bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential gene expression underlying the biosynthesis of Dufour’s gland signals in Bombus impatiens
Authors: Derstine Nathan , Galbraith David , Villar Gabriel , Amsalem Etya 
Published: April 2022

AbstractPheromones regulating social behavior are one of the most explored phenomena in social insects. However, compound identity, biosynthesis and their genetic regulation are known in only a handful of species. Here we conducted chemical and RNA-seq analyses of the Dufour’s gland in the bumble bee Bombus impatiens and examined the signals and the pathways regulating signal production in queens and workers. Across Hymenopterans, the Dufour’s gland contains mostly long-chained hydrocarbons and esters that signal reproductive and social status in several bee species. In bumble bees, the Dufour’s gland contains queen- and worker-specific esters, in addition to terpenes and terpene-esters only found in gynes and queens. These compounds are assumed to be synthesized de novo in the gland, however, their genetic regulation is unknown. A whole transcriptome gene expression analysis of the gland in queens, gynes, queenless and queenright workers showed distinct transcriptomic profiles, with thousands of differentially expressed genes between the groups. Workers and queens express genes associated with key enzymes in the biosynthesis of wax esters, while queens and gynes preferentially express key genes in terpene biosynthesis. In contrast, no genes were differentially expressed in queenless and queenright workers, despite differences in their Dufour’s gland chemistry and reproductive state, suggesting the quantitative differences in worker secretion are not regulated at the level of production. Overall, our data demonstrate gland-specific regulation of chemical signals associated with social behavior and identifies genes and pathways regulating caste-specific chemical signals in social insects.
Calibration allows accurate estimation of the axonal volume fraction with diffusion MRI
Authors: Papazoglou Sebastian , Ashtarayeh Mohammad , Oeschger Jan Malte , Callaghan Martina F. , Does Mark D. , Mohammadi Siawoosh 
Published: April 2022

AbstractBiophysical models enable the non-invasive estimation of microstructural tissue features of the central nervous system such as the axonal volume fraction using diffusion weighted imaging (DWI)-data. However, these models trade accuracy with complexity and demands for time-efficient data acquisition. In this study, we hypothesise that their accuracy can be improved substantially through biophysically motivated, linear calibration. We test this hypothesis in the context of axonal volume fraction estimation in four different DWI-models of different complexity using multi-modal data including ex-vivo diffusion MRI- and electron microscopy (EM)-data in mice with broad dynamic range, whereby the latter served as gold standard. We found that two calibration parameters, an offset accounting for the fraction of unmyelinated axons in severely hypomyelinated mice and a scaling accounting for the compartment-specific relaxation, substantially improved the accuracy of axonal volume fraction. Furthermore, we theoretically predict the scaling parameter, and demonstrate that similar accuracy improvement can be achieved for a subset of DWI-models, if the scaling parameter is fixed to the predicted value instead of estimating it on basis of data. This is of practical relevance because it allows to estimate the remaining offset calibration parameter from a limited amount of multi-modal data and thus makes the proposed method usable in human brain data.
Viral origin of eukaryotic type IIA DNA topoisomerases
Authors: Guglielmini Julien , Gaia Morgan , Da Cunha Violette , Criscuolo Alexis , Krupovic Mart , Forterre Patrick 
Published: April 2022

AbstractType II DNA topoisomerases of the family A (Topo IIA) are present in all bacteria (DNA gyrase) and eukaryotes. In eukaryotes, they play a major role in transcription, DNA replication, chromosome segregation and modulation of chromosome architecture. The origin of eukaryotic Topo IIA remains mysterious since they are very divergent from their bacterial homologues and have no orthologues in Archaea. Interestingly, eukaryotic Topo IIA have close homologues in viruses of the phylum Nucleocytoviricota, an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasmic large DNA viruses (NCLDV). Topo IIA are also encoded by some bacterioviruses of the class Caudoviricetes (tailed bacteriophages). To elucidate the origin of the eukaryotic Topo IIA, we performed in-depth phylogenetic analyses combining viral and cellular Topo IIA homologs. Topo IIA encoded by bacteria and eukaryotes form two monophyletic groups nested within Topo IIA encoded by Caudoviricetes and Nucleocytoviricota, respectively. Importantly, Nucleocytoviricota remained well separated from eukaryotes after removing both bacteria and Caudoviricetes from the dataset, indicating that the separation of Nucleocytoviricota and eukaryotes is probably not due to long branch attraction artefact. The topology of our tree suggests that the eukaryotic Topo IIA was probably acquired from an ancestral member of the Nucleocytoviricota of the class Megaviricetes, before the emergence of the last eukaryotic common ancestor (LECA). This result further highlights a key role of these viruses in eukaryogenesis and suggests that early proto-eukaryotes used a Topo IIB instead of a Topo IIA for solving their DNA topological problems.
The cellular poly(rC)-binding protein 2 prevents the early steps of hepatitis C virus virion assembly
Authors: Cousineau Sophie E. , Sagan Selena M. 
Published: April 2022

ABSTRACTPoly(rC)-binding protein 2 (PCBP2) was previously shown to bind to the hepatitis C virus (HCV) genome; however, its precise role in the viral life cycle remained unclear. Herein, we found that PCBP2 does not directly affect viral entry, translation, genome stability, replication, or virion egress. Rather, our data suggests that endogenous PCBP2 normally limits virion assembly, thereby indirectly promoting translation and replication by increasing the translating/replicating pool of viral RNAs. Additionally, we found that an alternative RNA conformation (SLIIalt) was important for efficient virion assembly, but functions in a PCBP2-independent manner. The latter may explain why the Japanese fulminant hepatitis 1 isolate is able to produce infectious particles in cell culture, while other HCV isolates are lost in translation. Taken together, our results suggest that PCBP2 and SLIIaltindependently modulate HCV genome packaging and alter the balance of viral RNAs in the translating/replicating pool and those engaged in virion assembly.Graphical Abstract
Genotype-dependent responses to long-term water stress in Chenopodium quinoa Willd
Authors: Maestro-Gaitán I. , Granado-Rodríguez S. , Orús M. , Matías J. , Cruz V , Bolaños L. , Reguera M. 
Published: April 2022

AbstractWithin the current climate context, freshwater resources have become scarce. Agriculture, especially in rain-fed conditions, should deal with the need for increasing yields to contribute to food security under limiting water availability. Exploring underutilized crops such as Chenopodium quinoa (quinoa) has become a unique opportunity as some of these crops possess the ability to tolerate several abiotic stresses, including drought. In line with this, this work aimed at evaluating the genotype-dependent response to drought by comparing the performance of different European-adapted cultivars (F14, F15, F16, and Titicaca). The results show that the cultivars here evaluated presented different mechanisms to cope with long-term water stress, including changes in phenology, morphology, or physiology. Among them, the cultivar F16 might be the most promising genotype to grow under water-limiting conditions as it was able to increase Water Use Efficiency (WUE), reducing the stomatal conductance and keeping CO2 assimilation rates similar to well-watered conditions, maintaining seed yield and increasing harvest index (HI) under water deficit conditions. Furthermore, based on these results, we propose a model in which differences between a tolerant and a sensitive genotype are presented. Altogether, we believe that this work will significantly contribute to broadening our understanding regarding how quinoa responds to long-term water stress highlighting genotype-related differences that will allow the selection of the best adapted genotypes for water-limiting environments.HighlightQuinoa physiological, phenological, and morphological distinct responses to long-term water stress depending on the genotype.
A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics
Authors: Tsai Chia-Feng , Wang Yi-Ting , Hsu Chuan-Chih , Kitata Reta Birhanu , Chu Rosalie K. , Velickovic Marija , Zhao Rui , Williams Sarai M. , Chrisler William B. , Jorgensen Marda L. , Moore Ronald J. , Zhu Ying , Rodland Karin D. , Smith Richard D. , Wasserfall Clive H. , Shi Tujin , Liu Tao 
Published: April 2022

AbstractEffective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily due to significant sample loss associated with non-specific surface adsorption during enrichment of low stoichiometric phosphopeptide. We developed a novel tandem tip phosphoproteomics sample preparation method that is capable of sample cleanup and enrichment without additional sample transfer, and its integration with our recently developed SOP (Surfactant-assisted One-Pot sample preparation) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling) approaches provides a streamlined workflow enabling sensitive, high-throughput nanoscale phosphoproteome measurements. This approach significantly reduces both sample loss and processing time, allowing the identification of >3,000 (>9,500) phosphopeptides from 1 (10) µg of cell lysate using the label-free method without a spectral library. It also enabled precise quantification of ∼600 phosphopeptides from 100 cells sorted by FACS (single-cell level input for the enriched phosphopeptides) and ∼700 phosphopeptides from human spleen tissue voxels with a spatial resolution of 200 µm (equivalent to ∼100 cells) in a high-throughput manner. The new workflow opens avenues for phosphoproteome profiling of mass-limited samples at the low nanogram level.
Coupling phenotype stability to growth rate overcomes limitations of bet-hedging strategies
Authors: de Groot Daan H. , Tjalma Age J. , Bruggeman Frank J. , van Nimwegen Erik 
Published: April 2022

AbstractMicrobes in the wild face highly variable and unpredictable environments, and are naturally selected for their average growth rate across environments. Apart from using sensory-regulatory systems to adapt in a targeted manner to changing environments, microbes employ bet-hedging strategies where cells in an isogenic population switch stochastically between alternative phenotypes. Yet, bet-hedging suffers from a fundamental trade-off: increasing the phenotype switching rate increases the rate at which maladapted cells explore alternative phenotypes, but also increases the rate at which cells switch out of a well-adapted state. Consequently, it is currently believed that bet-hedging strategies are only effective when the number of possible phenotypes is limited and when environments last for sufficiently many generations. However, recent experimental results show that gene expression noise generally decreases with growth rate, suggesting that phenotype switching rates may systematically decrease with growth rate. We here show that such growth rate dependent stability (GRDS) can almost completely overcome the trade-off that limits bet-hedging, allowing for effective adaptation even when environments are diverse and change rapidly. GRDS allows cells to be more explorative when maladapted, and more phenotypically stable when well-adapted. We further show that even a small decrease in switching rates of faster growing phenotypes can substantially increase long-term fitness of bet-hedging strategies. Together, our results suggest that stochastic strategies may play an even bigger role for microbial adaptation than hitherto appreciated.
Carbon dioxide regulates Mycobacterium tuberculosis PhoPR signaling and virulence
Authors: Dechow Shelby J. , Goyal Rajni , Johnson Benjamin K. , Abramovitch Robert B. 
Published: April 2022

AbstractThe Mycobacterium tuberculosis (Mtb) two-component regulatory system, PhoPR, is implicated in pH-sensing within the macrophage because it is strongly induced by acidic pH both in vitro and the macrophage phagosome. The carbonic anhydrase (CA) inhibitor ethoxzolamide (ETZ) inhibits PhoPR signaling supporting the hypothesis that CO2 may also play a role in regulating PhoPR. Here, we show that increasing CO2 concentration induces PhoPR signaling, and its induction is independent of medium pH. We also show that at acidic pH 5.7, a normally strong inducer of PhoPR signaling, that increasing CO2 from 0.5% to 5% further induces the pathway. Based on these findings, we propose that PhoPR functions as a CO2 sensor. Mtb has three CA (CanA, CanB, and CanC) and using CRISPR interference knockdowns and gene deletion mutants, we assessed which CAs regulate PhoPR signaling and virulence. We first examined if CA played a role in Mtb pathogenesis and observed that CanB was required for virulence in macrophages, where the knockdown strain had ~1 log reduction in virulence. To further define the interplay of CO2 and Mtb signaling, we conducted transcriptional profiling experiments at varying pH and CO2 concentrations. As hypothesized, we observed the induction of PhoPR at acidic pH is dependent on CO2 concentration, with a subset of core PhoPR regulon genes dependent on both 5% CO2 and acidic pH for their induction, including expression of the ESX-1 secretion system. Transcriptional profiling also revealed core CO2 responsive genes that were differentially expressed independently of the PhoPR regulon or the acidic pH-inducible regulon. Notably, genes regulated by a second two component regulatory system, TrcRS, are associated with adaptation to changes in CO2.
An updatedC. elegansnuclear body muscle transcriptome for studies in muscle formation and function
Authors: Schorr Anna L. , Mejia Alejandro Felix , Miranda Martina Y. , Mangone Marco 
Published: April 2022

ABSTRACTThe body muscle is an important tissue used in organisms for proper viability and locomotion. Although this tissue is generally well studied and characterized, and many pathways have been elucidated throughout the years, we still lack a comprehensive understanding of its transcriptome and how it controls muscle development and function. Here, we have updated a nuclear FACS sorting-based methodology to isolate and sequence a high-quality muscle transcriptome fromC. elegansmixed-stage animals. We have identified 2,848 muscle-specific protein-coding genes, including 78 transcription factors and 206 protein-coding genes containing an RNA binding domain. We studied their interaction network, performed a detailed promoter analysis, and identified novel muscle-specificcis-acting elements. We have also identified 16 high-quality muscle-specific miRNAs, studied their functionin vivousing fluorochrome-based analyses, and developed a high-qualityC. elegansmiRNA Interactome incorporating other muscle-specific datasets produced by our lab and others.Our study expands our understanding of how muscle tissue functions inC. elegansand in turn, provide results that can in the future be applied to humans to study muscular-related diseases.
A chromosome-scale genome assembly of aBacillus thuringiensisCry1Ac insecticidal protein resistant strain ofHelicoverpa zea
Authors: Stahlke Amanda R. , Chang Jennifer , Tembrock Luke R. , Sim Sheina B. , Chudalayandi Sivanandan , Geib Scott M. , Scheffler Brian E. , Perera Omaththage P. , Gilligan Todd M. , Childers Anna K. , Hackett Kevin J. , Coates Brad S. 
Published: April 2022

AbstractHelicoverpa zea(Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, includingBacillus thuringiensis(Bt) insecticidal proteins in transgenic cotton and maize.H. zeapopulations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a singleH. zeamale from Bt resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single-copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly forH. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.SignificanceWe established a chromosome-level reference assembly forHelicoverpa zea, an insect pest of multiple cultivated crops in the Americas. This assembly of aBacillus thuringiensisinsecticidal protein resistant strain, HzStark_Cry1AcR, will facilitate future research in areas such as population genomics and adaptations to agricultural control practices.
A recombinant murine rotavirus with Nano-Luciferase expression reveals tissue tropism, replication dynamics, and virus transmission
Authors: Zhu Yinxing , Sánchez-Tacuba Liliana , Hou Gaopeng , Kawagishi Takahiro , Feng Ningguo , Greenberg Harry B. , Ding Siyuan 
Published: April 2022

ABSTRACTRotaviruses (RVs) are one of the main causes of severe gastroenteritis, diarrhea, and death in children and young animals. Although suckling mice prove to be highly useful small animal models of RV infection and pathogenesis, direct visualization tools are lacking to track the temporal dynamics of RV replication and transmissibility in vivo. Here, we report the generation of the first recombinant murine RV that encodes a Nano-Luciferase reporter (NLuc) using a newly optimized RV reverse genetics system. The NLuc-expressing RV was replication-competent in cell culture and both infectious and virulent in neonatal mice in vivo. Strong luciferase signals were detected in the proximal and distal small intestines, colon, and mesenteric lymph nodes. We showed, via a noninvasive in vivo imaging system, that RV intestinal replication peaked at day 2 and day 5 post infection. Moreover, we successfully tracked RV transmission to uninoculated littermates as early as 3 days post infection, 1 day prior to clinically apparent diarrhea and 3 days prior to detectable fecal RV shedding in the uninoculated littermates. We also observed significantly increased viral replication in Stat1 knockout mice that lack the host interferon signaling. Our results suggest that the NLuc RV represents a non-lethal powerful tool for the studies of tissue tropism and host and viral factors that regulate RV replication and spread, as providing a new mechanism to facilitate the testing of prophylactic and therapeutic interventions in the future.
Phylogenomics and body shape morphometrics reveal recent diversification in the goatfishes (Syngnatharia: Mullidae)
Authors: Nash Chloe M. , Lungstrom Linnea L. , Hughes Lily C. , Westneat Mark W. 
Published: April 2022

AbstractClades of marine fishes exhibit many patterns of diversification, ranging from relatively constant throughout time to rapid changes in the rates of speciation and extinction. The goatfishes (Syngnatharia: Mullidae) are a family of marine, reef associated fishes with a relatively recent origin, distributed globally in tropical and temperate waters. Despite their abundance and economic importance, the goatfishes remain one of the few coral reef families for which the species level relationships have not been examined using genomic techniques. Here we use phylogenomic analysis of ultra-conserved elements (UCE) and exon data to resolve a well-supported, time-calibrated phylogeny for 72 species of goatfishes, supporting a recent crown age of the goatfishes at 21.9 million years ago. We used this framework to test hypotheses about the associations among body shape morphometrics, taxonomy, and phylogeny, as well as to explore relative diversification rates across the phylogeny. Body shape was strongly associated with generic-level taxonomy of goatfishes, with morphometric analyses showing evidence for high phylogenetic signal across all morphotypes. Rates of diversification in this clade reveal a recent sharp increase in lineage accumulation, with 92% of the goatfish species sampled across all clades and major body plans having originated in just the past 5 million years. We suggest that habitat diversity in the early Pliocene oceans and the generalist ecology of goatfishes are key factors in the unusual evolutionary tempo of the family Mullidae.
EstG is a novel esterase required for cell envelope integrity
Authors: Daitch Allison K. , Orsburn Benjamin C. , Chen Zan , Alvarez Laura , Eberhard Colten D. , Sundararajan Kousik , Zeinert Rilee , Kreitler Dale F , Jakoncic Jean , Chien Peter , Cava Felipe , Gabelli Sandra B. , Bumpus Namandjé N. , Goley Erin D. 
Published: April 2022

AbstractProper regulation of the bacterial cell envelope is critical for cell survival. Identification and characterization of enzymes that maintain cell envelope homeostasis is crucial, as they can be targets for effective antibiotics. In this study, we have identified a novel enzyme, called EstG, whose activity protects cells from a variety of lethal assaults in the ⍺-proteobacterium Caulobacter crescentus. Despite homology to transpeptidase family cell wall enzymes and an ability to protect against cell wall-targeting antibiotics, EstG does not demonstrate biochemical activity towards cell wall substrates. Instead, EstG is genetically connected to the periplasmic enzymes OpgH and BglX, responsible for synthesis and hydrolysis of osmoregulated periplasmic glucans (OPGs), respectively. The crystal structure of EstG revealed similarities to esterases and transesterases, and we demonstrated esterase activity of EstG in vitro. Using biochemical fractionation, we identified a cyclic hexamer of glucose as a likely substrate of EstG. This molecule is the first OPG described in Caulobacter and establishes a novel class of OPGs, the regulation and modification of which is important for stress survival and adaptation to fluctuating environments. Our data indicate that EstG, BglX, and OpgH comprise a previously unknown OPG pathway in Caulobacter. Ultimately, we propose that EstG is a novel enzyme that, instead of acting on the cell wall, acts on cyclic OPGs to provide resistance to a variety of cellular stresses.