bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Protein Subcellular Localization Prediction with Structural Prediction & Graph Neural Networks
Authors: Dubourg-Felonneau Geoffroy , Abbasi Arash , Akiva Eyal , Lee Lawrence 
Published: December 2022

AbstractThe majority of biological functions are carried out by proteins. Proteins perform their roles only upon arrival to their target location in the cell, hence elucidating protein subcellular localization is essential for better understanding their function. The exponential growth in genomic information and the high cost of experimental validation of protein localization call for the development of predictive methods. We present a method that improves subcellular localization prediction for proteins based on their sequence by leveraging structure prediction and Graph Neural Networks. We demonstrate how Language Models, trained on protein sequences, and Graph Neural Networks, trained on protein’s 3D structures, are both efficient approaches for this task. They both learn meaningful, yet different representations of proteins; hence, ensembling them outperforms the reigning state of the art method. Our architecture improves the localization prediction performance while being lighter and more cost-effective.
Validation of six commercial antibodies for detection of heterologous and endogenous TRPM8 ion channel expression
Authors: Hernández-Ortego Pablo , Torres-Montero Remedios , de la Peña Elvira , Viana Félix , Fernández-Trillo Jorge 
Published: December 2022

AbstractTRPM8 is a non-selective cation channel expressed in primary sensory neurons and other tissues, including prostate and urothelium. Its participation in different physiological and pathological processes such as thermoregulation, pain, itch, inflammation and cancer has been widely described, making it a promising target for therapeutic approaches. The detection and quantification of TRPM8 seems crucial for advancing in the knowledge of the mechanisms under-lying its role in these pathophysiological conditions. Antibody-based techniques are commonly used for protein detection and quantification, although their performance with many ion channels, including TRPM8, is suboptimal. Thus, the search for reliable antibodies is of utmost importance. In this study, we characterized the performance of six TRPM8 commercial antibodies in three immunodetection techniques: western blot, immunocytochemistry and immunohistochemistry. Different outcomes were obtained for the tested antibodies; two of them proved to be successful detecting TRPM8 in the three approaches while, in the conditions tested, the other four were acceptable only for specific techniques. Considering our results, we offer some insight into the usefulness of these antibodies for detection of TRMP8 depending on the methodology of choice.
FBXO42activity is required to prevent mitotic arrest, spindle assembly checkpoint activation, and lethality in glioblastoma and other cancers
Authors: Hoellerbauer Pia , Kufeld Megan , Arora Sonali , Girard Emily J. , Herman Jacob A. , Olson James M. , Paddison Patrick J. 
Published: December 2022

AbstractGlioblastoma (GBM) is the most common and aggressive brain tumor in adults. To identify genes differentially required for the viability of GBM stem-like cells (GSCs), we performed functional genomic lethality screens comparing GSCs and control human neural stem cells. Among top scoring hits in a subset of GBM cells was the F-box-containing geneFBXO42, which was also essential in ∼15% of cell lines derived from a broad range of cancers. Mechanistic studies revealed that, in sensitive cells,FBXO42activity prevents chromosome alignment defects, mitotic cell cycle arrest, and cell death. The cell cycle arrest, but not the cell death, triggered byFBXO42inactivation could be suppressed by brief exposure to a chemical inhibitor of Mps1, a key spindle assembly checkpoint (SAC) kinase.FBXO42’s cancer-essential function requires its F-box and Kelch domains, which are necessary for FBXO42’s substrate recognition and targeting by SCF ubiquitin ligase complex. However, none of FBXO42’s previously proposed targets, including ING4, p53, and RBPJ, were responsible for the observed phenotypes. Instead, our results suggest thatFBOX42activity suppresses the accumulation of one or more proteins that perturb chromosome-microtubule dynamics in cancer cells, which, in turn, leads to induction of the SAC and cell death.
Hippocampal engram networks for fear memory recruit new synapses and modify pre-existing synapsesin vivo
Authors: Lee Chaery , Lee Byung Hun , Jung Hyunsu , Lee Chiwoo , Sung Yongmin , Kim Hyopil , Kim Jooyoung , Shim Jae Youn , Kim Ji-il , Choi Dong Il , Park Hye Yoon , Kaang Bong-Kiun 
Published: December 2022

SummaryAs basic units of neural networks, ensembles of synapses underlie cognitive functions like learning and memory. These synaptic engrams show elevated synaptic density among engram cells following contextual fear memory formation. Subsequent analysis of the CA3-CA1 engram synapse revealed larger spine sizes, as the synaptic connectivity correlated to the memory strength. Here, we elucidate the synapse dynamics between CA3 and CA1 by tracking identical synapses at multiple time points by adapting two-photon microscopy and dual-eGRASP techniquein vivo. After memory formation, synaptic connections between engram populations are enhanced in conjunction with synaptogenesis within the hippocampal network. However, extinction learning specifically correlated with the disappearance of CA3 engram to CA1 engram (E-E) synapses. We observed “newly formed” synapses near pre-existing synapses, which clustered CA3-CA1 engram synapses after fear memory formation. Overall, we conclude that dynamics at CA3 to CA1 E-E synapses are key sites for modification during fear memory states.HighlightsWe adapted four-color two-photon microscopy with dual-eGRASP for a longitudinal observation of synaptic connections between CA3 and CA1.Synaptogenesis according to fear memory formation was specifically observed in E-E synapses.Extinction learning significantly correlated with the disappearance of E-E synapses.Particular distribution pattern of newly formed E-E synapses was observed after memory formation.
Drug Resistance Mutations In Transplant Recipients With Suspected Resistance
Authors: González Irene , Tarragó David 
Published: December 2022

ABSTRACTResistant CMV infections are challenging complications after SOT and HSCT. Prompt recognition of ARMs is imperative for appropriate therapy. 108 plasma samples from 96 CMV+ transplant recipients with suspected resistance were analysed in CNM in a retrospective nationwide study from January 2018 to July 2022 for resistance genotyping. ARMs in UL97 and UL54 were found in 26.87 % (18/67) and 10.60 % (7/66) of patients, respectively. Patients’ ARM distribution in UL97 was as follows: L595S n=3; L595S/M460I n=1; L595S/N510S n=1; L595W n=1; C603W n=4; A594V n=3; A594E n=1; C607Y n=1; L397R/T409M/H411L/M460I n=1; L397I n=1; H520Q n=1; four patients showed ARMs in UL54 as well (F412C n=1; T503I n=2; P522S n=1), whereas three patients exhibited ARMs in UL54 only (L501I/T503I/L516R/A834P n=1; A987G n=2). L516R in UL54 and L397R/I and H411L in UL97 have been found for the first time in a clinical sample. L595S/W was the most prevalent ARM found to lend resistance to GCV. In UL54 all ARMs lent resistance to GCV and CDV. In addition, A834P, found in one patient, also lent resistance to FOS. CMV load did not differ significantly in patients with or without ARMs, and no differences were found either between patients with ARMs in UL97 or in UL97 and UL54. Despite extensive use of classical antivirals for the treatment of CMV infection after HSCT and SOT, ARMs occurred mainly in viral UL97 kinase, which suggests that CDV and mostly FOS continue to be useful alternatives to nucleoside analogues after genotypic detection of ARMs.
Modeling the Sequence Dependence of Differential Antibody Binding in the Immune Response to Infectious Disease
Authors: Chowdhury Robayet , Taguchi Alexander T. , Kelbauskas Laimonas , Stafford Philip , Diehnelt Chris , Zhao Zhan-Gong , Williamson Phillip C. , Green Valerie , Woodbury Neal W. 
Published: December 2022

AbstractPast studies have shown that incubation of human serum samples on high density peptide arrays followed by measurement of total antibody bound to each peptide sequence allows detection and discrimination of humoral immune responses to a wide variety of infectious disease agents. This is true even though these arrays consist of peptides with near-random amino acid sequences that were not designed to mimic biological antigens. Previously, this immune profiling approach or “immunosignature” has been implemented using a purely statistical evaluation of pattern binding, with no regard for information contained in the amino acid sequences themselves. Here, a neural network is trained on immunoglobulin G binding to 122,926 amino acid sequences selected quasi-randomly to represent a sparse sample of the entire combinatorial binding space in a peptide array using human serum samples from uninfected controls and 5 different infectious disease cohorts infected by either dengue virus, West Nile virus, hepatitis C virus, hepatitis B virus orTrypanosoma cruzi. This results in a sequence-binding relationship for each sample that contains the differential disease information. Processing array data using the neural network effectively aggregates the sequence-binding information, removing sequence-independent noise and improving the accuracy of array-based classification of disease compared to the raw binding data. Because the neural network model is trained on all samples simultaneously, the information common to all samples resides in the hidden layers of the model and the differential information between samples resides in the output layer of the model, one column of a few hundred values per sample. These column vectors themselves can be used to represent each sample for classification or unsupervised clustering applications such as human disease surveillance.Author SummaryPrevious work from Stephen Johnston’s lab has shown that it is possible to use high density arrays of near-random peptide sequences as a general, disease agnostic approach to diagnosis by analyzing the pattern of antibody binding in serum to the array. The current approach replaces the purely statistical pattern recognition approach with a machine learning-based approach that substantially enhances the diagnostic power of these peptide array-based antibody profiles by incorporating the sequence information from each peptide with the measured antibody binding, in this case with regard to infectious diseases. This makes the array analysis much more robust to noise and provides a means of condensing the disease differentiating information from the array into a compact form that can be readily used for disease classification or population health monitoring.
Synthetic extremophiles: Species-specific formulations for microbial therapeutics and beyond
Authors: Jimenez Miguel , L’Heureux Johanna , Kolaya Emily , Martin Kyle B. , Villaverde Zachary , Khazi-Syed Afeefah , Cao Qinhao , Muller Benjamin , Byrne James D. , Traverso Giovanni 
Published: December 2022

AbstractMicroorganisms have been used for millennia to produce food and medicine and are now being developed as products themselves to treat disease and boost crop production. However, as required for these new applications, maintaining high viability throughout manufacturing, transportation and use remains a significant challenge requiring sophisticated cold-chains and packaging. In fact, we found that commercial microbial products (probiotics) provide a poor solution to this challenge, in particular for key industrial organisms likeE. coli. To overcome this technological gap, we report the development of synthetic extremophiles of industrially important gram-negative bacteria (E. coliNissle 1917,Ensifer meliloti), gram positive bacteria (Lactobacillusplantarum) and yeast (Saccharomyces boulardii). Specifically, we developed a high throughput pipeline to define species-specific materials that allow these organisms to survive drying, elevated temperatures, organic solvents and even ionizing radiation. We enhanced the stability ofE.coliNissle 1917 by >4 orders of magnitude over commercial formulations and demonstrate the capacity to remain viable while undergoing tableting and pharmaceutical methodologies involving organic solvents. The development of synthetic materials-based enhanced stabilization stands to transform our capacity to apply micro-organisms in extreme environments including those found on Earth as well as in space.One-Sentence SummaryFragile therapeutic bacteria can be made to survive the manufacturing extremes normally reserved for small molecule drugs.
Analysis of prokaryotic genes in an impaired Great Lakes harbour reveals seasonal metabolic shifts and a previously undetected cyanobacterium
Authors: Palermo Christine N. , Fulthorpe Roberta R. , Saati Rosemary , Short Steven M. 
Published: December 2022

ABSTRACTAs primary drivers of organic matter re-mineralization and trophic carbon transfer, bacteria promote biogeochemical cycling and shape ecosystems globally. We studied bacterial communities spatially and seasonally in an impaired harbour of Lake Ontario by extracting and sequencing community DNA from water samples collected biweekly from different sites. Assembled contigs were annotated at the phylum level, and Cyanobacteria were further characterized at order and species levels. Actinobacteria were most abundant in early summer, while Cyanobacteria were dominant in mid-summer.Microcystis aeruginosaandLimnoraphis robustawere most abundant throughout the sampling period, expanding the documented diversity of Cyanobacteria in Hamilton Harbour. Functional annotations were performed using the MG-RAST pipeline and SEED database, revealing that genes for photosynthesis, nitrogen metabolism and aromatic compound metabolism varied in relative abundances over the season, while phosphorus metabolism remained consistent, suggesting that these genes remain essential despite fluctuating environmental conditions and community succession. We observed seasonal shifts from anoxygenic to oxygenic phototrophy, and from ammonia assimilation to nitrogen fixation, coupled with decreasing heterotrophic bacteria and increasing cyanobacteria relative abundances. Our data contribute important insights into bacterial taxa and functional potentials in Hamilton Harbour, revealing seasonal and spatial dynamics that can be used to inform ongoing remediation efforts.
Hepatocyte Growth Factor and β1-integrin signalling axis drives tunneling nanotube formation in A549 lung adenocarcinoma cells
Authors: Awanis Griselda , Raveenthiraraj Sathuwarman , Johnson Robert , Gavrilovic Jelena , Warren Derek , Sobolewski Anastasia 
Published: December 2022

AbstractTunneling nanotubes (TNTs) are thin cytoplasmic protrusions involved in long-distance cellular communication. The presence of TNTs has been foundin vivoandin vitrostudies in non-small cell lung cancer (NSCLC). Cancer cells transport a range of organelles and signalling molecules along TNTs, to confer a survival phenotype for the recipient cell, contributing toward chemoresistance and malignancy. Despite its important role in cancer progression, the molecular mechanisms underlying TNT formation is not well defined. Within the tumour microenvironment (TME) of NSCLC, hepatocyte growth factor (HGF) and its receptor, c-Met, are mutationally upregulated causing growth, and invasion. In this study, we report a novel crosstalk between HGF/c-Met and β1-integrin involved in the formation of functional TNTs in A549 cells. Through pharmacological inhibitor studies, we discovered Arp2/3 complex, MAPK and PI3K pathways were activated downstream of this crosstalk signalling axis. Furthermore, paxillin was recruited during this key process, localising at the protrusion site of HGF-induced TNTs, and therefore serving as the central link between the upstream and downstream regulators involved. Overall, these results demonstrate a novel strategy to inhibit TNT formation in NSCLC through targeting the HGF/c-Met and β1-integrin signalling axis, thus highlighting the importance of personalised multi-drug targeting in NSCLC.
Mannose-coupled AAV2: a second generation AAV vector for increased retinal gene therapy efficiency
Authors: Mével Mathieu , Pichard Virginie , Bouzelha Mohammed , Alvarez-Dorta Dimitri , Lalys Pierre-Alban , Provost Nathalie , Allais Marine , Mendes Alexandra , Landagaray Elodie , Ducloyer Jean-Baptiste , Galy Anne , Brument Nicole , Lefevre Gaëlle M. , Gouin Sébastien G. , Isiegas Carolina , Le Meur Guylène , Cronin Thérèse , Le Guiner Caroline , Weber Michel , Moullier Philippe , Ayuso Eduard , Deniaud David , Adjali Oumeya 
Published: December 2022

AbstractInherited retinal diseases are a leading and untreatable cause of blindness and are therefore candidate diseases for gene therapy. Recombinant vectors derived from adeno-associated virus (rAAV) are currently the most promising vehicles forin vivotherapeutic gene delivery to the retina. However, there is a need for novel AAV-based vectors with greater efficacy for ophthalmic applications, as underscored by recent reports of dose-related inflammatory responses in clinical trials of rAAV-based ocular gene therapies. Improved therapeutic efficacy of vectors would allow for decreases in the dose delivered, with consequent reductions in immune reactions. Here, we describe the development of new rAAV vectors using bioconjugation chemistry to modify the rAAV capsid, thereby improving the therapeutic index. Covalent coupling of a mannose ligand,viathe formation of a thiourea bond, to the amino groups of the rAAV capsid significantly increases vector transduction efficiency of both rat and nonhuman primate retinas. These optimized rAAV vectors have important implications for the treatment of a wide range of retinal diseases.
Identification of combinatorial colistin resistance mutations inShewanella algae
Authors: Huang Yao-Ting , Mao Yan-Chiao , Tseng Chien-Hao , Liu Chia-Wei , Liu Po-Yu 
Published: December 2022

AbstractBackgroundColistin is one of the last-line antimicrobial agents against drug-resistant gram-negative bacteria. Currently, little is known about the genetic mechanisms underlying colistin resistance inShewanella algae, partly due to complex epistatic interactions among multiple genes.Methodology/Principal FindingsThis study sequenced, assembled, and compared the genomes of 23 mcr-negative colistin-resistantShewanella algaefrom marine, clam, oyster, and human. Comparative genomics and computational approach were applied to find combinatorial mutations. A combination of three mutations (PmrB451, PmrE168, PmrH292) was found to be strongly associated with colistin resistance inShewanella algae.Conclusions/SignificanceThis study demonstrates a computational approach for identifying epistatic-interacted mutations.Author summaryShewanella algaeis an emerging pathogen related to Neglected Tropical Diseases (NTDs), including cobra-bite wound infections, marine injuries or ingestion of contaminated seafood.Shewanella algaeis intrinsic resistant to various classes of β-lactams. Additionally, growing resistance to colistin inmcr-negativeShewanella algaefurther limits therapeutic options, especially in resource-limited regions. Currently, little is known about the genetic mechanisms underlying colistin resistance inShewanella algae, partly due to complex epistatic interactions among multiple genes. We conduct comparative genomics to identify combinatorial colistin resistance mutations inmcr-negative colistin-resistantShewanella algaeand a combination of three mutations (PmrB451, PmrE168, PmrH292) is strongly associated with colistin-resistance.
Competition between myosin II and βH-Spectrin regulates cytoskeletal tension
Authors: Ibar Consuelo , Chinthalapudi Krishna , Heissler Sarah M. , Irvine Kenneth D. 
Published: December 2022

ABSTRACTSpectrins are membrane cytoskeletal proteins generally thought to function as heterotetramers comprising two ⍺-spectrins and two β-spectrins. They influence cell shape and Hippo signaling, but the mechanism by which they influence Hippo signaling has remained unclear. We have investigated the role and regulation of theDrosophilaβ-heavy Spectrin (βH-Spectrin, encoded by thekarstgene) in wing imaginal discs. Our results establish that βH-Spectrin regulates Hippo signaling through the Jub biomechanical pathway due to its influence on cytoskeletal tension. While we find that ⍺-Spectrin also regulates Hippo signaling through Jub, unexpectedly, we find that βH-Spectrin localizes and functions independently of ⍺-Spectrin. Instead, βH-Spectrin co-localizes with and reciprocally regulates and is regulated by myosin. In vivo and in vitro experiments support a model in which βH-Spectrin and myosin directly compete for binding to apical F-actin. This competition can explain the influence of βH-Spectrin on cytoskeletal tension and myosin accumulation. It also provides new insight into how βH-Spectrin participates in ratcheting mechanisms associated with cell shape change.
Quantification of the diversity sampling bias resulting from rice root bacterial isolation on popular and nitrogen-free culture media, using 16S amplicon barcoding
Authors: Sondo Moussa , Wonni Issa , Klonowska Agnieszka , Koïta Kadidia , Moulin Lionel 
Published: December 2022

AbstractCulturing bacteria from plant material is well known to introduce a strong bias compared to the real diversity present in the original samples. This bias is related to cultivability of bacteria, the chemical composition of media and culture conditions. The bias of recovery is often observed but was never quantified on different media using an amplicon barcoding approach comparing plant microbiota DNA extractions versus DNA extracted from serial dilutions of the same plant tissues grown on bacterial culture media. In this study, we i) quantified the culturing diversity bias using 16S amplicon barcode sequencing by comparing a culture-dependent approach (CDA) on rice roots on four popular bacterial media (Tryptone Soybean Agar-TSA-at two concentrations, 10% and 50%; a plant-based media with rice flour; Norris Glucose Nitrogen Free Medium-NGN; and Nitrogen Free -NFb) versus a culture-independent approach (CIA) assessed from DNA extracted directly on root and rhizosphere samples; ii) assessed enriched and missing taxa detected on the different media; iii) use biostatistics functional predictions to predict which metabolic profiles are enriched in the CDA and CIA. A comparative analysis of the two approaches revealed that among the 22 phyla present in the microbiota of the studied rice root samples, only five were present on the culture media approach (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicrobia). TheProteobacteriaphylum was the most abundant in all cultured media samples, showing a high enrichment of gamma-Proteobacteria. The diversity of the combined culture media represented about 1/3 of the diversity of the total microbiota, and its genus diversity and frequency was documented. The functional prediction tool (PiCrust2) detected an enrichment of nitrogenase enzyme in bacterial taxa sampled from Nitrogen-free media, validating its predictive capacity. Further functional predictions also showed that the CDA missed mostly anaerobic, methylotrophic, methanotrophic and photosynthetic bacteria compared to the culture independent approach, delivering valuable insights to design ad-hoc culture media and conditions to increase cultivability of the rice-associated microbiota.