time-mean jets. It is also found that the jets are associated with alternating weak barriers to the meridional material transport, but the locations of these barriers are not unique and depend on the direction of the background flow and depth. Finally, if the channel is closed with meridional walls, then the jets become more latent but the eddy forcing properties do not change qualitatively.
    Description: Funding for PB was provided by NSF Grants OCE 0344094 and OCE 0725796 and by the research grant from the Newton Trust of the University of Cambridge. Funding for IK was provided by NSF Grants OCE 0346178 and 0749722. Funding for JP was provided by NSF Grant OCE 0451086.
    Keywords: Ocean dynamics ; Jets ; Kinematics
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    Upper-ocean response to Hurricane Frances (2004) observed by Profiling EM-APEX floats (2011)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2011. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 41 (2011): 1041–1056, doi:10.1175/2010JPO4313.1.
    Description: Three autonomous profiling Electromagnetic Autonomous Profiling Explorer (EM-APEX) floats were air deployed one day in advance of the passage of Hurricane Frances (2004) as part of the Coupled Boundary Layer Air–Sea Transfer (CBLAST)-High field experiment. The floats were deliberately deployed at locations on the hurricane track, 55 km to the right of the track, and 110 km to the right of the track. These floats provided profile measurements between 30 and 200 m of in situ temperature, salinity, and horizontal velocity every half hour during the hurricane passage and for several weeks afterward. Some aspects of the observed response were similar at the three locations—the dominance of near-inertial horizontal currents and the phase of these currents—whereas other aspects were different. The largest-amplitude inertial currents were observed at the 55-km site, where SST cooled the most, by about 2.2°C, as the surface mixed layer deepened by about 80 m. Based on the time–depth evolution of the Richardson number and comparisons with a numerical ocean model, it is concluded that SST cooled primarily because of shear-induced vertical mixing that served to bring deeper, cooler water into the surface layer. Surface gravity waves, estimated from the observed high-frequency velocity, reached an estimated 12-m significant wave height at the 55-km site. Along the track, there was lesser amplitude inertial motion and SST cooling, only about 1.2°C, though there was greater upwelling, about 25-m amplitude, and inertial pumping, also about 25-m amplitude. Previously reported numerical simulations of the upper-ocean response are in reasonable agreement with these EM-APEX observations provided that a high wind speed–saturated drag coefficient is used to estimate the wind stress. A direct inference of the drag coefficient CD is drawn from the momentum budget. For wind speeds of 32–47 m s−1, CD ~ 1.4 × 10−3.
    Description: The Office of Naval Research supported the development of the EM-APEX float system through SBIR Contract N00014-03-C-0242 to Webb Research Corporation and with a subcontract to APL-UW. Sanford and J. Girton were supported by the Office of Naval Research through GrantsN00014-04-1-0691 and N00014- 07-1-024, and J. Price was supported through Grant N00014-04-1-0109.
    Keywords: Hurricanes ; Ocean dynamics ; Profilers ; Air-sea interactions
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    Reconstructing the ocean's interior from surface data (2013)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 1611–1626, doi:10.1175/JPO-D-12-0204.1.
    Description: A new method is proposed for extrapolating subsurface velocity and density fields from sea surface density and sea surface height (SSH). In this, the surface density is linked to the subsurface fields via the surface quasigeostrophic (SQG) formalism, as proposed in several recent papers. The subsurface field is augmented by the addition of the barotropic and first baroclinic modes, whose amplitudes are determined by matching to the sea surface height (pressure), after subtracting the SQG contribution. An additional constraint is that the bottom pressure anomaly vanishes. The method is tested for three regions in the North Atlantic using data from a high-resolution numerical simulation. The decomposition yields strikingly realistic subsurface fields. It is particularly successful in energetic regions like the Gulf Stream extension and at high latitudes where the mixed layer is deep, but it also works in less energetic eastern subtropics. The demonstration highlights the possibility of reconstructing three-dimensional oceanic flows using a combination of satellite fields, for example, sea surface temperature (SST) and SSH, and sparse (or climatological) estimates of the regional depth-resolved density. The method could be further elaborated to integrate additional subsurface information, such as mooring measurements.
    Description: JW and AM were supported by NASA (NNX12AD47G) and NSF (OCE 0928617). JLM was supported by the Office of Naval Research and the Office of Science (BER), U.S. Department of Energy under DE-GF0205ER64119. GRF is supported by OCE-0752346 and JHL by NORSEE (Nordic Seas Eddy Exchanges) funded by the Norwegian Research Council.
    Description: 2014-02-01
    Keywords: Eddies ; Ocean dynamics ; Potential vorticity ; Surface pressure ; Surface temperature ; Inverse methods
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    Estuarine exchange flow is related to mixing through the salinity variance budget (2018)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 48 (2018): 1375-1384, doi:10.1175/JPO-D-17-0266.1.
    Description: The relationship between net mixing and the estuarine exchange flow may be quantified using a salinity variance budget. Here “mixing” is defined as the rate of destruction of volume-integrated salinity variance, and the exchange flow is quantified using the total exchange flow. These concepts are explored using an idealized 3D model estuary. It is shown that in steady state (e.g., averaging over the spring–neap cycle) the volume-integrated mixing is approximately given by Mixing ≅ SinSoutQr, where Sin and Sout are the representative salinities of in- and outflowing layers at the mouth and Qr is the river volume flux. This relationship provides an extension of the familiar Knudsen relation, in which the exchange flow is diagnosed based on knowledge of these same three quantities, quantitatively linking mixing to the exchange flow.
    Description: The work was supported by the National Science Foundation through Grants OCE-1736242 to PM and OCE-1736539 to WRG and by the German Research Foundation through Grants TRR 181 and GRK 2000 to HB.
    Keywords: Coastal flows ; Diapycnal mixing ; Ocean dynamics ; Streamflow ; Diagnostics ; Isopycnal coordinates
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    A time-dependent Sverdrup relation and its application to the Indian Ocean (2022)
    American Meteorological Society
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    Publication Date: 2022-11-27
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(6), (2022): 1233-1244, https://doi.org/10.1175/jpo-d-21-0223.1.
    Description: The Sverdrup relation is the backbone of wind-driven circulation theory; it is a simple relation between the meridional transport of the wind-driven circulation in the upper ocean and the wind stress curl. However, the relation is valid for steady circulation only. In this study, a time-dependent Sverdrup relation is postulated, in which the meridional transport in a time-dependent circulation is the sum of the local wind stress curl term and a time-delayed term representing the effect of the eastern boundary condition. As an example, this time-dependent Sverdrup relation is evaluated through its application to the equatorial circulation in the Indian Ocean, using reanalysis data and a reduced gravity model. Close examination reveals that the southward Somali Current occurring during boreal winter is due to the combination of the local wind stress curl in the Arabian Sea and delayed signals representing the time change of layer thickness at the eastern boundary.
    Description: This work is supported by NSFC (41822602, 41976016, 42005035, 42076021), the Strategic Priority Research Program of Chinese Academy of Sciences (XDB42000000, XDA 20060502), Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (GML2019ZD0306), Guangdong Basic and Applied Basic Research Foundation (2021A1515011534), Youth Innovation Promotion Association CAS, ISEE2021ZD01, and LTOZZ2002. The numerical simulation is supported by the High-Performance Computing Division in the South China Sea Institute of Oceanology.
    Description: 2022-11-27
    Keywords: Ocean circulation ; Ocean dynamics ; Rossby waves ; Wind stress curl
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    Deep-current intraseasonal variability interpreted as topographic Rossby waves and deep eddies in the Xisha Islands of the South China Sea (2022)
    American Meteorological Society
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    Publication Date: 2022-12-16
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(7), (2022): 1415–1430. https://doi.org/10.1175/JPO-D-21-0147.1.
    Description: Strong subinertial variability near a seamount at the Xisha Islands in the South China Sea was revealed by mooring observations from January 2017 to January 2018. The intraseasonal deep flows presented two significant frequency bands, with periods of 9–20 and 30–120 days, corresponding to topographic Rossby waves (TRWs) and deep eddies, respectively. The TRW and deep eddy signals explained approximately 60% of the kinetic energy of the deep subinertial currents. The TRWs at the Ma, Mb, and Mc moorings had 297, 262, and 274 m vertical trapping lengths, and ∼43, 38, and 55 km wavelengths, respectively. Deep eddies were independent from the upper layer, with the largest temperature anomaly being 〉0.4°C. The generation of the TRWs was induced by mesoscale perturbations in the upper layer. The interaction between the cyclonic–anticyclonic eddy pair and the seamount topography contributed to the generation of deep eddies. Owing to the potential vorticity conservation, the westward-propagating tilted interface across the eddy pair squeezed the deep-water column, thereby giving rise to negative vorticity west of the seamount. The strong front between the eddy pair induced a northward deep flow, thereby generating a strong horizontal velocity shear because of lateral friction and enhanced negative vorticity. Approximately 4 years of observations further confirmed the high occurrence of TRWs and deep eddies. TRWs and deep eddies might be crucial for deep mixing near rough topographies by transferring mesoscale energy to small scales.
    Description: This work was supported by the National Natural Science Foundation of China (92158204, 91958202, 42076019, 41776036, 91858203), the Open Project Program of State Key Laboratory of Tropical Oceanography (project LTOZZ2001), and Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (GML2019ZD0304).
    Description: 2022-12-16
    Keywords: Abyssal circulation ; Ocean circulation ; Ocean dynamics ; Intraseasonal variability
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    Interannual and seasonal along-shelf current variability and dynamics: seventeen years of observations from the southern New England inner shelf (2022)
    American Meteorological Society
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    Publication Date: 2022-12-21
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(12), (2022): 2923–2933, https://doi.org/10.1175/jpo-d-22-0064.1.
    Description: The characteristics and dynamics of depth-average along-shelf currents at monthly and longer time scales are examined using 17 years of observations from the Martha’s Vineyard Coastal Observatory on the southern New England inner shelf. Monthly averages of the depth-averaged along-shelf current are almost always westward, with the largest interannual variability in winter. There is a consistent annual cycle with westward currents of 5 cm s−1 in summer decreasing to 1–2 cm s−1 in winter. Both the annual cycle and interannual variability in the depth-average along-shelf current are predominantly driven by the along-shelf wind stress. In the absence of wind forcing, there is a westward flow of ∼5 cm s−1 throughout the year. At monthly time scales, the depth-average along-shelf momentum balance is primarily between the wind stress, surface gravity wave–enhanced bottom stress, and an opposing pressure gradient that sets up along the southern New England shelf in response to the wind. Surface gravity wave enhancement of bottom stress is substantial over the inner shelf and is essential to accurately estimating the bottom stress variation across the inner shelf.
    Description: The National Science Foundation, Woods Hole Oceanographic Institution, the Massachusetts Technology Collaborative, and the Office of Naval Research have supported the construction and maintenance of MVCO. The analysis presented here was partially funded by the National Science Foundation under Grants OCE 1558874 and OCE 1655686.
    Keywords: Continental shelf/slope ; Coastal flows ; Momentum ; Ocean dynamics ; Wind stress
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    Frontogenesis and variability in Denmark Strait and its influence on overflow water (2019)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(7), (2019): 1889-1904, doi:10.1175/JPO-D-19-0053.1.
    Description: A high-resolution numerical model, together with in situ and satellite observations, is used to explore the nature and dynamics of the dominant high-frequency (from one day to one week) variability in Denmark Strait. Mooring measurements in the center of the strait reveal that warm water “flooding events” occur, whereby the North Icelandic Irminger Current (NIIC) propagates offshore and advects subtropical-origin water northward through the deepest part of the sill. Two other types of mesoscale processes in Denmark Strait have been described previously in the literature, known as “boluses” and “pulses,” associated with a raising and lowering of the overflow water interface. Our measurements reveal that flooding events occur in conjunction with especially pronounced pulses. The model indicates that the NIIC hydrographic front is maintained by a balance between frontogenesis by the large-scale flow and frontolysis by baroclinic instability. Specifically, the temperature and salinity tendency equations demonstrate that the eddies act to relax the front, while the mean flow acts to sharpen it. Furthermore, the model reveals that the two dense water processes—boluses and pulses (and hence flooding events)—are dynamically related to each other and tied to the meandering of the hydrographic front in the strait. Our study thus provides a general framework for interpreting the short-time-scale variability of Denmark Strait Overflow Water entering the Irminger Sea.
    Description: MAS was supported by the National Science Foundation (NSF) under Grants OCE-1558742 and OCE-1534618. RSP, PL, and DM were supported by NSF under Grants OCE-1558742 and OCE-1259618. WJvA was supported by the Helmholtz Infrastructure Initiative FRAM. TWNH and MA were supported by NSF under Grants OCE-1633124 and OCE-118123.
    Description: 2020-07-01
    Keywords: Baroclinic flows ; Frontogenesis/frontolysis ; Meridional overturning circulation ; Ocean dynamics ; Topographic effects
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    Potential vorticity dynamics of the arctic halocline (2021)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(9), (2020): 2491-2506, doi:10.1175/JPO-D-20-0056.1.
    Description: An idealized two-layer shallow water model is applied to the study of the dynamics of the Arctic Ocean halocline. The model is forced by a surface stress distribution reflective of the observed wind stress pattern and ice motion and by an inflow representing the flow of Pacific Water through Bering Strait. The model reproduces the main elements of the halocline circulation: an anticyclonic Beaufort Gyre in the western basin (representing the Canada Basin), a cyclonic circulation in the eastern basin (representing the Eurasian Basin), and a Transpolar Drift between the two gyres directed from the upwind side of the basin to the downwind side of the basin. Analysis of the potential vorticity budget shows a basin-averaged balance primarily between potential vorticity input at the surface and dissipation at the lateral boundaries. However, advection is a leading-order term not only within the anticyclonic and cyclonic gyres but also between the gyres. This means that the eastern and western basins are dynamically connected through the advection of potential vorticity. Both eddy and mean fluxes play a role in connecting the regions of potential vorticity input at the surface with the opposite gyre and with the viscous boundary layers. These conclusions are based on a series of model runs in which forcing, topography, straits, and the Coriolis parameter were varied.
    Description: This study was supported by National Science Foundation Grant OPP-1822334. Comments and suggestions from two anonymous referees greatly helped to improve the paper.
    Description: 2021-02-17
    Keywords: Eddies ; Ekman pumping/transport ; Ocean circulation ; Ocean dynamics ; Potential vorticity ; Shallow-water equations
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    Kinematic structure and dynamics of the Denmark Strait Overflow from ship-based observations (2021)
    American Meteorological Society
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    Publication Date: 2022-05-27
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(11), (2020): 3235–3251, https://doi.org/10.1175/JPO-D-20-0095.1.
    Description: The dense outflow through Denmark Strait is the largest contributor to the lower limb of the Atlantic meridional overturning circulation, yet a description of the full velocity field across the strait remains incomplete. Here we analyze a set of 22 shipboard hydrographic–velocity sections occupied along the Látrabjarg transect at the Denmark Strait sill, obtained over the time period 1993–2018. The sections provide the first complete view of the kinematic components at the sill: the shelfbreak East Greenland Current (EGC), the combined flow of the separated EGC, and the North Icelandic Jet (NIJ), and the northward-flowing North Icelandic Irminger Current (NIIC). The total mean transport of overflow water is 3.54 ± 0.29 Sv (1 Sv ≡ 106 m3 s−1), comparable to previous estimates. The dense overflow is partitioned in terms of water mass constituents and flow components. The mean transports of the two types of overflow water—Atlantic-origin Overflow Water and Arctic-origin Overflow Water—are comparable in Denmark Strait, while the merged NIJ–separated EGC transports 55% more water than the shelfbreak EGC. A significant degree of water mass exchange takes place between the branches as they converge in Denmark Strait. There are two dominant time-varying configurations of the flow that are characterized as a cyclonic state and a noncyclonic state. These appear to be wind-driven. A potential vorticity analysis indicates that the flow through Denmark Strait is subject to symmetric instability. This occurs at the top of the overflow layer, implying that the mixing/entrainment process that modifies the overflow water begins at the sill.
    Description: Funding for the study was provided by National Science Foundation (NSF) Grants OCE-1259618, OCE-1756361, and OCE-1558742. The German research cruises were financially supported through various EU Projects (e.g. THOR, NACLIM) and national projects (most recently TRR 181 “Energy Transfer in Atmosphere and Ocean” funded by the German Research Foundation and RACE II “Regional Atlantic Circulation and Global Change” funded by the German Federal Ministry for Education and Research). GWKM acknowledges the support of the Natural Sciences and Engineering Research Council of Canada. LP was supported by NSF Grant OCE-1657870.
    Keywords: Currents ; Instability ; Ocean circulation ; Ocean dynamics ; Potential vorticity
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    On the origins of the oceanic ultraviolet catastrophe (2022)
    American Meteorological Society
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    Publication Date: 2022-09-25
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(4), (2022): 597–616, https://doi.org/10.1175/jpo-d-21-0121.1.
    Description: We provide a first-principles analysis of the energy fluxes in the oceanic internal wave field. The resulting formula is remarkably similar to the renowned phenomenological formula for the turbulent dissipation rate in the ocean, which is known as the finescale parameterization. The prediction is based on the wave turbulence theory of internal gravity waves and on a new methodology devised for the computation of the associated energy fluxes. In the standard spectral representation of the wave energy density, in the two-dimensional vertical wavenumber–frequency (m–ω) domain, the energy fluxes associated with the steady state are found to be directed downscale in both coordinates, closely matching the finescale parameterization formula in functional form and in magnitude. These energy transfers are composed of a “local” and a “scale-separated” contributions; while the former is quantified numerically, the latter is dominated by the induced diffusion process and is amenable to analytical treatment. Contrary to previous results indicating an inverse energy cascade from high frequency to low, at odds with observations, our analysis of all nonzero coefficients of the diffusion tensor predicts a direct energy cascade. Moreover, by the same analysis fundamental spectra that had been deemed “no-flux” solutions are reinstated to the status of “constant-downscale-flux” solutions. This is consequential for an understanding of energy fluxes, sources, and sinks that fits in the observational paradigm of the finescale parameterization, solving at once two long-standing paradoxes that had earned the name of “oceanic ultraviolet catastrophe.”
    Description: The authors gratefully acknowledge support from the ONR Grant N00014-17-1-2852. YL gratefully acknowledges support from NSF DMS Award 2009418.
    Description: 2022-09-25
    Keywords: Ocean ; Gravity waves ; Nonlinear dynamics ; Ocean dynamics ; Mixing ; Fluxes ; Isopycnal coordinates ; Nonlinear models
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    Turbulent mixing variability in an energetic standing meander of the Southern Ocean (2022)
    American Meteorological Society
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    Publication Date: 2022-08-29
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(8), (2022): 1593-1611, https://doi.org/10.1175/jpo-d-21-0180.1.
    Description: This study presents novel observational estimates of turbulent dissipation and mixing in a standing meander between the Southeast Indian Ridge and the Macquarie Ridge in the Southern Ocean. By applying a finescale parameterization on the temperature, salinity, and velocity profiles collected from Electromagnetic Autonomous Profiling Explorer (EM-APEX) floats in the upper 1600 m, we estimated the intensity and spatial distribution of dissipation rate and diapycnal mixing along the float tracks and investigated the sources. The indirect estimates indicate strong spatial and temporal variability of turbulent mixing varying from O(10−6) to O(10−3) m2 s−1 in the upper 1600 m. Elevated turbulent mixing is mostly associated with the Subantarctic Front (SAF) and mesoscale eddies. In the upper 500 m, enhanced mixing is associated with downward-propagating wind-generated near-inertial waves as well as the interaction between cyclonic eddies and upward-propagating internal waves. In the study region, the local topography does not play a role in turbulent mixing in the upper part of the water column, which has similar values in profiles over rough and smooth topography. However, both remotely generated internal tides and lee waves could contribute to the upward-propagating energy. Our results point strongly to the generation of turbulent mixing through the interaction of internal waves and the intense mesoscale eddy field.
    Description: The observations were funded through grants from the Australian Research Council Discovery Project (DP170102162) and Australia’s Marine National Facility. Surface drifters were provided by Dr. Shaun Dolk of the Global Drifter Program. AC was supported by an Australian Research Council Postdoctoral Fellowship. AC, HEP, and NLB acknowledge support from the Australian Government Department of the Environment and Energy National Environmental Science Program and the ARC Centre of Excellence in Climate Extremes. KP acknowledges the support from the National Science Foundation.
    Keywords: Diapycnal mixing ; Eddies ; Fronts ; Inertia-gravity waves ; Ocean dynamics
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    Kinetic energy transfers between mesoscale and submesoscale motions in the open ocean’s upper layers (2022)
    American Meteorological Society
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    Publication Date: 2022-09-15
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(1),(2022): 75–97, https://doi.org/10.1175/JPO-D-21-0099.1.
    Description: Mesoscale eddies contain the bulk of the ocean’s kinetic energy (KE), but fundamental questions remain on the cross-scale KE transfers linking eddy generation and dissipation. The role of submesoscale flows represents the key point of discussion, with contrasting views of submesoscales as either a source or a sink of mesoscale KE. Here, the first observational assessment of the annual cycle of the KE transfer between mesoscale and submesoscale motions is performed in the upper layers of a typical open-ocean region. Although these diagnostics have marginal statistical significance and should be regarded cautiously, they are physically plausible and can provide a valuable benchmark for model evaluation. The cross-scale KE transfer exhibits two distinct stages, whereby submesoscales energize mesoscales in winter and drain mesoscales in spring. Despite this seasonal reversal, an inverse KE cascade operates throughout the year across much of the mesoscale range. Our results are not incompatible with recent modeling investigations that place the headwaters of the inverse KE cascade at the submesoscale, and that rationalize the seasonality of mesoscale KE as an inverse cascade-mediated response to the generation of submesoscales in winter. However, our findings may challenge those investigations by suggesting that, in spring, a downscale KE transfer could dampen the inverse KE cascade. An exploratory appraisal of the dynamics governing mesoscale–submesoscale KE exchanges suggests that the upscale KE transfer in winter is underpinned by mixed layer baroclinic instabilities, and that the downscale KE transfer in spring is associated with frontogenesis. Current submesoscale-permitting ocean models may substantially understate this downscale KE transfer, due to the models’ muted representation of frontogenesis.
    Description: The OSMOSIS experiment was funded by the U.K. Natural Environment Research Council (NERC) through Grants NE/1019999/1 and NE/101993X/1. ACNG acknowledges the support of the Royal Society and the Wolfson Foundation, and XY that of a China Scholarship Council PhD studentship.
    Keywords: Ageostrophic circulations ; Dynamics ; Eddies ; Energy transport ; Frontogenesis/frontolysis ; Instability ; Mesoscale processes ; Nonlinear dynamics ; Ocean circulation ; Ocean dynamics ; Small scale processes ; Turbulence
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    Variations of the North Pacific Subtropical Mode Water from direct observations (2014)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 27 (2014): 2842–2860, doi:10.1175/JCLI-D-13-00227.1.
    Description: Mooring measurements from the Kuroshio Extension System Study (June 2004–June 2006) and from the ongoing Kuroshio Extension Observatory (June 2004–present) are combined with float measurements of the Argo network to study the variability of the North Pacific Subtropical Mode Water (STMW) across the entire gyre, on time scales from days, to seasons, to a decade. The top of the STMW follows a seasonal cycle, although observations reveal that it primarily varies in discrete steps associated with episodic wind events. The variations of the STMW bottom depth are tightly related to the sea surface height (SSH), reflecting mesoscale eddies and large-scale variations of the Kuroshio Extension and recirculation gyre systems. Using the observed relationship between SSH and STMW, gridded SSH products and in situ estimates from floats are used to construct weekly maps of STMW thickness, providing nonbiased estimates of STMW total volume, annual formation and erosion volumes, and seasonal and interannual variability for the past decade. Year-to-year variations are detected, particularly a significant decrease of STMW volume in 2007–10 primarily attributable to a smaller volume formed. Variability of the heat content in the mode water region is dominated by the seasonal cycle and mesoscale eddies; there is only a weak link to STMW on interannual time scales, and no long-term trends in heat content and STMW thickness between 2002 and 2011 are detected. Weak lagged correlations among air–sea fluxes, oceanic heat content, and STMW thickness are found when averaged over the northwestern Pacific recirculation gyre region.
    Description: This work was sponsored by the National Science Foundation (Grants OCE-0220161, OCE-0825152, and OCE-0827125).
    Description: 2014-10-15
    Keywords: Atmosphere-ocean interaction ; Mesoscale processes ; Mesoscale systems ; Ocean dynamics ; Eddies ; Water masses
    Repository Name: Woods Hole Open Access Server
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    The Arctic Ocean spices up (2016)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 1277-1284, doi:10.1175/JPO-D-16-0027.1.
    Description: The contemporary Arctic Ocean differs markedly from midlatitude, ice-free, and relatively warm oceans in the context of density-compensating temperature and salinity variations. These variations are invaluable tracers in the midlatitudes, revealing essential fundamental physical processes of the oceans, on scales from millimeters to thousands of kilometers. However, in the cold Arctic Ocean, temperature variations have little effect on density, and a measure of density-compensating variations in temperature and salinity (i.e., spiciness) is not appropriate. In general, temperature is simply a passive tracer, which implies that most of the heat transported in the Arctic Ocean relies entirely on the ocean dynamics determined by the salinity field. It is shown, however, that as the Arctic Ocean warms up, temperature will take on a new role in setting dynamical balances. Under continued warming, there exists the possibility for a regime shift in the mechanisms by which heat is transported in the Arctic Ocean. This may result in a cap on the storage of deep-ocean heat, having profound implications for future predictions of Arctic sea ice.
    Description: Support was provided by the National Science Foundation Division of Polar Programs Award 1350046 and Office of Naval Research Grant Number N00014-12-1-0110.
    Description: 2016-10-05
    Keywords: Geographic location/entity ; Arctic ; Circulation/ Dynamics ; Ocean dynamics
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  • 88
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    Two modes of Gulf Stream variability revealed in the last two decades of satellite altimeter data (2014)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 44 (2014): 149–163, doi:10.1175/JPO-D-13-0136.1.
    Description: Monthly mapped sea level anomalies (MSLAs) of the NW Atlantic in the region immediately downstream of the Gulf Stream (GS) separation point reveal a leading mode in which the path shifts approximately 100 km meridionally about a nominal latitude of 39°N, producing coherent sea level anomaly (SLA) variability from 72° to 50°W. This mode can be captured by use of a simple 16-point index based on SLA data taken along the maximum of the observed variability in the region 33°–46°N and 45°–75°W. The GS shifts between 2010 and 2012 are the largest of the last decade and equal to the largest of the entire record. The second group of EOF modes of variability describes GS meanders, which propagate mainly westward interrupted by brief periods of eastward or stationary meanders. These meanders have wavelengths of approximately 400 km and can be seen in standard EOFs by spatial phase shifting of a standing meander pattern in the SLA data. The spectral properties of these modes indicate strong variability at interannual and longer periods for the first mode and periods of a few to several months for the meanders. While the former is quite similar to a previous use of the altimeter for GS path, the simple index is a useful measure of the large-scale shifts in the GS path that is quickly estimated and updated without changes in previous estimates. The time-scale separation allows a low-pass filtered 16-point index to be reflective of large-scale, coherent shifts in the GS path.
    Description: Agencia Canaria de Investigación, Innovación y Sociedad de la Información (ACIISI) grant program of Apoyo al Personal Investigador en Formación and NSF Grant OCE-0726720
    Description: 2014-07-01
    Keywords: Atlantic Ocean ; Circulation/ Dynamics ; Boundary currents ; Indices ; Ocean dynamics ; Observational techniques and algorithms ; Altimetry ; Mathematical and statistical techniques ; Empirical orthogonal functions
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  • 89
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    The air-launched autonomous micro observer (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-08-05
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric and Oceanic Technology 39(4), (2022): 491–502, https://doi.org/10.1175/jtech-d-21-0046.1.
    Description: The Air-Launched Autonomous Micro Observer (ALAMO) is a versatile profiling float that can be launched from an aircraft to make temperature and salinity observations of the upper ocean for over a year with high temporal sampling. Similar in dimensions and weight to an airborne expendable bathythermograph (AXBT), but with the same capability as Argo profiling floats, ALAMOs can be deployed from an A-sized (sonobuoy) launch tube, the stern ramp of a cargo plane, or the door of a small aircraft. Unlike an AXBT, however, the ALAMO float directly measures pressure, can incorporate additional sensors, and is capable of performing hundreds of ocean profiles compared to the single temperature profile provided by an AXBT. Upon deployment, the float parachutes to the ocean, releases the air-deployment package, and immediately begins profiling. Ocean profile data along with position and engineering information are transmitted via the Iridium satellite network, automatically processed, and then distributed by the Global Telecommunications System for use by the operational forecasting community. The ALAMO profiling mission can be modified using the two-way Iridium communications to change the profiling frequency and depth. Example observations are included to demonstrate the ALAMO’s utility.
    Description: This work was supported by the National Oceanographic and Atmospheric Administration under Grants NA13OAR4830233 (as part of CINAR Sandy Supplemental funding from the Disaster Relief Appropriations Act of 2013) and NA14OAR4320158 and by Office of Naval Research under Grants N0001416WX01384, N0001416WX01262, and N000141512293. ALAMO floats are commercially available from MRV Systems, LLC (https://www.mrvsys.com).
    Keywords: Ocean ; Hurricanes ; Ocean dynamics ; Mixed layer ; Aircraft observations ; Instrumentation/sensors
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  • 90
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    On the development of SWOT in situ calibration/validation for short-wavelength ocean topography (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-11-01
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric and Oceanic Technology 39(5), (2022): 595–617, https://doi.org/10.1175/jtech-d-21-0039.1.
    Description: The future Surface Water and Ocean Topography (SWOT) mission aims to map sea surface height (SSH) in wide swaths with an unprecedented spatial resolution and subcentimeter accuracy. The instrument performance needs to be verified using independent measurements in a process known as calibration and validation (Cal/Val). The SWOT Cal/Val needs in situ measurements that can make synoptic observations of SSH field over an O(100) km distance with an accuracy matching the SWOT requirements specified in terms of the along-track wavenumber spectrum of SSH error. No existing in situ observing system has been demonstrated to meet this challenge. A field campaign was conducted during September 2019–January 2020 to assess the potential of various instruments and platforms to meet the SWOT Cal/Val requirement. These instruments include two GPS buoys, two bottom pressure recorders (BPR), three moorings with fixed conductivity–temperature–depth (CTD) and CTD profilers, and a glider. The observations demonstrated that 1) the SSH (hydrostatic) equation can be closed with 1–3 cm RMS residual using BPR, CTD mooring and GPS SSH, and 2) using the upper-ocean steric height derived from CTD moorings enable subcentimeter accuracy in the California Current region during the 2019/20 winter. Given that the three moorings are separated at 10–20–30 km distance, the observations provide valuable information about the small-scale SSH variability associated with the ocean circulation at frequencies ranging from hourly to monthly in the region. The combined analysis sheds light on the design of the SWOT mission postlaunch Cal/Val field campaign.
    Description: The research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004). All authors are supported by the SWOT project. J. T. Farrar was partially supported by NASA NNX16AH76G.
    Description: 2022-11-01
    Keywords: Internal waves ; Ocean dynamics ; Small scale processes ; Altimetry ; Global positioning systems (GPS) ; In situ oceanic observations ; Ship observations
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  • 91
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    Coupled ocean–atmosphere offshore decay scale of cold SST signals along upwelling eastern boundaries (2017)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 29 (2016): 8317-8331, doi:10.1175/JCLI-D-16-0109.1.
    Description: A simple analytic model is developed to represent the offshore decay of cold sea surface temperature (SST) signals that originate from wind-driven upwelling at a coastal boundary. The model couples an oceanic mixed layer to an atmospheric boundary layer through wind stress and air–sea heat exchange. The primary mechanism that controls SST is a balance between Ekman advection and air–sea exchange. The offshore penetration of the cold SST signal decays exponentially with a length scale that is the product of the ocean Ekman velocity and a time scale derived from the air–sea heat flux and the radiative balance in the atmospheric boundary layer. This cold SST signal imprints on the atmosphere in terms of both the boundary layer temperature and surface wind. Nonlinearities due to the feedback between SST and atmospheric wind, baroclinic instability, and thermal wind in the atmospheric boundary layer all slightly modify this linear theory. The decay scales diagnosed from two-dimensional and three-dimensional eddy-resolving numerical ocean models are in close agreement with the theory, demonstrating that the basic physics represented by the theory remain dominant even in these more complete systems. Analysis of climatological SST off the west coast of the United States also shows a decay of the cold SST anomaly with scale roughly in agreement with the theory.
    Description: MASwas supported by the Andrew W. Mellon Foundation Endowed Fund for Innovative Research and the National Science Foundation under Grant OCE-1433170 and PLR-1415489. NS was supported by the National Aeronautics and Space Administration under Grant NNX14AL83G, the Department of Energy, Office of Science Grant DE-SC0006766, and the Japan Agency for Marine-Earth Science and Technology as part of the JAMSTEC-IPRC Joint Investigations.
    Description: 2017-05-03
    Keywords: Coastal flows ; Ekman pumping/transport ; Ocean dynamics
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  • 92
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    Decadal to multidecadal variability of the mixed layer to the south of the Kuroshio Extension region (2021)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 33(17), (2020): 7697-7714, https://doi.org/10.1175/JCLI-D-20-0115.1.
    Description: The decadal to multidecadal mixed layer variability is investigated in a region south of the Kuroshio Extension (130°E–180°, 25°–35°N), an area where the North Pacific subtropical mode water forms, during 1948–2012. By analyzing the mixed layer heat budget with different observational and reanalysis data, here we show that the decadal to multidecadal variability of the mixed layer temperature and mixed layer depth is covaried with the Atlantic multidecadal oscillation (AMO), instead of the Pacific decadal oscillation (PDO). The mixed layer temperature has strong decadal to multidecadal variability, being warm before 1970 and after 1990 (AMO positive phase) and cold during 1970–90 (AMO negative phase), and so does the mixed layer depth. The dominant process for the mixed layer temperature decadal to multidecadal variability is the Ekman advection, which is controlled by the zonal wind changes related to the AMO. The net heat flux into the ocean surface Qnet acts as a damping term and it is mainly from the effect of latent heat flux and partially from sensible heat flux. While the wind as well as mixed layer temperature decadal changes related to the PDO are weak in the western Pacific Ocean. Our finding proposes the possible influence of the AMO on the northwestern Pacific Ocean mixed layer variability, and could be a potential predictor for the decadal to multidecadal climate variability in the western Pacific Ocean.
    Description: Xiaopei Lin is supported by the China’s national key research and development projects (2016YFA0601803) and the National Natural Science Foundation of China (41925025 and U1606402). Baolan Wu is supported by the China Scholarship Council (201806330010). Lisan Yu thanks NOAA for support for her study on climate change and variability.
    Keywords: Atmosphere-ocean interaction ; Boundary currents ; Hadley circulation ; Ocean dynamics ; Teleconnections
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    Influences of precipitation on water mass transformation and deep convection (2012)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 42 (2012): 1684–1700, doi:10.1175/JPO-D-11-0230.1.
    Description: The influences of precipitation on water mass transformation and the strength of the meridional overturning circulation in marginal seas are studied using theoretical and idealized numerical models. Nondimensional equations are developed for the temperature and salinity anomalies of deep convective water masses, making explicit their dependence on both geometric parameters such as basin area, sill depth, and latitude, as well as on the strength of atmospheric forcing. In addition to the properties of the convective water, the theory also predicts the magnitude of precipitation required to shut down deep convection and switch the circulation into the haline mode. High-resolution numerical model calculations compare well with the theory for the properties of the convective water mass, the strength of the meridional overturning circulation, and also the shutdown of deep convection. However, the numerical model also shows that, for precipitation levels that exceed this critical threshold, the circulation retains downwelling and northward heat transport, even in the absence of deep convection.
    Description: This study was supported by the National Science Foundation underGrantsOCE-0850416, OCE-0959381, andOCE-0859381.
    Description: 2013-04-01
    Keywords: Boundary currents ; Deep convection ; Eddies ; Meridional overturning circulation ; Ocean dynamics ; Stability
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    The wavenumber–frequency content of resonantly excited equatorial waves (2012)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 42 (2012): 1834–1858, doi:10.1175/JPO-D-11-0234.1.
    Description: The theoretical resonant excitation of equatorial inertia–gravity waves and mixed Rossby–gravity waves is examined. Contrary to occasionally published expectations, solutions show that winds that are broadband in both zonal wavenumber and frequency do not in general produce peaks in the wavenumber–frequency spectrum of sea surface height (SSH) at wavenumbers associated with vanishing zonal group velocity. Excitation of total wave energy in inertia–gravity modes by broadband zonal winds is virtually wavenumber independent when the meridional structure of the winds does not impose a bias toward negative or positive zonal wavenumbers. With increasing wavenumber magnitude |k|, inertia–gravity waves asymptote toward zonally propagating pure gravity waves, in which the magnitude of meridional velocity υ becomes progressively smaller relative to the magnitude of zonal velocity u and pressure p. When the total wave energy is independent of wavenumber, this effect produces a peak in |υ|2 near the wavenumber where group velocity vanishes, but a trough in |p|2 (or SSH variance). Another consequence of the shift toward pure gravity wave structure is that broadband meridional winds excite inertia–gravity modes progressively less efficiently as |k| increases and υ becomes less important to the wave structure. Broadband meridional winds produce a low-wavenumber peak in total wave energy leading to a subtle elevation of |p|2 at low wavenumbers, but this is due entirely to the decrease in the forcing efficiency of meridional winds with increasing |k|, rather than to the vanishing of the group velocity. Physical conditions that might alter the above conclusions are discussed.
    Description: This research was funded by NASA Grant NNX10AO93G.
    Description: 2013-05-01
    Keywords: Inertia-gravity waves ; Ocean dynamics
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  • 95
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    An idealized modeling study of the midlatitude variability of the wind-driven meridional overturning circulation (2021)
    American Meteorological Society
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    Publication Date: 2022-05-27
    Description: Author Posting. © American Meteorological Society, 2021. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 51(8),(2021): 2425–2441, https://doi.org/10.1175/JPO-D-20-0317.1.
    Description: The frequency and latitudinal dependence of the midlatitude wind-driven meridional overturning circulation (MOC) is studied using theory and linear and nonlinear applications of a quasigeostrophic numerical model. Wind forcing is varied either by changing the strength of the wind or by shifting the meridional location of the wind stress curl pattern. At forcing periods of less than the first-mode baroclinic Rossby wave basin crossing time scale, the linear response in the middepth and deep ocean is in phase and opposite to the Ekman transport. For forcing periods that are close to the Rossby wave basin crossing time scale, the upper and deep MOC are enhanced, and the middepth MOC becomes phase shifted, relative to the Ekman transport. At longer forcing periods the deep MOC weakens and the middepth MOC increases, but eventually for long enough forcing periods (decadal) the entire wind-driven MOC spins down. Nonlinearities and mesoscale eddies are found to be important in two ways. First, baroclinic instability causes the middepth MOC to weaken, lose correlation with the Ekman transport, and lose correlation with the MOC in the opposite gyre. Second, eddy thickness fluxes extend the MOC beyond the latitudes of direct wind forcing. These results are consistent with several recent studies describing the four-dimensional structure of the MOC in the North Atlantic Ocean.
    Description: This study was supported by National Science Foundation Grant OCE-1947290.
    Description: 2022-01-13
    Keywords: Eddies ; Large-scale motions ; Meridional overturning circulation ; Ocean dynamics ; Planetary waves
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    How spice is stirred in the Bay of Bengal (2021)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(9), (2020): 2669-2688, doi:10.1175/JPO-D-19-0077.1
    Description: The scale-dependent variance of tracer properties in the ocean bears the imprint of the oceanic eddy field. Anomalies in spice (which combines anomalies in temperature T and salinity S on isopycnal surfaces) act as passive tracers beneath the surface mixed layer (ML). We present an analysis of spice distributions along isopycnals in the upper 200 m of the ocean, calculated with over 9000 vertical profiles of T and S measured along ~4800 km of ship tracks in the Bay of Bengal. The data are from three separate research cruises—in the winter monsoon season of 2013 and in the late and early summer monsoon seasons of 2015 and 2018. We present a spectral analysis of horizontal tracer variance statistics on scales ranging from the submesoscale (~1 km) to the mesoscale (~100 km). Isopycnal layers that are closer to the ML-base exhibit redder spectra of tracer variance at scales ≲10 km than is predicted by theories of quasigeostrophic turbulence or frontogenesis. Two plausible explanations are postulated. The first is that stirring by submesoscale motions and shear dispersion by near-inertial waves enhance effective horizontal mixing and deplete tracer variance at horizontal scales ≲10 km in this region. The second is that the spice anomalies are coherent with dynamical properties such as potential vorticity, and not interpretable as passively stirred.
    Description: We are grateful to the captain and crew of the R/V Roger Revelle and the R/V Thomas G. Thompson, and all ASIRI-OMM and MISO-BOB scientists. We thank Prof. Andrew Thompson and an anonymous reviewer for suggestions that improved the manuscript. This work was carried out under the Office of Naval Research’s Air-Sea Interaction Regional Initiative (ASIRI) and Monsoon Intra-Seasonal Oscillations in the Bay of Bengal (MISO-BOB) research initiatives, in collaboration with the Indian Ministry of Earth Science’s Ocean Mixing and Monsoons (OMM) initiative supported by the Monsoon Mission. Support came from ONR Grants N00014-16-1-2470, N00014-13-1-0451, N00014-17-1-2390 (G.S.J. and A.M.), N00014-14-1-0455 (J.M. and J.N), N00014-17-1-2511 (J.M.), N00014-13-1-0489, N00014-17-1-2391 (A.L.), N00014-15-1-2634 (E.S.), N00014-13-1-0456, N00014-17-1-2355 (A.T.), and N00014-13-1-0453, N00014-17-1-2880 (J.F.).
    Description: 2021-02-28
    Keywords: Ocean dynamics ; Thermocline ; Water masses/storage ; In situ oceanic observations ; Tracers ; Spectral analysis/models/distribution
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  • 97
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    Potential Vorticity and Instability in the Pacific Equatorial Undercurrent West of the Galápagos Archipelago (2022)
    American Meteorological Society
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    Publication Date: 2023-02-01
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(8), (2022): 1927-1943, https://doi.org/10.1175/jpo-d-21-0124.1.
    Description: The Galápagos Archipelago lies on the equator in the path of the eastward flowing Pacific Equatorial Undercurrent (EUC). When the EUC reaches the archipelago, it upwells and bifurcates into a north and south branch around the archipelago at a latitude determined by topography. Since the Coriolis parameter (f) equals zero at the equator, strong velocity gradients associated with the EUC can result in Ertel potential vorticity (Q) having sign opposite that of planetary vorticity near the equator. Observations collected by underwater gliders deployed just west of the Galápagos Archipelago during 2013–16 are used to estimate Q and to diagnose associated instabilities that may impact the Galápagos Cold Pool. Estimates of Q are qualitatively conserved along streamlines, consistent with the 2.5-layer, inertial model of the EUC by Pedlosky. The Q with sign opposite of f is advected south of the Galápagos Archipelago when the EUC core is located south of the bifurcation latitude. The horizontal gradient of Q suggests that the region between 2°S and 2°N above 100 m is barotropically unstable, while limited regions are baroclinically unstable. Conditions conducive to symmetric instability are observed between the EUC core and the equator and within the southern branch of the undercurrent. Using 2-month and 3-yr averages, e-folding time scales are 2–11 days, suggesting that symmetric instability can persist on those time scales.
    Description: This work was supported by the National Science Foundation (Grants OCE-1232971 and OCE-1233282), the NASA Earth and Space Science Fellowship Program (Grant 80NSSC17K0443), and the Global Ocean Monitoring and Observing Program of the National Oceanographic and Atmospheric Administration (NA13OAR4830216). Color maps are from Thyng et al. (2016).
    Description: 2023-02-01
    Keywords: Currents ; In situ oceanic observations ; Instability ; Mixing ; Ocean dynamics ; Pacific Ocean ; Potential vorticity ; Tropics
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  • 98
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    On characterizing ocean kinematics from surface drifters (2022)
    American Meteorological Society
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    Publication Date: 2023-02-01
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric and Oceanic Technology 39(8), (2022): 1183-1198, https://doi.org/10.1175/jtech-d-21-0068.1.
    Description: Horizontal kinematic properties, such as vorticity, divergence, and lateral strain rate, are estimated from drifter clusters using three approaches. At submesoscale horizontal length scales O(1–10)km, kinematic properties become as large as planetary vorticity f, but challenging to observe because they evolve on short time scales O(hourstodays). By simulating surface drifters in a model flow field, we quantify the sources of uncertainty in the kinematic property calculations due to the deformation of cluster shape. Uncertainties arise primarily due to (i) violation of the linear estimation methods and (ii) aliasing of unresolved scales. Systematic uncertainties (iii) due to GPS errors, are secondary but can become as large as (i) and (ii) when aspect ratios are small. Ideal cluster parameters (number of drifters, length scale, and aspect ratio) are determined and error functions estimated empirically and theoretically. The most robust method—a two-dimensional, linear least squares fit—is applied to the first few days of a drifter dataset from the Bay of Bengal. Application of the length scale and aspect-ratio criteria minimizes errors (i) and (ii), and reduces the total number of clusters and so computational cost. The drifter-estimated kinematic properties map out a cyclonic mesoscale eddy with a surface, submesoscale fronts at its perimeter. Our analyses suggest methodological guidance for computing the two-dimensional kinematic properties in submesoscale flows, given the recently increasing quantity and quality of drifter observations, while also highlighting challenges and limitations.
    Description: This research was supported by the Office of Naval Research (ONR) Departmental Research Initiative ASIRI under Grant N00014-13-1-0451 (SE and AM) and Grant N00014-13-1-0477 (VH and LC). The authors thank the captain and crew of the R/V Roger Revelle, and Andrew Lucas with the Multiscale Ocean Dynamics group at the Scripps Institution for Oceanography for providing the FastCTD data collected in 2015, which was supported by ONR Grant N00014-13-1-0489, as well as Eric D’Asaro for helpful discussions and Lance Braasch for assistance with the drifter dataset. AM and SE further thank NSF (Grant OCE-I434788) and ONR (Grant N00014-16-1-2470) for support. VH and LC were additionally supported by ONR Grants N00014-15-1-2286, N00014-14-1-0183, N00014-19-1-26-91 and NOAA Global Drifter Program (GDP) Grant NA15OAR4320071.
    Description: 2023-02-01
    Keywords: Indian Ocean ; Eddies ; Frontogenesis/frontolysis ; Fronts ; Lagrangian circulation/transport ; Ocean circulation ; Ocean dynamics
    Repository Name: Woods Hole Open Access Server
    Type: Article
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