ALBERT

Description: Aims Understanding carbon (C) and nitrogen (N) dynamics and their dependence on the stand density of an even-aged, mature forest provides knowledge that is important for forest management. This study investigated the differences in ecosystem total C and N storage and flux between a low-density stand (LD) and a high-density stand (HD) and examined the effects of stand density on aboveground net primary productivity (ANPP), total belowground C allocation (TBCA) and net ecosystem production (NEP) in a naturally regenerated, 65- to 75-year-old Pinus densiflora S. et Z. forest. Methods LD (450 trees ha –1 ) and HD (842 trees ha –1 ) were established in an even-aged, mature P. densiflora forest in September 2006. The forest had been naturally regenerated following harvesting, and the stand density was naturally maintained without any artificial management such as thinning. The diameter at breast height (DBH ≥ 5.0cm) of all live stems within the stands was measured yearly from 2007 to 2011. To compare C and N storage and fluxes in LD and HD, C and N pools in aboveground and belowground biomass, the forest floor, coarse woody debris (CWD) and soil; soil CO 2 efflux ( R S ); autotrophic respiration ( R A ); litter production; and soil N availability were measured. Further, ANPP, TBCA and NEP were estimated from plot-based measurement data. Important Findings Ecosystem C (Mg C ha –1 ) and N (Mg N ha –1 ) storage was, respectively, 173.0±7.3 (mean ± SE) and 4.69±0.30 for LD and 162±11.8 and 4.08±0.18 for HD. There were no significant differences in C and N storage in the ecosystem components, except for soils, between the two stands. In contrast, there were significant differences in aboveground ANPP and TBCA between the two stands ( P 〈 0.05). Litterfall, biomass increment and R S were major C flux components with values of, respectively, 3.89, 3.74 and 9.07 Mg C ha –1 year –1 in LD and 3.15, 2.94 and 7.06 Mg C ha –1 year –1 in HD. Biometric-based NEP (Mg C ha –1 year –1 ) was 4.18 in LD and 5.50 in HD. Although the even-aged, mature P. densiflora forest had similar C and N allocation patterns, it showed different C and N dynamics depending on stand density. The results of the current study will be useful for elucidating the effects of stand density on C and N storage and fluxes, which are important issues in managing natural mature forest ecosystems.

Description: In a consortium including 23 637 breast cancer patients and 25 579 controls of East Asian ancestry, we investigated 70 single-nucleotide polymorphisms (SNPs) in 67 independent breast cancer susceptibility loci recently identified by genome-wide association studies (GWASs) conducted primarily in European-ancestry populations. SNPs in 31 loci showed an association with breast cancer risk at P 〈 0.05 in a direction consistent with that reported previously. Twenty-one of them remained statistically significant after adjusting for multiple comparisons with the Bonferroni-corrected significance level of 〈0.0015. Eight of the 70 SNPs showed a significantly different association with breast cancer risk by estrogen receptor (ER) status at P 〈 0.05. With the exception of rs2046210 at 6q25.1, the seven other SNPs showed a stronger association with ER-positive than ER-negative cancer. This study replicated all five genetic risk variants initially identified in Asians and provided evidence for associations of breast cancer risk in the East Asian population with nearly half of the genetic risk variants initially reported in GWASs conducted in European descendants. Taken together, these common genetic risk variants explain ~10% of excess familial risk of breast cancer in Asian populations.

Description: In 2007, Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr/ ) was publicly open with 65 genomes corresponding to 58 fungal and Oomycete species. The CFGP provided six bioinformatics tools, including a novel tool entitled BLASTMatrix that enables search homologous genes to queries in multiple species simultaneously. CFGP also introduced Favorite, a personalized virtual space for data storage and analysis with these six tools. Since 2007, CFGP has grown to archive 283 genomes corresponding to 152 fungal and Oomycete species as well as 201 genomes that correspond to seven bacteria, 39 plants and 105 animals. In addition, the number of tools in Favorite increased to 27. The Taxonomy Browser of CFGP 2.0 allows users to interactively navigate through a large number of genomes according to their taxonomic positions. The user interface of BLASTMatrix was also improved to facilitate subsequent analyses of retrieved data. A newly developed genome browser, Seoul National University Genome Browser (SNUGB), was integrated into CFGP 2.0 to support graphical presentation of diverse genomic contexts. Based on the standardized genome warehouse of CFGP 2.0, several systematic platforms designed to support studies on selected gene families have been developed. Most of them are connected through Favorite to allow of sharing data across the platforms.

Description: Temporal atmospheric pressure variations introduce an artifact into percolation measurements in free-draining lysimeters. This anomaly is associated with transient pressure gradients that occur as fluid and gas pressures within the lysimeter equilibrate with atmospheric pressure changes at the drain. On the basis of harmonic (Fourier) analysis of a large (20 m × 10 m × 1.8 m) free-draining lysimeter, hourly percolation was maximally affected by pressure variations of ∼2 cycles per day, with the effect decreasing with decreasing frequency. Compared to the calculated pressure differences at the drain, the measured phase delay between percolation and the atmospheric pressure was less by ∼45°, which we attribute to an additional phase lag existing between the percolation and pressure difference at the drain. These pressure-induced changes in percolation rate can influence the outcome of water balances conducted via free-draining lysimeters.

Description: DNA methylation and hydroxymethylation have been implicated in normal development and differentiation, but our knowledge is limited about the genome-wide distribution of 5-methylcytosine (5 mC) and 5-hydroxymethylcytosine (5 hmC) during cellular differentiation. Using an in vitro model system of gradual differentiation of human embryonic stem (hES) cells into ventral midbrain-type neural precursor cells and terminally into dopamine neurons, we observed dramatic genome-wide changes in 5 mC and 5 hmC patterns during lineage commitment. The 5 hmC pattern was dynamic in promoters, exons and enhancers. DNA hydroxymethylation within the gene body was associated with gene activation. The neurogenesis-related genes NOTCH1 , RGMA and AKT1 acquired 5 hmC in the gene body and were up-regulated during differentiation. DNA methylation in the promoter was associated with gene repression. The pluripotency-related genes POU5F1 , ZFP42 and HMGA1 acquired 5 mC in their promoters and were down-regulated during differentiation. Promoter methylation also acted as a locking mechanism to maintain gene silencing. The mesoderm development-related genes NKX2-8 , TNFSF11 and NFATC1 acquired promoter methylation during neural differentiation even though they were already silenced in hES cells. Our findings will help elucidate the molecular mechanisms underlying lineage-specific differentiation of pluripotent stem cells during human embryonic development.

Description: The effect of ambient medium viscosity on the motility and flagellar beating motion of the dinoflagellate Prorocentrum minimum was experimentally investigated. Prorocentrum minimum is a thecate desmokont dinoflagellate with two flagella that emerge from the flagellar pore at the anterior end of the cell. A digital holographic particle tracking velocimetry technique was employed to capture the swimming trajectories of hundreds of P. minimum cells and to extract the kinematic motion parameters. The viscosity of the surrounding medium was changed from 1.12 cP (natural sea water at 22°C) to 11.31 cP by adding methylcellulose to increase fluid viscosity. In natural sea water, the swimming speeds of P. minimum cells ( n = 77) in a helical motion ranged from 5.4 to 138.4 µm/s with a mean speed of 51.3 ± 27.9 µm/s. The helix radius and pitch of the swimming trajectories are 3.08 ± 0.64 and 25.34 ± 7.96 µm/s, respectively. The longitudinal flagellum beats with a planar wave at a beating frequency of 87.10 ± 10.96 Hz. On the other hand, the transverse flagellum beats with a helical wave at a beating frequency of 45.38 ± 13.61 Hz. As the ambient medium viscosity increases, the beating frequency of flagella decreased and consequently, the swimming speed of P. minimum was reduced.

Description: In the present study, we investigated the 3' untranslated region (UTR) of the mouse core clock gene cryptochrome 1 ( Cry1 ) at the post-transcriptional level, particularly its translational regulation. Interestingly, the 3'UTR of Cry1 mRNA decreased its mRNA levels but increased protein amounts. The 3'UTR is widely known to function as a cis -acting element of mRNA degradation. The 3'UTR also provides a binding site for microRNA and mainly suppresses translation of target mRNAs. We found that AU-rich element RNA binding protein 1 (AUF1) directly binds to the Cry1 3'UTR and regulates translation of Cry1 mRNA. AUF1 interacted with eukaryotic translation initiation factor 3 subunit B and also directly associated with ribosomal protein S3 or ribosomal protein S14, resulting in translation of Cry1 mRNA in a 3'UTR-dependent manner. Expression of cytoplasmic AUF1 and binding of AUF1 to the Cry1 3'UTR were parallel to the circadian CRY1 protein profile. Our results suggest that the 3'UTR of Cry1 is important for its rhythmic translation, and AUF1 bound to the 3'UTR facilitates interaction with the 5' end of mRNA by interacting with translation initiation factors and recruiting the 40S ribosomal subunit to initiate translation of Cry1 mRNA.

Description: Both the timing and mechanism for the removal of a ∼150–250 km wide forearc block from southern Mexico during the Cenozoic are controversial. Principal competing hypotheses are (1) removal due to sinistral strike-slip shear, in which slow, diachronous removal of the Chortis Block throughout the Cenozoic is inferred, and (2) removal due to subduction erosion, in which rapid removal of a large forearc block during the late Oligocene/early Miocene is inferred to be synchronous with the rapid landward migration of the southern Mexican arc. New data indicate northeast-directed back-thrusting in (1) the Chacalapa shear zone west of −96.5°E, with the timing of shear deformation bracketed by a 25.5 ± 0.5 Ma U/Pb zircon age and a 20.7 ± 0.6 Ma Ar/Ar biotite age, and (2) in an unnamed shear zone to the south, with the timing of deformation bracketed by a 27.5 ± 0.5 Ma U/Pb zircon age and a 25.1 ± 0.2 Ma Ar/Ar biotite age. Zircon and biotite ages date the emplacement and cooling of deformed plutons, respectively. The observed back-thrusting is consistent with a model of forearc removal due to subduction-erosion processes because it is evidence for subduction-orthogonal shortening occurring within the upper plate just before the landward migration of the southern Mexican arc. Rapid subduction of the southern Mexican forearc could have recycled continental lithosphere into the upper mantle at a rate up to half the global average rate of subduction erosion during the late Oligocene/early Miocene.

Description: Motivation: A number of long non-coding RNAs (lncRNAs) have been identified by deep sequencing methods, but their molecular and cellular functions are known only for a limited number of lncRNAs. Current databases on lncRNAs are mostly for cataloging purpose without providing in-depth information required to infer functions. A comprehensive resource on lncRNA function is an immediate need. Results: We present a database for functional investigation of lncRNAs that encompasses annotation, sequence analysis, gene expression, protein binding and phylogenetic conservation. We have compiled lncRNAs for six species (human, mouse, zebrafish, fruit fly, worm and yeast) from ENSEMBL, HGNC, MGI and lncRNAdb. Each lncRNA was analyzed for coding potential and phylogenetic conservation in different lineages. Gene expression data of 208 RNA-Seq studies (4995 samples), collected from GEO, ENCODE, modENCODE and TCGA databases, were used to provide expression profiles in various tissues, diseases and developmental stages. Importantly, we analyzed RNA-Seq data to identify coexpressed mRNAs that would provide ample insights on lncRNA functions. The resulting gene list can be subject to enrichment analysis such as Gene Ontology or KEGG pathways. Furthermore, we compiled protein–lncRNA interactions by collecting and analyzing publicly available CLIP-seq or PAR-CLIP sequencing data. Finally, we explored evolutionarily conserved lncRNAs with correlated expression between human and six other organisms to identify functional lncRNAs. The whole contents are provided in a user-friendly web interface. Availability and implementation: lncRNAtor is available at http://lncrnator.ewha.ac.kr/ . Contact: sanghyuk@ewha.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online.

Description: A seven-year time series of satellite radar images over Unimak Island, Alaska-site of Westdahl Volcano, Fisher Caldera and Shishaldin Volcano-was processed using a model-free Persistent Scatterer Interferometry (PSI) technique assisted by Numerical Weather Prediction (NWP) model. The deformation-only signals were optimally extracted from atmosphere-contaminated phase records. The reconstructed deformation time series maps are compared with campaign and continuous Global Positioning System (GPS) measurements as well as Small Baseline Subset (SBAS) InSAR results for quality assessment and geophysical interpretation. We observed subtle surface inflation at Westdahl Volcano that can be fit by a Mogi source located at approximately 3.6 km north of Westdahl peak and at depth of about 6.9 km that is consistent to the GPS estimated depth for the 1998 to 2001 time period. The magma chamber volume change decays during the period of 2003 to 2010. The deformation field over Fisher Caldera is steadily subsiding over time. Its best-fit analytical model is a sill source that is about 7.9 km in length, 0.54 km in width, and locates at about 5.5 km BSL underneath the center of Fisher Caldera with strike angle of N52°E. Very little deformation was detected near Shishaldin peak, however, a region approximately 15 km east of Shishaldin, as well as an area at the Tugamak range at about 30 km northwest of Shishaldin, show evidence for movement towards the satellite, with a temporal signature correlated with the 2004 Shishaldin eruption. The cause of these movements is unknown.