bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maintenance of Complex I and respiratory super-complexes by NDUF-11 is essential for respiratory function, mitochondrial structure and health inC. elegans
Authors: Knapp-Wilson Amber , Pereira Gonçalo C. , Buzzard Emma , Richardson Andrew , Corey Robin A. , Neal Chris , Verkade Paul , Halestrap Andrew P. , Gold Vicki A.M. , Kuwabara Patricia , Collinson Ian 
Published: January 2021

ABSTRACTMitochondrial super-complexes form around a conserved core of monomeric complex I and dimeric complex III; wherein subunit NDUFA11, of the former, is conspicuously situated at the interface. We identifiedB0491.5(NDUF-11) as theC. eleganshomologue, of which animals homozygous for a CRISPR-Cas9 generated knockout allele arrested at the L2 development stage. Reducing expression by RNAi allowed development to the adult stage, enabling characterisation of the consequences: destabilisation of complex I and its super-complexes, and perturbation of respiratory function. The loss of NADH-dehydrogenase activity is compensated by enhanced complex II activity, resulting in excessive detrimental ROS production. Meanwhile, electron cryo-tomography highlight aberrant cristae morphology and widening of the inter-membrane space and cristae junctions. The requirement of NDUF-11 for balanced respiration, mitochondrial morphology and development highlights the importance of complex I/ super-complex maintenance. Their perturbation by this, or other means, is likely to be the cause of metabolic stress and disease.
Recognition of a Tandem Lesion by DNA Glycosylases Explored Combining Molecular Dynamics and Machine Learning
Authors: Bignon Emmanuelle , Gillet Natacha , Chan Chen-Hui , Jiang Tao , Monari Antonio , Dumont Elise 
Published: January 2021

ABSTRACTThe combination of several closely spaced DNA lesions, which can be induced by a single radical hit, constitutes a hallmark in the DNA damage landscape and radiation chemistry. The occurrence of such tandem base lesions give rise to a strong coupling with the double helix degrees of freedom and induce important structural deformations, in contrast to DNA strands containing a single oxidized nucleobase. Although such complex lesions are known to be refractory to repair by DNA glycosylases, there is still a lack of structural evidence to rationalize these phenomena. In this contribution, we explore, by numerical modeling and molecular simulations, the behavior of the bacterial glycosylase responsible for base excision repair (MutM), specialized in excising oxidatively-damaged defects such as 7,8-dihydro-8-oxoguanine (8-oxoG). The difference in lesion recognition between a simple damage and a tandem lesions featuring an additional abasic site is assessed at atomistic resolution owing to microsecond molecular dynamics simulation and machine learning postprocessing, allowing to extensively pinpoint crucial differences in the interaction patterns of the damaged bases. This work advocates for the use of such high throughput numerical simulations for exploring the complex combinatorial chemistry of tandem DNA lesions repair and more generally multiple damaged sites of the utmost significance in radiation chemistry.
Are we missing the forest for the trees? Conspecific negative density dependence in a temperate deciduous forest
Authors: Barry Kathryn E. , Schnitzer Stefan A. 
Published: January 2021

AbstractOne of the central goals of ecology is to determine the mechanisms that enable coexistence among species. Evidence is accruing that conspecific negative density dependence (CNDD), the process by which plant seedlings are unable to survive in the area surrounding adults of their same species, is a major contributor to tree species coexistence. However, for CNDD to maintain diversity, three conditions must be met. First, CNDD must maintain diversity for the majority of the woody plant community (rather than merely specific groups). Second, the pattern of repelled recruitment must increase in with plant size. Third, CNDD must occurs across life history strategies and not be restricted to a single life history strategy. These three conditions are rarely tested simultaneously. In this study, we simultaneously test all three conditions in a woody plant community in a North American temperate forest. We examined whether the different woody plant growth forms (shrubs, understory trees, mid-story trees, canopy trees, and lianas) at different ontogenetic stages (seedling, sapling, and adult) were overdispersed – a spatial pattern indicative of CNDD – using spatial point pattern analysis across life history stages and strategies. We found that there was a strong signal of overdispersal at the community level. However, this pattern was driven by adult canopy trees. By contrast, understory plants, which can constitute up to 80% of temperate forest plant diversity, were not overdispersed as adults. The lack of overdispersal suggests that CNDD is unlikely to be a major mechanism maintaining understory plant diversity. The focus on trees for the vast majority of CNDD studies may have biased the perception of the prevalence of CNDD as a dominant mechanism that maintains community-level diversity when, according to our data, CNDD may be restricted largely to trees.
Incidence and Characteristics of Co-infection and Secondary Infection in Patients with COVID-19
Authors: Guo Yingyi , Qu Jiuxin , Cheng Lingling , Li Xiaohe , Liu Ningjing , Li Tungngai , Jiang Ying , Wan Qiao , Zhuo Chuyue , Xiao Shunian , Liu Baomo , Chen Yan , Fu lin , Chen Zhixu , Ma Mingcong , zhuo Chao , Zhong Nanshan 
Published: January 2021

ABSTRACTObjectiveThe etiology and epidemiology of co-infection and secondary infection in COVID-19 patients remain unknown. The study aims to investigate the occurrence and characteristics of co-infection and secondary infection in COVID-19 patients, mainly focusing on Streptococcus pneumoniae co-infections.MethodsThis study was a prospective, observational cohort study of the inpatients diagnosed with COVID-19 in two designated hospitals in south China enrolled between Jan 11 and Feb 22, 2020. The urine specimen was collected on admission and applied for pneumococcal urinary antigen tests (PUATs). Demographic, clinical and microbiological data of patients were recorded simultaneously.ResultA total of 146 patients with a confirm diagnosis of COVID-19 at the median age of 50.0 years (IQR 36.0-61.0) were enrolled, in which, 16 (11.0%) were classified as severe cases and 130 (89.0%) as non-severe cases. Of the enrolled patients, only 3 (2.1%) were considered to present the co-infection, in which 1 was co-infected with S.pneumoniae, 1 with B. Ovatus infection and the other one with Influenza A virus infection. Secondary infection occurred in 16 patients, with S. maltophilia as the most commonly isolated pathogen (43.8%), followed by P. aeruginosa (25.0%), E. aerogenes (25.0%), C. parapsilosis (25.0%) and A. fumigates (18.8%).ConclusionPatients with confirmed COVID-19 were rarely co-infected with Streptococcus pneumoniae or other pathogens, indicating that the application of antibiotics against CAP on admission may not be necessary in the treatment of COVID-19 cases.
Evolution to alternative levels of stable diversity leaves areas of niche space unexplored
Authors: Rubin Ilan N. , Ispolatov Iaroslav , Doebeli Michael 
Published: January 2021

AbstractOne of the oldest and most persistent questions in ecology and evolution is whether natural communities tend to evolve toward saturation and maximal diversity. Robert MacArthur’s classical theory of niche packing and the theory of adaptive radiations both imply that populations will diversify and fully partition any available niche space. However, the saturation of natural populations is still very much an open area of debate and investigation. Additionally, recent evolutionary theory suggests the existence of alternative evolutionary stable states (ESSs), which implies that some stable communities may not be fully saturated. Using models with classical Lokta-Volterra ecological dynamics and three formulations of evolutionary dynamics (a model using adaptive dynamics, an individual-based model, and a partial differential equation model), we show that following an adaptive radiation, communities can often get stuck in low diversity states when limited by mutations of small phenotypic effect. These low diversity metastable states can also be maintained by limited resources and finite population sizes. When small mutations and finite populations are considered together, it is clear that despite the presence of higher-diversity stable states, natural populations are likely not fully saturating their environment and leaving potential niche space unfilled. Additionally, within-species variation can further reduce community diversity from levels predicted by models that assume species-level homogeneity.Author summaryUnderstanding if and when communities evolve to saturate their local environments is imperative to our understanding of natural populations. Using computer simulations of classical evolutionary models, we study whether adaptive radiations tend to lead toward saturated communities, in which no new species can invade or remain trapped in alternative, lower diversity stable states. We show that with asymmetric competition and small effect mutations, evolutionary Red Queen dynamics can trap communities in low diversity metastable states. Moreover, limited resources not only reduces community population sizes, but also reduces community diversity, denying the formation of saturated communities and stabilizing low diversity, non-stationary evolutionary dynamics. Our results are directly relevant to the longstanding questions important to both ecological empiricists and theoreticians on the species packing and saturation of natural environments. Also, by showing the ease evolution can trap communities in low diversity metastable states, we demonstrate the potential harm in relying solely on ESSs to answer questions of biodiversity.
Predictors of virus prevalence and diversity across a wild bumblebee community
Authors: Pascall David J. , Tinsley Matthew C. , Clark Bethany L. , Obbard Darren J. , Wilfert Lena 
Published: January 2021

AbstractViruses are key regulators of natural populations. Despite this, we have limited knowledge of the diversity and ecology of viruses that lack obvious fitness effects on their host. This is even the case in wild host populations that provide ecosystem services, where small fitness effects may have major ecological and financial impacts in aggregate. One such group of hosts are the bumblebees, which have a major role in the pollination of food crops and have suffered population declines and range contractions in recent decades. In this study, we used a multivariate generalised linear mixed model to investigate the ecological factors that determine the prevalence of four recently discovered bumblebee viruses (Mayfield virus 1, Mayfield virus 2, River Liunaeg virus and Loch Morlich virus), and two previously known viruses that infect both wild bumblebees and managed honeybees (Acute bee paralysis virus and Slow bee paralysis virus). We show that the recently discovered bumblebee viruses were more genetically diverse than the viruses shared with honeybees, potentially due to spillover dynamics of shared viruses. We found evidence for ecological drivers of prevalence in our samples, with relatively weak evidence for a positive effect of precipitation on the prevalence of River Luinaeg virus. Coinfection is potentially important in shaping prevalence: we found a strong positive association between River Liunaeg virus and Loch Morlich virus presence after controlling for host species, location and other relevant ecological variables. This study represents a first step in the description of predictors of bumblebee infection in the wild not driven by spillover from honeybees.
Combining single-molecule super-resolved localization microscopy with fluorescence polarization imaging to study cellular processes
Authors: Shepherd Jack W , Payne-Dwyer Alex L , Lee Ji-Eun , Syeda Aisha , Leake Mark C 
Published: January 2021

AbstractSuper-resolution microscopy has catalyzed valuable insights into the sub-cellular, mechanistic details of many different biological processes across a wide range of cell types. Fluorescence polarization spectroscopy tools have also enabled important insights into cellular processes through identifying orientational changes of biological molecules typically at an ensemble level. Here, we combine these two biophysical methodologies in a single home-made instrument to enable the simultaneous detection of orthogonal fluorescence polarization signals from single fluorescent protein molecules used as common reporters on the localization of proteins in cellular processes. These enable measurement of spatial location to a super-resolved precision better than the diffraction-limited optical resolution, as well as estimation of molecular stoichiometry based on the brightness of individual fluorophores. In this innovation we have adapted a millisecond timescale microscope used for single-molecule detection to enable splitting of fluorescence polarization emissions into two separate imaging channels for s- and p-polarization signals, which are imaged onto separate halves of the same high sensitivity back-illuminated CMOS camera detector. We applied this fluorescence polarization super-resolved imaging modality to a range of test fluorescent samples relevant to the study of biological processes, including purified monomeric green fluorescent protein, single combed DNA molecules, and protein assemblies and complexes from live Escherichia coli and Saccharomyces cerevisiae cells. Our findings are qualitative but demonstrate promise in showing how fluorescence polarization and super-resolved localization microscopy can be combined on the same sample to enable simultaneous measurements of polarization and stoichiometry of tracked molecular complexes, as well as the translational diffusion coefficient.
The H3K36me2 writer-reader dependency in H3K27M-DIPG
Authors: Yu Jia-Ray , LeRoy Gary , Bready Devin , Frenster Joshua D. , Saldaña-Meyer Ricardo , Jin Ying , Descostes Nicolas , Stafford James M. , Placantonakis Dimitris G. , Reinberg Danny 
Published: January 2021

AbstractThe lysine-to-methionine mutation at residue 27 of histone H3 (H3K27M) is a driving mutation in Diffuse Intrinsic Pontine Glioma (DIPG), a highly aggressive form of pediatric brain tumor with no effective treatment and little chance of survival. H3K27M reshapes the epigenome through a global inhibition of PRC2 catalytic activity, the placement of methylation at lysine 27 of histone H3 (H3K27me2/3), promoting oncogenesis of DIPG. As a consequence, a histone modification H3K36me2, antagonistic to H3K27me2/3, is aberrantly elevated. Here, we investigate the role of H3K36me2 in H3K27M-DIPG by tackling its upstream catalyzing enzymes (writers) and downstream binding factors (readers). We determine that NSD1 and NSD2 are the key writers for H3K36me2. Loss of NSD1/2 in H3K27M-DIPG impedes cellular proliferation in vitro and tumorigenesis in vivo, and disrupts tumor-promoting gene expression programs. Further, we demonstrate that LEDGF and HDGF2 are the main readers that mediate the pro-tumorigenic effects downstream of NSD1/2-H3K36me2. Treatment with a chemically modified peptide mimicking endogenous H3K36me2 dislodges LEDGF/HDGF2 from chromatin and specifically inhibits the proliferation of H3K27M-DIPG. Together, our results indicate a functional pathway of NSD1/2-H3K36me2-LEDGF/HDGF2 as an acquired dependency in H3K27M-DIPG and suggest a possibility to target this pathway for therapeutic interventions.
Domain-general conflict monitoring predicts neural and behavioral indices of linguistic error processing during reading comprehension
Authors: Brothers Trevor , Zeitlin Margarita , Perrachione Arim Choi , Choi Connie , Kuperberg Gina 
Published: January 2021

AbstractThe ability to detect and respond to linguistic errors is critical for successful reading comprehension, but these skills can vary considerably across readers. In the current study, healthy adults (age 18-35) read short discourse scenarios for comprehension while monitoring for the presence of semantic anomalies. Using a factor analytic approach, we examined if performance in non-linguistic conflict monitoring tasks (Stroop, AX-CPT) would predict individual differences in neural and behavioral measures of linguistic error processing. Consistent with this hypothesis, domain-general conflict monitoring predicted both readers’ end-of-trial acceptability judgments and the amplitude of a late neural response (the P600) evoked by linguistic anomalies. Interestingly, the influence on the P600 was non-linear, suggesting that online neural responses to linguistic errors are influenced by both the effectiveness and efficiency of domain-general conflict monitoring. These relationships were also highly specific and remained after controlling for variability in working memory capacity and verbal knowledge. Finally, we found that domain-general conflict monitoring also predicted individual variability in measures of reading comprehension, and that this relationship was partially mediated by behavioral measures of linguistic error detection. These findings inform our understanding of the role of domain-general executive functions in reading comprehension, with potential implications for the diagnosis and treatment of language impairments.
The telomere regulatory gene POT1 responds to stress and predicts performance in nature: implications for telomeres and life history evolution
Authors: Wolf Sarah E. , Sanders Tiana L. , Beltran Sol E. , Rosvall Kimberly A. 
Published: January 2021

ABSTRACTLong telomeres have become nearly synonymous with a variety of fitness-related traits and may be mediators of ecologically relevant variation in life history strategies. Growing evidence suggests that telomere dynamics are more predictive of performance than length itself, but very little work considers how telomere regulatory mechanisms respond to environmental challenges or influence performance in nature. Here, we combine observational and experimental datasets from free-living tree swallows (Tachycineta bicolor) to assess how performance is predicted by the telomere regulatory gene POT1, which encodes a shelterin protein that sterically blocks telomerase from repairing the telomere. First, we show that lower POT1 gene expression was associated with higher female quality, i.e. earlier breeding, and heavier body mass. We next challenged mothers with an immune stressor (lipopolysaccharide injection) that led to ‘sickness’ in mothers and 24h of food restriction in their offspring. While POT1 did not respond to maternal injection, females with lower constitutive gene expression were better able to maintain feeding rates following treatment. Maternal injection also generated a one-day stressor for chicks, who responded with decreased POT1 gene expression and elongated telomeres. Other putatively stress-responsive mechanisms (i.e. glucocorticoids, antioxidants) were not significantly different between control and stress-exposed chicks. Model comparisons indicated that POT1 mRNA abundance was a largely better predictor of performance than telomere dynamics, indicating that telomere regulators may be powerful modulators of variation in life history strategies.
Endosomal cAMP production broadly impacts the cellular phosphoproteome
Authors: Tsvetanova Nikoleta G. , Trester-Zedlitz Michelle , Newton Billy W. , Peng Grace E. , Johnson Jeffrey R. , Jimenez-Morales David , Kurland Andrew P. , Krogan Nevan J. , von Zastrow Mark 
Published: January 2021

AbstractEndosomal signaling downstream of G protein-coupled receptors (GPCRs) has emerged as a novel paradigm with important pharmacological and physiological implications. Yet, our knowledge of the functional consequences of intracellular signaling is incomplete. To begin to address this gap, we combined an optogenetic approach for site-specific generation of the prototypical second messenger generated by active GPCRs, cyclic AMP (cAMP), with unbiased mass spectrometry-based analysis of phosphoproteomic effects. We identified 218 unique, highconfidence sites whose phosphorylation is either increased or decreased in response to cAMP production. We next determined that the same amount of cAMP produced from endosomes led to more robust changes in phosphorylation than the plasma membrane. Remarkably, this was true for the entire repertoire of identified targets, and irrespective of their annotated sub-cellular localization. Furthermore, we identified a particularly strong endosome bias for a subset of proteins that are dephosphorylated in response to cAMP. Through bioinformatics analysis, we established these targets as putative substrates for protein phosphatase 2A (PP2A), and we propose compartmentalized activation of PP2A-B56δ as the likely underlying mechanism. Altogether, our study extends the concept that endosomal signaling is a significant functional contributor to cellular responsiveness by establishing a unique role for localized cAMP production in defining categorically distinct phosphoresponses.
The Great Western Development policy: how it affected grain crop production, land use and rural poverty in western China
Authors: Li Pei , Tian Ye , Wu JunJie , Xu Wenchao 
Published: January 2021

PurposeThe purpose of this paper evaluates the effects of the Great Western Development (GWD) policy on agricultural intensification, land use, agricultural production and rural poverty in western China.Design/methodology/approachThe authors collect county-level data on land use, input application, grain crop production, income, poverty and geophysical characteristics for 1996–2005 and use a quasi-natural experimental design of difference-in-differences (DD) in the empirical analysis.FindingsResults suggest that the GWD policy significantly increased the grain crop production in western China. This increase resulted from higher yield, with increased fertilizer use and agricultural electricity consumption per hectare, and more land allocated to grow grain crops. The policy also increased land-use concentration, reduced crop diversity and alleviated rural poverty in western China.Originality/valueThis paper makes three contributions. First, the authors add to the growing literature on the GWD policy by evaluating its effects on farm household decisions and exploring the mechanisms and broad socioeconomic impacts in western China. Second, the authors take advantage of a quasi-natural experimental design to improve the identification strategy where input use, land allocation, production and off-farm labor participation are all endogenous in a farm household. Third, the authors explore a long list of variables within one integrated dataset to present a comprehensive picture of the impact of the GWD policy.