bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-domain cognitive assessment of male mice reveals whole body exposure to space radiation is not detrimental to high-level cognition and actually improves pattern separation
Authors: Whoolery Cody W. , Yun Sanghee , Reynolds Ryan P. , Lucero Melanie J. , Soler Ivan , Tran Fionya H. , Ito Naoki , Redfield Rachel L. , Richardson Devon R. , Shih Hung-ying , Rivera Phillip D. , Chen Benjamin P. C. , Birnbaum Shari G. , Stowe Ann M. , Eisch Amelia J. 
Published: October 2019

ABSTRACTAstronauts on interplanetary space missions - such as to Mars - will be exposed to space radiation, a spectrum of highly-charged, fast-moving particles that includes 56Fe and 28Si. Earth-based preclinical studies with mature, “astronaut-aged” rodents show space radiation decreases performance in low- and some high-level cognitive tasks. Given the prevalence of touchscreens in astronaut training and in-mission assessment, and the ability of rodent touchscreen tasks to assess the functional integrity of brain circuits and multiple cognitive domains in a non-aversive way, it is surprising the effect of space radiation on rodent touchscreen performance is unknown. To fill this knowledge gap, 6-month-old C57BL/6J male mice were exposed to whole-body space radiation and assessed on a touchscreen battery starting 1-month later. Relative to Sham, 56Fe irradiation did not overtly change performance on tasks of visual discrimination, reversal learning, rule-based, or object-spatial paired associates learning, suggesting preserved functional integrity of supporting brain circuits. Surprisingly, 56Fe irradiation led to better performance on a dentate gyrus-reliant task of pattern separation ability. Irradiated mice discriminated similar visual cues in ∼40% fewer days and ∼40% more accurately than control mice. Improved pattern separation was not touchscreen-, radiation-particle, or neurogenesis-dependent, as both 56Fe and 28Si irradiation led to faster context discrimination (e.g. Sham Block 5 vs. 56Fe Block 2) in a non-touchscreen task and 56Fe led to fewer new dentate gyrus neurons relative to Sham. These data urge revisitation of the broadly-held view that space radiation is detrimental to cognition.SIGNIFICANCE STATEMENTAstronauts on an interplanetary mission - such as to Mars - will be unavoidably exposed to galactic cosmic radiation, a spectrum of highly-charged, fast-moving particles. Rodent studies suggest space radiation is detrimental to cognition. However, here we show this is not universally true. Mature mice that received whole body exposure to Mars-relevant space radiation perform similarly to control mice on high-level cognitive tasks, reflecting the functional integrity of key neural circuits. Even more surprisingly, irradiated mice perform better than controls in both appetitive and aversive tests of pattern separation, a mission-critical task reliant on dentate gyrus integrity. Notably, improved pattern separation was not touchscreen-, radiation-particle-, or neurogenesis-dependent. Our work urges revisitation of the generally-accepted conclusion that space radiation is detrimental to cognition.
Shifting transmission risk for malaria in Africa with climate change: a framework for planning and intervention
Authors: Ryan Sadie J. , Lippi Catherine A. , Zermoglio Fernanda 
Published: October 2019

AbstractBackgroundMalaria continues to be a disease of massive burden in Africa, and the public health resources targeted at surveillance, prevention, control, and intervention comprise large outlays of expense. Malaria transmission is largely constrained by the suitability of the climate for Anopheles mosquitoes and Plasmodium parasite development. Thus, as climate changes, we will see shifts in geographic locations suitable for transmission, and differing lengths of seasons of suitability, which will require changes in the types and amounts of resources.MethodsWe mapped the shifting geographic risk of malaria transmission, in context of changing seasonality (i.e. endemic to epidemic, and vice-versa), and the number of people affected. We applied a temperature-dependent model of malaria transmission suitability to continental gridded climate data for multiple future climate model projections. We aligned the resulting outcomes with programmatic needs to provide summaries at national and regional scales for the African continent. Model outcomes were combined with population projections to estimate the population at risk at three points in the future, 2030, 2050, and 2080, under two scenarios of greenhouse gas emissions (RCP4.5 and RCP8.5).ResultsGeographic shifts in endemic and seasonal suitability for malaria transmission were observed across all future scenarios of climate change. The worst-case regional scenario (RCP8.5) of climate change places an additional 75.9 million people at risk from endemic (10-12 months) exposure to malaria transmission in Eastern and Southern Africa by the year 2080, with the greatest population at risk in Eastern Africa. Despite a predominance of reduction in season length, a net gain of 51.3 million additional people will be put at some level of risk in Western Africa by midcentury.ConclusionsThis study provides an updated view of potential malaria geographic shifts in Africa under climate change for the more recent climate model projections (AR5), and a tool for aligning findings with programmatic needs at key scales for decision makers. In describing shifting seasonality, we can capture transitions between endemic and epidemic risk areas, to facilitate the planning for interventions aimed at year-round risk versus anticipatory surveillance and rapid response to potential outbreak locations.
Multifaceted diversity traits of crucial microbial groups in biological soil crusts promote soil multifunctionality
Authors: Li Hua , Chen Youxin , Yu Gongliang , Rossi Federico , Huo Da , De Philippis Roberto , Cheng Xiaoli , Wang Weibo , Li Renhui 
Published: October 2019

AbstractsMicrobial diversity is one of the most important drivers on ecosystem to maintain the simultaneous performance of functions (multifunctionality, MF) under climatic oscillation. However, existing studies typically consider taxonomic richness or Shannon index at the community level in which relations between diversity and functioning are not highly consistent. To disentangle the underlying linkages in real-world ecosystems, we conducted field investigation on biological soil crusts of Tibetan Plateau and evaluated multiple diversity facets (i.e., richness, evenness, and phylogeny-related trait dissimilarity) of carbon- and nitrogen-fixing functional groups (FGs). Seven crucial variables of soil functioning were also identified to calculate MF. We found that the integrated index, invoking multiple diversity components, was a stronger predictor on MF than richness. Moreover, the divergent performance of different diversity facets determined the idiosyncratic diversity effect of each FG on the MF. Namely, richness was the dominant factor for diazotrophs to maximize MF, whereas phylogenetic dissimilarity was the most important one for phototrophs. The heterogeneity among the focal FGs derived from the significant differentiation of the extent of multifunctional redundancy. Collectively, we speculated that the multifaceted diversity pattern depicts the response ability of crucial FGs by which biocrusts stabilize MF under environmental perturbation. Taken together, our results provided a perspective to bridge the gap between taxonomic and trait-based approaches for elucidating the biodiversity-ecosystem functioning relationship, and could ultimately help to boost the practices of dryland management against global change.
An experimentally-derived measure of inter-replicate variation in reference samples: the same-same permutation methodology
Authors: Handler David C. , Haynes Paul A. 
Published: October 2019

AbstractThe multiple testing problem is a well-known statistical stumbling block in high-throughput data analysis, where large scale repetition of statistical methods introduces unwanted noise into the results. While approaches exist to overcome the multiple testing problem, these methods focus on theoretical statistical clarification rather than incorporating experimentally-derived measures to ensure appropriately tailored analysis parameters. Here, we introduce a method for estimating inter-replicate variability in reference samples for a quantitative proteomics experiment using permutation analysis. This can function as a modulator to multiple testing corrections such as the Benjamini-Hochberg ordered Q value test. We refer to this as a ‘same-same’ analysis, since this method incorporates the use of six biological replicates of the reference sample and determines, through non-redundant triplet pairwise comparisons, the level of quantitative noise inherent within the system. The method can be used to produce an experiment-specific Q value cut-off that achieves a specified false discovery rate at the quantitation level, such as 1%. The same-same method is applicable to any experimental set that incorporates six replicates of a reference sample. To facilitate access to this approach, we have developed a same-same analysis R module that is freely available and ready to use via the internet.
The PMK-3 (p38) Mitochondrial Retrograde Response Functions in Intestinal Cells to Extend Life via the ESCRT Machinery
Authors: Radetskaya Oxana , Lane Rebecca K. , Friedman Troy , Garrett Aria , Nguyen Michael , Borror Megan B. , Russell Joshua , Rea Shane L. 
Published: October 2019

ABSTRACTThe p38 mitogen-activated protein kinase (MAPK) PMK-3 controls a life-extending retrograde response in the nematodeCaenorhabditis elegansthat is activated following mitochondrial electron transport chain (ETC) disruption and is distinct from known longevity-promoting pathways. Here we show that the long isoform of PMK-3 expressed exclusively in the gut, rather than neurons, is sufficient to fully extend the life of animals exposed to mild ETC dysfunction. Surprisingly, constitutive activation of PMK-3 using a gain-of-function MAP3K/DLK-1 mutant does not extend the life of wild-type worms due to dampening of the DLK-1/PMK-3 signaling axis with age. We further show that core components of the ESCRT-III machinery, including ISTR-1, CHMP2B (CC01A4.2) and RAB-11.1, are required for life extension following ETC disruption. ESCRT proteins are needed for extracellular vesicle (EV) formation, lysosomal traffic and other functions requiring membrane encapsulation away from the cytoplasm. Together, our findings underscore PMK-3 as a pivotal factor controlling life extension in worms following mitochondrial ETC disruption and illustrate the importance of the endomembrane system to this process. Our findings raise the possibility that EVs may act as intra-organismal signaling vehicles to control aging.
Fluorescent reporter plasmids for single-cell and bulk-level composition assays inE. faecalis
Authors: Hallinen Kelsey M. , Guardiola-Flores Keanu A. , Wood Kevin B. 
Published: October 2019

ABSTRACTFluorescent reporters are an important tool for monitoring dynamics of bacterial populations at the single cell and community level. While there are a large range of reporter constructs available–particularly for common model organisms likeE. coli–fewer options exist for other species, includingE. faecalis, a gram-positive opportunistic pathogen. To expand the potential toolkit available forE. faecalis, we modified a previously developed reporter plasmid (pBSU101) to express one of nine different fluorescent reporters and confirmed that all constructs exhibited detectable fluorescence in singleE. faecaliscells and mixed biofilm communities. To identify promising constructs for bulk-level experiments, we then measured the fluorescence spectra fromE. faecalispopulations in microwell plate (liquid) cultures during different growth phases. Cultures showed density- and reporter-specific variations in fluorescent signal, though spectral signatures of all reporters become clear in late-exponential and stationary-phase populations. Based on these results, we identified six pairs of reporters that can be combined with simple spectral unmixing to accurately estimate population composition in 2-strain mixtures at or near stationary phase. This approach offers a simple and scalable method for selection and competition experiments in simple two-species populations. Finally, we modified the construct to express codon-optimized variants of blue (BFP) and red (RFP) reporters and show that they lead to increased fluorescence in exponentially growing cells. As a whole, the results inform the scope of application of different reporters and identify both single reporters and reporter pairs that are promising for fluorescence-based assays at bulk and single-cell levels inE. faecalis.
REP-X: An Evolution-guided Strategy for the Rational Design of Cysteine-less Protein Variants
Authors: Dalton Kevin , Lopez Tom , Pande Vijay , Frydman Judith 
Published: October 2019

AbstractSite-specific labeling of proteins is often a prerequisite for biophysical and biochemical characterization. Chemical modification of a unique cysteine residue is among the most facile methods for site-specific labeling of proteins. However, many proteins have multiple reactive cysteines, which must be mutated to other residues to enable labeling of unique positions. This trial-and-error process often results in cysteine-free proteins with reduced activity or stability. Herein we describe a general methodology to rationally engineer cysteine-less proteins. Briefly, natural variation across orthologues is exploited to identify suitable cysteine replacements compatible with protein activity and stability. As a proof-of-concept, we recount the successful engineering of a cysteine-less mutant of the group II chaperonin from methanogenic archaeon Methanococcus maripaludis. A webapp, REP-X (Replacement at Endogenous Positions from eXtant sequences), which enables users to design their own cysteine-less protein variants, will make this rational approach widely available.
Autonomous bioluminescence imaging of single mammalian cells with the bacterial bioluminescence system
Authors: Gregor Carola , Pape Jasmin K. , Gwosch Klaus C. , Gilat Tanja , Sahl Steffen J. , Hell Stefan W. 
Published: October 2019

AbstractBioluminescence based imaging of living cells has become an important tool in biological and medical research. However, many bioluminescence imaging applications are limited by the requirement of an externally provided luciferin substrate and the low bioluminescence signal which restricts the sensitivity and spatiotemporal resolution. The bacterial bioluminescence system is fully genetically encodable and hence produces autonomous bioluminescence without an external luciferin, but its brightness in cell types other than bacteria has so far not been sufficient for imaging single cells. We coexpressed codon-optimized forms of the bacterialluxCDABEandfrpgenes from multiple plasmids in different mammalian cell lines. Our approach produces high luminescence levels that are comparable to firefly luciferase, thus enabling autonomous bioluminescence microscopy of mammalian cells.Significance statementBioluminescence is generated by luciferases that oxidize a specific luciferin. The enzymes involved in the synthesis of the luciferin from widespread cellular metabolites have so far been identified for only two bioluminescence systems, those of bacteria and fungi. In these cases, the complete reaction cascade is genetically encodable, meaning that heterologous expression of the corresponding genes can potentially produce autonomous bioluminescence in cell types other than the bacterial or fungal host cells. However, the light levels achieved in mammalian cells so far are not sufficient for single-cell applications. Here we present, for the first time, autonomous bioluminescence images of single mammalian cells by coexpression of the genes encoding the six enzymes from the bacterial bioluminescence system.
Ratiometric bioluminescent sensors towards in vivo imaging of bacterial signaling
Authors: Dippel A. B , Anderson W. A. , Park J. H. , Yildiz F. H. , Hammond M.C. 
Published: October 2019

ABSTRACTSecond messenger signaling networks allow cells to sense and adapt to changing environmental conditions. In bacteria, the nearly ubiquitous second messenger molecule cyclic di-GMP coordinates diverse processes such as motility, biofilm formation, and virulence. In bacterial pathogens, these signaling networks allow the bacteria to survive changing environment conditions that are experienced during infection of a mammalian host. While studies have examined the effects of cyclic di-GMP levels on virulence in these pathogens, it has previously not been possible to visualize cyclic di-GMP levels in real time during the stages of host infection. Towards this goal, we generate the first ratiometric, chemiluminescent biosensor scaffold that selectively responds to c-di-GMP. By engineering the biosensor scaffold, a suite of Venus-YcgR-NLuc (VYN) biosensors is generated that provide extremely high sensitivity (KD < 300 pM) and large BRET signal changes (up to 109%). As a proof-of-concept that VYN biosensors can image cyclic di-GMP during host infection, we show that the VYN biosensors function in the context of a tissue phantom model, with only ∼103-104 biosensor-expressing cells required for the measurement. Furthermore, the stable BRET signal suggests that the sensors could be used for long-term imaging of cyclic di-GMP dynamics during host infection. The VYN sensors developed here can serve as robust in vitro diagnostic tools for high throughput screening, as well as genetically encodable tools for monitoring the dynamics of c-di-GMP in live cells, and lay the groundwork for live cell imaging of c-di-GMP dynamics in bacteria during host infection, and other complex environments.
Two brain pathways initiate distinct forward walking programs inDrosophila
Authors: Bidaye Salil S. , Laturney Meghan , Chang Amy K. , Liu Yuejiang , Bockemühl Till , Büschges Ansgar , Scott Kristin 
Published: October 2019

SummaryAn animal at rest or engaged in stationary behaviors can instantaneously initiate goal-directed walking. How descending brain inputs trigger rapid transitions from a non-walking state to an appropriate walking state is unclear. Here, we identify two specific neuronal classes in theDrosophilabrain that drive two distinct forward walking programs in a context-specific manner. The first class, named P9, consists of descending neurons that drive forward walking with ipsilateral turning. P9 receives inputs from central courtship-promoting neurons and visual projection neurons and is necessary for a male to track a female during courtship. The second class comprises novel, higher order neurons, named BPN, that drives straight, forward walking. BPN is required for high velocity walking and is active during long, fast, straight walking bouts. Thus, this study reveals separate brain pathways for object-directed steering and fast straight walking, providing insight into how the brain initiates different walking programs.
The conserved DNMT1 dependent methylation regions in human cells are vulnerable to environmental rotenone
Authors: Freeman Dana M. , Lou Dan , Li Yanqiang , Martos Suzanne N. , Wang Zhibin 
Published: October 2019

AbstractAllele-specific DNA methylation (ASM) describes genomic loci that maintain CpG methylation at only one inherited allele rather than having coordinated methylation across both alleles. The most prominent of these regions are germline ASMs (gASMs) that control the expression of imprinted genes in a parent of origin-dependent manner and are associated with disease. However, our recent report reveals numerous ASMs at non-imprinted genes. These non-germline ASMs are dependent on DNA methyltransferase 1 (DNMT1) and strikingly show the feature of random, switchable monoallelic methylation patterns in the mouse genome. The significance of these ASMs to human health has not been explored. Due to their shared allelicity with gASMs, herein, we propose that non-traditional ASMs are sensitive to exposures in association with human disease. We first explore their conservancy in the human genome. Our data show that our putative non-germline ASMs were in conserved regions of the human genome and located adjacent to genes vital for neuronal development and maturation. We next tested the hypothesized vulnerability of these regions by exposing human embryonic kidney cell HEK293 with the neurotoxicant rotenone for 24h. Indeed,14 genes adjacent to our identified regions were differentially expressed from RNA-sequencing. We analyzed the base-resolution methylation patterns of the predicted non-germline ASMs at two neurological genes,HCN2andNEFM, with potential to increase the risk of neurodegeneration. Both regions were significantly hypomethylated in response to rotenone. Our data indicate that non-germline ASMs seem conserved between mouse and human genomes, overlap important regulatory factor binding motifs, and regulate the expression of genes vital to neuronal function. These results support the notion that ASMs are sensitive to environmental factors and may alter the risk of neurological disease later in life by disrupting neuronal development.
Estimating the genome-wide contribution of selection to temporal allele frequency change
Authors: Buffalo Vince , Coop Graham 
Published: October 2019

AbstractRapid phenotypic adaptation is often observed in natural populations and selection experiments. However, detecting the genome-wide impact of this selection is difficult, since adaptation often proceeds from standing variation and selection on polygenic traits, both of which may leave faint genomic signals indistinguishable from a noisy background of genetic drift. One promising signal comes from the genome-wide covariance between allele frequency changes observable from temporal genomic data, e.g. evolve-and-resequence studies. These temporal covariances reflect how heritable fitness variation in the population leads changes in allele frequencies at one timepoint to be predictive of the changes at later timepoints, as alleles are indirectly selected due to remaining associations with selected alleles. Since genetic drift does not lead to temporal covariance, we can use these covariances to estimate what fraction of the variation in allele frequency change through time is driven by linked selection. Here, we reanalyze three selection experiments to quantify the effects of linked selection over short timescales using covariance among time-points and across replicates. We estimate that at least 17% to 37% of allele frequency change is driven by selection in these experiments. Against this background of positive genome-wide temporal covariances we also identify signals of negative temporal covariance corresponding to reversals in the direction of selection for a reasonable proportion of loci over the time course of a selection experiment. Overall, we find that in the three studies we analyzed, linked selection has a large impact on short-term allele frequency dynamics that is readily distinguishable from genetic drift.Significance StatementA long-standing problem in evolutionary biology is to understand the processes that shape the genetic composition of populations. In a population without migration, the two processes that change allele frequencies are selection, which increases beneficial alleles and removes deleterious ones, and genetic drift which randomly changes frequencies as some parents contribute more or less alleles to the next generation. Previous efforts to disentangle these processes have used genomic samples from a single timepoint and models of how selection affects neighboring sites (linked selection). Here, we use genomic data taken through time to quantify the contributions of selection and drift to genome-wide frequency changes. We show selection acts over short timescales in three evolve-and-resequence studies and has a sizable genome-wide impact.