bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomes of the extinct Bachman’s Warbler shows high divergence and no evidence of admixture with other extantVermivoraWarblers
Authors: Wood Andrew W. , Szpiech Zachary A. , Lovette Irby , Smith Brian Tilson , Toews David P. L. 
Published: December 2022

AbstractBachman’s Warbler (Vermivora bachmanii) – last sighted in 1988 – is one of the few North American passerines that have gone extinct. Given the extensive ongoing hybridization of its two extant congeners – the Blue-Winged Warbler (V. cyanoptera) and Golden-Winged Warbler (V. chrysoptera) – and shared patterns of plumage variation between Bachman’s Warbler and hybrids between those extant species, it has been suggested that Bachman’s Warbler might have also had a component of hybrid ancestry. Here, we use historic DNA (hDNA) and whole genome sequencing of Bachman’s Warblers collected at the turn of the 20thcentury to address this possibility. We combine these data with genomes of the two extantVermivoraspecies to examine patterns of population differentiation, inbreeding, and gene flow. In contrast to the admixture hypothesis, the genomic evidence is consistent withV. bachmaniibeing a highly divergent, reproductively isolated species, with no evidence of introgression. We show that bothV. bachmaniiandV. chrysopterahave elevated runs of homozygosity compared toV. cyanoptera, consistent with the effects of a small effective population size or population bottlenecks in the former two species. We also found—using population branch statistic estimates of all three species—previously undocumented evidence of lineage-specific evolution inV. chrysopteranear a novel pigmentation gene candidate for warblers,CORIN, which is a known modifier ofASIP, which is in turn involved in melanic throat and mask coloration in this family of birds. Together, these genomic results also highlight how natural history collections are such invaluable repositories of information about extant and extinct species.SignificanceFew common North American passerines have gone extinct. Bachman’s Warbler is, unfortunately, one that has—the last sighting was in 1988. Here we use whole genome historical DNA from museum specimens of Bachman’s warblers collected at the turn of the 20thcentury to learn about the evolution of this species and test whether there was evidence for hybridization and gene flow between it and two extant members of the same genus which, today, hybridize extensively. We find Bachman’s warbler was highly divergent with no evidence of gene flow. We also find evidence of elevated “runs of homozygosity” in both Bachman’s warbler and one of the two extantVermivoraspecies, suggesting the effects of a small population size or population bottlenecks.
Multiplex qPCR assays for detection of two imperiled anuran species,Anaxyrus californicusandSpea hammondii, from environmental DNA
Authors: Rodgers Torrey W. , Lovich Robert E. , Walton James A. , Prince Daniel J. , Gonzalez Bernardo R. , Shaffer H. Bradley , Mock Karen E. 
Published: December 2022

AbstractWe developed a species-specific, quantitative PCR assay multiplex for the detection of two threatened and endangered anuran species, arroyo toad (Anaxyrus californicus)and western spadefoot (Spea hammondii), from environmental DNA (eDNA). Both species have experienced range wide declines over the last century, mostly as a result of habitat loss. Given these declines and their cryptic life histories, improved tools for detecting and monitoring both species are needed. Species-specificity and sensitivity of assays were empirically tested in the lab, and the multiplexed assays were validated with field-collected eDNA samples. Both assays were species-specific, sensitive, and effectively detected the target species from streams, rivers and ponds, although detection was imperfect. These assays provide an efficient and economical tool that will aid in the detection, monitoring, management, and conservation of these at-risk species.
Simulation-guided sloppy DNA probe design for mismatch tolerant hybridization
Authors: Bugga Pallavi , Asthana Vishwaratn , Drezek Rebekah 
Published: December 2022

AbstractThe ability to both sensitively and specifically assess the sequence composition of a nucleic acid strand is an ever-growing field. Designing a detection scheme that can perform this function when the sequence of the target being detected deviates significantly from the canonical sequence however is difficult in part because probe/primer design is based on established Watson-Crick base-pairing rules. We present here a robust and tunable toehold-based exchange probe that can detect a sequence with a variable number of SNPs of unknown identity by inserting a series of controlled, sequential mismatches into the protector seal of the toehold probe, in an effort to make the protector seal “sloppy”. We show that the mismatch tolerant system follows predicted behavior closely even with targets containing up to four mismatches and thermodynamically deviating from the canonical sequence by up to 15 kcal/mole. The system also performs faithfully regardless of the global mismatch position on either the protector seal or target. Lastly, we demonstrate the generalizability of the approach by testing the increasingly sloppy protectors on HIV clinical samples and show that the system is capable of resolving multiple, iteratively mutated sequences derived from numerous HIV sub-populations with remarkable precision.
Spatially distinct phytohormone responses of individualArabidopsis thalianaroot cells to infection and colonization byFusarium oxysporum
Authors: Calabria Jacob , Wang Liu , Rast-Somssich Madlen I. , Chen Hsiang-Wen , Watt Michelle , Persson Staffan , Idnurm Alexander , Somssich Marc 
Published: December 2022

AbstractJasmonic acid (JA), ethylene (ET) and salicylic acid (SA) are the three major phytohormones coordinating a plant’s defense response to pathogenic attack. While JA and ET are assumed to primarily control the defense against necrotrophic pathogens, SA-induced defense responses target mainly biotrophic microbes, and can include drastic measures such as programmed cell death as part of the plant’s hypersensitive response (HR).Fusarium oxysporumis a hemibiotrophic fungal pathogen of several plant species, including many important food crops, and the model plant speciesArabidopsis thaliana. Colonization of the plant’s root vascular tissue by the fungus eventually results in wilting and plant death. A general role for JA, ET and SA in combating infection and colonization of the plant byF. oxysporumhas been demonstrated, but their distinct roles and modes of action have so far not been described. Here, using high resolution microscopy with fluorescent marker lines ofA. thalianaroots infected withF. oxysporumwe show that SA acts spatially separate from JA, in a distinct set of root cells immediately neighboring the fungal colonization site. There, SA induces HR to stop the spread of colonization. JA acts in a different, but also clearly defined set of cells, slightly removed from the colonization site, where it initiates a defense response to actively resist the invader. ET is activated in a stretch of cells that covers both, the cells with activated SA and JA signaling, and may be involved in creating these two distinct zones. These results show how the three phytohormones act together, but spatially and functionally separate from each other, to fight this hemibiotrophic pathogen. Such a high-resolution analysis to resolve the plant’s immune response to pathogenic infection on an individual cell level and in intact tissue has so far been lacking.Graphical AbstractColonization of theA.thalianaroot tip byF.oxysporumstrainFo5176 leads to immediate cell death of the colonized and surrounding tissue.As the colonization front progresses through the vasculature, the cell death front moves along with it through not only the vasculature, but also the surrounding tissues.WRKY70 positively regulates salicylic acid (SA) biosynthesis in cells immediately adjacent to the colonized tissue, inducing a hypersensitive response (HR), thereby killing off the cells deemed lost to the intruder, establishing the cell death front.Slightly further removed from the HR zone, WRKY11 induces jasmonate (JA) biosynthesis in cells of the vasculature to launch a defense response aimed at actively repelling the fungus.
Newly repopulated spinal cord microglia exhibit a unique transcriptome and correlate with pain resolution
Authors: Donovan Lauren J. , Bridges Caldwell M. , Nippert Amy R. , Wang Meng , Wu Shaogen , Forman Thomas E. , Haight Elena S. , Huck Nolan A. , Bond Sabrina F. , Jordan Claire E. , Gardner Aysha S. , Nair Ramesh V. , Tawfik Vivianne L. 
Published: December 2022

SummaryMicroglia contribute to the initiation of pain, however, a translationally viable approach addressing how or when to modulate these cells remains elusive. We used a targeted, inducible, genetic microglial depletion strategy at both acute and acute-to-chronic transition phases in the clinically-relevant tibial fracture/casting pain model to determine the contribution of microglia to the initiation and maintenance of pain. We observed complete resolution of pain after transient microglial depletion at the acute-to-chronic phase, which coincided with the timeframe of full repopulation of microglia. These repopulated microglia were morphologically distinct from control microglia, signifying they may exhibit a unique transcriptome. RNA sequencing of repopulated spinal cord microglia identified genes of interest using weighted gene co-expression network analysis (WGCNA). We intersected these genes with a newly-generated single nuclei microglial dataset from human spinal cord dorsal horn and identified human-relevant genes that may ultimately promote pain resolution after injury. This work presents a novel approach to gene discovery in pain and provides comprehensive datasets for the development of future microglial-targeted therapeutics.
Clinically defined mutations inMEN1alter its tumor-suppressive function through increased menin turnover
Authors: Duan Suzann , Sheriff Sulaiman , Elvis-Offiah Uloma B. , Sawyer Travis W. , Sundaresan Sinju , Cierpicki Tomasz , Grembecka Jolanta , Merchant Juanita L. 
Published: December 2022

AbstractLoss of the tumor suppressor protein menin is a critical event underlying the formation of neuroendocrine tumors (NETs) in hormone-expressing tissues including gastrinomas. While aberrant expression of menin impairs its tumor suppression, few studies explore the structure– function relationship of clinical Multiple Endocrine Neoplasia, type 1 (MEN1) mutations in the absence of a complete loss of heterozygosity at both loci. Here, we determined whether clinicalMEN1mutations render nuclear menin unstable and lead to its functional inactivation. We studied the structural and functional implications of three clinicalMEN1mutations (R516fs, E235K, and A541T) recently identified in a cohort of ten patients with GEP-NETs. We evaluated the subcellular localization and half-lives of these mutated menin variants inMen1-null mouse embryo fibroblast cells and in hormone-expressing human gastric adenocarcinoma and murine enteroendocrine tumor cell lines. Loss of menin function was assessed by cell proliferation and gastrin gene expression assays. Lastly, we evaluated the effect of the small molecule compound MI-503 on stabilizing nuclear menin expression and functionin vitroand in a previously reported mouse model of gastric NET development. Both the R516fs and E235K variants exhibited severe defects in total and subcellular expression of menin, and this was consistent with reduced half-lives of these mutants. Mutated menin variants exhibited loss of function in suppressing tumor cell proliferation and gastrin expression. Treatment with MI-503 rescued nuclear menin expression and attenuated hypergastrinemia and gastric hyperplasia in NET-bearing mice.ImplicationClinically defined germline and somaticMEN1mutations confer pathogenicity by destabilizing nuclear menin expression.
motifNet: A Neural Network Approach for Learning Functional Sequence Patterns in mRNA
Authors: Deng Kaifeng , Li Zhengchang , Wei Wenqing , Liu Yang 
Published: December 2022

AbstractWe present a new approach for predicting functional sequence patterns in mRNA, known as motifs. These motifs play an important role in understanding the mechanisms of the cell life cycle in clinical research and drug discovery. However, many existing neural network models for mRNA event prediction only take the sequence as input, and do not consider the positional information of the sequence. In contrast, motifNet is a lightweight neural network that uses both the sequence and its positional information as input. This allows for the implicit neural representation of the various motif interaction patterns in human mRNA sequences. The model can then be used to interactively generate motif patterns and the positional effect score in mRNA activities. Additionally, motifNet can identify violations of motif patterns in real human mRNA variants that are associated with disease-related cell dysfunction.
Supervised discovery of interpretable gene programs from single-cell data
Authors: Kunes Russell Z. , Walle Thomas , Nawy Tal , Pe’er Dana 
Published: December 2022

AbstractFactor analysis can drive biological discovery by decomposing single-cell gene expression data into a minimal set of gene programs that correspond to processes executed by cells in a sample. However, matrix factorization methods are prone to technical artifacts and poor factor interpretability. We have developed Spectra, an algorithm that identifies user-provided gene programs, modifies them to dataset context as needed, and detects novel programs that together best explain expression covariation. Spectra overcomes the dominance of cell-type signals by modeling cell-type-specific programs, and can characterize interpretable cell states along a continuum. We show that it outperforms existing approaches in challenging tumor immune contexts; Spectra finds factors that change under immune checkpoint therapy, disentangles the highly correlated features of CD8+T-cell tumor reactivity and exhaustion, finds a novel program that explains continuous macrophage state changes under therapy, and identifies cell-type-specific immune metabolic programs.
Haplotype resolved chromosome level genome assembly ofCitrus australisreveals disease resistance and other citrus specific genes
Authors: Nakandala Upuli , Masouleh Ardashir Kharabian , Smith Malcolm W. , Furtado Agnelo , Mason Patrick , Constantin Lena , Henry Robert J. 
Published: December 2022

ABSTRACTRecent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus. Relatively few genomes have been anchored at the chromosome level and/or are haplotype phased, with the available genomes of varying accuracy and completeness. We now report a phased high-quality chromosome level genome assembly for an Australian native citrus species;Citrus australis(round lime) using highly accurate PacBio HiFi long reads, complemented with Hi-C scaffolding. Hifiasm with Hi-C integrated assembly resulted in a 331 Mb genome ofC. australiswith two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness (BUSCO). Repeat analysis showed that more than 50% of the genome contained interspersed repeats. Among them, LTR elements were the predominant type (21.0%), of which LTR Gypsy (9.8 %) and LTR copia (7.7 %) elements were the most abundant repeats. A total of 29,464 genes and 32,009 transcripts were identified in the genome. Of these, 28,222 CDS (25,753 genes) had BLAST hits and 21,401 CDS (75.8%) were annotated with at least one GO term. Citrus specific genes for antimicrobial peptides, defense, volatile compounds and acidity regulation were identified. This chromosome scale, and haplotype resolvedC. australisgenome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species.
Hypothalamic supramammillary neurons that project to the medial septum control wakefulness
Authors: Liang Mengru , Jian Tingliang , Jin Wenjun , Chen Qianwei , Yang Xinyu , Wang Rui , Xiao Jingyu , Yang Zhiqi , Liao Xiang , Chen Xiaowei , Wang Liecheng , Qin Han 
Published: December 2022

AbstractThe hypothalamic supramammillary nucleus (SuM) plays a key role in controlling wakefulness, but the downstream target regions participating in this control process remain unknown. Here, using circuit-specific fiber photometry and single-neuron electrophysiology together with electroencephalogram, electromyogram and behavioral recordings, we find approximately half of SuM neurons that project to the medial septum (MS) are wake-active. Optogenetic stimulation of axonal terminals of SuM-MS projection induces a rapid and reliable transition to wakefulness from NREM or REM sleep, and chemogenetic activation of SuMMSprojecting neurons significantly increases wakefulness time and prolongs latency to sleep. Consistently, chemogenetically inhibiting these neurons significantly reduces wakefulness time and latency to sleep. Therefore, these results identify the MS as a functional downstream target of SuM and provide evidence for a causal role for this hypothalamic-septal projection in wakefulness control.
Recurrent hypoxia in a rat model of sleep apnea during pregnancy leads to microglia-dependent respiratory deficits and persistent neuroinflammation in adult male offspring
Authors: Mickelson Carly R. , Ewald Andrea C. , Gumnit Maia G. , Meza Armand L. , Radcliff Abigail B. , Johnson Stephen M. , Ouellette Jonathan N. , Kermath Bailey A. , Roopra Avtar S. , Cahill Michael E. , Watters Jyoti J. , Baker Tracy L. 
Published: December 2022

ABSTRACTSleep apnea (SA) during pregnancy is detrimental to the health of the pregnancy and neonate, but little is known regarding long-lasting consequences of maternal SA during pregnancy on adult offspring. SA is characterized by repeated cessations in breathing during sleep, resulting in intermittent hypoxia (IH). We show that gestational IH (GIH) in rats reprograms the male fetal neuroimmune system toward enhanced inflammation in a region- and sex-specific manner, which persists into adulthood. Male GIH offspring also had deficits in the neural control of breathing, specifically in the ability to mount compensatory responses to central apnea, an effect that was rescued by a localized anti-inflammatory or microglial depletion. Female GIH offspring appeared unaffected. These results indicate that SA during pregnancy sex- and region-dependently skews offspring microglia toward a pro-inflammatory phenotype, which leads to long-lasting deficits in the capacity to elicit important forms of respiratory neuroplasticity in response to breathing instability. These studies contribute to the growing body of recent evidence indicating that SA during pregnancy may lead to sex-specific neurological deficits in offspring that persist into adulthood.
A genome-wide screen in macrophages defines host genes regulating the uptake ofMycobacterium abscessus
Authors: Gilliland Haleigh N. , Beckman Olivia K. , Olive Andrew J. 
Published: December 2022

ABSTRACTThe interactions between a host cell and a pathogen can dictate disease outcomes and are important targets for host-directed therapies.Mycobacterium abscessus(Mab) is a highly antibiotic resistant, rapidly growing non-tuberculous mycobacterium that infects patients with chronic lung diseases. Mab can infect host immune cells, such as macrophages, which contribute to its pathogenesis. However, our understanding of initial host-Mab interactions remains unclear. Here, we developed a functional genetic approach to define these host-Mab interactions by coupling a Mab fluorescent reporter with a genome-wide knockout library in murine macrophages. We used this approach to conduct a forward genetic screen to define host genes that contribute to the uptake of Mab by macrophages. We identified known regulators of phagocytosis, such as the integrin ITGB2, and uncovered a key requirement for glycosaminoglycan (sGAG) synthesis for macrophages to efficiently take up Mab. CRISPR-Cas9 targeting of three key sGAG biosynthesis regulators,Ugdh, B3gat3 and B4galt7resulted in reduced uptake of both smooth and rough Mab variants by macrophages. Mechanistic studies suggest that sGAGs function upstream of pathogen engulfment and are required for the uptake of Mab, but notEscherichia colior latex beads. Further investigation found that the loss of sGAGs reduced the surface expression, but not the mRNA expression, of key integrins suggesting an important role for sGAGs in modulating surface receptor availability. Together, these studies globally define and characterize important regulators of macrophage-Mab interactions and are a first step to understanding host genes that contribute to Mab pathogenesis and disease.IMPORTANCEPathogen interactions with immune cells like macrophages contribute to pathogenesis, yet the mechanisms underlying these interactions remain largely undefined. For emerging respiratory pathogens, likeMycobacterium abscessus, understanding these host-pathogen interactions is important to fully understand disease progression. Given thatM. abscessusis broadly recalcitrant to antibiotic treatments, new therapeutic approaches are needed. Here, we leveraged a genome-wide knockout library in murine macrophages to globally define host genes required forM. abscessusuptake. We identified new macrophage uptake regulators duringM. abscessusinfection, including a subset of integrins and the glycosaminoglycan synthesis (sGAG) pathway. While ionic characteristics of sGAGs are known to drive pathogen-cell interactions, we discovered a previously unrecognized requirement for sGAGs to maintain robust surface expression of key uptake receptors. Thus, we developed a flexible forward-genetic pipeline to define important interactions duringM. abscessusinfection and more broadly identified a new mechanism by which sGAGs control pathogen uptake.