bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forecasting ocean acidification impacts on kelp forest ecosystems
Authors: Schlenger Adam J. , Beas-Luna Rodrigo , Ambrose Richard F. 
Published: July 2020

AbstractOcean acidification is one the biggest threats to marine ecosystems worldwide, but its ecosystem wide responses are still poorly understood. This study integrates field and experimental data into a mass balance food web model of a temperate coastal ecosystem to determine the impacts of specific OA forcing mechanisms as well as how they interact with one another. Specifically, we forced a food web model of a kelp forest ecosystem near its southern distribution limit in the California large marine ecosystem to a 0.5 pH drop over the course of 50 years. This study utilizes a modeling approach to determine the impacts of specific OA forcing mechanisms as well as how they interact. Isolating OA impacts on growth (Production), mortality (Other Mortality), and predation interactions (Vulnerability) or combining all three mechanisms together leads to a variety of ecosystem responses, with some taxa increasing in abundance and other decreasing. Results suggest that carbonate mineralizing groups such as coralline algae, abalone, snails, and lobsters display the largest decreases in biomass while macroalgae, urchins, and some larger fish species display the largest increases. Low trophic level groups such as giant kelp and brown algae increase in biomass by 16% and 71%, respectively. Due to the diverse way in which OA stress manifests at both individual and population levels, ecosystem-level effects can vary and display nonlinear patterns. Combined OA forcing leads to initial increases in ecosystem and commercial biomasses followed by a decrease in commercial biomass below initial values over time, while ecosystem biomass remains high. Both biodiversity and average trophic level decrease over time. These projections indicate that the kelp forest community would maintain high productivity with a 0.5 drop in pH, but with a substantially different community structure characterized by lower biodiversity and relatively greater dominance by lower trophic level organisms.
Language processing in brains and deep neural networks: computational convergence and its limits
Authors: Caucheteux Charlotte , King Jean-Rémi 
Published: July 2020

AbstractDeep Learning has recently led to major advances in natural language processing. Do these models process sentences similarly to humans, and is this similarity driven by specific principles? Using a variety of artificial neural networks, trained on image classification, word embedding, or language modeling, we evaluate whether their architectural and functional properties lead them to generate activations linearly comparable to those of 102 human brains measured with functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG). We show that image, word and contextualized word embeddings separate the hierarchical levels of language processing in the brain. Critically, we compare 3,600 embeddings in their ability to linearly map onto these brain responses. The results show that (1) the position of the layer in the network and (2) the ability of the network to accurately predict words from context are the main factors responsible for the emergence of brain-like representations in artificial neural networks. Together, these results show how perceptual, lexical and compositional representations precisely unfold within each cortical region and contribute to uncovering the governing principles of language processing in brains and algorithms.
Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison)
Authors: Harper Lynsey R. , Watson Hayley V. , Donnelly Robert , Hampshire Richard , Sayer Carl D. , Breithaupt Thomas , Hänfling Bernd 
Published: July 2020

AbstractIn the UK, the native European otter (Lutra lutra) and invasive American mink (Neovison vison) have experienced concurrent declines and expansions. Currently, the otter is recovering from persecution and waterway pollution, whereas the mink is in decline due to population control and probable interspecific interaction with the otter. We explored the potential of DNA metabarcoding for investigating diet and niche partitioning between these mustelids. Otter spraints (n= 171) and mink scats (n= 19) collected from three sites (Malham Tarn, River Hull, and River Glaven) in northern and eastern England were screened for vertebrates using high-throughput sequencing. Otter diet mainly comprised aquatic fishes (81.0%) and amphibians (12.7%), whereas mink diet predominantly consisted of terrestrial birds (55.9%) and mammals (39.6%). The mink used a lower proportion (20%) of available prey (n= 40 taxa) than the otter, and low niche overlap (0.267) was observed between these mustelids. Prey taxon richness of mink scats was lower than otter spraints, and beta diversity of prey communities was driven by taxon turnover (i.e. the otter and mink consumed different prey taxa). Considering otter diet only, prey taxon richness was higher in spraints from the River Hull catchment, and beta diversity of prey communities was driven by taxon turnover (i.e. the otter consumed different prey taxa at each site). Studies using morphological faecal analysis may misidentify the predator as well as prey items. Faecal DNA metabarcoding can resolve these issues and provide more accurate and detailed dietary information. When upscaled across multiple habitat types, DNA metabarcoding should greatly improve future understanding of resource use and niche overlap between the otter and mink.
EyeLoop: An open-source, high-speed eye-tracker designed for dynamic experiments
Authors: Arvin Simon , Rasmussen Rune , Yonehara Keisuke 
Published: July 2020

AbstractEye-tracking is a method for tracking the position of the eye and size of the pupil, often employed in neuroscience laboratories and clinics. Eye-trackers are widely used, from studying brain dynamics to investigating neuropathology and disease models. Despite this broad utility, eye-trackers are expensive, hardware-intensive, and proprietary, which have limited this approach to high-resource facilities. Besides, experiments have largely been confined to static open-loop designs and post hoc analysis due to the inflexibility of current systems. Here, we developed an open-source eye-tracking system, named EyeLoop, tailored to dynamic experiments. This Python-based software easily integrates custom functions via a modular logic, tracks a multitude of eyes, including rodent, human, and non-human primate eyes, and it operates well on inexpensive consumer-grade hardware. One of the most appealing applications of EyeLoop is closed-loop experiments, in which the eyes evoke stimulus feedback, such as rapid neuronal optogenetic stimulation. By using EyeLoop, we demonstrate its utility in an open-loop, a closed-loop, and a biomedical experiment. With a remarkably low minimal hardware cost amounting to 29 USD, EyeLoop makes dynamic eye-tracking accessible to low-resource facilities, such as high schools, small laboratories, and small clinics.
Induction of C4genes evolved through changes incisallowing integration into ancestral C3gene regulatory networks
Authors: Singh Pallavi , Stevenson Sean R. , Reyna-Llorens Ivan , Reeves Gregory , Schreier Tina B. , Hibberd Julian M. 
Published: July 2020

ABSTRACTC4photosynthesis has evolved independently in over sixty lineages and in so doing repurposed existing enzymes to drive a carbon pump that limits the RuBisCO oxygenation reaction. In all cases, gene expression is modified such that C4proteins accumulate to levels matching those of the photosynthetic apparatus. To better understand this rewiring of gene expression we undertook RNA- and DNaseI-SEQ on de-etiolating seedlings of C4Gynandropsis gynandra, which is sister to C3Arabidopsis. Changes in chloroplast ultrastructure and C4gene expression were coordinated and rapid. C3photosynthesis and C4genes showed similar induction patterns, but C4genes fromG. gynandrawere more strongly induced than orthologs from Arabidopsis. A gene regulatory network predicted transcription factors operating at the top of the de-etiolation network, including those responding to light, act upstream of C4genes. Light responsive elements, especially G-, E- and GT-boxes were over-represented in accessible chromatin around C4genes. Moreover,in vivobinding of many G-, E- and GT-boxes was detected. Overall, the data support a model in which rapid and robust C4gene expression following light exposure is generated through modifications incisto allow integration into high-level transcriptional networks including those underpinned by conserved light responsive elements.
Impact of parasitic lifestyle and different types of centromere organization on chromosome and genome evolution in the plant genusCuscuta
Authors: Neumann Pavel , Oliveira Ludmila , Čížková Jana , Jang Tae-Soo , Klemme Sonja , Novák Petr , Stelmach Katarzyna , Koblížková Andrea , Doležel Jaroslav , Macas Jiří 
Published: July 2020

SummaryThe parasitic genusCuscuta(Convolvulaceae) is exceptional among plants with respect to centromere organization, including both monocentric and holocentric chromosomes, and substantial variation in genome size and chromosome number. We investigated 12 species representing the diversity of the genus in a phylogenetic context to reveal the molecular and evolutionary processes leading to diversification of their genomes.We measured genome sizes and investigated karyotypes and centromere organization using molecular cytogenetic techniques. We also performed low-pass whole genome sequencing and comparative analysis of repetitive DNA composition.A remarkable 102-fold variation in genome sizes (342–34,734 Mbp/1C) was detected for monocentricCuscutaspecies, while genomes of holocentric species were of moderate sizes (533–1,545 Mbp/1C). The genome size variation was primarily driven by the differential accumulation of repetitive sequences. The transition to holocentric chromosomes in the subgenusCuscutawas associated with loss of histone H2A phosphorylation and elimination of centromeric retrotransposons. In addition, the basic chromosome number (x) decreased from 15 to 7, presumably due to chromosome fusions.We demonstrated that the transition to holocentricity inCuscutawas accompanied by significant changes in epigenetic marks, chromosome number and the repetitive DNA sequence composition.
Human ANKLE1 is a nuclease specific for branched DNA
Authors: Song Junfang , Freeman Alasdair D. J. , Knebel Axel , Gartner Anton , Lilley David M. J. 
Published: July 2020

ABSTRACTAll physical connections between sister chromatids must be broken before cells can divide, and eukaryotic cells have evolved multiple ways in which to process branchpoints connecting DNA molecules separated both spatially and temporally. A single DNA link between chromatids has the potential to disrupt cell cycle progression and genome integrity, so it is highly likely that cells require a nuclease that can process remaining unresolved and hemi-resolved DNA junctions and other branched species at the very late stages of mitosis. We argue that ANKLE1 probably serves this function in human cells (LEM-3 inC. elegans). LEM-3 has previously been shown to be located at the cell mid-body, and we show here that human ANKLE1 is a nuclease that cleaves a range of branched DNA species. It thus has the substrate selectivity consistent with an enzyme required to process a variety of unresolved and hemi-resolved branchpoints in DNA. Our results imply that ANKLE1 acts as a catch-all enzyme of last resort that allows faithful chromosome segregation and cell division to occur.
A photosynthesis operon in the chloroplast genome drives speciation in evening primroses
Authors: Zupok Arkadiusz , Kozul Danijela , Schöttler Mark Aurel , Niehörster Julia , Garbsch Frauke , Liere Karsten , Malinova Irina , Bock Ralph , Greiner Stephan 
Published: July 2020

AbstractIncompatibility between the cytoplasm and the nucleus is considered as major factor in species formation, but mechanistic understanding is poor. In evening primroses, a model plant for organelle genetics and population biology, hybrid offspring regularly displays chloroplast-nuclear incompatibility. These incompatibilities affect photosynthesis, a trait under selection in changing environments. Here we show that light-dependent misregulation of the plastidpsbBoperon (encoding core subunits of photosystem II and the cytochromeb6fcomplex), can lead to hybrid incompatibility, thus ultimately driving speciation. This misregulation results in an impaired light acclimation response in incompatible plants. Moreover, as a result of their different chloroplast genotypes, the parental lines differ in their photosynthesis performance upon exposure to different light conditions. Significantly, the incompatible chloroplast genome is naturally found in xeric habitats with high light intensities, whereas the compatible one is limited to mesic habitats. Consequently, our data raise the possibility that the hybridization barrier evolved as a result of adaptation to specific climatic conditions.
A global resource for genomic predictions of antimicrobial resistance and surveillance ofSalmonellaTyphi at Pathogenwatch
Authors: Argimón Silvia , Yeats Corin A. , Goater Richard J. , Abudahab Khalil , Taylor Benjamin , Underwood Anthony , Sánchez-Busó Leonor , Wong Vanessa K. , Dyson Zoe A. , Nair Satheesh , Park Se Eun , Marks Florian , Page Andrew J. , Keane Jacqueline A. , Baker Stephen , Holt Kathryn E. , Dougan Gordon , Aanensen David M. 
Published: July 2020

AbstractBackgroundMicrobial whole-genome sequencing (WGS) is now increasingly used to inform public health investigations of infectious disease. This approach has transformed our understanding of the global population structure ofSalmonella entericaserovar Typhi (S.Typhi), the causative agent of typhoid fever. WGS has been particularly informative for understanding the global spread of multi-drug resistant (MDR) typhoid. As WGS capacity becomes more decentralised, there is a growing opportunity for collaboration and sharing of surveillance data within and between countries to inform disease control policies. This requires freely available, community driven tools that reduce the barriers to access genomic data for public health surveillance and that deliver genomic data on a global scale.MethodsHere we present the Pathogenwatch (https://pathogen.watch/styphi) scheme forS.Typhi, a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data to identify high-risk clones at a population level. Data are delivered in single genome reports or in collections of genomes combined with geographic and other data using trees, maps and tables.ResultsWe show that the clustering ofS.Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are largely concordant with phenotypic drug susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from over 4,300 public genomes available in the application.ConclusionsPathogenwatch democratises genomic epidemiology ofS.Typhi by providing an intuitive entry point for the analysis of WGS and linked epidemiological data, enabling international public health monitoring of the emergence and spread of high risk clones.
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction ofNeisseria gonorrhoeaeat Pathogenwatch
Authors: Sánchez-Busó Leonor , Yeats Corin A. , Taylor Benjamin , Goater Richard J. , Underwood Anthony , Abudahab Khalil , Argimón Silvia , Ma Kevin C. , Mortimer Tatum D. , Golparian Daniel , Cole Michelle J. , Grad Yonatan H. , Martin Irene , Raphael Brian H. , Shafer William M. , Spiteri Gianfranco , Town Katy , Wi Teodora , Harris Simon R. , Unemo Magnus , Aanensen David M. 
Published: July 2020

AbstractBackgroundAntimicrobial resistant (AMR)Neisseria gonorrhoeaeis an urgent threat to public health, as strains resistant to at least one of the two last line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be used to identify new AMR clones, transmission networks and inform the development of point-of-care tests for antimicrobial susceptibility, novel antimicrobials and vaccines. Community driven tools that provide an easy access to and analysis of genomic and epidemiological data is the way forward for public health surveillance.MethodsHere we present a public health focussed scheme for genomic epidemiology ofN. gonorrhoeaeat Pathogenwatch (https://pathogen.watch/ngonorrhoeae). An international advisory group of experts in epidemiology, public health, genetics and genomics ofN. gonorrhoeaewas convened to inform on the utility of current and future analytics in the platform. We implement backwards compatibility with MLST, NG-MAST and NG-STAR typing schemes as well as an exhaustive library of genetic AMR determinants linked to a genotypic prediction of resistance to eight antibiotics. A collection of over 12,000N. gonorrhoeaegenome sequences from public archives has been quality-checked, assembled and made public together with available metadata for contextualization.ResultsAMR prediction from genome data revealed specificity values over 99% for azithromycin, ciprofloxacin and ceftriaxone and sensitivity values around 99% for benzylpenicillin and tetracycline. A case study using the Pathogenwatch collection ofN. gonorrhoeaepublic genomes showed the global expansion of an azithromycin resistant lineage carrying a mosaicmtrover at least the last 10 years, emphasizing the power of Pathogenwatch to explore and evaluate genomic epidemiology questions of public health concern.ConclusionsTheN. gonorrhoeaescheme in Pathogenwatch provides customized bioinformatic pipelines guided by expert opinion that can be adapted to public health agencies and departments with little expertise in bioinformatics and lower resourced settings with internet connection but limited computational infrastructure. The advisory group will assess and identify ongoing public health needs in the field of gonorrhoea, particularly regarding gonococcal AMR, in order to further enhance utility with modified or new analytic methods.
Hyperkalemia, not apoptosis, accurately predicts chilling injury in individual locusts
Authors: Carrington Jessica , Andersen Mads Kuhlmann , Brzezinski Kaylen , MacMillan Heath 
Published: July 2020

AbstractDuring prolonged or severe chilling, the majority of insects accrue chilling injuries that are typically quantified by scoring neuromuscular function after rewarming. In the cold, these chill susceptible insects, like the migratory locust (Locusta migratoria) suffer a loss of ion and water balance that is hypothesized to initiate cell death. Whether apoptotic or necrotic cell death pathways are responsible for this chilling injury is unclear. Here, we use a caspase-3 specific assay to indirectly quantify apoptosis in three locust tissues (muscle, nerves, and midgut) following prolonged chilling and recovery from an injury-inducing cold exposure. Furthermore, we obtain matching measurements of injury, hemolymph [K+], and muscle caspase-3 activity in individual locusts to gain further insight into mechanistic nature of chilling injury. We hypothesized that apoptotic cell death in both muscle and nerve tissue drives motor defects following cold exposure in insects, and that there would be a strong association between cold- induced injury, hyperkalemia, and muscle caspase-3 activity. We found a significant increase in muscle caspase-3 activity, but no such increase was observed in either nervous or gut tissue from the same animals, suggesting that chill injury primarily relates to apoptotic muscle cell death. However, the levels of chilling injury measured at the whole animal level prior to tissue sampling were strongly correlated with the degree of hemolymph hyperkalemia, but not apoptosis. These results support the notion that cold-induced ion balance disruption triggers cell death but also that apoptosis is not the main cell death pathway driving injury in the cold.Significance StatementTemperature has profound effects on animal fitness and sets limits to animal distribution. To understand and model insect responses to climate, we need to know how temperature sets limits to their survival. There is strong evidence that a collapse of ion and water balance occurs in insects in the cold, and it is generally held that the resulting cold injury is caused by activation of programmed cell death (apoptosis). Here, we directly test this idea and show for the first time that although the loss of ion balance is a strong predictor of individual survival outcomes, apoptosis is not the primary cause of cold-induced injury.
Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression
Authors: Kong Nikki R. , Bassal Mahmoud A. , Tan Hong Kee , Kurland Jesse V. , Yong Kol Jia , Young John J. , Yang Yang , Li Fudong , Lee Jonathan , Liu Yue , Wu Chan-Shuo , Stein Alicia , Luo Hongbo , Silberstein Leslie E. , Bulyk Martha L. , Tenen Daniel G. , Chai Li 
Published: July 2020

SummaryThe zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, down-regulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive target for designing therapeutic strategies. However, whether SALL4 binds DNA directly to regulate gene expression is unclear and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) experiments, we identified and validated the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA-seq analyses after SALL4 knockdown, we discovered hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of Histone 3 Lysine 9-specific Demethylases (KDMs). Taken together, these results elucidated the mechanism of SALL4 DNA binding and revealed novel pathways and molecules to target in SALL4-dependent tumors.