bluuebunny/crossref_metadata_2025_split huggingface dataset:
PandoraRL: DQN and Graph Convolution based ligand pose learning for SARS-COV1 Mprotease
Authors: Jose Justin , Alam Ujjaini , Arora Pooja , Singh Divye , Jatana Nidhi 
Published: June 2022

ABSTRACTThe ability to predict the correct ligand binding pose for proteinligand complex is vital for drug design. Recently several machine learning methods have suggested knowledge based scoring functions for binding energy prediction. In this study, we propose a reinforcement learning (RL) based model, PandoraRL, where the RL agent helps the ligand traverse to the optimal binding pose. The underlying representation of molecules utilizes generalized graph convolution to represent the protein ligand complex with various atomic and spatial features. The representation consists of edges formed on the basis of inter molecular interactions such as hydrogen bonds, hydrophobic interactions, etc, and nodes representing atomic features. This study presents our initial model which can train on a protein-ligand pair and predict optimal binding pose for a different ligand with the same protein. To the best of our knowledge, this is the first time an RL based approach has been put forward for predicting optimized ligand pose.CCS CONCEPTSComputing methodologies → Reinforcement learning.
Explainable deep graph learning accurately modeling the peptide secondary structure prediction
Authors: Jiang Yi , Wang Ruheng , Feng Jiuxin , Jin Junru , Liang Sirui , Li Zhongshen , Yu Yingying , Ma Anjun , Su Ran , Zou Quan , Ma Qin , Wei Leyi 
Published: June 2022

AbstractAccurately predicting peptide secondary structures remains a challenging task due to the lack of discriminative information in short peptides. In this study, we propose PHAT, a deep graph learning framework for the prediction of peptide secondary structures. The framework includes a novel interpretable deep hypergraph multi-head attention network that uses residue-based reasoning for structure prediction. Our algorithm can incorporate sequential semantic information from large-scale biological corpus and structural semantic information from multi-scale structural segmentation, leading to better accuracy and interpretability even with extremely short peptides. Our interpretable models are able to highlight the reasoning of structural feature representations and the classification of secondary substructures. We further demonstrate the importance of secondary structures in peptide tertiary structure reconstruction and downstream functional analysis, highlighting the versatility of our models. To facilitate the use of our model, we establish an online server which is accessible via http://inner.wei-group.net/PHAT/. We expect our work to assist in the design of functional peptides and contribute to the advancement of structural biology research.
Skeletal muscle lineage is dispensable for appendage regeneration in axolotl
Authors: Hu Yan , Pan Xiangyu , Shi Yu , Qiu Yuanhui , Wang Liqun , Murawala Prayag , Liu Yanmei , Xing Wanjin , Tanaka Elly M , Fei Ji-Feng 
Published: June 2022

AbstractRegeneration of a complex appendage structure such as limb requires hierarchical coordination of multiple types of tissues. Muscles, as one of the major cell masses in limbs, have been reported recently to be critical to guide other tissue regeneration in planaria, but its function and relationship to other cells in vertebrate complex regeneration have been unclear. Here, we use Pax7 mutant axolotls, in which the limb muscle is developmentally lost, to investigate limb regeneration in the absence of skeletal muscle. We find that the pattern of regenerated limbs is normal in Pax7 mutants compared to the controls. Lack of muscles do not affect the proliferation of fibroblasts, another major population in limbs. Furthermore, using single cell RNA-sequencing, we demonstrate that the cell type composition in completely regenerated limbs in Pax7 mutants is similar to that in the controls, except the lack of cell types in muscle lineage. Our study reveals skeletal muscle is not required for the guidance of complex tissue regeneration in axolotls, and provides new views of the tissue hierarchy in vertebrate appendage regeneration.
Transcriptomic analysis reveals hub genes and pathways in response to acetic acid stress in Kluyveromyces marxianus during high-temperature ethanol fermentation
Authors: Li Yumeng , Hou Shiqi , Ren Ziwei , Fu Shaojie , Wang Sunhaoyu , Chen Mingpeng , Dang Yan , Li Hongshen , Li Shizhong , Li Pengsong 
Published: June 2022

AbstractThe thermotolerant yeast Kluyveromyces marxianus has great potential for high-temperature ethanol fermentation, but it produces excess acetic acid during high-temperature fermentation, which inhibits ethanol production. The mechanisms of K. marxianus’s responses to acetic acid have not been fully understood. In this study, the transcriptomic changes of K. marxianus DMKU3-1042 resulted from acetic acid stress during high-temperature ethanol fermentation were investigated based on high-throughput RNA sequencing. We identified 611 differentially expressed genes (DEGs) under acetic acid stress (fold change > 2 or < 0.5, P-adjust <0.05), with 166 up-regulated and 445 down-regulated. GO terms and pathways enriched in these DEGs were identified. Protein-protein interaction (PPI) networks were constructed based on the interactions between proteins coded by the DEGs, and hub genes and key modules in the PPI networks were identified. The results in this study indicated that during high-temperature fermentation, acetic acid stress promoted protein catabolism but repressed protein synthesis, which affected the growth and metabolism of K. marxianus and led to the decrease of ethanol production. The findings in this study provide a better understanding of the response mechanism of K. marxianus to acetic acid stress, and provide a basis for subsequent increase of ethanol production by K. marxianus.
Modelling the mechanical cross-talk between cells and fibrous extracellular matrix using hybrid cellular Potts and molecular dynamics methods
Authors: Tsingos Erika , Bakker Bente Hilde , Keijzer Koen A.E. , Hupkes Hermen Jan , Merks Roeland M.H. 
Published: June 2022

AbstractThe mechanical interaction between cells and the extracellular matrix (ECM) is fundamental to coordinate collective cell behavior in multicellular tissues. Relating individual cell-level mechanics to tissue-scale collective behavior is an outstanding challenge which cell-based models such as the cellular Potts model (CPM) are well-positioned to address. These models generally represent the ECM with mean-field approaches, which assume substrate homogeneity. This assumption breaks down with fibrous ECM, which has non-trivial structure and mechanics. Here, we extend the CPM with a bead-spring chain model of ECM fiber networks modelled using molecular dynamics. We model contractile cells pulling with discrete focal adhesion-like sites on the ECM fiber network, and demonstrate agreement with experimental spatiotemporal fiber densification and displacement. We show that contractile cell forces propagate over multiple cell radii scaling with power law exponent of ≈ −0.5 typical of viscoelastic ECM. Further, we use in silico atomic force microscopy to measure local cell-induced network stiffening consistent with experiments. Our model lays the foundation to investigate how local and long-ranged cell-ECM mechanobiology contributes to multicellular morphogenesis.
Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance
Authors: Vaughn Justin N. , Branham Sandra E. , Abernathy Brian L. , Hulse-Kemp Amanda M. , Rivers Adam , Levi Amnon , Wechter William P. 
Published: June 2022

AbstractThe genomic sequences segregating in experimental populations are often highly divergent from the community reference and from one another. Such divergence is problematic under various short-read-based genotyping strategies. In addition, large structural differences are often invisible despite being strong candidates for causal variation. These issues are exacerbated in specialty crop breeding programs with fewer, lower-quality sequence resources. We examined the benefits of complete genomic information, based on long-read assemblies, in a biparental mapping experiment segregating at numerous disease resistance loci in the non-model crop, melon (Cucumis melo). We find that a graph-based approach, which uses both parental genomes, results in 19% more variants callable across the population and raw allele calls with a 2 to 3-fold error-rate reduction, even relative to single reference approaches using a parent genome. We show that structural variation has played a substantial role in shaping twoFusariumwilt resistance loci with known causal genes. We also report on the genetics of powdery mildew resistance, where copy number variation and local recombination suppression are directly interpretable via parental genome alignments. Benefits observed, even in this low-resolution biparental experiment, will inevitably be amplified in more complex populations.
Fitness seascapes are necessary for realistic modeling of the evolutionary response to drug therapy
Authors: King Eshan S. , Maltas Jeff , Weaver Davis T. , Barker-Clarke Rowan , Pelesko Julia , Dolson Emily , Scott Jacob G. 
Published: June 2022

ABSTRACTA persistent challenge in evolutionary medicine is predicting the evolution of drug resistance, which is complicated further when the drug concentration varies in time and space within a patient. Evolutionary trade-offs, or fitness costs of resistance, cause the evolutionary landscape to change dramatically as the drug selective pressure changes. In this work, we show how fitness seascapes, or collections of genotype-specific dose-response curves, more accurately describe dose-dependent evolution and the arrival of drug resistance. We measure a novel empirical fitness seascape inE. colisubject to cefotaxime, finding substantial growth rate penalties in exchange for drug resistance. In two computational experiments we show how the fitness seascape framework may be used to model evolution in changing environments. First, we show that the probability of evolutionary escape from extinction is dependent on the rate of environmental change, aligning with priorin vitroresults. Then, we simulate patients undergoing a daily drug regimen for an infection with varying rates of nonadherence. We find that early drug regimen adherence is critical for successfully eliminating the infection, lending evidence to a “two strike” model of disease extinction. Our work integrates an empirical fitness seascape into an evolutionary model with realistic pharmacological considerations. Future work may leverage this platform to optimize dosing regimens or design adaptive therapies to avoid resistance.
Ion exchange biomaterials to capture daptomycin and prevent resistance evolution in off-target bacterial populations
Authors: Yeh Shang-Lin , Narasimhalu Naveen , vom Steeg Landon G. , Muthami Joy , LeConey Sean , He Zeming , Pitcher Mica , Cassady Harrison , Morley Valerie J. , Cho Sung Hyun , Bator Carol , Koshani Roya , Woods Robert J. , Hickner Michael , Read Andrew F. , Sheikhi Amir 
Published: June 2022

AbstractDaptomycin (DAP), a cyclic anionic lipopeptide antibiotic, is among the last resorts to treat multidrug resistant (vancomycin resistant Enterococcus faecium or methicillin resistant Staphylococcus aureus) Gram-positive bacterial infections. DAP is administered intravenously and biliary excretion results in the introduction of DAP (∼5-10 % of the intravenous DAP dose) arriving in the gastrointestinal (GI) tract where it drives resistance evolution in off-target populations of Enterococcus faecium bacteria. Previously, we have shown that the oral administration of cholestyramine, an ion exchange biomaterial (IXB) sorbent, prevents DAP treatment from enriching DAP-resistance in populations of E. faecium shed from mice. Here, we engineer the biomaterial-DAP interfacial interactions to uncover the antibiotic removal mechanisms. The IXB-mediated DAP capture from aqueous media was measured in both controlled pH/electrolyte solutions and in simulated intestinal fluid (SIF) to uncover the molecular and colloidal mechanisms of DAP removal from the GI tract. Our findings show that the IXB electrostatically adsorbs the anionic antibiotic via a time-dependent diffusion-controlled process. Unsteady-state diffusion-adsorption mass balance describes the dynamics of adsorption well, and the maximum removal capacity is beyond the electric charge stoichiometric ratio because of DAP self-assembly. This study may open new opportunities for optimizing cholestyramine adjuvant therapy to prevent DAP resistance, as well as designing novel biomaterials to remove off-target antibiotics from the GI tract.TOC
A lipopolysaccharide-dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance
Authors: Warring Suzanne L. , Malone Lucia M. , Jayaraman Jay , Easingwood Richard A. , Rigano Luciano A. , Frampton Rebekah A. , Visnovsky Sandra B. , Addison Shea M. , Hernandez Loreto , Pitman Andrew R. , Acedo Elena Lopez , Kleffmann Torsten , Templeton Matthew D. , Bostina Mihnea , Fineran Peter C. 
Published: June 2022

SummaryBacterial pathogens are major causes of crop diseases, leading to significant production losses. For instance, kiwifruit canker, caused by the phytopathogen Pseudomonas syringae pv. actinidiae (Psa), has posed a global challenge to kiwifruit production. Treatment with copper and antibiotics, whilst initially effective, is leading to the rise of bacterial resistance, requiring new biocontrol approaches. Previously, we isolated a group of closely related Psa phages with biocontrol potential, which represent environmentally sustainable antimicrobials. However, their deployment as antimicrobials requires further insight into their properties and infection strategy. Here, we provide an in-depth examination of the genome of ΦPsa374-like phages and show that they use lipopolysaccharides (LPS) as their main receptor. Through proteomics and cryo-electron microscopy of ΦPsa374, we revealed the structural proteome and that this phage possess a T=9 capsid triangulation, unusual for myoviruses. Furthermore, we show that ΦPsa374 phage resistance arises in planta through mutations in a glycosyltransferase involved in LPS synthesis. Lastly, through in vitro evolution experiments we showed that phage-resistance is overcome by mutations in a tail fiber and structural protein of unknown function in ΦPsa374. This study provides new insight into the properties of ΦPsa374-like phages that informs their use as antimicrobials against Psa.Originality-Significance StatementThe rise of phytopathogen resistance to agrichemicals poses a significant threat to crop production, and requires urgent attention. The work presented here examines a phage genus, members of which utilize LPS as a receptor, and show potential as biocontrol agents of Psa. Studies in planta showed the development of Psa resistance to the phage, whilst maintaining bacterial virulence. This finding underscores the importance of examining phages in their ecological context for the informed design of phage cocktails that are effective in phytopathogen control.
A universal stress protein acts as a metabolic rheostat controlling carbon flux in mycobacteria
Authors: Lougheed Kathryn E. , Thomson Michael , Koziej Lukasz S. , Larrouy-Maumus Gerald , Williams Huw D 
Published: June 2022

AbstractUniversal stress proteins (USPs) are ubiquitous amongst prokaryotes and have empirically determined roles in adaptation to stress, while their specific biochemical function in cellular processes is opaque. The most frequently encountered USP is a small ~15kDa protein comprised of a single domain (PF00582). In Mycobacterium tuberculosis Rv1636 is the sole single domain protein amongst its 10 USPs. We were unable to delete rv1636 from M. tuberculosis, supporting previous data that it is essential for growth. We deleted its orthologue, MS3811, from M. smegmatis, and in exponential phase competition experiments we observed that the advantage switched between wildtype and the mutant depending on the growth environment. In rich medium the wildtype had the competitive advantage, but in a defined medium with a single carbon source the competitive advantage switched, with the mutant rapidly taking over the culture. We hypothesised the USP is regulating metabolic flux, with its deletion leading to increased flux and more rapid turn-over of central-carbon metabolites. We tested this by performing 13C-stable isotope tracing, using [U-13C6] glucose as sole carbon source for growth of the parental and deletion strains. The findings were unequivocal; deletion of the USP led to an increase in label incorporation in central carbon metabolites and a profound change in the isotopologue distribution. Furthermore, in vivo protein-crosslinking provided evidence that Rv1636 interacts directly with key central metabolic enzymes, including the glycolytic enzymes pyruvate kinase, pyruvate dehydrogenase, pyruvate synthase. We propose the mycobacterial single domain USP acts as a metabolic rheostat to regulate central carbon metabolism.ImportanceThere are more than 62,000 universal stress proteins (USPs) found mostly in prokaryotes, but very few examples where the role of a USP is unequivocally linked to a specific biological or biochemical function. For the first time we were able to assign a role in metabolic regulation to a bacterial single domain universal stress protein. We demonstrate a mycobacterial USP regulates flux through central catabolic pathways, and our evidence, based on 13C-stable isotope tracing, indicates that the USP acts as a brake on carbon flux, and we assign to it a role as a metabolic rheostat.
A two-step in vivo CRISPR screen unveils pervasive RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a therapeutic target
Authors: Vujovic Ana , de Rooij Laura P.M.H. , Chahi Ava Keyvani , Chen He Tian , Yee Brian , Loganathan Sampath K , Liu Lina , Chan Derek C.H. , Tajik Amanda , Tsao Emily , Moreira Steven , Joshi Pratik , Xu Joshua , Wong Nicholas , Zandi Sasan , Aigner Stefan , Dick John E. , Minden Mark D. , Schramek Daniel , Yeo Gene W. , Hope Kristin J. 
Published: June 2022

SUMMARYAcute myeloid leukemia (AML) progression and relapse is fueled by self-renewing leukemic stem cells (LSCs) whose molecular determinants have been difficult to discern from normal hematopoietic stem cells (HSCs) or to uncover in screening approaches focused on general AML cell properties. We have identified a unique set of RNA binding proteins (RBPs) that are enriched in human AML LSCs but repressed in HSCs. Using an in vivo two step CRISPR-Cas9-mediated screening approach to specifically score for cancer stem cell functionality, we found 32 RBPs essential for LSC propagation and self-renewal in MLL-AF9 translocated AML. Using knockdown or small molecule approaches we show that targeting key hit RBP ELAVL1 impaired LSC-driven in vivo leukemic reconstitution and selectively depleted primitive AML cells vs. normal hematopoietic stem and progenitors. Importantly, knockdown of Elavl1 spared HSCs while significantly reducing LSC numbers across genetically diverse leukemias. Integrative RNA-seq and eCLIP-seq profiling revealed hematopoietic differentiation, RNA splicing and mitochondrial metabolism as key features defining the leukemic ELAVL1-mRNA interactome with the mitochondrial import protein TOMM34 being a direct ELAVL1-stabilized target whose inhibition impairs AML propagation. Altogether, through the use of a stem cell-adapted in vivo CRISPR dropout screening strategy, this work demonstrates that a wide variety of post-transcriptionally acting RBPs are important regulators of LSC-survival and self-renewal and, as exemplified by ELAVL1, highlights their potential as therapeutic targets in AML.
Distinguishing biophysical stochasticity from technical noise in single-cell RNA sequencing usingMonod
Authors: Gorin Gennady , Pachter Lior 
Published: June 2022

AbstractWe present the Python packageMonodfor the analysis of single-cell RNA sequencing count data through biophysical modeling.Monodnaturally “integrates” unspliced and spliced count matrices, and provides a route to identifying and studying differential expression patterns that do not cause changes in average gene expression. TheMonodframework is open-source and modular, and may be extended to more sophisticated models of variation and further experimental observables.TheMonodpackage can be installed from the command line using pip install monod. The source code is available and maintained athttps://github.com/pachterlab/monod. A separate repository, which contains sample data and Python notebooks for analysis withMonod, is accessible athttps://github.com/pachterlab/monod_examples/. Structured documentation and tutorials are hosted athttps://monod-examples.readthedocs.io/.
Neural plate progenitors give rise to both anterior and posterior pituitary cells
Authors: Chen Qiyu , Leshkowitz Dena , Li Hanjie , van Impel Andreas , Schulte-Merker Stefan , Amit Ido , Rizzoti Karine , Levkowitz Gil 
Published: June 2022

SummaryThe pituitary is the master neuroendocrine gland, which regulates body homeostasis. It consists of the anterior pituitary/adenohypophysis (AH), which harbors hormones producing cells and the posterior pituitary/neurohypophysis (NH), which relays the direct passage of hormones from the brain to the periphery. It is widely accepted that the AH originates from the oral ectoderm (Rathke’s pouch) whereas the neural ectoderm contributes to the NH. Using single cell transcriptomics of the zebrafish pituitary we characterizedcyp26b1-positive pituicyte of the NH andprop1-positive adenohypophyseal progenitors. We found that these cell types expressed common markers implying lineage relatedness. Genetic tracing revealed that in contrast to the prevailing dogma, neural plate precursors of both zebrafish (her4.3+) and mouse (Sox1+) contribute to both the neurohypophyseal and adenohypophyseal cells. We further show that pituicytes andprop1+progenitors reside in close anatomical proximity and pituicyte-derived RA-degrading enzyme Cyp26b1 fine-tunes differentiation ofprop1+progenitors into hormone-producing cells. These results challenge the notion that AH cells are exclusively derived from non-neural ectoderm and demonstrate that a cross-talk between neuro- and adeno-hypophyseal cells fine-tunes the development of pituitary neuroendocrine cells.
Membrane compression by synaptic vesicle exocytosis triggers ultrafast endocytosis
Authors: Jing Haoyuan , Ogunmowo Tyler , Raychaudhuri Sumana , Kusick Grant F. , Imoto Yuuta , Li Shuo , Itoh Kie , Chapman Edwin R. , Ha Taekjip , Watanabe Shigeki , Liu Jian 
Published: June 2022

AbstractCompensatory endocytosis keeps the surface area of secretory cells constant following exocytosis. At chemical synapses, clathrin-independent ultrafast endocytosis maintains such homeostasis. This endocytic pathway is temporally and spatially coupled to exocytosis, initiating within 50 ms at the region immediately next to where vesicles fuse: the active zone. How synaptic vesicle exocytosis induces ultrafast endocytosis is unknown. Here, we demonstrate that actin filaments are enriched in the region surrounding active zone at mouse hippocampal synapses and that the membrane area conservation due to this actin corral is necessary for exo-endocytic coupling. Simulations suggest that flattening of fused vesicles exerts lateral membrane pressure in the plasma membrane against the actin corral, resulting in rapid formation of endocytic pits at the border between the active zone and the surrounding actin-enriched region. Consistent with our simulations, ultrafast endocytosis does not initiate when actin organization is disrupted, either pharmacologically or by ablation of the actin-binding protein Epsin1. These data suggest that endocytosis is mechanically coupled to exocytosis at synapses.