bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of HSV-1 strains circulating in Finland demonstrates the uncoupling of whole-genome relatedness and phenotypic outcomes of viral infection
Authors: Bowen Christopher D. , Paavilainen Henrik , Renner Daniel W. , Palomäki Jussi , Lehtinen Jenni , Vuorinen Tytti , Norberg Peter , Hukkanen Veijo , Szpara Moriah L. 
Published: September 2018

AbstractA majority of adults in Finland are seropositive carriers of herpes simplex viruses (HSV). Infection occurs at epithelial or mucosal surfaces, after which virions enter innervating nerve endings, eventually establishing lifelong infection in neurons of the sensory or autonomic nervous system. Recent data have highlighted the genetic diversity of HSV-1 strains, and demonstrated apparent geographic patterns in strain similarity. Though multiple HSV-1 genomes have been sequenced from Europe to date, there is a lack of sequenced genomes from Nordic countries. Finland’s history includes at least two major waves of human migration, suggesting the potential for diverse viruses to persist in the population. Here we used HSV-1 clinical isolates from Finland to test the relationship between viral phylogeny, genetic variation, and phenotypic characteristics. We found that Finnish HSV-1 isolates separated into two distinct phylogenetic groups, potentially reflecting historical waves of human (and viral) migration into Finland. Each HSV-1 isolate harbored a distinct set of phenotypes in cell culture, including differences in virus production, extracellular virus release, and cell-type-specific fitness. Importantly, the phylogenetic clusters were not predictive of any detectable pattern in phenotypic differences, demonstrating that whole-genome relatedness is not a proxy for overall viral phenotype. Instead, we highlight specific gene-level differences that may contribute to observed phenotypic differences, and we note that strains from different phylogenetic groups contain the same genetic variations.ImportanceHerpes simplex viruses (HSV) infect a majority of adults. Recent data have highlighted the genetic diversity of HSV-1 strains, and demonstrated apparent genomic relatedness between strains from the same geographic region. We use HSV-1 clinical isolates from Finland to test the relationship between viral genomic and geographic relationships, differences in specific genes, and characteristics of viral infection. We found that viral isolates from Finland separated into two distinct groups of genomic and geographic relatedness, potentially reflecting historical patterns of human and viral migration into Finland. These Finland HSV-1 isolates had distinct infection characteristics in multiple cell types tested, which were specific to each isolate and did not group according to genomic and geographic relatedness. This demonstrates that HSV-1 strain differences in specific characteristics of infection are set by a combination of host cell type and specific viral gene-level differences.
Multiplex logic processing isothermal diagnostic assays for an evolving virus
Authors: Bhadra Sanchita , Saldaña Miguel A. , Han Hannah Grace , Hughes Grant L. , Ellington Andrew D. 
Published: September 2018

AbstractWe have developed a generalizable ‘smart molecular diagnostic’ capable of accurate point-of-care (POC) detection of variable nucleic acid targets. Our one-pot isothermal assay relies on multiplex execution of four loop-mediated isothermal amplification reactions, with primers that are degenerate and redundant, thereby increasing the breadth of targets while reducing the probability of amplification failure. An easy-to-read visual answer is computed directly by a multi-input Boolean OR gate signal transducer that uses degenerate strand exchange probes to assess any combination of amplicons. We demonstrate our platform by using the same assay to detect divergent Asian and African lineages of the evolving Zika virus (ZIKV), while maintaining selectivity against non-target viruses. Direct analysis of biological specimens proved possible, with 20 virions / µl being directly detected in human saliva within 90 minutes, and crudely macerated ZIKV-infected Aedes aegypti mosquitoes being identified with 100% specificity and sensitivity. The ease-of-use with minimal instrumentation, broad programmability, and built-in fail-safe reliability make our smart molecular diagnostic attractive for POC use.
Protein inference using PIA workflows and PSI standard file formats
Authors: Uszkoreit Julian , Perez-Riverol Yasset , Eggers Britta , Marcus Katrin , Eisenacher Martin 
Published: September 2018

AbstractProteomics using LC-MS/MS has become one of the main methods to analyze the proteins in biological samples in high-throughput. But the existing mass spectrometry instruments are still limited with respect to resolution and measurable mass ranges, which is one of the main reasons why shotgun proteomics is the major approach. Here, proteins are digested, which leads to the identification and quantification of peptides instead. While often neglected, the important step of protein inference needs to be conducted to infer from the identified peptides to the actual proteins in the original sample.In this work, we highlight some of the previously published and newly added features of the tool PIA – Protein Inference Algorithms, which helps the user with the protein inference of measured samples. We also highlight the importance of the usage of PSI standard file formats, as PIA is the only current software supporting all available standards used for spectrum identification and protein inference. Additionally, we briefly describe the benefits of working with workflow environments for proteomics analyses and show the new features of the PIA nodes for the KNIME Analytics Platform. Finally, we benchmark PIA against a recently published dataset for isoform detection.PIA is open source and available for download on GitHub (https://github.com/mpc-bioinformatics/pia) or directly via the community extensions inside the KNIME analytics platform.
Atypically larger variability of resource allocation accounts for visual working memory deficits in schizophrenia
Authors: Zhao Yi-Jie , Ma Tianye , Ran Xuemei , Zhang Li , Zhang Ru-Yuan , Ku Yixuan 
Published: September 2018

AbstractSchizophrenia patients are known to have profound deficits in visual working memory (VWM), and almost all previous studies attribute the deficits to decreased memory capacity. This account, however, ignores the potential contributions of other VWM components (e.g., memory precision). Here, we measure the VWM performance of schizophrenia patients and healthy control subjects on two classical delay-estimation tasks. Moreover, we thoroughly evaluate several established computational models of VWM to compare the performance of the two groups. We find that the model assuming variable precision across items and trials is the best model to explain the performance of both groups. According to the variable-precision model, schizophrenia subjects exhibit abnormally larger variability of allocating memory resources rather than resources per se. These results invite a rethink of the widely accepted decreased-capacity theory and propose a new perspective on the diagnosis and rehabilitation of schizophrenia.
Snail shell colour evolution in urban heat islands detected via citizen science
Authors: Kerstes Niels A. G. , Breeschoten Thijmen , Kalkman Vincent , Schilthuizen Menno 
Published: September 2018

AbstractThe extreme environmental conditions that prevail in cities are known to cause selection pressures leading to adaptive changes in wild, city-dwelling, organisms (“urban evolution”). The urban heat island, elevated temperatures in the city centre due to a combination of generation, reflection, and trapping of heat, is one of the best recognised and most widespread urban environmental factors. Here, we used a citizen-science approach to study the effects of urban heat on genetically-determined shell colour in the land snailCepaea nemoralisin the Netherlands. We used smartphone applications to obtain colour data on almost 8,000 snails throughout the country. Our analysis shows that snails in urban centres are more likely to be yellow than pink, an effect predicted on the basis of thermal selection. Urban yellow snails are also more likely to carry dark bands at the underside of the shell; these bands might affect thermoregulation in yet underexplored ways.
Extinction times in diffusive public good population dynamics
Authors: Kimmel Gregory J. , Gerlee Philip , Altrock Philipp M. 
Published: September 2018

AbstractThe co-evolutionary dynamics of competing populations can be strongly affected by frequency-dependent selection and population structure in space. As co-evolving populations grow into a spatial domain, their initial spatial arrangement, as well as their growth rate differences determine the dynamics. Here, we are interested in the dynamics of producers and free-rider co-evolution in the context of an ecological public good that is produced by a sub-population but evokes growth benefits to all individuals. We consider the spatial growth dynamics in one, two and three dimensions by modeling producer cell, free-rider cell and public good densities in space, driven by birth, death and diffusion. Typically, one population goes extinct. We find that uncorrelated initial spatial structures do not influence the time to extinction in comparison to the well-mixed system. We derive a slow manifold solution in order to estimate the time to extinction of either free-riders or producers. For invading populations, i.e. for populations that are initially highly segregated, we observe a traveling wave, whose speed can be calculated to improve the extinction time estimate by a simple superposition of the two times. Our results show that local effects of spatial dynamics evolve independently of the dynamics of the mean populations. Our considerations provide quantitative predictions for the transient dynamics of cooperative traits under pressure of extinction, and a potential experiment to derive elusive details of the fitness function of an ecological public goods game through extinction time observations.Author SummaryEcological public goods (PG) relationships emerge in growing cellular populations, for example between bacteria and cancer cells. We study the eco-evolutionary dynamics of a PG in populations that grow in space. In our model, public good-producer cells and free-rider cells can grow according to their own birth and death rates. Co-evolution occurs due to public good-driven surplus in the intrinsic growth rates and a cost to producers. A net growth rate benefit to free-riders leads to the well-known tragedy of the commons in which producers go extinct. What is often omitted from discussions is the time scale on which this extinction can occur, especially in spatial populations. We derive analytical estimates of the time to extinction in different spatial settings, and identify spatial scenarios in which extinction takes long enough such that the tragedy of the commons never occurs within the lifetime of the populations. Using numerical simulations we analyze the deviations from analytical predictions. Our results have direct implications for inferring ecological public good game properties from in vitro and in vivo experimental observations.
A Hybridde novoAssembly of the Sea Pansy (Renilla muelleri) Genome
Authors: Jiang Justin , Quattrini Andrea M. , Francis Warren R. , Ryan Joseph F. , Rodríguez Estefanía , McFadden Catherine S. 
Published: September 2018

AbstractBackgroundOver 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral “forests” which provide unique niches and three-dimensional living space for other organisms. The octocoral genusRenillainhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans.Renillais especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several cnidarian genomes are currently available, the majority are from hexacorals. Here, we present ade novoassembly of theR. muellerigenome, making this the first complete draft genome from an octocoral.FindingsWe generated a hybridde novoassembly using the Maryland Super-Read Celera Assembler v.3.2.6 (MaSuRCA). The final assembly included 4,825 scaffolds and a haploid genome size of 172 Mb. A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustusab initiogene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone,Nematostella vectensis,or to the Uniprot database. Although theR. muellerigenome is smaller (172 Mb) than other publicly available, hexacoral genomes (256-448 Mb), theR. muellerigenome is similar to the hexacoral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models.ConclusionsTheR. muellerihybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.
Biophysical model of axonal stimulation in epiretinal visual prostheses
Authors: Beyeler Michael 
Published: September 2018

AbstractVisual prostheses aim to restore vision to people blinded from degenerative photoreceptor diseases by electrically stimulating surviving neurons in the retina. However, a major challenge with epiretinal prostheses is that they may accidentally activate passing axon fibers, causing severe perceptual distortions. To investigate the effect of axonal stimulation on the retinal response, we developed a computational model of a small population of morphologically and biophysically detailed retinal ganglion cells, and simulated their response to epiretinal electrical stimulation. We found that activation thresholds of ganglion cell somas and axons varied systematically with both stimulus pulse duration and electrode-retina distance. These findings have important implications for the improvement of stimulus encoding methods for epiretinal prostheses.
Carbonic anhydrase network of genes trigger cytosolic pH enabling differentiation from quiescence
Authors: Yasin Jeshima Khan , Chaudhary Sakshi , Verma Nidhi , Vennila Sengottaiyan 
Published: September 2018

AbstractBackgroundCarbonic anhydrase regulates various cellular processes. Intracellular pH flux impacted by carbonic anhydrase alters the enzyme’s allosteric active site which effects several downstream cellular processes. Earlier, we reported that, the catalytic activity of carbonic anhydrase is independent, but direction of catalysis is affected by cellular pH level. On the other hand carbonic anhydrase alters the cytosolic pH level to facilitate allosteric phosphorylation of proteins which further leads to cellular differentiation through a process being regulated by ncRNAs.ResultsThis study illustrates various ways of cell differentiation/ organ development regulation via carbonic anhydrase interacting network of proteins involved in various cellular processes. It is involved in protein degradation process of other proteins like RPT, 26S proteasome, AT3G15120 and its variant producing ncRNA, etc. Carbonic anhydrase indirectly involved in signaling process along with MAPK in providing innate resistance against biotic and abiotic stresses. It is also indirectly linked to cell membrane transporters like H+-ATPase and V-ATPase B.ConclusionsThough carbonic anhydrase is not directly linked with EMS1 as revealed by network analyses and protein-protein interaction there could be a suitable condition generated by the carbonic anhydrase for EMS1 to be active. Hence, we report that carbonic anhydrase, along with other pH regulating gene complexes plays a major role for making EMS1 functional.
When do shifts in trait dynamics precede population declines?
Authors: Baruah Gaurav , Clements Christopher F. , Guillaume Fréderic , Ozgul Arpat 
Published: September 2018

AbstractPredicting population responses to environmental change is an on-going challenge in ecology. Studies investigating the links between fitness-related phenotypic traits and demography have shown that trait dynamic responses to environmental change can sometimes precede population dynamic responses, and thus, can be used as an early warning signal. However, it is still unknown under which ecological and evolutionary circumstances, shifts in fitness-related traits can precede population responses to environmental perturbation. Here, we take a trait-based demographic approach and investigate both trait and population dynamics in a density-regulated population in response to a gradual change in the environment. We explore the ecological and evolutionary constraints under which shifts in a fitness-related trait precedes a decline in population size. We show both analytically and with experimental data that under medium-to-slow rate of environmental change, shifts in trait value can precede population decline. We further show the positive influence of environmental predictability, average reproductive rate, plasticity, and genetic variation on shifts in trait dynamics preceding potential population declines. These results still hold under non-constant genetic variation and environmental stochasticity. Our study highlights ecological and evolutionary circumstances under which a fitness-related trait can be used as an early warning signal of an impending population decline.
Cdh2 coordinates Myosin-II dependent internalisation of the zebrafish neural plate
Authors: Araya Claudio , Häkkinen Hanna-Maria , Carcamo Luis , Cerda Mauricio , Savy Thierry , Rookyard Christopher , Peyriéras Nadine , Clarke Jonathan D 
Published: September 2018

AbstractTissue internalisation is a key morphogenetic mechanism by which embryonic tissues generate complex internal organs and a number of studies of epithelia have outlined a general view of tissue internalisation. Here we have used quantitative live imaging and mutant analysis to determine whether similar mechanisms are responsible for internalisation in a tissue that apparently does not have a typical epithelial organisation – the zebrafish neural plate. We found that although zebrafish embryos begin neurulation without a conventional epithelium, medially located neural plate cells adopt strategies typical of epithelia in order to constrict their dorsal surface membrane during cell internalisation. Furthermore, we show that Myosin-II activity is a significant driver of this transient cell remodeling which also depends on Cdh2 (N-cadherin). Abrogation of Cdh2 results in defective Myosin-II distribution, mislocalised internalisation events and defective neural plate morphogenesis. Our work suggests Cdh2 coordinates Myosin-II dependent internalisation of the zebrafish neural plate.
A Sparse Unreliable Distributed Code Underlies the Limits of Behavioral Discrimination
Authors: Sriram Balaji , Cruz-Martin Alberto , Li Lillian , Reinagel Pamela , Ghosh Anirvan 
Published: September 2018

ABSTRACTThe cortical code that underlies perception must enable subjects to perceive the world at timescales relevant for behavior. We find that mice can integrate visual stimuli very quickly (<100 ms) to reach plateau performance in an orientation discrimination task. To define features of cortical activity that underlie performance at these timescales, we measured single unit responses in the mouse visual cortex at timescales relevant to this task. In contrast to high contrast stimuli of longer duration, which elicit reliable activity in individual neurons, stimuli at the threshold of perception elicit extremely sparse and unreliable responses in V1 such that the activity of individual neurons do not reliably report orientation. Integrating information across neurons, however, quickly improves performance. Using a linear decoding model, we estimate that integrating information over 50-100 neurons is sufficient to account for behavioral performance. Thus, at the limits of perception the visual system is able to integrate information across a relatively small number of highly unreliable single units to generate reliable behavior.
Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum L.)
Authors: Songsomboon Kittikun , Crawford Ryan , Crawford Jamie , Hansen Julie , Cummings Jaime , Mattson Neil , Bergstrom Gary , Viands Donald 
Published: September 2018

ABSTRACTSwitchgrass (Panicum virgatum L.), a northern native perennial grass, suffers from yield reduction from Bipolaris leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoe-maker. This study aimed for determining the resistant populations via multiple phenotyping approaches and identifying potential resistance genes to the disease from genome-wide association studies in the switchgrass northern association panel. The disease resistance was evaluated from both natural (field evaluations in NY and PA) and artificial inoculations (detached leaf and leaf disk assays). There are ten out of the 66 populations showed the most resistant based on a combination of detached leaf, leaf disk, and mean from two locations. The GWAS from five subgroups from the association panel to different disease evaluation combinations yielded 27 significant SNPs on 12 chromosomes: 1K, 2K, 2N, 3K, 3N, 4N, 5K, 5N, 6N, 7K, 7N, and 9N accumulatively explaining phenotypic variance of BLUPs of detached leaf percent lesion via image analysis 26.52% at most and BLUPs of leaf disk percent lesion via image analysis 3.28% at least. Within linkage disequilibrium of 20 kb, these SNP markers linked with the potential resistance genes including genes encoding for NBS-LRR, PPR, cell wall related proteins, homeostatic proteins, anti-apoptotic proteins, and ABC transporters.
A Theory of Centriole Duplication Based on Self-Organized Spatial Pattern Formation
Authors: Takao Daisuke , Yamamoto Shohei , Kitagawa Daiju 
Published: September 2018

SUMMARYIn each cell cycle, centrioles are duplicated to produce a single copy of each pre-existing centriole. At the onset of centriole duplication, the master regulator Polo-like kinase 4 (Plk4) undergoes a dynamic change in its spatial pattern on the periphery of the pre-existing centriole, forming a single duplication site. However, the significance and mechanisms of this pattern transition remain largely unknown. Using super-resolution imaging, we found that centriolar Plk4 exhibits periodic discrete patterns resembling pearl necklaces, frequently with single prominent foci. We constructed mathematical models that simulated the pattern formation of Plk4 to gain insight into the discrete ring patterns. The simulations incorporating the self-organization properties of Plk4 successfully generated the experimentally observed patterns. We therefore propose that the self-patterning of Plk4 is crucial for the regulation of centriole duplication. These results, defining the mechanisms of self-organized regulation, provide a fundamental principle for understanding centriole duplication.