ALBERT

Beschreibung: The Kidnappers [~1200 km 3 dense rock equivalent (DRE)] and Rocky Hill (~200 km 3 DRE) caldera-forming events in the Taupo Volcanic Zone, New Zealand, were erupted in close succession from the Mangakino volcanic centre. They have identical radiometric ages at ~1 Ma, yet erosion along the contact between the two deposits suggests that some years to decades separated the two eruptions. Field constraints and the similarities of crystal textures and compositions and glass chemistries of both eruption deposits demonstrate that they came from one overall magmatic system with a common crystal mush source. However, second-order variations in these parameters confirm that the Kidnappers and Rocky Hill deposits represent distinct events and are not the products of a single zoned magma chamber. The systematically zoned Kidnappers fall deposits provide evidence for the tapping of three discrete magma bodies, whereas the succeeding Kidnappers ignimbrite is compositionally more diverse. The transition from fall to flow deposition marks a change in the style of caldera collapse and the simultaneous evacuation of discrete but compositionally diverse melts, each of which underwent a distinct evolution and was held at slightly different P–T conditions prior to eruption. Contrasting plagioclase and orthopyroxene zonation patterns are present in pumices originating from three discrete magma bodies. Less evolved mafic melts interacted with the system, which mobilized portions of the final erupted melt through heating and volatile or chemical exchange in the mush. The two largest Kidnappers melt-dominant bodies were re-tapped in modified form, or re-established from their common mush source, prior to the Rocky Hill event. Rocky Hill pumices contain common, fluid-affected antecrystic crystal clots derived from chamber wall material. Amphibole compositions from each eruption reflect melt evolution processes and, in particular, the contemporaneous crystallization of biotite and breakdown of orthopyroxene. Plagioclase and orthopyroxene from Rocky Hill pumices share common zonation patterns with those from the two largest magma bodies in the Kidnappers. The rapid production of new melt-dominant bodies and the triggering of the Rocky Hill eruption reflect the ability of the magmatic system to rejuvenate on a geologically short timescale. The Mangakino centre did not follow a typical cycle of decreased activity after the supervolcanic Kidnappers event, instead producing a second caldera-forming eruption, within years to decades from the same system.

Beschreibung: Transposable elements (TEs) comprise large fractions of many eukaryotic genomes and imperil host genome integrity. The host genome combats these challenges by encoding proteins that silence TE activity. Both the introduction of new TEs via horizontal transfer and TE sequence evolution requires constant innovation of host-encoded TE silencing machinery to keep pace with TEs. One form of host innovation is the adaptation of existing, single-copy host genes. Indeed, host suppressors of TE replication often harbor signatures of positive selection. Such signatures are especially evident in genes encoding the p iwi- i nteracting-RNA pathway of gene silencing, for example, the female germline-restricted TE silencer, HP1D/Rhino . Host genomes can also innovate via gene duplication and divergence. However, the importance of gene family expansions, contractions, and gene turnover to host genome defense has been largely unexplored. Here, we functionally characterize Oxpecker , a young, tandem duplicate gene of HP1D/rhino . We demonstrate that Oxpecker supports female fertility in Drosophila melanogaster and silences several TE families that are incompletely silenced by HP1D/Rhino in the female germline. We further show that, like Oxpecker , at least ten additional, structurally diverse, HP1D/rhino -derived daughter and "granddaughter" genes emerged during a short 15-million year period of Drosophila evolution. These young paralogs are transcribed primarily in germline tissues, where the genetic conflict between host genomes and TEs plays out. Our findings suggest that gene family expansion is an underappreciated yet potent evolutionary mechanism of genome defense diversification.

Beschreibung: The motion of cells and molecules through biological environments is often hindered by the presence of other cells and molecules. A common approach to modeling this kind of hindered transport is to examine the mean squared displacement (MSD) of a motile tracer particle in a lattice-based stochastic random walk in which some lattice sites are occupied by obstacles. Unfortunately, stochastic models can be computationally expensive to analyze because we must average over a large ensemble of identically prepared realizations to obtain meaningful results. To overcome this limitation we describe an exact method for analyzing a lattice-based model of the motion of an agent moving through a crowded environment. Using our approach we calculate the exact MSD of the motile agent. Our analysis confirms the existence of a transition period where, at first, the MSD does not follow a power law with time. However, after a sufficiently long period of time, the MSD increases in proportion to time. This latter phase corresponds to Fickian diffusion with a reduced diffusivity owing to the presence of the obstacles. Our main result is to provide a mathematically motivated, reproducible, and objective estimate of the amount of time required for the transport to become Fickian. Our new method to calculate this crossover time does not rely on stochastic simulations.

Beschreibung: We outline a modeling study of an extrinsic semiconductor interface formed from the interaction of nanostructured metal oxide decorated porous silicon and used for sensing gas phase analytes. We consider simple conductometric sensors that operate at room temperature and atmospheric pressure. Nanostructured metal oxide deposition provides a matrix of responses to various analytes, facilitating the extraction of ambient gas concentrations from sensor responses. The sensors are simulated in four stages with an emphasis to the continual improvement of the modeling effort. Stage 1 focuses solely on the diffusion mechanics of an analyte gas into and out of a micro/nanoporous interface and the observed linear response at low concentrations. Stage 2 focuses on the non-linearity resulting primarily from the quenching of sensor response at higher concentrations and introduces an absorption response mechanism. Here, stage 3 demonstrates how the consideration of charge carrier density leads to the development of a new Fermi-distribution based response mechanism. Stage 4 establishes a combined absorption-Fermi-distribution response mechanism.

Beschreibung: Throughout their evolutionary history, genomes acquire new genetic material that facilitates phenotypic innovation and diversification. Developmental processes associated with reproduction are particularly likely to involve novel genes. Abundant gene creation impacts the evolution of chromosomal gene content and general regulatory mechanisms such as dosage compensation. Numerous studies in model organisms have found complex and, at times contradictory, relationships among these genomic attributes highlighting the need to examine these patterns in other systems characterized by abundant sexual selection. Therefore, we examined the association among novel gene creation, tissue-specific gene expression, and chromosomal gene content within stalk-eyed flies. Flies in this family are characterized by strong sexual selection and the presence of a newly evolved X chromosome. We generated RNA-seq transcriptome data from the testes for three species within the family and from seven additional tissues in the highly dimorphic species, Teleopsis dalmanni . Analysis of dipteran gene orthology reveals dramatic testes-specific gene creation in stalk-eyed flies, involving numerous gene families that are highly conserved in other insect groups. Identification of X-linked genes for the three species indicates that the X chromosome arose prior to the diversification of the family. The most striking feature of this X chromosome is that it is highly masculinized, containing nearly twice as many testes-specific genes as expected based on its size. All the major processes that may drive differential sex chromosome gene content—creation of genes with male-specific expression, development of male-specific expression from pre-existing genes, and movement of genes with male-specific expression—are elevated on the X chromosome of T. dalmanni . This masculinization occurs despite evidence that testes expressed genes do not achieve the same levels of gene expression on the X chromosome as they do on the autosomes.

Beschreibung: The GeneWeaver data and analytics website ( www.geneweaver.org ) is a publically available resource for storing, curating and analyzing sets of genes from heterogeneous data sources. The system enables discovery of relationships among genes, variants, traits, drugs, environments, anatomical structures and diseases implicitly found through gene set intersections. Since the previous review in the 2012 Nucleic Acids Research Database issue, GeneWeaver's underlying analytics platform has been enhanced, its number and variety of publically available gene set data sources has been increased, and its advanced search mechanisms have been expanded. In addition, its interface has been redesigned to take advantage of flexible web services, programmatic data access, and a refined data model for handling gene network data in addition to its original emphasis on gene set data. By enumerating the common and distinct biological molecules associated with all subsets of curated or user submitted groups of gene sets and gene networks, GeneWeaver empowers users with the ability to construct data driven descriptions of shared and unique biological processes, diseases and traits within and across species.

Beschreibung: Understanding epigenetic differences that distinguish neurons and glia is of fundamental importance to the nascent field of neuroepigenetics. A recent study used genome-wide bisulfite sequencing to survey differences in DNA methylation between these two cell types, in both humans and mice. That study minimized the importance of cell type-specific differences in CpG methylation, claiming these are restricted to localized genomic regions, and instead emphasized that widespread and highly conserved differences in non-CpG methylation distinguish neurons and glia. We reanalyzed the data from that study and came to markedly different conclusions. In particular, we found widespread cell type-specific differences in CpG methylation, with a genome-wide tendency for neuronal CpG-hypermethylation punctuated by regions of glia-specific hypermethylation. Alarmingly, our analysis indicated that the majority of genes identified by the primary study as exhibiting cell type-specific CpG methylation differences were misclassified. To verify the accuracy of our analysis, we isolated neuronal and glial DNA from mouse cortex and performed quantitative bisulfite pyrosequencing at nine loci. The pyrosequencing results corroborated our analysis, without exception. Most interestingly, we found that gene-associated neuron vs. glia CpG methylation differences are highly conserved across human and mouse, and are very likely to be functional. In addition to underscoring the importance of independent verification to confirm the conclusions of genome-wide epigenetic analyses, our data indicate that CpG methylation plays a major role in neuroepigenetics, and that the mouse is likely an excellent model in which to study the role of DNA methylation in human neurodevelopment and disease.

Beschreibung: Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata ( emdatabank.org ). We provide here an overview of the rapidly growing 3DEM structural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Bank. In addition, we describe progress and approaches toward development of validation protocols and methods, working with the scientific community, in order to create a validation pipeline for 3DEM data.

Beschreibung: A series of indirectly driven capsule implosions has been performed on the National Ignition Facility to assess the relative contributions of ablation-front instability growth vs. fuel compression on implosion performance. Laser pulse shapes for both low and high-foot pulses were modified to vary ablation-front growth and fuel adiabat, separately and controllably. Three principal conclusions are drawn from this study: (1) It is shown that reducing ablation-front instability growth in low-foot implosions results in a substantial (3-10X) increase in neutron yield with no loss of fuel compression. (2) It is shown that reducing the fuel adiabat in high-foot implosions results in a significant (36%) increase in fuel compression together with a small (10%) increase in neutron yield. (3) Increased electron preheat at higher laser power in high-foot implosions, however, appears to offset the gain in compression achieved by adiabat-shaping at lower power. These results taken collectively bridge the space between the higher compression low-foot results and the higher yield high-foot results.