bluuebunny/crossref_metadata_2025_split huggingface dataset:
An IS-mediated, RecA-dependent, bet-hedging strategy inBurkholderia thailandensis
Authors: Lowrey Lillian C. , Kent Leslie A. , Rios Bridgett M. , Ocasio Angelica B. , Cotter Peggy A. 
Published: November 2022

ABSTRACTAdaptation to fluctuating environmental conditions is difficult to achieve. Phase variation mechanisms can overcome this difficulty by altering genomic architecture in a subset of individuals, creating a phenotypically heterogeneous population with subpopulations optimized to persist when conditions change, or are encountered, suddenly. We have identified a phase variation system inBurkholderia thailandensisthat generates a genotypically and phenotypically heterogeneous population. Genetic analyses revealed that RecA-mediated homologous recombination between a pair of insertion sequence (IS)2-like elements duplicates a 208.6 kb region that contains 157 coding sequences. RecA-mediated homologous recombination also resolves merodiploids, and hence copy number of the region is varied and dynamic within populations. We showed that the presence of two or more copies of the region is advantageous for growth in a biofilm, and a single copy is advantageous during planktonic growth. While IS elements are well-known to contribute to evolution through gene inactivation, polar effects on downstream genes, and altering genomic architecture, we believe that this system represents a rare example of IS element-mediated evolution in which the IS elements provide homologous sequences for amplification of a chromosomal region that provides a selective advantage under specific growth conditions, thereby expanding the lifestyle repertoire of the species.
Managing invasive hybrids through habitat restoration in an endangered salamander system
Authors: Cooper Robert D. , Shaffer H. Bradley 
Published: November 2022

AbstractInvasive species present one of the greatest threats to the conservation of biodiversity. When invasives hybridize with endangered native taxa, they introduce novel challenges ranging from the identification of hybrids in the field, to hybrid vigor and the erosion of species identity as genotypes are lost. Across a large swath of central California, a hybrid swarm consisting of admixed endangered California tiger salamanders (“CTS”,Ambystoma californiense) and introduced barred tiger salamander (Ambystoma mavortium) has replaced native populations, threatening CTS with genomic extinction. Here we employ a large-scale, genomically-informed field ecological experiment to test whether habitat restoration can reinstate natural selection favoring native salamander genotypes. We constructed 14 large, semi-natural ponds and manipulated their hydroperiods to evaluate larval survival and mass at metamorphosis. Consistent with earlier work, we found overwhelming evidence of hybrid superiority which persisted across all hydroperiod treatments. Short duration ponds substantially reduced the mass and survival probability of both native and hybrid larvae, likely exerting strong selective pressure in the wild. We identified 86 candidate genes, representing 1.8% of 4,723 screened loci, that significantly responded to this hydroperiod-driven selection. In contrast to previous mesocosm-based studies, native CTS never exhibited greater fitness than hybrids, suggesting that hydroperiod management alone will not shift selection to favor native genotypes. However, shortening pond hydroperiod may represent a cost-effective strategy to limit the overall productivity of ponds with non-native genotypes, complimenting additional strategies such as targeted hybrid removal. At a broader level, our experimental approach leverages extensive ecological knowledge, modern genomic tools, and a naturalistic,in situreplicated design to critically evaluate and expand the potential toolkit that managers can use to address this, and other recalcitrant biological invasions. We believe that this strategy may be an important tool for managing the growing number of complex invasion scenarios threatening global biodiversity.
Multi-omics analysis identifies symbionts and pathogens of blacklegged ticks (Ixodes scapularis) from a Lyme disease hotspot in southeastern Ontario, Canada
Authors: Paulson Amber R. , Lougheed Stephen C. , Huang David , Colautti Robert I. 
Published: November 2022

AbstractTicks in the familyIxodidaeare important vectors of zoonoses including Lyme disease (LD), which is caused by spirochete bacteria from theBorreliella(Borrelia)burgdorferisensu lato (Bbsl) complex. The blacklegged tick (Ixodes scapularis) continues to expand across Canada, creating hotspots of elevated LD risk at the leading edge of its expansion range. Current efforts to understand the risk of pathogen transmission associated withI. scapularisin Canada focus primarily on targeted screens, while variation in the tick microbiome remains poorly understood. Using multi-omics consisting of 16S metabarcoding and ribosome-depleted, whole-shotgun RNA transcriptome sequencing, we examined the microbial communities associated with adultI. scapularis(N = 32), sampled from four tissue types (whole tick, salivary glands, midgut, and viscera) and three geographical locations within a LD hotspot near Kingston, Ontario, Canada. The communities consisted of both endosymbiotic and known or potentially pathogenic microbes, including RNA viruses, bacteria, and aBabesiasp. intracellular parasite. We show that β-diversity is significantly higher between individual tick salivary gland and midgut bacterial communities, compared to whole ticks; while linear discriminant analysis (LDA) effect size (LEfSe) determined that the three potentially pathogenic bacteria detected by V4 16S rDNA sequencing also differed among dissected tissues only, including aBorreliafrom theBbslcomplex,Borrelia miyamotoi, andAnaplasma phagocytophilum. Importantly, we find co-infection ofI. scapularisby multiple microbes, in contrast to diagnostic protocols for LD, which typically focus on infection from a single pathogen of interest (B. burgdorferisensu stricto).IMPORTANCEA vector of human health concern, blacklegged ticks,Ixodes scapularis, transmit pathogens that cause tick-borne diseases (TBDs), including Lyme disease (LD). Several hotspots of elevated LD risk have emerged across Canada asI. scapularisexpands its range. Focusing on a hotspot in southeastern Ontario, we used high-throughput sequencing on whole ticks and dissected salivary glands and midguts. Compared to whole ticks, analysis of salivary glands and midguts revealed greater β-diversity among microbiomes that are less dominated byRickettsiaendosymbiont bacteria and enriched for pathogenic bacteria including aBbsl-associatedBorrelia,Borrelia miyamotoi, andAnaplasma phagocytophilum. We also find evidence of co-infection ofI. scapularisin this region by multiple microbes. Overall, our study highlights the challenges and opportunities associated with the surveillance of the microbiome ofI. scapularisfor pathogen detection using metabarcoding and metatranscriptome approaches.
BatCount: A software program to count moving animals
Authors: Bentley Ian , Kuczynska Vona , Eddington Valerie M. , Armstrong Mike , Kloepper Laura N. 
Published: November 2022

AbstractOne of the biggest challenges with species conservation is collecting accurate and efficient information on population sizes, especially from species that are difficult to count. Bats worldwide are declining due to disease, habitat destruction, and climate change, and many species lack reliable population information to guide management decisions. Current approaches for estimating population sizes of bats in densely occupied colonies are time-intensive, may negatively impact the population due to disturbance, and/or have low accuracy. Research-based video tracking options are rarely used by conservation or management agencies for animal counting due to the perceived training required to operate. In this paper, we present BatCount, a free software program created in direct consultation with end-users designed to automatically count aggregations of bats at cave roosts with a streamlined and user-friendly interface. We report on the software package and provide performance metrics for different recording habitat conditions. Our analysis demonstrates that BatCount is an efficient and reliable option for counting bats in flight and has important implications for range- and species-wide population monitoring. Furthermore, this software can be extended to count any organisms moving across a camera including birds, mammals, fish or insects.
Accurate Detection of Incomplete Lineage Sorting via Supervised Machine Learning
Authors: Rosenzweig Benjamin , Kern Andrew , Hahn Matthew 
Published: November 2022

AbstractGene tree discordance due to incomplete lineage sorting or introgression has been described in numerous genomic datasets. Among distantly related taxa, however, it is difficult to differentiate these biological sources of discordance from discordance due to errors in gene tree reconstruction, even when supervised machine learning techniques are used to infer individual gene trees. Here, rather than applying machine learning to the problem of inferring single tree topologies, we develop a model to infer important properties of a particular internal branch of the species tree via genome-scale summary statistics extracted from individual alignments and inferred gene trees. We show that our model can effectively predict the presence/absence of discordance, estimate the probability of discordance, and infer the correct species tree topology in the presence of multiple, common sources of error. While gene tree topology counts are the most salient predictors of discordance at short time scales, other genomic features become relevant for distantly related species. We validate our approach through simulation, and apply it to data from the deepest splits among metazoans. Our results suggest that the base of Metazoa experienced significant gene tree discordance, implying that discordant traits among current taxa can be explained without invoking homoplasy. In addition, we find support for Porifera as the sister clade to the rest of Metazoa. Overall, these results demonstrate how machine learning can be used to answer important phylogenetic questions, while marginalizing over individual gene tree—and even species tree—topologies.
Essential Gene Phenotypes Reveal Antibiotic Mechanisms and Synergies inAcinetobacter baumannii
Authors: Ward Ryan D. , Tran Jennifer S. , Banta Amy B. , Bacon Emily E. , Rose Warren E. , Peters Jason M. 
Published: November 2022

AbstractThe emergence of multidrug-resistant Gram-negative bacteria underscores the need to define genetic vulnerabilities in relevant pathogens. The Gram-negative pathogen,Acinetobacter baumannii, poses an urgent threat by evading antibiotic treatment through both intrinsic and acquired mechanisms. Antibiotics kill bacteria by targeting essential gene products, but antibiotic-essential gene interactions have not been studied systematically inA. baumannii. Here, we use CRISPR interference (CRISPRi) to comprehensively phenotypeA. baumanniiessential genes. We show that certain essential genes are acutely sensitive to knockdown, providing a set of promising therapeutic targets. Screening our CRISPRi library against last-resort antibiotics revealed essential pathways that modulate beta-lactam resistance, an unexpected link between NADH dehydrogenase function and polymyxin killing, and the genetic basis for synergy between polymyxins and rifamycins. Our results demonstrate the power of systematic genetic approaches to identify weaknesses in Gram-negative pathogens and uncover antibiotic mechanisms that better inform combination therapies.SignificanceAcinetobacter baumanniiis a hospital-acquired pathogen that is resistant to common antibiotic treatments.A. baumanniiinfections, we need to identify promising therapeutic targets and effective antibiotic combinations. Here, we characterize genes critical forA. baumanniiviability and their interactions with antibiotics. We find that genes involved in proton gradient formation required for oxygen-dependent energy generation are central toA. baumanniiphysiology and represent appealing drug targets. We show that polymyxins interact with proton gradient genes, explaining how these antibiotics inhibit growth at sub-lethal concentrations and their efficacy in combination therapies. Our studies reveal antibiotic-gene interactions inA. baumanniithat can inform future therapies.
Preferential consumption of benthic cyanobacterial mats by Caribbean parrotfishes
Authors: Manning Joshua C. , McCoy Sophie J. 
Published: November 2022

AbstractCyanobacteria are ubiquitous on coral reefs and perform important ecosystem functions. Benthic cyanobacterial mats (BCMs) have become increasingly abundant on degraded reefs. While epilithic and endolithic benthic cyanobacteria are the primary trophic resource for many parrotfishes, mat-forming benthic cyanobacteria are generally considered unpalatable to reef fishes. Regardless, recent studies have documented substantial grazing of BCMs by reef fishes, including parrotfishes. Here, we observed foraging in five Caribbean parrotfishes on the fringing coral reefs of Bonaire, Netherlands, to investigate BCM consumption relative to other benthic substrates. All species overwhelmingly targeted reef substrates composed of algal turfs and crustose coralline algae, which are typically associated with epilithic and endolithic microalgal and cyanobacterial communities. Additionally, three species preferentially consumed BCMs. As such, our work is consistent with and provides direct evidence supporting the recently proposed trophic role for parrotfishes as microphages. Contrasting observations of reef fishes avoiding substrates dominated by BCMs on other reefs suggests variation in the palatability of BCMs to grazing reef fishes, or species-specific differences in preference for these potentially nutritional trophic resources.
memento: Generalized differential expression analysis of single-cell RNA-seq with method of moments estimation and efficient resampling
Authors: Kim Min Cheol , Gate Rachel , Lee David S. , Lu Andrew , Gordon Erin , Shifrut Eric , Marson Alexander , Ntranos Vasilis , Ye Chun Jimmie 
Published: November 2022

AbstractDifferential expression analysis of scRNA-seq data is central for characterizing how experimental factors affect the distribution of gene expression. However, it remains challenging to distinguish biological and technical sources of cell-cell variability and to assess the statistical significance of quantitative comparisons between groups of cells. We introducemementoto address these limitations and enable accurate and efficient differential expression analysis of the mean, variability, and gene correlation from scRNA-seq. We usedmementoto analyze 70,000 tracheal epithelial cells to identify interferon response genes with distinct variability and correlation patterns, 160,000 T cells perturbed with CRISPR-Cas9 to reconstruct gene-regulatory networks that control T cell activation, and 1.2 million PMBCs to map cell-type-specificcisexpression quantitative trait loci (eQTLs). In all cases,mementoidentified more significant and reproducible differences in mean expression but also identified differences in variability and gene correlation that suggest distinct modes of transcriptional regulation imparted by cytokines, genetic perturbations, and natural genetic variation. These results demonstratemementoas a first-in-class method for the quantitative comparisons of scRNA-seq data scalable to millions of cells and thousands of samples.
Structures of the Ndc80 complex and its interactions at the yeast kinetochore-microtubule interface
Authors: Zahm Jacob , Jenni Simon , Harrison Stephen 
Published: November 2022

ABSTRACTThe conserved Ndc80 kinetochore complex, Ndc80c, is the principal link between spindle microtubules and centromere associated proteins during chromosome segregation. We used AlphaFold 2 to obtain structural predictions of the Ndc80 “loop” region and the Ndc80:Nuf2 globular head domains that interact with the Dam1 subunit of the decameric DASH/Dam1 complex (Dam1c). The predictions guided design of constructs that readily yielded crystal structures, essentially congruent with the predicted ones. The Ndc80 “loop” is a stiff, straight α-helical “switchback” structure, and flexibility within the long Ndc80c rod occurs instead at a hinge point between the globular head and the loop. Conserved stretches of the Dam1 C terminus bind Ndc80c with a short α helix followed by an extended segment such that phosphorylation of Dam1 serines 257, 265, and 292 by the mitotic kinase Ipl1/Aurora B can release this contact during error correction of mis-attached kinetochores. We integrate the structural results presented here into our current molecular model of the kinetochore-microtubule interface. The model illustrates how multiple interactions between Ndc80c, DASH/Dam1c and the microtubule lattice stabilize kinetochore attachments.
Tumor-specific CD4 T cells instruct monocyte differentiation in pancreatic ductal adenocarcinoma
Authors: Patterson Michael T. , Burrack Adam L. , Xu Yingzheng , Schmiechen Zoe C. , Schrank Patricia R. , Kennedy Ainsley E. , Firulyova Maria M. , Miller Ebony A. , Cruz-Hinojoza Eduardo , Zaitsev Konstantin , Williams Jesse W. , Stromnes Ingunn M. 
Published: November 2022

SummaryPancreatic ductal adenocarcinoma (PDA) is a lethal malignancy resistant to immunotherapy. The pancreatic tumor microenvironment is shaped and maintained by myeloid cells that outnumber tumor cells. Here, using monocyte fate-mapping PDA mouse models and human tumor tissues, we identify monocytes give rise to most heterogeneous macrophage subpopulations in PDA. We show that monocyte differentiation is governed by the local presence of CD4, but not CD8, T cells. We demonstrate that tumor specific CD4 T cells induce monocyte differentiation into antitumor MHCIIhiproinflammatory macrophages dependent on non-redundant IFNγ and CD40 signaling pathways that suppress tumor growth. Pancreatic tissue-resident macrophages exhibit an immunosuppressive pro-tumor state that is refractory to the modulatory effects of antitumor CD4 T cells. Intratumoral monocytes adopt a pro-tumor fate indistinguishable from tissue-resident macrophages following CD4 T cell depletion. Thus, tumor-specific CD4 T cell governance of monocyte fate promotes immune-mediated control of solid tumors.Highlights▪Circulating monocytes are progenitors to most heterogeneous macrophage subsets in PDA▪Monocyte-derived macrophage acquisition of an MHCIIhiphenotype is dependent on tumor-specific CD4 T cells▪In the absence of CD4 T cells, monocyte-derived macrophages acquire tissue resident macrophage traits and tumors rapidly progress▪IFNγ and CD40 signaling are nonredundant and critical determinants of intratumoral monocyte fate
Quisinostat is a brain-penetrant radiosensitizer in glioblastoma
Authors: Cascio Costanza Lo , Margaryan Tigran , Melendez Ernesto Luna , McNamara James B. , White Connor I. , Knight William , Ganta Saisrinidhi , Opachich Zorana , Yoo Wonsuk , Sanai Nader , Tovmasyan Artak , Mehta Shwetal 
Published: November 2022

ABSTRACTIn recent years, histone deacetylase inhibitors (HDACi) have garnered considerable interest for the treatment of adult and pediatric malignant brain tumors. However, owing to their broad-spectrum nature and inability to effectively penetrate the blood-brain barrier, HDACi have failed to provide significant clinical benefit to glioblastoma (GBM) patients to date. Moreover, global inhibition of HDACs results in widespread toxicity, highlighting the need for selective isoform targeting. While no isoform-specific HDACi are currently available, the second-generation hydroxamic acid-based HDACi quisinostat possesses sub-nanomolar specificity for class I HDAC isoforms, particularly HDAC1 and 2. Recently, we demonstrated that HDAC1 is the essential HDAC in GBM. Here, we provide the first report on the neuro-pharmacokinetic, pharmacodynamic and radiation-sensitizing properties of quisinostat in preclinical models of GBM. We demonstrate that quisinostat is a well-tolerated and brain-penetrant molecule that significantly extends survival when administered in combination with radiationin vivo. The pharmacokinetic-pharmacodynamic-efficacy relationship was established by correlating free drug concentrations and evidence of target modulation in the brain with survival benefit. Together, these data provide a strong rationale for clinical development of quisinostat as a radiosensitizer for the treatment of GBM.
Plant pathogenicRalstoniaphylotypes evolved divergent respiratory strategies and behaviors to thrive in xylem
Authors: Truchon Alicia N. , Dalsing Beth L. , Khokhani Devanshi , MacIntyre April , McDonald Bradon R. , Ailloud Florent , Klassen Jonathan , Gonzalez-Orta Enid T. , Currie Cameron , Prior Philippe , Lowe-Power Tiffany M. , Allen Caitilyn 
Published: November 2022

ABSTRACTBacterial pathogens in theRalstonia solanacearumspecies complex (RSSC) infect the water-transporting xylem vessels of plants, causing bacterial wilt disease. Strains in RSSC phylotypes I and III can reduce nitrate to dinitrogen via complete denitrification. The four-step denitrification pathway enables bacteria to use inorganic nitrogen species as terminal electron acceptors, supporting their growth in oxygen-limited environments like biofilms or plant xylem. Reduction of nitrate, nitrite, and nitric oxide all contribute to virulence of a model phylotype I strain. However, little is known about the physiological role of the last denitrification step, the reduction of nitrous oxide to dinitrogen by NosZ. We found that phylotypes I and III need NosZ for full virulence. However, strains in phylotypes II and IV are highly virulent despite lacking NosZ. The ability to respire by reducing nitrate to nitrous oxide does not greatly enhance growth of phylotype II and IV strains. These partial denitrifying strains reach high cell densities during plant infection and cause typical wilt disease. However, unlike phylotype I and III strains, partial denitrifiers cannot grow well under anaerobic conditions or form thick biofilms in culture or in tomato xylem vessels. Furthermore, aerotaxis assays show that strains from different phylotypes have different oxygen and nitrate preferences. Together, these results indicate that the RSSC contains two subgroups that occupy the same habitat but have evolved divergent energy metabolism strategies to exploit distinct metabolic niches in the xylem.IMPORTANCEPlant pathogenicRalstonia spp. are a heterogeneous globally distributed group of bacteria that colonize plant xylem vessels.Ralstoniacells multiply rapidly in plants and obstruct water transport, causing fatal wilting and serious economic losses of many key food security crops. Virulence of these pathogens depends on their ability to grow to high cell densities in the low-oxygen xylem environment. Plant pathogenicRalstoniacan use denitrifying respiration to generate ATP. The last denitrification step, nitrous oxide reduction by NosZ, contributes to energy production and virulence for only one of the three phytopathogenicRalstoniaspecies. These complete denitrifiers form thicker biofilms in culture and in tomato xylem, suggesting they are better adapted to hypoxic niches. Strains with partial denitrification physiology form less biofilm and are more often planktonic. They are nonetheless highly virulent. Thus, these closely related bacteria have adapted their core metabolic functions to exploit distinct micro-niches in the same habitat.