bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disease driven extinction in the wild of the Kihansi spray toad (Nectophrynoides asperginis)
Authors: Weldon C. , Channing A. , Misinzo G. , Cunningham A.A. 
Published: June 2019

AbstractThe Kihansi spray toad, Nectophrynoides asperginis, became extinct in the wild despite population monitoring and conservation management of its habitat in the Kihansi gorge, Tanzania. Anecdotal evidence has indicated human induced habitat modification, predators, pesticides and disease as possible causes of a rapid population decline and the species extirpation. Here, we systematically investigate the role of disease in the extinction event of the wild toad population. The amphibian chytrid fungus, Batrachochytrium dendrobatidis, was detected in spray toads that died during the extinction event and subsequently in other amphibian species in Kihansi Gorge and the adjacent Udagaji Gorge, but not in any toads collected prior to this. Following the population decline, the remnant spray toad population gradually disappeared over a nine-month period. We demonstrate how demographic and behavioral attributes predisposed the spray toads to chytridiomycosis, due to B. dendrobatidis infection, and how epidemic disease could have been exacerbated by altered environmental conditions in the spray wetlands. Our results show that chytridiomycosis was the proximate cause of extinction in the wild of N. asperginis. This represents the first known case of extinction by disease of an amphibian species in Africa. A captive breeding program in the US and Tanzania ensures the survival of the species and a reintroduction program is underway. However, we caution that chytridiomycosis remains an existing threat that requires a comprehensive mitigation strategy before the desired conservation outcome of an established population of repatriated toads can be achieved.
Impact of white spotting alleles, includingW20, on phenotype in the American Paint Horse
Authors: Brooks Samantha A. , Palermo Katelyn M. , Kahn Alisha , Hein Jessica 
Published: June 2019

SummaryThe American Paint Horse Association (APHA) records pedigree and performance information for their breed, a stock-type horse valued as a working farm or ranch horse and as pleasure horses. As the name implies, the breed is also valued for attractive white spotting patterns on the coat. The APHA utilizes visual inspections of photographs to determine if coat spotting exceeds threshold anatomical landmarks considered characteristic of desirable patterns. Horses with sufficient white patterning enter the “Regular” registry, rather than the “Solid Paint-bred” division, providing a threshold modeled phenotype. Genetic studies previously defined sequence variants corresponding to 35 alleles for white spotting in the horse. Here, we calculate the allele frequency for nine common white spotting alleles in the American Paint horse using a sample of 1,054 registered animals. The APHA spotting phenotype is altered by additive interactions among spotting loci, and epistatically by theMC1RandASIPgenes controlling pigment production. TheW20allele within theKITgene, independent of other known spotting alleles, was strongly associated with the APHA-defined white spotting phenotype (p = 1.86 x10−18), refuting reports thatW20acts only as a modifier of other underlying white spotting patterns. The parentage of an individual horse, either American Paint or American Quarter Horse, did not alter the likelihood of entering the APHA Regular registry. An empirical definition of the action of these genetic loci on the APHA-defined white spotting phenotype will allow more accurate application of genome-assisted selection for improving color production and marketability of APHA horses.
Habitat specificity is not universal proxy for sensitivity to habitat conversion among rodents on the Canadian Prairies
Authors: Heisler Leanne M. , Simpson Gavin L. , Poulin Ray G. , Wellicome Troy I. , Hall Britt D. 
Published: June 2019

AbstractConverting habitat for agricultural production threatens biodiversity loss worldwide and has significant implications for human well-being. Debates on how to conserve biodiversity as the demand for agriculture products rises is being informed by studies using habitat specificity as a proxy for sensitivity to land modification, assuming all species respond to habitat loss and fragmentation relative to their affinity towards the habitat type being converted. Here, we test this assumption among rodent assemblages on the Canadian Prairies, hypothesizing negative responses among grassland obligates and neutral or positive responses among habitat generalists to landscape change along a gradient of increasing agricultural intensity. We found complex, sometimes contradictory responses among rodent species, which depended on the magnitude of habitat loss that had occurred and did not always reflect each species’ relative affinity for grassland habitat. Our results suggest future studies should avoid assuming a single habitat type appropriately characterizes resource limitation among all species, and instead carefully consider which dimension of the ecological niche defines specificity for each species. Our results indicate habitat specificity is not always a reliable proxy for sensitivity to land modification, with significant implications for biodiversity conservation when used to inform agriculture and land use policies.
The evolution of realized niches within freshwater Synechococcus
Authors: Tromas Nicolas , Taranu Zofia E. , Castelli Mathieu , Pimentel Juliana S. M. , Pereira Daniel A. , Marcoz Romane , Shapiro B. Jesse , Giani Alessandra 
Published: June 2019

SummaryUnderstanding how ecological traits have changed over evolutionary time is a fundamental question in biology. Specifically, the extent to which more closely-related organisms share similar ecological preferences due to phylogenetic conservation – or if they are forced apart by competition – is still debated. Here we explored the co-occurrence patterns of freshwater cyanobacteria at the sub-genus level to investigate whether more closely-related taxa share more similar niches, and to what extent these niches were defined by abiotic or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several abiotic environmental parameters (nutrients, temperature, etc.) in water samples collected over time and space in Furnas Reservoir, Brazil. We found that relatively more closely-related Synechococcus (in the continuous range of 93-100% nucleotide identity in 16S) had an increased tendency to co-occur with one another (i.e. had similar realized niches). This tendency could not be easily explained by shared preferences for measured abiotic niche dimensions. Thus, commonly measured abiotic parameters might not be sufficient to characterize, nor to predict community assembly or dynamics. Rather, co-occurrence between Synechococcus and the surrounding community (whether or not they represent true biological interactions) may be a more sensitive measure of realized niches. Overall, our results suggest that realized niches are phylogenetically conserved, at least at the sub-genus level and at the resolution of the 16S marker. Determining how these results generalize to other genera and at finer genetic resolution merits further investigation.Originality-Significance StatementWe address a fundamental question in ecology and evolution: how do niche preferences change over evolutionary time? Using time-series analysis of 16S rRNA gene amplicon sequencing data, we develop an approach to highlight the importance of biotic factors in defining realized niches, and show how niche preferences change proportionally with the 16S gene molecular clock within the genus Synechococcus. Ours is also one of few studies on the ecology of freshwater Synechococcus, adding significantly to our knowledge about this abundant and widespread lineage of Cyanobacteria.
Empirical characterization factors assessing the effects of hydroelectricity on fish richness across three large biomes
Authors: Turgeon Katrine , Trottier Gabrielle , Turpin Christian , Bulle Cécile , Margni Manuele 
Published: June 2019

AbstractHydroelectricity is often presented as a clean, reliable, and renewable energy source, but is also recognized for its potential impacts on aquatic ecosystem biodiversity. We used empirical data on change in fish species richness following impoundment to develop Characterisation Factors (CF) and Impact Scores (IS) for hydroelectricity production for use in Life Cycle Assessment (LCA). We used data collected on 89 sampling stations (63 upstream and 26 downstream of a dam) belonging to 27 reservoirs from three biomes (boreal, temperate and tropical). Overall, the impact of hydroelectricity production on fish species richness was significant in the tropics, of smaller amplitude in temperate and minimal in boreal biome, stressing for the need of regionalisation. The impact of hydroelectricity production was also quite consistent across scales (i.e., same directionality and statistical significance across sampling stations, reservoirs and biomes) but was sensitive to the duration of the study (i.e., the period over which data have been collected after impoundment), highlighting the need for a clear understanding of transient situations before reaching steady states. Our CFs and ISs contribute to fill a gap to assist decision makers using LCA to evaluate alternative technologies, such as hydropower, to decarbonize the worldwide economy.HighlightsThis paper is the first to develop global and empirically based characterization factors of the impact of hydroelectricity production on aquatic ecosystems biodiversity, to be used in LCA;The impact of hydroelectricity production on fish species richness was significant in the tropics, of smaller amplitude in temperate and minimal in boreal biome;The impact of hydroelectricity production on fish richness was consistent across scales - same directionality and statistical significance across sampling stations, reservoirs and biomes;The impact of hydroelectricity production on fish richness was sensitive to the duration of the study, highlighting the need for a clear understanding of transient situations before reaching steady states in LCA.
A subset of SMN complex members have a specific role in tissue regeneration via ERBB pathway-mediated proliferation
Authors: Pei Wuhong , Xu Lisha , Chen Zelin , Slevin Claire C , Pettie Kade P , Wincovitch Stephen ,   NISC Comparative Sequencing Program, Burgess Shawn M 
Published: June 2019

AbstractSpinal Muscular Atrophy (SMA) is the most common genetic disease in childhood. SMA is generally caused by mutations inSMN1. The Survival of Motor Neurons (SMN) complex consists of SMN1, Gemins (2–8) and Strap/Unrip. We previously demonstratedsmn1andgemin5inhibited tissue regeneration in zebrafish. Here we investigated each individual SMN complex member and identifiedgemin3as another regeneration-essential gene. These three genes are likely pan-regenerative since they affect the regeneration of hair cells, liver and caudal fin. RNA-Seq and miRNA-Seq analyses reveal thatsmn1, gemin3, andgemin5are linked to a common set of genetic pathways, including the tp53 and ErbB pathways. Additional studies indicated all three genes facilitate regeneration by inhibiting the ErbB pathway, thereby allowing cell proliferation in the injured neuromasts. This study provides a new understanding of the SMN complex and a potential etiology for SMA and potentially other rare unidentified genetic diseases with similar symptoms.
Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically-relevant bacteria
Authors: Botelho João , Mourão Joana , Roberts Adam P. , Peixe Luísa 
Published: June 2019

AbstractCarbapenemases inactivate most β-lactam antibiotics, including carbapenems and have been frequently reported amongEnterobacteriaceae,Acinetobacterspp. andPseudomonasspp. Traditionally, the horizontal gene transfer of carbapenemase encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted anin-silicoanalysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182,663). We detected 17,520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically-relevant bacteria asPseudomonas aeruginosa,Klebsiella pneumoniaeandEscherichia coli). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFTand MPFFclasses and often encode resistance to other antibiotics (e.g., aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.Author NotesAll supporting data has been provided within the article or through supplementary data files. Supplementary material is available with the online version of this article.Impact StatementCarbapenems are commonly used to treat severe infections in humans. Resistance is often mediated by carbapenemases. These enzymes degrade carbapenems and are frequently present in plasmids. Here, we demonstrate that common carbapenemase-encoding genes (CEGs) found in clinical isolates (e.g.blaKPC,blaGES,blaIMP,blaNDM,blaVIM) can also be located within integrative and conjugative elements (ICEs). CEG-bearing ICEs belong to three mating-pair formation families. These mobile elements may be particularly important in bacteria where plasmids do not seem to play a significant role in the spread of antibiotic resistance genes, asPseudomonasspp. This study considerably expands the knowledge of the repertoire of CEGs-bearing ICEs among clinically-relevant bacterial pathogens, such asPseudomonas aeruginosa,Klebsiella pneumoniaeandEscherichia coli.Data SummaryAll the bacterial genomes scanned in this study have been deposited previously in the National Center for Biotechnology Information genome database and are listed on the supplementary tables. The extracted 66 ICEs in fasta format and the outputs for the profile HMMs scanned on the 386 putative MGEs identified in this study are deposited on figshare athttps://figshare.com/projects/_Comprehensive_genome_data_analysis_establishes_a_triple_whammy_of_carbapenemases_ICEs_and_multiple_clinically-relevant_bacteria/78369.
Natural selection towards wild-type in composite cross populations of winter wheat
Authors: Knapp Samuel , Döring Thomas F. , Jones Hannah E. , Snape John , Wingen Luzie U. , Wolfe Martin S. , Leverington-Waite Michelle , Griffiths Simon 
Published: June 2019

AbstractMost of our crops are grown in monoculture with single genotypes grown over wide acreage. An alternative approach, where segregating populations are used as crops is an exciting possibility, but outcomes of natural selection upon this type of crop are not well understood. We tracked allelic frequency changes in evolving composite cross populations (CCPs) of wheat grown over ten generations under organic and conventional farming. At three generations, each population was genotyped with 19 SSR and 8 SNP markers. The latter were diagnostic for major functional genes. Gene diversity was constant at SSR markers but decreased over time for genic markers. Population differentiation between the four locations could not be detected, suggesting that organic vs. non-organic crop management did not drive allele frequency changes. However, we did see changes for genes controlling plant height and phenology in all populations independently and consistently. We interpret these changes as the result of a consistent natural selection towards wild-type. Independent selection for alleles that are associated with plant height suggests that competition for light was central, resulting in the predominance of stronger intraspecific competitors, and highlighting a potential trade-off between individual and population performance.
Transcriptional Activation of Arabidopsis Zygotes Is Required for Their Initial Division
Authors: Kao Ping , Nodine Michael 
Published: June 2019

SUMMARYCommonly referred to as the maternal-to-zygotic transition, the shift of developmental control from maternal-to-zygotic genomes is a key event during animal and plant embryogenesis. Together with the degradation of parental gene products, the increased transcriptional activities of the zygotic genome remodels the early embryonic transcriptome during this transition. Although evidence from multiple flowering plants suggests that zygotes become transcriptionally active soon after fertilization, the timing and developmental requirements of zygotic genome activation inArabidopsis thaliana(Arabidopsis) remained a matter of debate until recently. In this report, we optimized an expansion microscopy technique for robust immunostaining of Arabidopsis ovules and seeds. This enabled the detection of marks indicative of active transcription in zygotes before the first cell division. Moreover, we employed a live-imaging culture system together with transcriptional inhibitors to demonstrate that such active transcription is required in zygotes. Our results indicate that zygotic genome activation occurs soon after fertilization and is physiologically required prior to the initial zygotic division in Arabidopsis.
Interplay of ERα binding and DNA methylation in the intron-2 determines the expression and estrogen regulation of Cystatin A in breast cancer cells
Authors: John Mary Dixcy Jaba Sheeba , Sikarwar Girija , Kumar Ajay , Limaye Anil Mukund 
Published: June 2019

AbstractDespite advances in early detection and treatment, invasion and metastasis of breast tumors remains a major hurdle. Cystatin A (CSTA, also called stefin A), an estrogen-regulated gene in breast cancer cells, is an inhibitor of cysteine cathepsins, and a purported tumor suppressor. Loss of CSTA expression in breast tumors evidently shifts the balance in favor of cysteine cathepsins, thereby promoting extracellular matrix remodeling, tumor invasion and metastasis. However, the underlying mechanism behind the loss of CSTA expression in breast tumors is not known. Here, we have analyzed CSTA expression, and methylation of upstream and intron-2 CpG sites within the CSTA locus in human breast cancer cell lines and breast tumors of the TCGA cohort. Results showed an inverse relationship between expression and methylation. Sequence analysis revealed a potential estrogen response element (ERE) in the intron-2. Analysis of ChIP-seq data (ERP000380) and our own ChIP experiments showed that 17β-estradiol (E2) enhanced ERα binding to this ERE in MCF-7 cells. This ERE was located amidst the differentially methylated intron-2 CpG sites, which provoked us to examine the possible conflict between estrogen-regulation of CSTA and DNA methylation in the intron-2. We analyzed the expression of CSTA and its regulation by estrogen in MDA-MB-231 and T47D cells subjected to global demethylation by 5-azacytidine (5-aza). 5-aza, not only enhanced CSTA expression in these cell lines but also restored estrogen-regulation of CSTA in these cells. Taken together, our results indicate that DNA methylation-dependent silencing could play a significant role in the loss of CSTA expression in breast tumors. The potential of DNA methylation as an indicator of CSTA expression or as a marker of tumor progression can be explored in future investigations. Furthermore, our results indicate the convergence of ERα-mediated estrogen regulation and DNA methylation in the intron-2, thereby offering a novel context to understand the role of estrogen-ERα signaling axis in breast tumor invasion and metastasis.
Inference based decisions in a hidden state foraging task: differential contributions of prefrontal cortical areas
Authors: Vertechi Pietro , Lottem Eran , Sarra Dario , Godinho Beatriz , Treves Isaac , Quendera Tiago , Oude Lohuis Matthijs Nicolai , Mainen Zachary F. 
Published: June 2019

AbstractEssential features of the world are often hidden and must be inferred by constructing internal models based on indirect evidence. Here, to study the mechanisms of inference we established a foraging task that is naturalistic and easily learned, yet can distinguish inference from simpler strategies such as the direct integration of sensory data. We show that both mice and humans learn a strategy consistent with optimal inference of a hidden state. However, humans acquire this strategy more than an order of magnitude faster than mice. Using optogenetics in mice we show that orbitofrontal and anterior cingulate cortex inactivation impact task performance, but only orbitofrontal inactivation reverts mice from an inference-based to a stimulus-bound decision strategy. These results establish a cross-species paradigm for studying the problem of inference-based decision-making and begin to dissect the network of brain regions crucial for its performance.
Transposable elements strongly contribute to cell-specific and species-specific looping diversity in mammalian genomes
Authors: Diehl Adam G , Ouyang Ningxin , Boyle Alan P 
Published: June 2019

AbstractBackgroundChromatin looping is exceedingly important to gene regulation and a host of other nuclear processes. Many recent insights into 3D chromatin structure across species and cell types have contributed to our understanding of the principles governing chromatin looping. However, 3D genome evolution and how it relates to Mendelian selection remain largely unexplored. CTCF, an insulator protein found at most loop anchors, has been described as the “master weaver” of mammalian genomes, and variations in CTCF occupancy are known to influence looping divergence. A large fraction of mammalian CTCF binding sites fall within transposable elements (TEs) but their contributions to looping variation are unknown. Here we investigated the effect of TE-driven CTCF binding site expansions on chromatin looping in human and mouse.ResultsTEs have broadly contributed to CTCF binding and loop boundary specification, primarily forming variable loops across species and cell types and contributing nearly 1/3 of species-specific and cell-specific loops.ConclusionsOur results demonstrate that TE activity is a major source of looping variability across species and cell types. Thus, TE-mediated CTCF expansions explain a large fraction of population-level looping variation and may play a role in adaptive evolution.
RIPK3 upregulation confers robust proliferation and collateral cystine-dependence on breast cancer recurrence
Authors: Lin Chao-Chieh , Mabe Nathaniel , Lin Yi-Tzu , Yang Wen-Hsuan , Tang Xiaohu , Hong Lisa , Sun Tianai , Yao Tso-Pang , Alvarez James , Chi Jen-Tsan 
Published: June 2019

AbstractThe molecular and genetic basis of tumor recurrence is complex and poorly understood. RIPK3 is a key effector in programmed necrotic cell death and, therefore, its expression is frequently suppressed in primary tumors. In a transcriptome profiling between primary and recurrent breast tumor cells from a murine model of breast cancer recurrence, we found that RIPK3, while absent in primary tumor cells, is dramatically re-expressed in recurrent breast tumor cells by an epigenetic mechanism. Unexpectedly, we found that RIPK3 knockdown in recurrent tumor cells reduced clonogenic growth, causing cytokinesis failure, p53 stabilization, and repressed the activities of YAP/TAZ. These data uncover a surprising role of the pro-necroptotic RIPK3 kinase in enabling productive cell cycle during tumor recurrence. Remarkably, high RIPK3 expression also rendered recurrent tumor cells exquisitely dependent on extracellular cystine and undergo programmed necrosis upon cystine deprivation. The induction of RIPK3 in recurrent tumors unravels an unexpected mechanism that paradoxically confers on tumors both growth advantage and necrotic vulnerability, providing potential strategies to eradicate recurrent tumors.