bluuebunny/crossref_metadata_2025_split huggingface dataset:
One-pot Golden Gate Assembly of an avian infectious bronchitis virus reverse-genetics system
Authors: Bilotti Katharina , Keep Sarah , Sikkema Andrew P. , Pryor John M. , Kirk James , Foldes Katalin , Doyle Nicole , Wu Ge , Freimanis Graham , Dowgier Giulia , Adeyemi Oluwapelumi , Tabatabaei S. Kasra , Lohman Gregory J.S. , Bickerton Erica 
Published: November 2023

AbstractAvian infectious bronchitis is an acute respiratory disease of poultry of particular concern for global food security. Investigation of Infectious Bronchitis Virus (IBV), the causative agent of avian infectious bronchitis, via reverse genetics enables deeper understanding of virus biology and a rapid response to emerging variants. Classic methods of reverse genetics for IBV can be time consuming, rely on recombination for the introduction of mutations, and, depending on the system, can be subject to genome instability and unreliable success rates. In this study, we have applied data-optimized Golden Gate Assembly design to create a rapidly executable, flexible, and faithful reverse genetics system for IBV. The IBV genome was divided into 12 fragments at high-fidelity fusion site breakpoints. All fragments were synthetically produced and propagated inE. coliplasmids, amenable to standard molecular biology techniques for DNA manipulation. The assembly can be carried out in a single reaction, with the products used directly in subsequent viral rescue steps. We demonstrate the use of this system for generation of point mutants and gene replacements. This Golden Gate Assembly-based reverse genetics system will enable rapid response to emerging variants of IBV, particularly important to vaccine development for controlling spread within poultry populations.
Identification and characterization of new structural scaffolds modulating the activity ofMycobacterium tuberculosisdihydroneopterin aldolase (FolB)in vitro
Authors: Falcão Virginia Carla de Almeida , Czeczot Alexia de Matos , Alam Mohammad Maqusood , Park Kyu-Ho Paul , Heo Jinyeong , Woo Minjeong , Camini Ana Micaela , Timmers Luis Fernando Saraiva Macedo , Shum David , Perelló Marcia Alberton , Basso Luiz Augusto , Machado Pablo , Bizarro Cristiano Valim , Delorme Vincent 
Published: November 2023

AbstractAntifolates were among the first broad-spectrum compounds used as antimycobacterial agents and can still be of use when no other therapeutic options are available. The discovery of compounds targeting this essential pathway could lead to new therapeutic agents to treat tuberculosis (TB). In particular, the enzyme required for the conversion of 7,8-dihydroneopterin (DHNP) to 6-hydroxymethyl-7,8-dihydropterin (HP) and glycolaldehyde (GA) in the folate pathway (MtbFolB, a dihydroneopterin aldolase - DHNA, EC 4.1.2.25), has received little attention as a potential drug target. Here, we conducted a small-scale diversity screening to identifyMtbFolB inhibitors using a microplate-based enzyme inhibition assay. About 6,000 compounds were assembled for the screening and 19 hits were identified, spanning 5 independent clusters. These compounds were tested in dose-response studies and active compounds selected for kinetic inhibition and time-dependent inhibition studies, leading to compounds with IC50values ranging from 2.6 to 47 µM. A preliminary structure activity analysis was performed, revealing that bi-sulfonamide compounds could be explored for further optimizations. Docking studies highlighted two modes of binding for pyrazol-3-one compounds and, for the sulfonamide series, indicated several interactions with the catalytic Tyrosine-54 (Tyr54D) and Lysine-99 (Lys99A) residues ofMtbFolB. The sulfonamide compound13represents the first identified compound directed againstMtbFolB with an antimycobacterial activity.
Stable long-term individual variation in chimpanzee technological efficiency
Authors: Berdugo S. , Cohen E. , Davis A. J. , Matsuzawa T. , Carvalho S. 
Published: November 2023

AbstractUsing tools to access hard-to-reach and high-quality resources, such as termites, honey, and nuts, initiated a fundamental adaptive shift in human and nonhuman primate cognitive and behavioural evolution. Variation in the efficiency of extracting calorie-rich and nutrient-dense resources directly impacts energy expenditure, and potentially has significant repercussions for cultural transmission where model selection biases are employed during skill acquisition. Assessing variation in efficiency is key to understanding the evolution of complex behavioural traits in primates. Yet, individual-level differences beyond age- and sex-class in primate extractive foraging efficiency have never been investigated. Here, we used 25 years (1992– 2017) of video data of the Bossou chimpanzee community (Guinea), to investigate whether individual differences in nut-cracking efficiency exist across the life span of chimpanzees aged ≥ 6 years. Data from 3,882 oil-palm nut-cracking bouts from over 800 hours of observation were collected. We found long-term stable and reliable individual differences in four (out of five) measures of efficiency. We found no sex effect, challenging previous research on a female bias in chimpanzee tool use. These life-long differences in extractive foraging impacts daily energy budgets, which potentially have significant individual fitness and life history consequences. Additionally, the establishment of long-term individual variation in chimpanzee stone tool use has implications for interpreting archaeological records of hominins. Our findings highlight the importance of longitudinal data from long-term field sites when investigating underlying cognitive and behavioural diversity across individual lifespans and between populations.
The transcriptomic and proteomic ramifications of segmental amplification
Authors: Fritts Ryan K. , Ebmeier Christopher C. , Copley Shelley D. 
Published: November 2023

AbstractGene amplification can drive adaptation by rapidly increasing the cellular dosage of critical gene products. Segmental amplifications often encompass large genomic regions surrounding the gene(s) under selection for higher dosage. Overexpression of co-amplified neighboring genes imposes a substantial metabolic burden. While compensatory mutations can decrease inappropriate overexpression of co-amplified genes, it takes time for such mutations to arise. The extent to which intrinsic regulatory mechanisms modulate expression of co-amplified genes in the immediate aftermath of segmental amplification is largely unknown. To address the collateral effects of segmental amplification, we evolved replicate cultures of anEscherichia colimutant under conditions that select for higher dosage of an inefficient enzyme whose weak activity limits growth rate. Segmental amplifications encompassing the gene encoding the weak-link enzyme arose in all populations. Amplicons ranged in size (9 to 125 kb) and copy number (2 to 12 copies). We performed RNA-seq and label-free proteomics to quantify expression of amplified genes present at 2, 6, and 12 copies. mRNA expression generally scales with gene copy number, but protein expression scales less well with both gene copy number and mRNA expression. We characterize the molecular mechanisms underlying discrepancies between gene copy number and expression for several cases. We also show that segmental amplifications can have system-wide consequences by indirectly altering expression of non-amplified genes. Our findings indicate that the fitness benefit derived from segmental amplification depends on the combined effects of amplification size, gene content, and copy number as well as collateral effects on non-amplified genes.Significance StatementGene amplification frequently drives rapid adaptation when organisms are challenged by harsh conditions. However, gene amplification rarely amplifies only the gene(s) under selection for higher dosage. Segmental amplifications often include many co-amplified neighbor genes. Because segmental amplifications can reach very high copy number, overexpression of co-amplified genes can impose an energetic burden and perturb physiology, yet this aspect of gene amplification has received little attention. Here, we performed transcriptomic and proteomic analysis of laboratory-evolvedEscherichia colistrains containing large, high-copy-number amplifications. We found that mRNA levels, but often not protein levels, scale well with gene copy number. We identified amplified genes that exhibit discrepancies between gene copy number and mRNA/protein expression and examine the molecular mechanisms underlying these discrepancies.
Epstein-Barr virus-encoded BART9 and BART15 miRNAs are elevated in exosomes of cerebrospinal fluid from relapsing-remitting multiple sclerosis patients
Authors: Mohammadinasr Mina , Montazersaheb Soheila , Hosseini Vahid , Kahroba Houman , Talebi Mahnaz , Molavi Ommoleila , Ayromlou Hormoz , Hejazi Mohammad Saeid 
Published: November 2023

AbstractEpstein-Barr virus (EBV) infection is approved as the main environmental trigger of multiple sclerosis (MS). In this path, we quantified EBV-encoded BART9-3p and BART15 miRNAs in exosomes of cerebrospinal fluid (CSF) of untreated relapsing-remitting MS (RRMS) patients in comparison with the control group. Interestingly, patients displayed significant upregulation of BART9-3p (18.4-fold) and BART15 (3.1-fold) expression in CSF exosomes. Moreover, the expression levels of miR-21-5p and miR-146a-5p were found to be significantly elevated in the CSF samples obtained from the patient group in comparison to those obtained from the HC group. The levels of Interferon gamma (IFN-γ), interleukin-1β (IL-1β), interleukin- 6 (IL-6), interleukin-17 (IL-17), interleukin-23 (IL-23), transforming growth factor beta (TGF- β), and tumor necrosis factor alpha (TNF-α) were observed to be significantly elevated in the serum and CSF exosomes of the patients. The highest increase was observed in TGF-β (8.5- fold), followed by IL-23 (3.9-fold) in CSF exosomes. These findings are in agreement with the association between EBV infection and inflammatory cytokines induction. Furthermore, the ratios of TGF-β:TNF-α and TGF-β:IFN-γ attained values of 4 to 16.4 and 1.3 to 3.6, respectively, in the CSF exosomes of the patients, in comparison to those of the control group. Remarkable stimulation of EBV BART9-3p, BART15 miRNAs, and inflammatory cytokines expression in CSF exosomes confers a substantial link between EBV in MS onset and also the infection-to-MS transition.
FrameDiPT: SE(3) Diffusion Model for Protein Structure Inpainting
Authors: Zhang Cheng , Leach Adam , Makkink Thomas , Arbesú Miguel , Kadri Ibtissem , Luo Daniel , Mizrahi Liron , Krichen Sabrine , Lang Maren , Tovchigrechko Andrey , Lopez Carranza Nicolas , Şahin Uğur , Beguir Karim , Rooney Michael , Fu Yunguan 
Published: November 2023

AbstractProtein structure prediction field has been revolutionised by deep learning with protein folding models such as AlphaFold 2 and ESMFold. These models enable rapidin silicoprediction and have been integrated intode novoprotein design and protein-protein interaction (PPI) prediction. However, biologically relevant features dependent on conformational distributions cannot be estimated with these models. Diffusion models, a novel class of generative models, have been developed to learn conformational distributions and applied tode novoprotein design. Limited work has been done on protein structure inpainting, where a masked section is recovered by simultaneously conditioning on its sequence and the rest of the structure. In this work, we proposeFrameDiffinPainTing (FrameDiPT), a generalised model for protein inpainting. This is important for T-cells given the hyper-variability of the complementarity determining region (CDR) loops. We evaluated the model on CDR loop design for T-cell receptors and achieved comparable prediction accuracy to ProteinGenerator and RFdiffusion with limited training data and learnable parameters. Different from deterministic structure prediction models, FrameDiPT captures the conformational distribution at different regions and binding states, highlighting a key advantage of generative models. The model and inference code have been released1.
Exploring TAS2R46 Biomechanics through Molecular Dynamics and Network Analysis
Authors: Cannariato Marco , Fanunza Riccardo , Zizzi Eric A. , Miceli Marcello , Di Benedetto Giacomo , Deriu Marco A. , Pallante Lorenzo 
Published: November 2023

AbstractUnderstanding the intricate interplay between structural features and signal-processing events is crucial for unravelling the mechanisms of biomolecular systems. G protein-coupled receptors (GPCRs), a pervasive protein family in humans, serve a wide spectrum of vital functions. TAS2Rs, a subfamily of GPCRs, play a primary role in recognizing bitter molecules and triggering events leading to the perception of bitterness, a crucial defence mechanism against spoiled or poisonous food. Beyond taste, TAS2Rs function is associated with many diseases as they are expressed in several extra-oral tissues. Since the precise mechanism of TAS2R activation is poorly understood, this work aims to characterize the mechanisms underlying the signal transduction on the recently experimentally solved human TAS2R46 bitter taste receptor using molecular dynamics simulations coupled with network-based analysis. The results show that the allosteric activation of the receptor is associated with more correlated dynamics of the receptor and the formation of an interaction between two helices which mainly convey the signal transferring from the extracellular to the intracellular region. By elucidating the hallmarks of the allosteric network of TAS2R46 under varying conditions (ligand-bound, ligand-free, and transition states), this study has enabled the identification of the unique functional mechanisms of this receptor, thereby establishing a foundation for a more profound characterisation of this intriguing class of receptors.HighlightsThe dynamics of TAS2R46 in different states were studied through molecular dynamics and network analysis.The presence of the bitter agonist increases intra-protein correlations.TM3 and TM6 helices mediate the allosteric network in Holo TAS2R46.The rotation of Y2416.48residue is pivotal in the allosteric network for the Holo TAS2R46.
AOPWIKI-EXPLORER: An Interactive Graph-based Query Engine leveraging Large Language Models
Authors: Kumar Saurav , Deepika Deepika , Slater Luke T , Kumar Vikas 
Published: November 2023

AbstractBackgroundAdverse Outcome Pathways (AOPs) provide a basis for non-animal testing, by outlining and encoding the cascade of molecular and cellular events initiated upon stressor exposure, leading to adverse effects. AOPs are therefore considered an integral part of the New Approach Methodology (NAMs) to human health risk assessment. Over the last few years, the scientific community has shown immense interest in developing AOPs with crowdsourcing, with the results of those efforts being archived in the AOP wiki: a centralized repository coordinated by the OECD, which hosts nearly 512 AOPs. However, the AOP-wiki platform currently lacks a versatile querying system, which would enable developers to integrate and explore the AOP network data in a manner that would permit their practical use in risk assessment.ImplementationThis work proposes to expose the full potential of the AOP wiki archive by adapting its data into a Labeled Property Graph (LPG) database. In addition, the solution provides both database-specific query and natural language query interfaces to support retrieval and integration of the graph data, including the ability to chain stepwise queries. To evaluate the platform, a case study is presented, with three levels of use case scenarios (simple, moderate, and complex query). This tool is freely available on GitHub (InSilicoVida/AOPWiki-explorer) for wider community usability and further enhancement.ConclusionsThe presented query engine increases the potential of AOP exploration, by reducing the time, human resources, and technical ability needed to make practical use of the data they contain. Also, its dynamic prompt generation capability, will lead to precise query generation as the interaction increases. We, therefore, anticipate that the approach will be integral to the future realisation of new approach methodologies in chemical risk assessment.
A deep-learning-based screening platform in aging-relevant human motor neurons to identify therapeutic compounds for amyotrophic lateral sclerosis
Authors: Jalnapurkar Bhagawati , Le David , Shainin William , Zarcone Ryan , Bhatnagar Rajat , Chin Joshua , Corbin Conor , Curt Charles , Hodge Brian , Martinez Fernando , Mikita Thomas , Pipathsouk Anne , Rosen Jesse , Rando Thomas A. , Rodgers Joseph T. , Linsley Jeremy W. 
Published: November 2023

AbstractAge is the primary risk factor for most neurodegenerative diseases including amyo-trophic lateral sclerosis (ALS). Despite the clear importance of age on the development and progression of ALS, age is rarely considered a factor in cellular or animal models of ALS. The recent advent of direct reprogramming methodologies, whereby somatic cells such as fibroblasts can be converted into neurons while retaining the age signature of the host, has facilitated the study of age-relevant human cellsin vitrofor the first time. Despite the promise of this technology, age is a complex, multidimensional, and dy-namic phenotype that makes the interpretation of the interplay between age and dis-ease a great challenge. To circumvent these challenges, we developed a screening platform for directly reprogrammed neurons in an age-relevant human cellular model to better model and identify disease-modifying targets and pathways for ALS. This plat-form uses deep learning image analysis to screen compounds for efficacy against ALS-associated cellular phenotypes and efficiently classifies ALS-like phenotypic signatures as well as predicts the age of the original fibroblast donor. Notably, our work identified NCB-0846, a TNIK/MAP4K7 inhibitor, as a novel compound with the ability to revert ALS-like phenotypes. Moreover, we show that chronic dosing of NCB-0846 in the SOD1G93A mouse model of ALS significantly reduced serum neurofilament-L levels. Our findings establish the power of a platform that combines direct reprogramming of human cells and deep learning as a powerful tool for combatting aging and age-related diseases.
Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2
Authors: Nguyen Ai , Zhao Huaying , Myagmarsuren Dulguun , Srinivasan Sanjana , Wu Di , Chen Jiji , Piszczek Grzegorz , Schuck Peter 
Published: November 2023

AbstractGenetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also exhibiting functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
Unicellular life balances asymmetric allocation and repair of somatic damage representing the origin of r/K selection
Authors: Biba Dmitry A. , Wolf Yuri I. , Koonin Eugene V. , Rochman Nash D. 
Published: November 2023

AbstractOver the course of multiple divisions, cells accumulate diverse non-genetic, somatic damage including misfolded and aggregated proteins and cell wall defects. If the rate of damage accumulation exceeds the rate of dilution through cell growth, a dedicated mitigation strategy is required to prevent eventual population collapse. Strategies for somatic damage control can be divided into two categories, asymmetric allocation and repair, which are not, in principle, mutually exclusive. Through mathematical modelling, we identify the optimal strategy, maximizing the total cell number, over a wide range of environmental and physiological conditions. The optimal strategy is primarily determined by extrinsic (damage-independent) mortality and the physiological model for damage accumulation that can be either independent (linear) or increasing (exponential) with respect to the prior accumulated damage. Under the linear regime, the optimal strategy is either exclusively repair or asymmetric allocation whereas under the exponential regime, the optimal strategy is mixed. Repair is preferred when extrinsic mortality is low, whereas at high extrinsic mortality, asymmetric damage allocation becomes the strategy of choice. We hypothesize that optimization over somatic damage repair and asymmetric allocation in early cellular life forms gave rise to therandKselection strategies.
Identification of a highly drought-resistantpp7l hda6mutant
Authors: Xu Duorong , Leister Dario , Kleine Tatjana 
Published: November 2023

AbstractPlants have evolved efficient strategies to cope with drought stress, including stomata closure, significant changes in nuclear gene expression, and epigenetic mechanisms. Previously, we identifiedArabidopsis thalianaPROTEIN PHOSPHATASE7-LIKE (PP7L) as an extrachloroplastic protein that promotes chloroplast development and high light, and salt tolerance. Here, we demonstrate that thepp7lmutant can withstand prolonged periods of drought stress. Interestingly, chloroplast development inpp7lrecovers under drought conditions, despite growth of the mutant is impaired under normal growth conditions. To assess the (post)transcriptional changes occurring in thepp7lmutant under different durations of drought exposure, we used long non-coding RNA-sequencing. Compared to the previously reported drought-responsive changes in the wild type, the drought-responsive changes detected in thepp7lmutant were negligible. Our analysis of data generated in this study and previously motivated us to create app7l hda6mutant, which exhibits remarkable drought resistance. Notably, the growth penalty associated withpp7lwas alleviated in the double mutant, ruling out a dwarf effect on the drought-tolerant trait of this genotype.