bluuebunny/crossref_metadata_2025_split huggingface dataset:
A billion years arms-race between viruses, virophages and eukaryotes
Authors: Nino Barreat Jose Gabriel , Katzourakis Aris 
Published: April 2021

AbstractBamfordviruses are arguably the most diverse group of viruses infecting eukaryotes. They include the Nucleocytoplasmic Large DNA viruses (NCLDVs), virophages, adenoviruses,Mavericksand Polinton-like viruses. Two main hypotheses for their origins have been proposed: the “nuclear-escape” and “virophage-first” hypotheses. The “nuclear-escape” hypothesis proposes an endogenous,Maverick-like ancestor which escaped from the nucleus and gave rise to adenoviruses and NCLDVs. In contrast, the “virophage-first” hypothesis proposes that NCLDVs coevolved with protovirophages;Mavericksthen evolved from virophages that became endogenous, with adenoviruses escaping from the nucleus at a later stage. Here, we test the predictions made by both models and consider alternative evolutionary scenarios. We use a data set of the four core virion proteins sampled across the diversity of the lineage, together with Bayesian and maximum-likelihood hypothesis-testing methods, and estimate rooted phylogenies. We find strong evidence that adenoviruses and NCLDVs are not sister groups, and thatMavericksand Mavirus acquired the rve-integrase independently. We also found strong support for a monophyletic group of virophages (familyLavidaviridae) and a most likely root placed between virophages and the other lineages. Our observations support alternatives to the nuclear-escape scenario and a billion years evolutionary arms-race between virophages and NCLDVs.
CRISPR/Cas9 modifiedAn. gambiaecarrying kdr mutation L1014F functionally validate its contribution in insecticide resistance and interaction with metabolic enzymes
Authors: Grigoraki Linda , Cowlishaw Ruth , Nolan Tony , Donnelly Martin , Lycett Gareth , Ranson Hilary 
Published: April 2021

AbstractInsecticide resistance inAnophelesmosquitoes is a major obstacle in maintaining the momentum in reducing the malaria burden; mitigating strategies require improved understanding of the underlying mechanisms. Mutations in the target site of insecticides (the voltage gated sodium channel for the most widely used pyrethroid class) and over-expression of detoxification enzymes are commonly reported, but their relative contribution to phenotypic resistance remain poorly understood. Here we present a genome editing pipeline to introduce single nucleotide polymorphisms inAn. gambiaewhich we have used to study the effect of the classical kdr mutation L1014F (L995F based onAn. gambiaenumbering), one of the most widely distributed resistance alleles. Introduction of 1014F in an otherwise fully susceptible genetic background increased levels of resistance to all tested pyrethroids and DDT ranging from 9.9-fold for permethrin to >24-fold for DDT. The introduction of the 1014F allele was sufficient to reduce mortality of mosquitoes after exposure to deltamethrin treated bednets, even as the only resistance mechanism present. When 1014F was combined with over-expression of glutathione transferase Gste2, resistance to permethrin increased further demonstrating the critical combined effect between target site resistance and detoxification enzymesin vivo. We also show that mosquitoes carrying the 1014F allele in homozygosity showed fitness disadvantages including increased mortality at the larval stage and a reduction in fecundity and adult longevity, which can have consequences for the strength of selection that will apply to this allele in the field.Author SummaryEscalation of pyrethroid resistance inAnophelesmosquitoes threatens to reduce the effectiveness of our most important tools in malaria control. Studying the mechanisms underlying insecticide resistance is critical to design mitigation strategies. Here, using genome modified mosquitoes, we functionally characterize the most prevalent mutation in resistant mosquitoes, showing that it confers substantial levels of resistance to all tested pyrethroids and undermines the performance of pyrethroid-treated nets. Furthermore, we show that combining this mutation with elevated levels of a detoxification enzyme further increases resistance. The pipeline we have developed provides a robust approach to quantifying the contribution of different combinations of resistance mechanisms to the overall phenotype, providing the missing link between resistance monitoring and predictions of resistance impact.
Enrichment analyses identify shared associations for 25 quantitative traits in over 600,000 individuals from seven diverse ancestries
Authors: Smith Samuel Pattillo , Shahamatdar Sahar , Cheng Wei , Zhang Selena , Paik Joseph , Graff Misa , Haiman Christopher , Matise T.C. , North Kari E , Peters Ulrike , Kenny Eimear , Gignoux Chris , Wojcik Genevieve , Crawford Lorin , Ramachandran Sohini 
Published: April 2021

AbstractSince 2005, genome-wide association (GWA) datasets have been largely biased toward sampling European ancestry individuals, and recent studies have shown that GWA results estimated from self-identified European individuals are not transferable to non-European individuals due to various confounding challenges. Here, we demonstrate that enrichment analyses which aggregate SNP-level association statistics at multiple genomic scales—from genes to genomic regions and pathways—have been underutilized in the GWA era and can generate biologically interpretable hypotheses regarding the genetic basis of complex trait architecture. We illustrate examples of the robust associations generated by enrichment analyses while studying 25 continuous traits assayed in 566,786 individuals from seven diverse self-identified human ancestries in the UK Biobank and the Biobank Japan, as well as 44,348 admixed individuals from the PAGE consortium including cohorts of African-American, Hispanic and Latin American, Native Hawaiian, and American Indian/Alaska Native individuals. We identify 1,000 gene-level associations that are genome-wide significant in at least two ancestry cohorts across these 25 traits, as well as highly conserved pathway associations with triglyceride levels in European, East Asian, and Native Hawaiian cohorts.
Behavioral interactions between bacterivorous nematodes and predatory bacteria in a synthetic community
Authors: Mayrhofer Nicola , Velicer Gregory J. , Schaal Kaitlin A. , Vasse Marie 
Published: April 2021

AbstractTheory and empirical studies in metazoans predict that apex predators should shape the behavior and ecology of mesopredators and prey at lower trophic levels. Despite the ecological importance of microbial communities, few studies of predatory microbes examine such behavioral responses and the multiplicity of trophic interactions. Here, we sought to assemble a three-level microbial food chain and to test for behavioral interactions between the predatory nematodeCaenorhabditis elegansand the predatory social bacteriumMyxococcus xanthuswhen cultured together with two basal prey bacteria that both predators can eat -Escherichia coliandFlavobacterium johnsoniae. We find that >90% ofC. elegansworms failed to interact withM. xanthuseven when it was the only potential prey species available, whereas most worms were attracted to pure patches ofE. coliandF. johnsoniae. In addition,M. xanthusaltered nematode predatory behavior on basal prey, repellingC. elegansfrom two-species patches that would be attractive withoutM. xanthus, an effect similar to that ofC. eleganspathogens. The nematode also influenced the behavior of the bacterial predator:M. xanthusincreased its predatory swarming rate in response toC. elegansin a manner dependent both on basal-prey identity and on worm density. Our results suggest thatM. xanthusis an unattractive prey for some soil nematodes and is actively avoided when more lucrative prey are available. Most broadly, we find that nematode and bacterial predators mutually influence one another’s predatory behavior, with likely consequences for coevolution within complex microbial food webs.
Antibiotic breakdown by susceptible bacteria enhances the establishment of β-lactam resistant mutants
Authors: Saebelfeld Manja , Das Suman G. , Brink Jorn , Hagenbeek Arno , Krug Joachim , de Visser J. Arjan G.M. 
Published: April 2021

AbstractFor a better understanding of the evolution of antibiotic resistance, it is imperative to study the factors that determine the initial establishment of mutant resistance alleles. In addition to the antibiotic concentration, the establishment of resistance alleles may be affected by interactions with the surrounding susceptible cells from which they derive, for instance via the release of nutrients or removal of the antibiotic. Here, we investigate the effects of social interactions with surrounding susceptible cells on the establishment ofEscherichia colimutants with increasing β-lactamase activity (i.e. the capacity to hydrolyze β-lactam antibiotics) from single cells under the exposure of the antibiotic cefotaxime on agar plates. We find that mutant establishment probability is increased in the presence of susceptible cells due to the active breakdown of the antibiotic, but the rate of breakdown by the susceptible strain is much higher than expected based on its low enzymatic activity. A detailed theoretical model suggests that this observation can be explained by cell filamentation causing delayed lysis. While susceptible cells may hamper the spread of higher-resistant β-lactamase mutants at relatively high frequencies, our findings show that they could promote establishment during their emergence.
Sphingolipid-Induced Programmed Cell Death Is a Salicylic Acid and EDS1-Dependent Phenotype in Arabidopsis
Authors: König Stefanie , Gömann Jasmin , Zienkiewicz Agnieszka , Zienkiewicz Krzysztof , Meldau Dorothea , Herrfurth Cornelia , Feussner Ivo 
Published: April 2021

AbstractCeramides and long chain bases (LCBs) are plant sphingolipids involved in the induction of plant programmed cell death (PCD). Thefatty acid hydroxylasemutantfah1 fah2exhibits high ceramide levels and moderately elevated LCB levels. Salicylic acid (SA) is strongly induced in these mutants, but no cell death is visible. To determine the effect of ceramides with different chain lengths,fah1 fah2was crossed withceramide synthasemutantslongevity assurance gene one homologue1-3(loh1,loh2andloh3). Surprisingly, only triple mutants withloh2show a cell death phenotype under the selected conditions. Sphingolipid profiling revealed that the greatest differences between the triple mutant plants are in the LCB and LCB-phosphate (LCB-P) fraction.fah1 fah2 loh2plants accumulate LCB d18:0 and LCB-P d18:0. Crossingfah1 fah2 loh2with the SA synthesis mutantsid2-2, and with the SA signaling mutantsenhanced disease susceptibility 1-2(eds1-2) andphytoalexin deficient 4-1(pad4-1), revealed that lesions are SA- and EDS1-dependent. These quadruple mutants also suggest that there may be a feedback loop between SA and sphingolipid metabolism as they accumulated less ceramides and LCBs. In conclusion, PCD infah1 fah2 loh2is a SA and EDS1-dependent phenotype, which is likely due to accumulation of LCB d18:0.
Alzheimer’s disease-associatedTM2Dgenes regulate Notch signaling and neuronal function inDrosophila
Authors: Salazar Jose L. , Yang Sheng-An , Lin Yong Qi , Li-Kroeger David , Marcogliese Paul C. , Deal Samantha L. , Neely G. Gregory , Yamamoto Shinya 
Published: April 2021

AbstractTM2 domain containing (TM2D) proteins are conserved in metazoans and encoded by three separate genes in each species. Rare variants inTM2D3are associated with Alzheimer’s disease (AD) and its fly orthologalmondexis required for embryonic Notch signaling. However, the functions of this gene family remain elusive. We knocked-out all threeTM2Dgenes (almondex, CG11103/amaretto,CG10795/biscotti) inDrosophilaand found that they share the same maternal-effect neurogenic defect. Triple null animals are not phenotypically worse than single nulls, suggesting these genes function together. Overexpression of the most conserved region of the TM2D proteins acts as a potent inhibitor of Notch signaling at the γ-secretase cleavage step. Lastly, Almondex is detected in the brain and its loss causes shortened lifespan accompanied by progressive electrophysiological defects. The functional links between all threeTM2Dgenes are likely to be evolutionarily conserved, suggesting that this entire gene family may be involved in AD.
Post-weaning social isolation increases reward-seeking behavior in a sex-specific manner in mice
Authors: Noback Michael , Barrow James C. , Carr Gregory V. 
Published: April 2021

AbstractSocial isolation is a growing concern in public health. Although isolation at any age is harmful, previous studies have shown that isolation during adolescence, correlating with critical periods of brain development, can impair cognitive function and increase the risk for psychiatric illness later in life. In this study, we utilized a mouse model of adolescent social isolation (SI) and compared performance of isolated and group-housed mice on touchscreen-based continuous performance test (CPT) and fixed ratio/progressive ratio (FR/PR) tasks in adulthood. SI increased sensitivity in the CPT in male mice and had no effect in female mice. The increase in sensitivity was consistent across time bins within the 45-minute testing session and there were no SI effects on reaction times or reward retrieval latencies. A possible confound for performance in the CPT would be SI-induced changes in reward-seeking or motivation for the strawberry milk reward. We next compared the SI mice to their group-housed littermate controls on both FR and PR schedules of reinforcement and found that male SI mice earned significantly more reinforcers on FR schedules of reinforcement and had higher breakpoints on PR schedules compared to their group-housed littermates. SI had no effect on FR or PR performance in female mice. These data indicate that SI during adolescence has striking, sex-specific effects on reward-seeking behavior in adult mice and may provide a useful behavioral model for studying the link between SI and risk for neuropsychiatric disorders.
Continuous multiplexed population representations of task context in the mouse primary visual cortex
Authors: Hajnal Márton Albert , Tran Duy , Einstein Michael , Martelo Mauricio Vallejo , Safaryan Karen , Polack Pierre-Olivier , Golshani Peyman , Orbán Gergő 
Published: April 2021

SummaryPrimary visual cortex (V1) neurons integrate motor and multisensory information with visual inputs during sensory processing. However, whether V1 neurons also integrate and encode higher-order cognitive variables is less understood. We trained mice to perform a context-dependent cross-modal decision task where the interpretation of identical audio-visual stimuli depends on task context. We performed silicon probe population recordings of neuronal activity in V1 during task performance and showed that task context (whether the animal should base its decision on visual or auditory stimuli) can be decoded during both intertrial intervals and stimulus presentations. Context and visual stimuli were represented in overlapping populations but were orthogonal in the population activity space. Context representation was not static but displayed distinctive dynamics upon stimulus onset and offset. Thus, activity patterns in V1 independently represent visual stimuli and cognitive variables relevant to task execution.
A Synthetic, Closed-Looped Gene Circuit for the Autonomous Regulation of RUNX2 Activity during Chondrogenesis
Authors: Kaur Gurcharan , Wu Biming , Murali Sunjana , Lanigan Thomas , Coleman Rhima M. 
Published: April 2021

AbstractThe transcription factor RUNX2 is a key regulator of chondrocyte phenotype during development, making it an ideal target for prevention of undesirable chondrocyte maturation in cartilage tissue engineering strategies. Here, we engineered an autoregulatory gene circuit (cisCXp-shRunx2) that negatively controls RUNX2 activity in chondrogenic cells via RNA interference initiated by a tunable syntheticCol10a1-like promoter (cisCXp). ThecisCXp-shRunx2gene circuit is designed based on the observation that induced RUNX2 silencing after early chondrogenesis enhances the accumulation of cartilaginous matrix in ATDC5 cells. We show that thecisCXp-shRunx2initiates RNAi of RUNX2 in maturing chondrocytes in response to the increasing intracellular RUNX2 activity without interfering with early chondrogenesis. The induced loss of RUNX2 activity in turn negatively regulates the gene circuit itself. Moreover, the efficacy of RUNX2 suppression fromcisCXp-shRunx2can be controlled by modifying the sensitivity ofcisCXp promoter. Finally, we show the efficacy of inhibiting RUNX2 in preventing matrix loss in human MSC-derived cartilage under conditions that induce chondrocyte hypertrophic differentiation, including inflammation. Overall, our results demonstrated that the negative modulation of RUNX2 activity with our autoregulatory gene circuit enhanced matrix synthesis and resists ECM degradation by reprogrammed MSC-derived chondrocytes in response to the microenvironment of the degenerative joint.
Trade-offs in biosensor optimization for dynamic pathway engineering
Authors: Verma Babita K. , Mannan Ahmad A. , Zhang Fuzhong , Oyarzún Diego A. 
Published: April 2021

AbstractRecent progress in synthetic biology allows the construction of dynamic control circuits for metabolic engineering. This technology promises to overcome many challenges encountered in traditional pathway engineering, thanks to their ability to self-regulate gene expression in response to bioreactor perturbations. The central components in these control circuits are metabolite biosensors that read out pathway signals and actuate enzyme expression. However, the construction of metabolite biosensors is a major bottleneck for strain design, and a key challenge is to understand the relation between biosensor dose-response curves and pathway performance. Here we employ multiobjective optimization to quantify performance trade-offs that arise in the design and calibration of metabolite biosensors. Our approach reveals strategies for tuning dose-response curves along an optimal trade-off between production flux and the cost of an increased expression burden on the host. We explore properties of control architectures built in the literature, and identify their advantages and caveats in terms of performance and robustness to growth conditions and leaky promoters. We demonstrate the optimality of a control circuit for glucaric acid production inEscherichia coli, which has been shown to increase titer by 2.5-fold as compared to static designs. Our results lay the groundwork for the automated design of control circuits for pathway engineering, with applications in the food, energy and pharmaceutical sectors.
Anaerobic growth ofListeria monocytogeneson rhamnose is stimulated by Vitamin B12 and bacterial microcompartment dependent 1,2-propanediol utilization
Authors: Zeng Zhe , Li Siming , Boeren Sjef , Smid Eddy J. , Notebaart Richard A. , Abee Tjakko 
Published: April 2021

AbstractThe food-borne pathogenListeria monocytogenesis able to form proteinaceous organelles called bacterial microcompartments (BMCs) that optimize the utilization of substrates, such as 1,2-propanediol, and confer an anaerobic growth advantage. Rhamnose is a deoxyhexose sugar abundant in a range of environments including the human intestine, and can be degraded in anaerobic conditions into 1,2-propanediol, next to acetate and lactate. Rhamnose-derived 1,2-propanediol has been found to link with BMCs in a limited number of commensal human colonic species and some human pathogens such asSalmonella enterica, but the involvement of BMCs in rhamnose metabolism and potential physiological effects onL. monocytogenesare still unknown. In this study, we firstly test the effect of rhamnose uptake and utilization on anaerobic growth ofL. monocytogenesEGDe without and with added vitamin B12, followed by metabolic analysis. We unveil that the vitamin B12-dependent activation ofpdustimulates metabolism and anaerobic growth ofL. monocytogenesEGDe on rhamnose via 1,2-propanediol degradation into 1-propanol and propionate. Transmission electron microscopy ofpdu-induced cells shows that BMCs are formed and additional proteomics experiments confirm expression ofpduBMC shell proteins and enzymes. Finally, we discuss physiological effects and energy efficiency ofL. monocytogenes pduBMC-driven anaerobic rhamnose metabolism and impact on competitive fitness in environments such as the human intestine.
Heterologous reporter expression in the planarianSchmidtea mediterraneathrough somatic mRNA transfection
Authors: Hall Richard Nelson , Weill Uri , Drees Leonard , Leal-Ortiz Sergio , Li Hongquan , Chai Chew , Alvarado Alejandro Sánchez , Melosh Nicholas A. , Fire Andrew Z. , Rink Jochen C. , Wang Bo 
Published: April 2021

AbstractPlanarians have long been studied for their regenerative abilities. Moving forward, tools for ectopic expression of non-native proteins will be of substantial value. Using a luminescent reporter to overcome the strong autofluorescence background of planarian tissues, we demonstrate heterologous protein expression in planarian cells and live animals. Our approach is based on the introduction of mRNA through several nanotechnological and chemical transfection methods. We improve reporter expression by altering untranslated region (UTR) sequences and codon bias, facilitating measurement of expression kinetics both in isolated cells and in whole planarians using luminescence imaging. We also examine protein expression as a function of variations in the UTRs of delivered mRNA, demonstrating a framework to investigate gene regulation at the post-transcriptional level. Together, these advances expand the toolbox for the mechanistic analysis of planarian biology and establish a strong foundation for the development and expansion of transgenic techniques in this unique model system.MotivationThe study of planarians has contributed to advances in our understanding of regeneration, stem cell dynamics, and many other fundamental biological processes. However, the persistent challenge of expressing transgenes in planarians has led to the speculation that they may be resistant to transfection. In this work, we develop methods to express exogenous mRNAs in both isolated planarian cells and whole animals by optimizing delivery techniques, genetic constructs, and detection methods. These methods allow us to study transfection kinetics and post-transcriptional regulation of gene expression in a quantitative manner. Beyond planarian research, this work should also provide a broadly applicable strategy to develop similar tools for animals that are also challenging to modify genetically.
Recognition of Divergent Viral Substrates by the SARS-CoV-2 Main Protease
Authors: MacDonald Elizabeth A. , Frey Gary , Namchuk Mark N. , Harrison Stephen C. , Hinshaw Stephen M. , Windsor Ian W. 
Published: April 2021

ABSTRACTThe main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease (COVID-19), is an ideal target for pharmaceutical inhibition. It is required for infection, it cleaves the viral polyprotein at multiple sites, and it is conserved among coronaviruses and distinct from human proteases. We present crystal structures of SARS-CoV-2 Mprobound to two viral substrate peptides. The structures show how Mprorecognizes substrates and how the peptide sequence can dictate catalytic efficiency by influencing the position of the scissile bond. One peptide, constituting the junction between viral non-structural proteins 8 and 9 (nsp8/9), has P1’ and P2’ residues that are unique among SARS-CoV-2 cleavage sites but conserved among nsp8/9 junctions in coronaviruses. Mprocleaves nsp8/9 inefficiently, and amino acid substitutions at P1’ or P2’ can enhance catalysis. Visualization of Mprowith intact substrates provides new templates for antiviral drug design and suggests that the coronavirus lifecycle selects for finely tuned substrate-dependent catalytic parameters.