bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification by cryoEM of a densovirus causing mass mortality in mass-reared larval darkling beetles (Zophobas morio)
Authors: Penzes Judit J , Kaelber Jason T 
Published: May 2022

AbstractA reared colony of larval superworms (Zophobas morio) experienced the swift and unexplained death of about 90% of its population. We isolated a high-abundance virus from dead larvae and, using cryoEM, identified it as a novel densovirus, which we name Zophobas morio black wasting virus (ZmBWV). Densoviruses (DVs) are small, ssDNA viruses of the family Parvoviridae that infect protostome and deuterostome invertebrates. The vast majority of DVs have been associated with severe pathology, especially in larval stage insects. By cryoEM we resolved the high-resolution capsid structure of this new DV at 2.9 Å resolution for the genome-packaging, infectious particles and at a resolution of 3.3 Å in case of the empty particles, both purified directly from the infected Z. morio larvae. The capsid structure of ZmBWV provides the first insights into the capsid morphology of a structurally previously-uncharacterized genus, Blattambidensovirus. Consequently, the ZmBWV capsid harbors a unique surface morphology within the family, yet shows the T=1 icosahedral symmetry, the eight-stranded jelly roll core, as well as general features of multimer interactions previously found typical of subfamily Densovirinae. Although we have not inoculated healthy larvae with ZmBWV, on the basis of its prodigious abundance in infected larvae and the prior probability of larval pathology with viruses of this subfamily, ZmBWV is the most probable cause of the observed mass mortality event.
Structural-guided fragment-based drug discovery applied to antitoxin, MAB3862 opens a new possibility of exploring the Toxin and Antitoxin for antibiotics
Authors: Kim So Yeon , Eun Hyun-Jong , Lee JooYeon , Lee Wonsuk , Thomas Sherine Elizabeth , Brear Paul , Vedithi Sundeep Chaitanya , Abell Chris , Lee Bong-Jin , Blundell Tom L. 
Published: May 2022

AbstractMycobacterium abscessus (Mab) is a rapidly growing multidrug-resistant species among nontuberculous mycobacteria (NTM). Pulmonary infections caused by M. abscessus are difficult to treat and often result in an accelerated condition and premature death of immunosuppressed patients such as those with cystic fibrosis, putting them at a greater risk of other infections and increasing the urgency of developing a novel class of antibiotics. Here, we explore the use of toxin and antitoxin (TA) as an interesting and promising new class of target in a fragment-based drug-discovery approach. A de novo structure of Mab3862, an antitoxin of type 2 TA class in M. abscessus was elucidated and followed by drug discovery work. Very small molecules (fragments) are used to bind the antitoxin and then elaborated into drug-sized molecule that potentially trigger conformational change to prevent formation of toxin-antitoxin complex. Biophysical screening methods and binding-mode guidance from in silico docking were conducted. Grouping of fragments based on the binding site, creating a pharmacophore model, can facilitate further studies for rational design of inhibitors. Although targeting the TA complex for developing antibiotics is relatively novel and challenging, this could possibly open the gate for exploring it as potential drug target. Targeting one of the TA pairs might not be completely bactericidal. However, using this approach strategically with other antibiotics for synergic effect might be effective for patients with a persistence phenotype requiring prolonged therapy.
Site-specific decreases in DNA methylation in replicating cells following exposure to oxidative stress
Authors: Seddon Annika R. , Das Andrew B. , Hampton Mark B. , Stevens Aaron J. 
Published: May 2022

AbstractOxidative stress is a common feature of inflammation-driven cancers, and promotes genomic instability and aggressive tumour phenotypes. It is known that oxidative stress transiently modulates gene expression through the oxidation of transcription factors and associated regulatory proteins. Activated neutrophils produce hypochlorous acid and chloramines that can disrupt DNA methylation via methionine oxidation. The goal of the current study was to determine whether chloramine exposure results in sequence-specific modifications in DNA methylation that enable long-term alterations in transcriptional output. Proliferating Jurkat T-lymphoma cells were exposed to sublethal doses of glycine chloramine and differential methylation patterns were compared using Illumina EPIC 850K bead chip arrays. There was a substantial genome-wide decrease in methylation four hours after exposure that correlated with altered RNA expression for 24 and 48 hours, indicating sustained impacts on exposed cells. A large proportion of the most significant differentially methylated CpG sites were situated towards chromosomal ends, suggesting that these regions are most susceptible to inhibition of maintenance DNA methylation. This may contribute to epigenetic instability of chromosomal ends in rapidly dividing cells, with potential implications for the regulation of telomere length and cellular longevity.
Onsager regression characterizes living systems in passive measurements
Authors: Muenker Till M. , Knotz Gabriel , Krüger Matthias , Betz Timo 
Published: May 2022

AbstractUnderstanding life is arguably among the most complex scientific problems faced in modern research. From a physics perspective, living systems are complex dynamic entities that operate far from thermodynamic equilibrium.1–3This active, non-equilibrium behaviour, with its constant hunger for energy, allows life to overcome the ever dispersing forces of entropy, and drives cellular organisation.4, 5Unfortunately, most analysis methods provided by the toolbox of statistical mechanics cannot be used in such non-equilibrium situations, forcing researchers to use sophisticated and often invasive approaches to study the mechanistic processes inside living organisms. Here we introduce a new observable coined the mean back relaxation. Based on three-point probabilities, and exploiting Onsager’s regression hypothesis, it extracts additional information from passively observed trajectories compared to classical observables such as the mean squared displacement. We mathematically prove that the mean back relaxation is able to detect broken detailed balance in systems confined in stationary or actively diffusing potentials. We show in experiment and theory that it gives access to the non-equilibrium generating energy and the viscoelastic material properties of a well controlled artificial system, and we experimentally demonstrate that it does so even for a variety of living systems, revealing an astonishing relation between the mean back relaxation and the active mechanical energy. Based on these findings, we conclude that it acts as a new marker of non-equilibrium dynamics. Combining, in a next step, passive fluctuations with the extracted active energy allows to overcome a fundamental barrier in the study of living systems; it gives access to the viscoelastic material properties from passive measurements.
PAX4 loss of function alters human endocrine cell development and influences diabetes risk
Authors: Lau Hwee Hui , Krentz Nicole A. J. , Abaitua Fernando , Perez-Alcantara Marta , Chan Jun-Wei , Ajeian Jila , Ghosh Soumita , Champon Benoite , Sun Han , Jha Alokkumar , Hoon Shawn , Tan Nguan Soon , Gardner Daphne , Kao Shih Ling , Tai E Shyong , Gloyn Anna L , Teo Adrian Kee Keong 
Published: May 2022

AbstractDiabetes is a major chronic disease with an excessive healthcare burden on society1. A coding variant (p.Arg192His) in the transcription factorPAX4is uniquely and reproducibly associated with an altered risk for type 2 diabetes (T2D) in East Asian populations2–7, whilst rarePAX4alleles have been proposed to cause monogenic diabetes8. In mice,Pax4is essential for beta cell formation but neither the role of diabetes-associated variants inPAX4nor PAX4 itself on human beta cell development and/or function are known. Here, we demonstrate that non-diabetic carriers of either thePAX4p.Arg192His or a newly identified p.Tyr186X allele exhibit decreased pancreatic beta cell function. In the human beta cell model, EndoC-βH1,PAX4knockdown led to impaired insulin secretion, reduced total insulin content, and altered hormone gene expression. Deletion ofPAX4in isogenic human induced pluripotent stem cell (hiPSC)-derived beta-like cells resulted in derepression of alpha cell gene expression whilstin vitrodifferentiation of hiPSCs from carriers ofPAX4p.His192 and p.X186 alleles exhibited increased polyhormonal endocrine cell formation and reduced insulin content.In silicoandin vitrostudies showed that thesePAX4alleles cause either reduced PAX4 expression or function. Correction of the diabetes-associatedPAX4alleles reversed these phenotypic changes. Together, we demonstrate the role of PAX4 in human endocrine cell development, beta cell function, and its contribution to T2D-risk.
Chromatin-modifying enzymes as modulators of nuclear size during lineage differentiation
Authors: Meng Lingjun 
Published: May 2022

AbstractThe mechanism of nuclear size determination and alteration during normal lineage development and cancer pathologies which is not fully understood. As recently reported, chromatin modification can change nuclear morphology. Therefore, we screened a range of pharmacological chemical compounds that impact the activity of chromatin-modifying enzymes, in order to get a clue of the specific types of chromatin-modifying enzymes that remarkably effect nuclear size and shape. We found that interrupted activity of chromatin-modifying enzymes is associated with nuclear shape abnormalities. Furthermore, the activity of chromatin-modifying enzymes perturbs cell fate determination in cellular maintenance and lineage commitment. Our results indicated that chromatin-modifying enzyme regulates cell fate decision during lineage differentiation and is associate with nuclear size alteration.SignificanceHere we described for the first time the modulation of chromatin-modifying enzymes remarkably effects nuclear shape, and perturbs cell fate determination in cellular maintenance and lineage fate commitment in normal stem cells and leukemia cancer cells. We found that the irregularities of nuclear contour were highly related to pharmacological inhibition of chromatin-modifying enzyme activity. After manipulating a histone demethylase named GASC1, we found that upregulation of GASC1 impairs the differentiation of hESCs to terminally differentiated neural cells. Moreover, upregulation of GASC1 impairs the proliferation of leukemia cells due to cell cycle arrest in the G0/G1 phase and indicates misshapen nuclei. This study suggested that chromatin-modifying enzyme regulates the nuclear contour related cell fate decision also including cancer cell fate determination.
Hepatic AMPK activation in response to dynamic REDOX balance is a biomarker of exercise to improve blood glucose control
Authors: Wu Meiling , Zhao Anda , Yan Xingchen , Gao Hongyang , Zhang Chunwang , Liu Xiaomin , Luo Qiwen , Xie Feizhou , Liu Shanlin , Shi Dongyun 
Published: May 2022

AbstractAntioxidant intervention is considered to inhibit reactive oxygen species (ROS) and alleviates hyperglycemia. Paradoxically, moderate exercise can produce ROS to improve diabetes. The exact redox mechanism of these two different approaches remains largely unclear. Here, by comparing exercise and antioxidants intervention on type 2 diabetic rats, we found moderate exercise upregulated compensatory antioxidant capability and reached a higher level of redox balance in the liver. In contrast, antioxidant intervention achieved a low-level redox balance by inhibiting oxidative stress. Both of these two interventions could promote glycolysis and aerobic oxidation mediated by hepatic AMPK activation, ameliorating diabetes. During exercise, different levels of ROS generated by exercise have differential regulations on the activity and expression of hepatic AMPK. Moderate exercise-derived ROS promoted hepatic AMPK glutathionylation activation. However, excess exercise increased oxidative damage, and inhibited the activity and expression of AMPK. Overall, our results illustrate that both exercise and antioxidant intervention improve blood glucose in diabetes by promoting redox balance, despite the levels of redox balance are different. Moreover, the activation and expression of AMPK could act as a biomarker to reflect the effective treatment range for diabetes. This finding provides theoretical evidence for the precise regulation of diabetes by antioxidants and exercise.
The temporal dynamics of lncRNAFirre-mediated epigenetic and transcriptional regulation
Authors: Much Christian , Lasda Erika L. , Pereira Isabela T. , Vallery Tenaya K. , Ramirez Daniel , Lewandowski Jordan P. , Dowell Robin D. , Smallegan Michael J. , Rinn John L. 
Published: May 2022

AbstractNumerous studies have now demonstrated that lncRNAs can influence gene expression programs leading to cell and organismal phenotypes. Typically, lncRNA perturbations and concomitant changes in gene expression are measured on the timescale of many hours to days. Thus, we currently lack a temporally grounded understanding of the primary, secondary, and tertiary relationships of lncRNA-mediated transcriptional and epigenetic regulation – despite being a prerequisite to elucidating lncRNA mechanisms. To begin to address when and where a lncRNA regulates gene expression, we genetically engineered cell lines to temporally induce the lncRNAFirre. Using this approach, we were able to monitor lncRNA transcriptional regulatory events from 15 min to four days. We observed that upon induction,FirreRNA regulates epigenetic and transcriptional states,in trans, within 30 min. These early regulatory events result in much larger transcriptional changes after twelve hours, well before current studies monitor lncRNA regulation. Moreover,Firre-mediated gene expression changes are epigenetically remembered for days. Overall, this study suggests that lncRNAs can rapidly regulate gene expression by establishing persistent epigenetic and transcriptional states.
MaLAdapt reveals novel targets of adaptive introgression from Neanderthals and Denisovans in worldwide human populations
Authors: Zhang Xinjun , Kim Bernard , Singh Armaan , Sankararaman Sriram , Durvasula Arun , Lohmueller Kirk E. 
Published: May 2022

AbstractAdaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, these outlier-based approaches are vulnerable to a high false-negative rate as the power of different methods vary, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals as AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present an ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selection sweeps, heterosis, and demographic misspecifications. Further, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and on a validation of empirical signals through visual impaction of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data, and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.
Prophylactic treatment of Glycyrrhiza glabra mitigates COVID-19 pathology through inhibition of pro-inflammatory cytokines in the hamster model and NETosis
Authors: Rizvi Zaigham Abbas , Babele Prabhakar , Sadhu Srikanth , Madan Upasna , Tripathy Manas Ranjan , Goswami Sandeep , Mani Shailendra , Kumar Sachin , Awasthi Amit , Dikshit Madhu 
Published: May 2022

AbstractSevere coronavirus disease (COVID-19) is accompanied with acute respiratory distress syndrome & pulmonary pathology, and is presented mostly with inflammatory cytokine release, dysregulated immune response, skewed neutrophil/ lymphocyte ratio, and hypercoagulable state. Though vaccinations have proved effective in reducing the COVID-19 related mortality, the limitation of use of vaccine against immunocompromised, comorbidity, and emerging variants remains a concern. In the current study we investigate for the first-time the efficacy of Glycyrrhiza glabra (GG) extract, a potent immunomodulator, against SARS-CoV-2 infection in hamsters. Prophylactic treatment with GG showed protection against loss in body weight and 35-40% decrease in lung viral load along with reduced lung pathology in the hamster model. Remarkably, GG reduced the mRNA expression of pro-inflammatory cytokines and Plasminogen activator inhibito-1 (PAI-1). In-vitro, GG acted as potent immunomodulator by reducing Th2 and Th17 differentiation and IL-4 and IL-17A cytokine production. In addition, GG also showed robust potential to suppress ROS, mtROS and NETs generation in a concentration dependent manner in both human polymorphonuclear neutrophils (PMNs) and murine bone marrow derived neutrophils (BMDNs). Taken together, we provide evidence for the protective efficacy of GG against COVID-19 and its putative mechanistic insight, which might be developed as a future immunomodulatory approach against various pathologies with high cytokine production, aberrant neutrophil activation including coronavirus infection.
Enzymatically-active bacterial microcompartments follow substrate gradients and are protected from aggregation in a cell-free system
Authors: Steinkühler Jan , Abrahamson Charlotte H. , Agudo-Canalejo Jaime , Golestanian Ramin , Tullman-Ercek Danielle , Kamat Neha P. 
Published: May 2022

AbstractThe ability to dynamically control organelle movement and position is essential for cellular function. Yet the underlying mechanisms driving this organization have not been fully resolved. Here, we draw from recent experimental observations and theoretical models of enzyme chemotaxis to demonstrate the chemotaxis of a bacterial organelle, the 1,2 propanediol (1,2-PD) utilization bacterial microcompartment (MCP) from Salmonella enterica. Upon encapsulating MCPs in a cell-like, biomimetic compartment, we observed the directed movement of MCPs along an external gradient of substrate. Our analysis shows that MCPs not only chemotax towards their substrate but also that enzymatic activity and substrate turnover protect them against large-scale aggregation. Our results provide a first experimental demonstration of organelle chemotaxis in a synthetic cellular system and support a recent theoretical model of chemotaxis. Together this work reveals a potentially significant driver of organelle organization while contributing to the construction of synthetic cell-like materials.
De Novo Protein Fold Design Through Sequence-Independent Fragment Assembly Simulations
Authors: Pearce Robin , Huang Xiaoqiang , Omenn Gilbert S. , Zhang Yang 
Published: May 2022

AbstractDe novo protein design generally consists of two steps, including structure and sequence design. However, many protein design studies have focused on sequence design with scaffolds adapted from native structures in the PDB, which renders novel areas of protein structure and function space unexplored. Here we developed FoldDesign to create novel protein folds from specific secondary structure (SS) assignments through sequence-independent replica-exchange Monte Carlo (REMC) simulations. The method was tested on 354 non-redundant topologies, where FoldDesign consistently created stable structural folds, while recapitulating on average 87.7% of the SS elements. Meanwhile, the FoldDesign scaffolds had well-formed structures with buried residues and solvent exposed areas that closely matched their native counterparts. Despite the high fidelity to the input SS restraints and local structural characteristics of native proteins, a large portion of the designed scaffolds possessed global folds that were completely different from natural proteins in the PDB, highlighting the ability of FoldDesign to explore novel areas of protein fold space. Detailed data analyses demonstrated that the major contributions to the successful fold design lay in the optimal energy force field, which contains a balanced set of fragment and secondary structure packing terms, and the REMC simulations, which utilize multiple auxiliary movements to efficiently search the conformational space. These results demonstrate FoldDesign’s strong potential to explore both structural and functional space through computational design simulations that natural proteins have not reached through evolution.SignificanceNatural proteins were generated following billions of years of evolution and therefore possess limited structural folds and biological functions. There is considerable interest in de novo protein design to generate artificial proteins with novel structures and functions beyond those created by nature. However, the success rate of computational de novo protein design remains low, where extensive user-intervention and large-scale experimental optimization are typically required to achieve successful designs. To address this issue, we developed a new automated open-source program, FoldDesign, for de novo protein fold design which shows improved performance in creating high fidelity stable folds compared to other state-of-the-art methods. The success of FoldDesign should enable the creation of desired protein structures with promising clinical and industrial potential.
Investigating and Modeling the Factors that Affect Genetic Circuit Performance
Authors: Zilberzwige-Tal Shai , Fontanarrosa Pedro , Bychenko Darya , Dorfan Yuval , Gazit Ehud , Myers Chris J. 
Published: May 2022

AbstractOver the past two decades, synthetic biology has yielded ever more complex genetic circuits able to perform sophisticated functions in response to specific signals. Yet, genetic circuits are not immediately transferable to an outside-the-lab setting where their performance is highly compromised. We propose introducing a scale step to the design-build-test workflow to include factors that might contribute to unexpected genetic circuit performance. As a proof-of-concept, we designed and tested a genetic circuit under different temperatures, mediums, inducer concentrations, and bacterial growth phases. We determined that the circuit’s performance is dramatically altered when these factors differ from the optimal lab conditions. Based on these results, a scaling effort, coupled with a learning process, proceeded to generate model predictions for the genetic circuit’s performance under untested conditions, which is currently lacking in synthetic biology application design. As the synthetic biology discipline transitions from proof-of-concept genetic programs to appropriate and safe application implementations, more emphasis on a scale step is needed to ensure correct and robust performances.