bluuebunny/crossref_metadata_2025 huggingface dataset:
The Behavior of Molecular Measures of Natural Selection after a Change in Population Size
Authors: Müller Rebekka , Kaj Ingemar , Mugal Carina F.
Published: December 2020

A common model to describe natural selection at the molecular level is the nearly neutral theory, which emphasizes the importance of mutations with slightly deleterious fitness effects as they have a chance to get fixed due to genetic drift. Since genetic drift is stronger in smaller than in larger populations, a negative relationship between molecular measures of selection and population size is expected within the nearly neutral theory. Originally, this hypothesis was formulated under equilibrium conditions. A change in population size, however, pushes the selection-drift balance off equilibrium leading to alterations in the efficacy of selection. To investigate the nonequilibrium behavior, we relate measures of natural selection and genetic drift to each other, considering both, measures of micro- and macroevolution. Specifically, we use a Poisson random field framework to modelπN/πSandωas time-dependent measures of selection and assess genetic drift by an effective population size. This analysis reveals a clear deviation from the expected equilibrium selection-drift balance during nonequilibrium periods. Moreover, we find that microevolutionary measures quickly react to a change in population size and reflect a recent change well, at the same time as they quickly lose the knowledge about it. Macroevolutionary measures, on the other hand, react more slowly to a change in population size but instead capture the influence of ancient changes longer. We therefore conclude that it is important to be aware of the different behaviors of micro- and macroevo- lutionary measures when making inference in empirical studies, in particular when comparing results between studies.
Functional tagging of endogenous proteins and rapid selection of cell pools (Rapid generation of endogenously taggedpiwiin ovarian somatic sheath cells.)
Authors: Andrews Celine Marlin , Konstantinidou Parthena , Genzor Pavol , Stoyko Daniel , Elchert Alexandra R. , Benner Leif , Sobti Sushil , Katz Esther Y. , Meng Qingcai , Haase Astrid D.
Published: December 2020

The combination of genome-editing and epitope tagging provides a powerful strategy to study proteins with high affinity and specificity while preserving their physiological expression patterns. However, stably modifying endogenous genes in cells that do not allow for clonal selection has been challenging. Here, we present a simple and fast strategy to generate stable, endogenously tagged alleles in a non-transformed cell culture model. At the example ofpiwiinDrosophilaovarian somatic sheath cells, we show that this strategy enables the generation of an N-terminally tagged protein that emulates the expression level and subcellular localization of the wild type protein and forms functional Piwi-piRNA complexes. We present a concise workflow to establish modified cells, characterize the edited allele and probe the function of the tagged protein.
Disentangling environmental drivers of circadian metabolism in desert-adapted mice
Authors: Colella Jocelyn P. , Blumstein Danielle M. , MacManes Matthew D.
Published: December 2020

Metabolism is a complex phenotype shaped by natural environmental rhythms, as well as behavioral, morphological, and physiological adaptations. Although historically studied under constant environmental conditions, continuous metabolic phenotyping through environmental transitions now offers a window into the physiological responses of organisms to changing environments. Here, we use flow-through respirometry to compare metabolic responses of the desert-adapted cactus mouse (Peromyscus eremicus) between diurnally variable and constant environmental conditions. We contrast metabolic responses to circadian cycles in photoperiod, temperature, and humidity, against those recorded under constant hot-and-dry and constant cold-and-wet conditions. We found significant sexual dimorphism in metabolic responses, despite no measurable difference in body weight. Males seem to be more heat tolerant and females more cold tolerant. Under circadian environmental cycling, the ratio of CO2produced to O2consumed (the respiratory quotient or respiratory exchange ratio) reached greater than one, a pattern that strongly suggests that lipogenesis is contributing to the production of energy and endogenous water in this species. This hypothesis is consistent with the results of previous dehydration experiments in this species, which documented significant weight loss in response to dehydration, without other physiological impairment. Our results are also consistent with historical descriptions of circadian torpor in this species (torpid by day, active by night), but reject the hypothesis that this pattern is driven by food restriction or negative water balance, as both resources were available to animals throughout the experiments.

SUMMARY STATEMENT

Continuous metabolic phenotyping of desert-adapted cactus mice (Peromyscus eremicus) identifies significant metabolic differences between the sexes and circadian patterning consistent with lipogenesis and environmental entrainment.
Enhanced reproductive thermotolerance is associated with increased accumulation of flavonols in pollen of the tomatohigh-pigment2 mutant
Authors: Rutley Nicholas , Miller Golan , Wang Fengde , Harper Jeffrey F , Miller Gad , Lieberman-Lazarovich Michal
Published: December 2020

Climate change has created an environment where heat stress conditions are becoming more frequent as temperatures continue to rise in crop production areas around the world. This situation leads to decreased crop production due to plant sensitivity to heat stress. Reproductive success is critically dependent on plants’ ability to produce functional pollen grains, which are the most thermo-sensitive tissue. Flavonols are plant secondary metabolites known for their potent antioxidative activity, essential for male fertility in several species including tomato, and implicated in heat stress tolerance. Since flavonols are highly abundant in fruits of the tomatohigh pigment-2(hp2) mutant, we tested the level of flavonols in pollen of this mutant, under the hypothesis that increased accumulation of flavonols would render pollen more tolerant to heat stress. Indeed, pollen from three alleles of thehp2mutant were found to have flavonols levels increased by 40% on average compared with wild-type under moderate chronic heat stress conditions. This mutant produced on average 7.8-fold higher levels of viable pollen and displayed better germination competence under heat stress conditions. The percentage of fully seeded fruits and the number of seeds per fruit were maintained in the mutant under heat stress conditions while decreased in wild-type plants. Our results strongly suggest that increased pollen flavonols content enhances pollen thermotolerance and reproductive success under heat stress conditions. Thus, the high flavonols trait may help frame the model for improving crop resilience to heat stress.
Activation of MrgprA3 and MrgprC11 on bladder-innervating afferents induces peripheral and central hypersensitivity to bladder distension
Authors: Grundy Luke , Caldwell Ashlee , Garcia-Caraballo Sonia , Grundy David , Spencer Nick J. , Dong Xinzhong , Castro Joel , Harrington Andrea M. , Brierley Stuart M.
Published: December 2020

Understanding the sensory mechanisms innervating the bladder is paramount to developing efficacious treatments for chronic bladder hypersensitivity conditions. The contribution of Mas-gene-related G protein-coupled receptors (Mrgpr) to bladder signalling is currently unknown. Here we show in mice with single-cell RT-PCR that sub-populations of dorsal root ganglion (DRG) neurons innervating the mouse bladder expressMrgprA3(14%) andMrgprC11 (38%), either individually or in combination, with high levels of co-expression withTrpv1(81-89%). Calcium imaging studies demonstrated MrgprA3 and MrgprC11 agonists (chloroquine, BAM8-22 and neuropeptide FF) activated sub-populations of bladder-innervating DRG neurons, showing functional evidence of co-expression between MrgprA3, MrgprC11 and TRPV1. Inex vivobladder-nerve preparations chloroquine, BAM8-22 and neuropeptide FF all evoked mechanical hypersensitivity in sub-populations (20-41%) of bladder afferents. These effects were absent in recordings fromMrgpr-clusterΔ−/−mice.In vitrowhole-cell patch clamp recordings showed that application of an MrgprA3/C11 agonist cocktail induced neuronal hyper-excitability in 44% of bladder-innervating DRG neurons. Finally,in vivoinstillation of an MrgprA3/C11 agonist cocktail into the bladder of wild-type mice induced a significant activation of dorsal horn neurons within the lumbosacral spinal cord, as quantified by pERK-immunoreactivity. This MrgprA3/C11 agonist-induced activation was particularly apparent within the superficial dorsal horn and the sacral parasympathetic nuclei of wild-type, but notMrgpr-clusterΔ−/−mice. This study demonstrates, for the first time, functional expression of MrgprA3 and MrgprC11 in bladder afferents. Activation of these receptors is not required for normal bladder function but does trigger hypersensitivity to distension, a critically valuable factor for therapeutic target development.

Significance statement

Determining how bladder afferents become sensitized is the first step in finding effective treatments for common urological disorders such as overactive bladder and interstitial cystitis/bladder pain syndrome. Here we show that two of the key receptors, MrgprA3 and MrgprC11, that mediate itch from the skin are also expressed on afferents innervating the bladder. Activation of these receptors results in sensitization of bladder afferents, resulting in sensory signals being sent into the spinal cord that prematurely indicate bladder fullness. Targeting bladder afferents expressing MrgprA3 or MrgprC11 and preventing their sensitisation may provide a novel approach for treating overactive bladder and interstitial cystitis/bladder pain syndrome.
Sterilizing immunity against SARS-CoV-2 in hamsters conferred by a novel recombinant subunit vaccine
Authors: Wu Yangtao , Huang Xiaofen , Yuan Lunzhi , Wang Shaojuan , Zhang Yali , Xiong Hualong , Chen Rirong , Ma Jian , Qi Ruoyao , Nie Meifeng , Xu Jingjing , Zhang Zhigang , Chen Liqiang , Wei Min , Zhou Ming , Cai Minping , Shi Yang , Zhang Liang , Yu Huan , Hong Junping , Wang Zikang , Hong Yunda , Yue Mingxi , Li Zonglin , Chen Dabing , Zheng Qingbing , Li Shaowei , Chen Yixin , Cheng Tong , Zhang Jun , Zhang Tianying , Zhu Huachen , Zhao Qinjian , Yuan Quan , Guan Yi , Xia Ningshao
Published: December 2020

A safe and effective SARS-CoV-2 vaccine is essential to avert the on-going COVID-19 pandemic. Here, we developed a subunit vaccine, which is comprised of CHO-expressed spike ectodomain protein (StriFK) and nitrogen bisphosphonates-modified zinc-aluminum hybrid adjuvant (FH002C). This vaccine candidate rapidly elicited the robust humoral response, Th1/Th2 balanced helper CD4 T cell and CD8 T cell immune response in animal models. In mice, hamsters, and non-human primates, 2-shot and 3-shot immunization of StriFK-FH002C generated 28- to 38-fold and 47- to 269-fold higher neutralizing antibody titers than the human COVID-19 convalescent plasmas, respectively. More importantly, the StriFK-FH002C immunization conferred sterilizing immunity to prevent SARS-CoV-2 infection and transmission, which also protected animals from virus-induced weight loss, COVID-19-like symptoms, and pneumonia in hamsters. Vaccine-induced neutralizing and cell-based receptor-blocking antibody titers correlated well with protective efficacy in hamsters, suggesting vaccine-elicited protection is immune-associated. The StriFK-FH002C provided a promising SARS-CoV-2 vaccine candidate for further clinical evaluation.
Multiple infiltration and cross-species transmission of foamy viruses across Paleozoic to Cenozoic era
Authors: Chen Yicong , Zhang Yu-Yi , Wei Xiaoman , Cui Jie
Published: December 2020

Foamy viruses (FVs) are complex retroviruses that can infect humans and other animals. In this study, by integrating transcriptomic and genomic data, we discovered 412 FVs from 6 lineages in amphibians, which significantly increased the known set of FVs in amphibians. Among these lineages, salamander FVs maintained a co-evolutionary pattern with their hosts that could be dated back to the Paleozoic era, while, on the contrary, frog FVs were much more likely acquired from cross-species (class level) transmission in the Cenozoic era. In addition, we found three distinct FV lineages had integrated into the genome of a salamander. Unexpectedly, we identified a potential exogenous form of FV circulated in caecilian, demonstrating the existence of exogenous form of FV besides mammals. Our discovery of rare phenomena in amphibian FVs has overturned our collective understanding of the macroevolution of the complex retrovirus.

Importance

Foamy viruses (FVs) represent, more so than other viruses, the best model of co-evolution between a virus and a host. This study represents so far, the largest investigation of amphibian FVs and revealed 412 FVs of 6 distinct lineages from three major orders of amphibians. Besides co-evolutionary pattern, cross-species and repeated infection were also observed during evolution of amphibian FVs. Remarkably, expressed FVs including a potential exogenous form were discovered, suggesting live FVs could be underestimated in nature. These findings revealed the multiple origin and complex evolution of amphibian FVs started from the Paleozoic era.
COMPARATIVE ANALYSIS OF TRIPLET COMPOSITION OF COMMON MITOCHONDRIAL AND CHLOROPLAST GENES OF THE SAME SPECIES
Authors: Sadovsky Michael G. , Fedotovskaya Viktoriya D.
Published: December 2020

We studied the relation between the genes encoding the same protein (ATP synthase) in mitochondria and chloroplasts, of the same species. 85 species are studied. The relation is revealed through the unsupervised clustering via elastic map implementation of the points in 64-dimensional space of the triplet frequencies of the genes. The triplet composition was counted with a nucleotide shift of the reading frame along a gene. Three types of clustering have been analyzed: for mitochondria genes solely, for chloroplast genes solely, and for the merged set of the genes from the genomes of both organellae. It was found that the encoded function is the feature in clustering: all the clusters in all three versions of clustering patterns clearly exhibit distinct separation of the genes encoding the same subunit into a separate cluster. This behaviour was found for all three types of cluster patterns.
Reconciling Membrane Protein Simulations with Experimental DEER Spectroscopy Data
Authors: Mittal Shriyaa , Shukla Diwakar
Published: December 2020

Spectroscopy experiments are crucial to study membrane proteins for which traditional structure determination methods still prove challenging. Double electron-electron resonance (DEER) spectroscopy experiments provide protein residue-pair distance distributions that are indicative of their conformational heterogeneity. Atomistic molecular dynamics (MD) simulations are another tool that have proved vital to study the structural dynamics of membrane proteins such as to identify inward-open, occluded, and outward-open conformations of transporter membrane proteins, among other partially open or closed states of the protein. Yet, studies have reported that there is no direct consensus between distributional data from DEER experiments and MD simulations, which has challenged validation of structures obtained from long-timescale simulations and using simulations to design experiments. Current coping strategies for comparisons rely on heuristics, such as mapping nearest matching peaks between two ensembles or biased simulations. Here we examine the differences in residue-pair distance distributions arising due to choice of membrane around the protein and covalent modification of a pair of residues to nitroxide spin labels in DEER experiments. Through comparing MD simulations of two proteins, PepTSoand LeuT - both of which have been characterized using DEER experiments previously - we show that the proteins’ dynamics are similar despite the choice of the detergent micelle as a membrane mimetic in DEER experiments. On the other hand, covalently modified residues show slight local differences in their dynamics and a huge divergence when the spin labels’ anointed oxygen atom pair distances are measured rather than protein backbone distances. Given the computational expense associated with pairwise MTSSL labeled MD simulations, we examine the use of biased simulations to explore the conformational dynamics of the spin labels only to reveal that such simulations alter the underlying protein dynamics. Our study identifies the main cause for the mismatch between DEER experiments and MD simulations and will accelerate developing potential mitigation strategies to improve simulation observables match with DEER spectroscopy experiments.
Protocol for an interdisciplinary cross-sectional study investigating the social, biological and community-level drivers of antimicrobial resistance (AMR): Holistic Approach to Unravelling Antibiotic Resistance in East Africa (HATUA)
Authors: Asiimwe Benon B. , Kiiru John , Mshana Stephen E. , Neema Stella , Keenan Katherine , Kesby Mike , Mwanga Joseph R. , Sloan Derek J. , Mmbaga Blandina T. , Smith V Anne , Gillespie Stephen , Lynch Andy G. , Sandeman Alison , Stelling John , Elliott Alison , Aanensen David M. , Kibiki Gibson S. , Sabiiti Wilber , Holden Matthew T. G. ,   HATUA CONSORTIUM, Kansiime Catherine , Mushi Martha F. , Decano Arun Gonzales , Green Dominique L. , Mwaniki John , Ntinginya Nyanda E , Bazira Joel
Published: December 2020

Introduction

Antimicrobial resistance (AMR) is a global health threat that requires urgent research using a multidisciplinary approach. The biological drivers of AMR are well understood, but factors related to treatment-seeking and the social contexts of antibiotic (AB) use behaviours are less understood. Here we describe the Holistic Approach to Unravelling Antibacterial Resistance in East Africa (HATUA), a multi-centre consortium that investigates the diverse drivers of drug-resistance in urinary tract infections (UTIs) in East Africa.

Methods and Analysis

This study will take place in Uganda, Kenya and Tanzania. We will conduct geospatial mapping of AB sellers, and conduct mystery client studies and in-depth interviews (IDI) with drug sellers to investigate AB provision practices. In parallel, we will conduct IDIs with doctors, alongside community focus groups. Clinically diagnosed UTI patients will be recruited from healthcare centres, provide urine samples, and complete a questionnaire capturing retrospective treatment pathways, socio-demographic characteristics, attitudes and knowledge. Bacterial isolates from urine and stool samples will be subject to culture and antibiotic susceptibility testing (C&AST). Genomic DNA from bacterial isolates will be extracted with a subset being sequenced. A follow-up household interview will be conducted with 1800 UTI-positive patients, where further environmental samples will be collected. A sub-sample of patients will be interviewed using qualitative tools. Questionnaire data, microbiological analysis and qualitative data will be linked at the individual level. Quantitative data will be analysed using statistical modelling including Bayesian network analysis, and all forms of qualitative data analysed through iterative thematic content analysis.

Ethics and Dissemination

Approvals have been obtained from all national and local ethical review bodies in East Africa and the UK. Results will be disseminated in communities, with local and global policy stakeholders, and in academic circles. They will have great potential to inform policy, improve clinical practice and build regional pathogen surveillance capacity.
Healthcare worker intentions to receive a COVID-19 vaccine and reasons for hesitancy: A survey of 16,158 health system employees on the eve of vaccine distribution
Authors: Meyer Michelle N. , Gjorgjieva Tamara , Rosica Daniel
Published: December 2020

Healthcare workers (HCWs) have been recommended to receive first priority for limited COVID-19 vaccines. They have also been identified as potential ambassadors of COVID-19 vaccine acceptance, helping to ensure that sufficient members of a hesitant public accept COVID-19 vaccines to achieve population immunity. Yet HCWs themselves have shown vaccine hesitancy in other contexts and the few prior surveys of U.S. HCW intentions to receive a COVID-19 vaccine report acceptance rates of only 28% to 34%. However, it is unknown whether HCW acceptance remains low following mid-November announcements of the efficacy of the first COVID-19 vaccines and the issuance of two emergency use authorizations (EUA) in December. We report the results of a December 2020 survey (N= 16,158; response rate 61%) administered by a large Pennsylvania health system to determine the intentions of its employees to receive a vaccine when it is offered to them. In a mixed sample of individuals serving in patient-facing and other roles, 55% would decide to receive a COVID-19 vaccine when offered, 16.4% would not, and 28.5% reported being undecided. The distribution of responses varied little across hospital campuses, between those in patient-facing roles and other HCWs, or by area or department of work. The higher rate of COVID-19 vaccine acceptance we observe may reflect the framing and timing of our survey. Among hesitant respondents, an overwhelming majority (90.3%) reported concerns about unknown risks and insufficient data. Other commonly reported concerns included known side effects (57.4%) and wanting to wait until they see how it goes with others (44.4%). We observed a substantial increase in self-reported intent to receive a COVID-19 vaccine after an FDA advisory committee voted to recommend an EUA. Among respondents who completed the survey after that point in time, 79% intend to receive a COVID-19 vaccine (n= 1155). Although only suggestive, this trend offers hope that rates of COVID-19 vaccine acceptance may be higher among HCWs and, perhaps, the general public than more hypothetical survey results have indicated.
Conservative treatment of partial-thickness rotator cuff tears and tendinopathy with platelet-rich plasma: a systematic review and meta-analysis
Authors: Xiang Xiao-Na , Deng Jie , Liu Yan , Yu Xi , Cheng Biao , He Hong-Chen
Published: December 2020

Purpose

To assess the effect of platelet-rich plasma (PRP) as a conservative therapy on individuals with partial-thickness rotator cuff tears (PTRCs) or tendinopathy in terms of pain, and function.

Methods

A systematic review and meta-analysis of randomized controlled trials were conducted. Short-term (6±1 months) and long-term (≥1 year) outcomes were analysed, including the visual analogue scale (VAS), Constant-Murley score (CMS), Shoulder Pain and Disability Index (SPADI), as well as American Shoulder and Elbow Surgeons (ASES) score. The weighted mean difference (MD) with 95% confidence interval (CI) was used.

Results

Ten studies were eligible in this review, nine studies with 561 patients were included in this meta-analysis. The meta-analysis showed statistically significant differences in the decrease in short-term VAS (MD=-1.56; 95% CI -2.82 to -0.30), and increase in CMS (MD=16.48; 95% CI 12.57 to 20.40), and SPADI (MD=-18.78 95% CI -36.55 to -1.02). Nonetheless, no long-term effect was observed on pain and function, except CMS (MD=24.30). The results of mean important differences (MIDs) reached the minimal clinically important differences, except ASES. For subgroup analysis, short-term VAS scores were decreased in PRP-treated patients with double centrifugation (MD=-1.99), single injection (MD=-0.71) and post-injection rehabilitation (MD=-1.59).

Conclusion

PRP-treated patients with PTRCs and rotator cuff tendinopathy demonstrated improvements in pain and function, although the effect may not last for a long time. Overall, our results suggest that PRP may have positive clinical outcomes, but limited data, and study heterogeneity hinder firm conclusions.
Naa12compensates forNaa10in mice in the amino-terminal acetylation pathway
Authors: Kweon Hyae Yon , Lee Mi-Ni , Dörfel Max , Seo Seungwoon , Gottlieb Leah , Papazyan Thomas , McTiernan Nina , Ree Rasmus , Bolton David , Garcia Andrew , Flory Michael , Crain Jonathan , Sebold Alison , Lyons Scott , Ismail Ahmed , Marchi Elaine , Sonn Seong-keun , Jeong Se-Jin , Jeon Sejin , Ju Shinyeong , Conway Simon J. , Kim TaeSoo , Kim Hyun-Seok , Lee Cheolju , Roh Tae-Young , Arnesen Thomas , Marmorstein Ronen , Oh Goo Taeg , Lyon Gholson J.
Published: December 2020

Amino-terminal acetylation is catalyzed by a set of N-terminal acetyltransferases (NATs). The NatA complex (including X-linked Naa10 and Naa15) is the major acetyltransferase, with 40-50% of all mammalian proteins being potential substrates. However, the overall role of amino-terminal acetylation on a whole-organism level is poorly understood, particularly in mammals. Male mice lackingNaa10show no globally apparentin vivoamino-terminal acetylation impairment and do not exhibit complete embryonic lethality. RatherNaa10nulls display increased neonatal lethality, and the majority of surviving undersized mutants exhibit a combination of hydrocephaly, cardiac defects, homeotic anterior transformation, piebaldism and urogenital anomalies.Naa12is a previously unannotatedNaa10-like paralogue with NAT activity that genetically compensates forNaa10. Mice deficient forNaa12have no apparent phenotype, whereas mice deficient forNaa10andNaa12display embryonic lethality. The discovery ofNaa12adds to the currently known machinery involved in amino-terminal acetylation in mice.
Enhancing cassava reproductive development does not negatively impact shoot to root ratio and dry matter content in storage roots
Authors: Deborah Oluwasanya , Tim Setter
Published: December 2020

From previous studies we developed treatments that significantly improved cassava female flower and fruit development, using a combination of the anti-ethylene, silver thiosulfate (STS), and the cytokinin, benzyladenine (BA); collectively referred to as plant growth regulators (PGR). In this study, we investigated whether the benefit derived from this treatment altered partitioning of photosynthate to other sinks and general vegetative growth of cassava in the first six months of plants growth, when reproductive growth initiates and peaks. Our flower enhancing treatment did not significantly alter shoot and storage root fresh weight, partitioning index on a fresh weight basis and percent dry matter content of storage roots between Months 2 and 5. With the onset of the dry season in Month 6, PGR treated plants had higher shoot and storage root fresh weight than controls but these plant parts responded proportionally and so partitioning index between controls and treated plants was not significantly different. The nighttime starch export under PGR treatments was reduced at Months 2, 4 and 5 but this was not correlated with flower development at these months. The survival of PGR treated plants until harvest was however reduced owing to increased mortality arising from phytotoxicity and increased susceptibility to disease. We therefore conclude that PGRs have effects more directly on flower and fruit reproductive signaling and regulatory pathways rather than on an indirect effect on resource partitioning.
Tuning the transglycosylation reaction of a GH11 xylanase by a delicate enhancement of its thumb flexibility
Authors: Marneth Kim , van den Elst Hans , Cramer-Blok Anneloes , Codee Jeroen , Overkleeft Hermen S. , Aerts Johannes M. F. G. , Ubbink Marcellus , Bdira Fredj Ben
Published: December 2020

Glycoside hydrolases (GH) are attractive tools for multiple biotechnological applications. In conjunction with their hydrolytic function, GH can perform transglycosylation reaction under specific conditions. In nature, oligosaccharides synthesis is performed by glycosyltransferase (GT). However, the industrial utilization of GT is limited by their instability in solution. A key difference between GT and GH is the flexibility of their binding sites architecture. In this report, we used the xylanase fromBacillus circulans(BCX) to study the interplay between active site flexibility and the transglycosylation reaction. Residues of the BCX thumb were substituted to increase the flexibility of the enzyme binding site. Replacement of the highly conserved residue P116 with glycine shifted the balance of the BCX enzymatic reaction toward transglycosylation. The effects of this point mutation on the structure and dynamics of BCX were investigated by NMR spectroscopy. The P116G mutation induces subtle changes in the configuration of the thumb and enhances the millisecond dynamics of the active site. Based on our findings, we propose the remodeling of the GH enzymes glycon site flexibility as a strategy to improve the transglycosylation efficiency of these biotechnologically important catalysts.
Evolutionary coupling range varies widely among enzymes depending on selection pressure
Authors: Echave Julian
Published: December 2020

Recent studies proposed that enzyme active sites induce evolutionary constraints at long distances. The physical origin of such long-range evolutionary coupling is unknown. Here, I use a recent biophysical model of evolution to study the relationship between physical and evolutionary couplings on a diverse data set of monomeric enzymes. I show that evolutionary coupling is not universally long-range. Rather, range varies widely among enzymes, from 2Å to 20Å. Furthermore, the evolutionary coupling range of an enzyme does not inform on the underlying physical coupling, which is short-range for all enzymes. Rather, evolutionary coupling range is determined by functional selection pressure.

SIGNIFICANCE

Until recently, only residues near enzyme active sites were thought to be evolutionarily constrained. However, recent studies proposed that active sites induce long-range evolutionary constraints. This seems to conflict with the common finding that physical couplings in proteins are short-range. This raises the question of how short-range physical couplings may cause long-range evolutionary couplings. Here, I show that the function that maps physical coupling into evolutionary coupling depends on functional selection pressure. Under weak selection, both couplings are similarly short-range; under strong selection, short-range physical coupling is non-linearly turned into long-range evolutionary coupling. Thus, due to a huge variation of selection pressure, evolutionary coupling range varies widely among enzymes, from very short (2 Å) to very long (20 Å).
Co-translational folding of the first transmembrane domain of ABC-transporter CFTR is supported by assembly with the first cytosolic domain
Authors: Kleizen Bertrand , van Willigen Marcel , Mijnders Marjolein , Peters Florence , Grudniewska Magda , Hillenaar Tamara , Thomas Ann , Kooijman Laurens , Peters Kathryn W. , Frizzell Raymond , van der Sluijs Peter , Braakman Ineke
Published: December 2020

ABC-transporters transport a wealth of molecules across membranes and consist of transmembrane and cytosolic domains. Their activity cycle involves a tightly regulated and concerted domain choreography. Regulation is driven by the cytosolic domains and function by the transmembrane domains. Folding of these polytopic multidomain proteins to their functional state is a challenge for cells, which is mitigated by co-translational and sequential events. We here reveal the first stages of co-translational domain folding and assembly of CFTR, the ABC-transporter defective in the most abundant rare inherited disease cystic fibrosis. We have combined biosynthetic radiolabeling with protease-susceptibility assays and domain-specific antibodies. The most N-terminal domain, TMD1 (transmembrane domain 1), folds both its hydrophobic and soluble helices during translation: the transmembrane helices pack tightly and the cytosolic N- and C-termini assemble with the first cytosolic helical loop ICL1, leaving only ICL2 exposed. This N-C-ICL1 assembly is strengthened by two independent events: i) assembly of ICL1 with the N-terminal subdomain of the next domain, cytosolic NBD1 (nucleotide-binding domain 1); and ii) in the presence of corrector drug VX-809, which rescues cell-surface expression of a range of disease-causing CFTR mutants. Both lead to increased shielding of the CFTR N-terminus, and their additivity implies different modes of action. Early assembly of NBD1 and TMD1 is essential for CFTR folding and positions both domains for the required assembly with TMD2. Altogether, we have gained insights into this first, nucleating, VX-809-enhanced domain-assembly event during and immediately after CFTR translation, involving structures conserved in type-I ABC exporters.
Nesting strategy shapes territorial aggression but not testosterone: a comparative approach in female and male birds
Authors: Lipshutz SE , Rosvall KA
Published: December 2020

Our understanding of the proximate and ultimate mechanisms shaping competitive phenotypes primarily stems from research on male-male competition for mates, even though female-female competition is also widespread. Obligate secondary cavity-nesting has evolved repeatedly across avian lineages, providing a useful comparative context to explore how competition over limited nest cavities shapes aggression and its underlying mechanisms across species. Although evidence from one or another cavity-nesting species suggests that territorial aggression is adaptive in both females and males, this has not yet been tested in a comparative framework. We tested the hypothesis that cavity-nesting generates more robust territorial aggression, in comparison to close relatives with less restrictive nesting strategies. Our focal species were two obligate secondary cavity-nesting species and two related species with more flexible nesting strategies in the same avian family: tree swallow (Tachycineta bicolor) vs. barn swallow (Hirundo rustica); Eastern bluebird (Sialia sialis) vs. American robin (Turdus migratorius). We assayed conspecific territorial aggression, and found that cavity-nesting species physically attacked a simulated intruder more often than their close relatives. This pattern held for both females and males. Because territorial aggression is often associated with elevated testosterone, we also hypothesized that cavity-nesting species would exhibit higher testosterone levels in circulation. However, cavity-nesting species did not have higher testosterone in circulation for either sex, despite some correlative evidence that testosterone is associated with higher rates of physical attack in female tree swallows. Our focus on a competitive context that is relevant to both sexes – competition over essential breeding resources – provides a useful comparative framework for co-consideration of proximate and ultimate drivers of reproductive competition in females and males.
COVID-19: An analysis of social media and research publication activity during the early stages of the pandemic
Authors: Taneja Sonia L. , Passi Monica , Bhattacharya Sumona , Schueler Samuel A. , Gurram Sandeep , Koh Christopher
Published: December 2020

Objectives

The COVID-19 pandemic has highlighted the importance of rapid dissemination of scientific and medical discovery. Social media (SoMe) has become an invaluable platform in science and medicine. This study analyzed activity of SoMe (Twitter), preprints, and publications related to COVID-19 and gastroenterology (GI) during the COVID-19 pandemic.

Methods

Data from Twitter, preprint servers and PubMed was collected and analyzed from December 2019 through May 2020. Global and regional geographic and gastrointestinal organ specific social media trends were compared to preprint and publication activity; any associations were identified.

Results

Over the 6-month period, there were 73,079 tweets from 44,609 users, 7,164 publications, and 4,702 preprints. Twitter activity peaked during March while preprints and publications peaked in April 2020. Strong correlations were identified between Twitter and both preprints and publications activity (p<0.001 for both). While COVID-19 data across the 3 platforms concentrated on pulmonology/critical care, the majority of GI tweets pertained to pancreatology, most publications focused on hepatology, and most preprints covered hepatology and luminal GI (LGI). There were significant associations between Twitter activity and research for all GI subfields (p=0.009 for LGI, p=0.006 for hepatology and IBD, p=0.007 for endoscopy), except pancreatology (p=0.2). Twitter activity was highest in the US (7,331 tweets) whereas PubMed activity was highest in China (1,768 publications).

Conclusions

The COVID-19 pandemic has highlighted the utility of SoMe as a vehicle for disseminating scientific information during a public health crisis. Scientists and clinicians should consider the use of SoMe in augmenting public awareness of their scholarly pursuits.
Infection and chronic disease activate a brain-muscle signaling axis that regulates muscle performance
Authors: Yang Shuo , Tian Meijie , Dai Yulong , Feng Shengyong , Wang Yunyun , Chhangani Deepak , Ou Tiffany , Li Wenle , Yang Ze , McAdow Jennifer , Rincon-Limas Diego E. , Yin Xin , Tai Wanbo , Cheng Gong , Johnson Aaron
Published: December 2020

Graphic abstract

Infections and neurodegenerative diseases induce neuroinflammation, but affected individuals often show a number of non-neural symptoms including muscle pain and muscle fatigue. The molecular pathways by which neuroinflammation causes pathologies outside the central nervous system (CNS) are poorly understood, so we developed three models to investigate the impact of neuroinflammation on muscle performance. We found that bacterial infection, COVID-like viral infection, and expression of a neurotoxic protein associated with Alzheimer′ s disease promoted the accumulation of reactive oxygen species (ROS) in the brain. Excessive ROS induces the expression of the cytokine Unpaired 3 (Upd3) in insects, or its orthologue IL-6 in mammals, and CNS-derived Upd3/IL-6 activates the JAK/Stat pathway in skeletal muscle. In response to JAK/Stat signaling, mitochondrial function is impaired and muscle performance is reduced. Our work uncovers a brain-muscle signaling axis in which infections and chronic diseases induce cytokine-dependent changes in muscle performance, suggesting IL-6 could be a therapeutic target to treat muscle weakness caused by neuroinflammation.
Fatty Acid Synthase inhibitor TVB-3166 prevents S-acylation of the Spike protein of human coronaviruses
Authors: Mekhail Katrina , Lee Minhyoung , Sugiyama Michael , Astori Audrey , St-Germain Jonathan , Latreille Elyse , Khosraviani Negar , Wei Kuiru , Li Zhijie , Rini James , Lee Warren L. , Antonescu Costin , Raught Brian , Fairn Gregory D.
Published: December 2020

The Spike protein of SARS-CoV2 and other coronaviruses mediate host cell entry and are S-acylated on multiple phylogenetically conserved cysteine residues. Multiple protein acyltransferase enzymes of the ZDHHC family have been reported to modify Spike proteins post-translationally. Using resin-assisted capture mass spectrometry, we demonstrate that the Spike protein is S-acylated in SARS-CoV2 infected human and monkey cells. We further show that increased abundance of the human acyltransferase ZDHHC5 results in increased S-acylation of the SARS-CoV2 Spike protein, whereasZDHHC5knockout cells had a 40% reduction in the incorporation of an alkynyl-palmitate using click chemistry detection. We also find that the S-acylation of the Spike protein is not limited to palmitate, as clickable versions of myristate and stearate were also found on the immunocaptured protein. Yet, ZDHHC5 was highly selective for palmitate, suggesting that other ZDHHC enzymes mediated the incorporation of other fatty acyl chains. Thus, since multiple ZDHHC isoforms may modify the Spike protein, we examined the ability of the fatty acid synthase inhibitor TVB-3166 to prevent the S-acylation of the Spike proteins of SARS-CoV-2 and human CoV-229E. Treating cells with TVB-3166 inhibited S-acylation of ectopically expressed SARS-CoV2 Spike and attenuated the ability of SARS-CoV2 and human CoV-229E to spreadin vitro.Additionally, treatment of mice with a comparatively low dose of TVB-3166 promoted survival from an otherwise fatal murine coronavirus infection. Our findings further substantiate the necessity of CoV Spike protein S-acylation and the potential use of fatty acid synthase inhibitors.
Molecular recognition of sugar binding in a melibiose transporter MelB by X-ray crystallography
Authors: Guan Lan , Hariharan Parameswaran
Published: December 2020

The symporter melibiose permease MelB is the best-studied representative from MFS_2 family and the only protein in this large family with crystal structure determined. Previous thermodynamic studies show that MelB utilizes cooperative binding as the core mechanism for its obligatory symport. Here we present two sugar-bound X-ray crystal structures of a Salmonella typhimurium MelB D59C uniport mutant that binds and catalyzes melibiose transport uncoupled to either cation, as determined by biochemical and biophysical studies. The two structures with bound nitrophenyl-α-D-galactoside or dodecyl-α-D-melibioside, which were refined to a resolution of 3.05 or 3.15 Å, respectively, are virtually identical at an outward-facing conformation; each one contains a α-galactoside molecule in the middle of protein. In the substrate-binding site, the galactosyl moiety on both ligands are at an essentially same configuration, so a galactoside specificity determinant pocket can be recognized, and hence the molecular recognition mechanism for the binding of sugar in MelB is deciphered. The conserved cation-binding pocket is also assigned, which is directly connected to the sugar specificity pocket. These key structural findings resolve the long-standing question on the sugar binding in MelB.
Modeling of astrocyte networks: towards realistic topology and dynamics
Authors: Verveyko D. V. , Verisokin A. Yu. , Postnov D. E. , Brazhe A. R.
Published: December 2020

Neuronal firing and neuron-to-neuron synaptic wiring are currently widely described as orchestrated by astrocytes — elaborately ramified glial cells tiling the cortical and hippocampal space into non-overlapping domains, each covering hundreds of individual dendrites and hundreds thousands synapses. A key component to astrocytic signaling is the dynamics of cytosolic Ca2+which displays multiscale spatiotemporal patterns from short confined elemental Ca2+events (puffs) to Ca2+waves expanding through many cells. Here we synthesize the current understanding of astrocyte morphology, coupling local synaptic activity to astrocytic Ca2+in perisynaptic astrocytic processes and morphology-defined mechanisms of Ca2+regulation in a distributed model. To this end, we build simplified realistic data-driven spatial network templates and compile model equations as defined by local cell morphology. The input to the model is spatially uncorrelated stochastic synaptic activity. The proposed modeling approach is validated by statistics of simulated Ca2+transients at a single cell level. In multicellular templates we observe regular sequences of cell entrainment in Ca2+waves, as a result of interplay between stochastic input and morphology variability between individual astrocytes. Our approach adds spatial dimension to the existing astrocyte models by employment of realistic morphology while retaining enough flexibility and scalability to be embedded in multiscale heterocellular models of neural tissue. We conclude that the proposed approach provides a useful description of neuron-driven Ca2+-activity in the astrocyte syncytium.
Stem cell derived astrocytes withPOLGmutations and mitochondrial dysfunction including abnormal NAD+ metabolism is toxic for neurons
Authors: Liang Kristina Xiao , Kianian Atefeh , Chen Anbin , Kristiansen Cecilie Katrin , Hong Yu , Furriol Jessica , Høyland Lena Elise , Ziegler Mathias , Kråkenes Torbjørn , Tzoulis Charalampos , Sullivan Gareth John , Bindoff Laurence A.
Published: December 2020

The inability to reliably replicate mitochondrial DNA (mtDNA) by mitochondrial DNA polymerase gamma (POLG) leads to a subset of common mitochondrial diseases associated with neuronal death and depletion of neuronal mtDNA. Defining disease mechanisms remains difficult due to the limited access to human tissue. Astrocytes are highly abundant in the brain, playing a crucial role in the support and modulation of neuronal function. Astrocytes also respond to insults affecting the brain. Following damage to the center neural system, which can be hypoxia, inflammation or neurodegeneration, astrocytes become activated and lose their supportive role and gain toxic functions that induce rapid death of neurons and oligodendrocytes. The role of astrocyte reactivation and the consequences this has for neuronal homeostasis in mitochondrial diseases has not been explored. Here, using patient cells carryingPOLGmutations, we generated iPSCs and then differentiated into astrocytes. We demonstrated that POLG-astrocytes exhibited both mitochondrial dysfunctions, including loss of mitochondrial membrane potential, energy failure, complex I and IV defects, disturbed NAD+/NADH metabolism, and mtDNA depletion. Further, POLG derived astrocytes presented an A1-like reactive phenotype with increased proliferation, invasion, upregulation of pathways involved in response to stimulus, immune system process, cell proliferation and cell killing. Under direct and indirect co-culture with neurons, POLG-astrocytes exhibited a toxic effect leading to the death of neurons. Our findings demonstrate that mitochondrial dysfunction caused byPOLGmutations leads not only to intrinsic defects in energy metabolism affecting both neurons and astrocytes, but also to neurotoxic damage driven by astrocytes. Our studies provide a robust astroglia-neuronal interaction model for future investigation of mitochondrial involvement in neurogenesis and neurodegenerative diseases.

Highlights

▪ Patient-specific astrocytes harbouring aPOLGmutation showed lower mitochondrial membrane potential and mtDNA depletion.

▪ POLG-astrocytes generated elevated L-lactate as the end glycolytic product.

▪ Patient-specific astrocytes withPOLGmutations exhibited mitochondrial respiratory chain disruption accompanied with abnormal UCP2/SirT1/SirT3 mediated NAD+metabolism.

▪ Suppressed complex I and IV-driven respiration contributed to the pathological mechanisms in POLG-related disease.

▪ POLG-astrocytes exhibit A1-reactive phenotype and neurotoxic potential.

Graphic abstract
Metal microdrive and head cap system for silicon probe recovery in freely moving rodent
Authors: Vöröslakos Mihály , Petersen Peter C. , Vöröslakos Balázs , Buzsáki György
Published: December 2020

High-yield electrophysiological extracellular recording in freely moving rodents provides a unique window into the temporal dynamics of neural circuits. Recording from unrestrained animals is critical to investigate brain activity during natural behaviors. The use and implantation of high-channel-count silicon probes represent the largest cost and experimental complexity associated with such recordings making a recoverable and reusable system desirable. To address this, we have designed and tested a novel 3D printed head-gear system for freely moving mice and rats. The system consists of a recoverable microdrive printed in stainless steel and a plastic head cap system, allowing researchers to reuse the silicon probes with ease, decreasing the effective cost, and the experimental effort and complexity. The cap designs are modular and provide structural protection and electrical shielding to the implanted hardware and electronics. We provide detailed procedural instructions allowing researchers to adapt and flexibly modify the head-gear system.