bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coevolution in Small Heat Shock Protein 1 (HSPB1) is Promoted by Interactions between the Alpha-Crystallin Domain and the Disordered Regions
Authors: Racigh Vanesa , Rodriguez Sawicki Luciana , Bravo Facundo Nicolas Eric , Fornasari Maria Silvina 
Published: December 2024

AbstractHuman HSPB1, a member of the small heat shock protein (sHSP) family, functions as an ATP-independent molecular chaperone crucial for protein quality control and is implicated in several pathologies, including Charcot-Marie-Tooth neuropathy. This study investigates the coevolution of the disordered N-terminal and C-terminal regions (NTR and CTR) with the structured Alpha-Crystallin domain (ACD) of human HSPB1, focusing on interactions that regulate its chaperone activity.Using a manually curated dataset of HSPB1 orthologs, the composition of critical motifs within the NTR (6VPFSLL11) and CTR (179ITIPV183) that interact with the ACD was analyzed and evolutionary rates per site for the human HSPB1 sequence were estimated. Additionally, structural modeling with AlphaFold 2 was employed to assess the prevalence of these contacts in human HSPB1 models.The results reveal that while the disordered regions globally evolve faster than the structured ACD, specific residues within the6VPFSLL11and179ITIPV183motifs exhibit reduced evolutionary rates, reflecting evolutionary constraints imposed by the conservation of the protein’s function. Structural modeling further indicates that coevolutionary-like information about the interaction between the6VPFSLL11motif and the ACD is encoded in the multiple sequence alignment used by Alphafold 2.Altogether, these findings suggest that the disordered regions and the ACD of human HSPB1 likely coevolved, preserving interactions crucial for its chaperone activity self-regulation. This evolutionary mechanism may also be extended to other sHSP featuring interacting motifs in the NTR, CTR, or both, and provides a framework to elucidate why pathogenic variants occurring in regions involved in these contacts contribute to disease.
OST Catalytic Subunit Redundancy Enables Therapeutic Targeting of N-Glycosylation
Authors: Baro Marta , Lee Hojin , Kelley Vanessa , Lou Rongliang , Phoomak Chatchai , Politi Katerina , Zeiss Caroline J. , Van Zandt Michael , Contessa Joseph N. 
Published: December 2024

ABSTRACTProtein asparagine (N)-glycosylation, which promotes folding and trafficking of cell surface receptors such as the EGFR, has not been considered a viable target in oncology due to the essential and non-redundant enzymatic activities required for glycan synthesis and transfer. In mammals an exception to this rule is the presence of the oligosaccharyltransferase (OST) catalytic subunit paralogs, STT3A and STT3B. Here we delineate the chemical biology of OST inhibitors and develop an approach for limited inhibition of N-glycosylation optimized for downstream effects on EGFR. Small molecules with enhanced pharmacokinetic properties and preferences for STT3A or STT3B were synthesized, characterizedin vitro, and advanced toin vivotesting. The lead from this series, NGI-189, causes tumor regression or growth delay of patient derived and TKI resistant EGFR-mutant lung cancer xenografts without toxicity. Together these results suggest that bioavailable OST inhibitors can be developed as therapeutic agents for oncology.SUMMARYA mechanistic approach for partial inhibition of N-glycosylation delivers small molecules with anti-tumor activity in EGFR mutant NSCLC.
Evolutionary Constraints on Positional Sequence, Collective Properties and Sequence Style of Tropoelastin Dictated by Fundamental Requirements for Formation and Function of the Extracellular Elastic Matrix
Authors: Keeley Fred W. 
Published: December 2024

AbstractElastin is an unusual extracellular matrix protein responsible for the properties of extension and energy-efficient elastic recoil of large blood vessels, heart valves, lung parenchyma and many other vertebrate tissues requiring such resilience. Polymeric elastin is assembled from monomeric tropoelastin by a process involving liquid-liquid phase separation, followed by maturation into an extended elastic matrix, covalently cross-linked through the side chains of lysine residues in the protein and producing a robust biomaterial with the structural integrity to withstand hundreds of millions of cycles of extension and recoil without mechanical failure. Elastin functions as an entropic elastomer, whose properties are the direct result of the inability of the protein to fold into a fixed, stable structure.Previous investigations of how the unusual properties of polymeric elastin arise from the sequence of tropoelastin have depended primarily on modeling using molecular biological and biophysical methodologies. This study takes a unique alternative approach, using a well-curated database of tropoelastin sequences from more than 80 representative species of Amniotes to identify characteristics that are conserved over more than 300 million years of evolution in order to provide assembly and conformational flexibility requirements of elastins.Conserved characteristics included preservation not only of regions of linear or positional sequence, but also of collective or compositional characteristics, derived from the sequence but not strictly dependent on positional sequence. A plausible overall consensus sequence for Amniote tropoelastins allowed quantification of residue-by-residue, domain-by-domain and region-by-region levels of sequence conservation, identifying distinct regions of high and low positional sequence conservation. Regions of low positional sequence conservation nevertheless maintained a recognizable, low complexity sequence style characterized by tandem repeats and partial repeats of short, non-polar motifs. Analysis of these motifs indicated hPGhGG, with numerous mutations, insertions and deletions, as the underlying repeating unit in all Amniote tropoelastins.Together these data identify significant evolutionary constraints dictated by fundamental requirements for formation and functionality of the extracellular elastin matrix. Mutations/polymorphisms in human tropoelastin affecting such well-conserved characteristics might be expected to have phenotypic consequences.
Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients
Authors: Randolph Haley E , Aguirre-Gamboa Raúl , Brunet-Ratnasingham Elsa , Nakanishi Tomoko , Locher Veronica , Ketter Ellen , Brandolino Cary , Larochelle Catherine , Prat Alexandre , Arbour Nathalie , Dumaine Anne , Finzi Andrés , Durand Madeleine , Richards J Brent , Kaufmann Daniel E , Barreiro Luis B 
Published: December 2024

AbstractGenome-wide association studies performed in patients with coronavirus disease 2019 (COVID-19) have uncovered various loci significantly associated with susceptibility to SARS-CoV-2 infection and COVID-19 disease severity. However, the underlyingcis-regulatory genetic factors that contribute to heterogeneity in the response to SARS-CoV-2 infection and their impact on clinical phenotypes remain enigmatic. Here, we used single-cell RNA-sequencing to quantify genetic contributions tocis-regulatory variation in 361,119 peripheral blood mononuclear cells across 63 COVID-19 patients during acute infection, 39 samples collected in the convalescent phase, and 106 healthy controls. Expression quantitative trait loci (eQTL) mapping across cell types within each disease state group revealed thousands ofcis-associated variants, of which hundreds were detected exclusively in immune cells derived from acute COVID-19 patients. Patient-specific genetic effects dissipated as infection resolved, suggesting that distinct gene regulatory networks are at play in the active infection state. Further, 17.2% of tested loci demonstrated significant cell state interactions with genotype, with pathways related to interferon responses and oxidative phosphorylation showing pronounced cell state-dependent variation, predominantly in CD14+monocytes. Overall, we estimate that 25.6% of tested genes exhibit gene-environment interaction effects, highlighting the importance of environmental modifiers in the transcriptional regulation of the immune response to SARS-CoV-2. Our findings underscore the importance of expanding the study of regulatory variation to relevant cell types and disease contexts and argue for the existence of extensive gene-environment effects among patients responding to an infection.
Contact Lens Wear Alters Transcriptional Responses toPseudomonas aeruginosain Both the Corneal Epithelium and the Bacteria
Authors: Kumar Naren G. , Grosser Melinda R , Wan Stephanie , Schator Daniel , Ahn Eugene , Jedel Eric , Nieto Vincent , Evans David J. , Fleiszig Suzanne M. J. 
Published: December 2024

AbstractPurposeHealthy corneas resist colonization by virtually all microbes yet contact lens wear can predispose the cornea to sight-threatening infection withPseudomonas aeruginosa. Here, we explored how lens wear changes corneal epithelium transcriptional responses toP. aeruginosaand its impact on bacterial gene expression.MethodsMale and female C57BL/6J mice were fitted with a contact lens on one eye for 24 h. After lens removal, corneas were immediately challenged for 4 h withP. aeruginosa. A separate group of naïve mice were similarly challenged with bacteria. Bacteria-challenged eyes were compared to uninoculated naive controls as was lens wear alone. Total RNA-sequencing determined corneal epithelium and bacterial gene expression.ResultsPrior lens wear profoundly altered the corneal response toP. aeruginosa, including: upregulated pattern-recognition receptors (tlr3, nod1), downregulated lectin pathway of complement activation (masp1), amplified upregulation oftcf7,gpr55, ifi205, wfdc2(immune defense) and further suppression ofefemp1(corneal stromal integrity). Without lens wear,P. aeruginosaupregulated mitochondrial and ubiquinone metabolism genes. Lens wear alone upregulatedaxl, grn, tcf7, gpr55(immune defense) and downregulated Ca2+-dependent genesnecab1, snx31 and npr3.P. aeruginosaexposure to prior lens wearing vs. naïve corneas upregulated bacterial genes of virulence (popD), its regulation (rsmY, PA1226) and antimicrobial resistance (arnB,oprR).ConclusionPrior lens wear impacts corneal epithelium gene expression altering its responses toP. aeruginosaand howP. aeruginosaresponds to it favoring virulence, survival and adaptation. Impacted genes and associated networks provide avenues for research to better understand infection pathogenesis.
Utility of gut-brain electrophysiological coupling in predicting L-Dopa induced dyskinesia in Parkinson’s Disease
Authors: Houde Sanket , Kaur Mansimran , Tiwari Hari Prakash , Priyanka B Nandini , BP Rathore , Balasubramani Pragathi P. 
Published: December 2024

AbstractIn this study, we focus on Levodopa induced dyskinesia (LID) condition in Parkinson’s Disease (PD) and investigate the mechanistic role of gut-brain coupling in explaining the dyskinesia severity. Earlier studies have provided evidences for abnormal dynamics in the cortico-basal ganglia loops and also in the gut functioning, for explaining LID. However to our knowledge, assessing gut-brain coupling isn’t a standard practice for development of the treatment strategy in LID patients for understanding the odds of dyskinesia onset and progression. In this study, we use scalable data acquisition technologies such as electroencephalography (EEG) and electrogastrography (EGG) for investigating the gut-brain coupling, and for the first time assess its utility to inform about dyskinesia severity in PD patients. We collected data from N=67 subjects (healthy = 26) in middle to old age adulthood and acquire their gut-brain coupling data during various cognitive engagement tasks, using simultaneous EEG and EGG recording setup. Some of our results include that gut-brain coupling can predict the severity of dyskinesia in PD during interoception, especially in hyperventilating and eyes closed resting state paradigms. Second, specific frequencies of gut coupling activity are more sensitive to explaining motor complications. Third, the gut activity differentially couples with different brain regions to explain the symptom severity. The most salient features of our model were the normogastric gut coupling with the temporo-occipital brain region, normogastric gut coupling with the frontal region, and the tachygastric gut coupling with the centro-parietal region. Furthermore of translational significance, the latter two features also significantly interacted with cardiac measures, and the model was able to predict sensitive heart rate variability levels for reducing the symptom severity. Altogether, our study paves way for utitlizing gut-brain coupling as a clinical measure for strategizing interventions in PD.
Chimeric aggregative multicellularity in absence of kin discrimination
Authors: Weltzer Michael L. , Govaerts Jack , Wall Daniel 
Published: December 2024

AbstractAggregative multicellularity is a cooperative strategy employed by some microorganisms. Unlike clonal expansion within protected environments during multicellular eukaryotic development, an aggregation strategy introduces the potential for genetic conflicts and exploitation by cheaters, threatening the stability of the social system.Myxococcus xanthus, a soil-dwelling bacterium, employs aggregative multicellularity to form multicellular fruiting bodies that produce spores in response to starvation. Studies of natural fruiting bodies show that this process is restricted to close kin or clonemates. Here, we investigate the mechanisms underlying kin recognition during development inM. xanthus. By co-culturing two distantly relatedM. xanthusstrains under vegetative and starvation conditions, we observed that the strains segregate in both contexts. During vegetative growth, one strain antagonized the other using the type VI secretion system (T6SS). T6SS-mediated antagonism was also observed during development, resulting in monoclonal fruiting bodies when WT strains were mixed. In contrast, mixtures of T6SS knockout strains formed chimeric fruiting bodies, that produced viable spores from both strains. These findings suggest that T6SS is the primary mechanism of kin discrimination in distantly relatedM. xanthusstrains, and its use ensures the development of monoclonal fruiting bodies and social integrity.
Usutu virus African 3.1 lineage, Portugal, 2021-2023
Authors: Queirós João , Silva Tatiana , Fontoura-Gonçalves Catarina , Magalhães Inês , Moraga Alberto , Contreras Marinela , Almeida Tereza , Lopes Ana M. , Abrantes Joana , da Silva Luís P. , Rodrigues Marisa , Costa João Basso , de Mello Gonçalo , Gonçalves David , Alves Paulo Célio , Höfle Ursula 
Published: December 2024

AbstractBackgroundUsutu virus (Orthoflavivirus usutuense, USUV), a neurotropic arthropod-borne RNA virus of the family Flaviviridae, is a zoonotic virus that has spread throughout the European continent over the last three decades, since its emergence in Italy in 1996. However, no cases of USUV have been reported in Portugal so far.Material and methodsIn the scope of an active surveillance program forOrthoflavivirus, we collected growing feather samples from 249 red-legged partridges (Alectoris rufa) hunted in southern Portugal during the 2021-2023 hunting seasons. Samples positive for USUV were subjected to whole genome sequencing and strain characterization.ResultsTwo partridges tested positive for USUV. Phylogenetic analyses of whole and partial genomes assigned the USUV strains to the African 3 lineage, specifically the African 3.1 sub-lineage.ConclusionsOur study confirms, for the first time, the circulation of USUV in wild birds in Portugal. Active surveillance of hunted partridges proved to be a useful, accessible, and cost-effective method for USUV monitoring, further supporting their value as effective sentinels forOrthoflavivirussurveillance. Given the ongoing circulation of USUV and the increasing risk of its spillover to other domestic and wild animals, and humans, additional efforts are needed to improve virus surveillance in Portugal from a One Health perspective.
Generation of an induced pluripotent stem cell line ERCi003-A derived from a patient with maturity-onset diabetes of the young type 10 caused by a heterozygousINSmutation
Authors: Bastrich Asya , Antonov Daniil , Podzhilkova Aleksandra , Petrova Darya A. , Pylina Svetlana V. , Laptev Dmitriy N. , Sechko Elena A. , Kuznetsov Sergey N. , Vetchinkina Ekaterina A. , Mokrysheva Natalia G. 
Published: December 2024

AbstractMaturity-onset diabetes of the young type 10 (MODY10) is inherited in an autosomal dominant manner, characterized by islet cell dysfunction, impaired insulin synthesis and secretion. MODY10 is relatively rare, and is caused by a mutation of the 11p15.5 site on chromosome 11 encoding insulin. We obtained iPSCs (ERCi003-A line) from dermal fibroblasts derived from a patient with MODY10 carrying a previously undescribed pathogenic heterozygous mutation in theINSgene (c.93C>G, p.C31W) into iPSCs using transfection with self-replicating RNA vector. iPSCs proliferate in dense monolayer cell colonies, have a normal karyotype (46,XY), express pluripotency markers (OCT4, SOX2, TRA-1-60). The functional pluripotency of iPSCs was confirmed by their ability to form embryoid bodies and differentiate into the three germ layers (ecto-, endo-, and mesoderm). Sanger sequencing of iPSCs confirmed the presence of pathogenic heterozygous mutation in theINSgene. This cell line could be useful to thoroughly modeling of MODY10 to improve clinical understanding of the disease.
Membrane wetting by biomolecular condensates is facilitated by mobile tethers
Authors: GrandPre Trevor , Pyo Andrew G. T. , Wingreen Ned. S. 
Published: December 2024

AbstractBiomolecular condensates frequently rely on membrane interactions for localization, recruitment, and chemical substrates. These interactions are often mediated by membrane- anchored tethers, a feature overlooked by traditional wetting models. Using a surface free-energy framework that couples surface tension with tether density, we solve for the contact angle and tether density in a spherical cap geometry, generalizing the Young-Dupré equation. While the contact angle retains its force-balance form, the tether density depends nontrivially on the form and strength of tether-condensate interactions. We solve for this dependence within a simple interaction model, and find a wetting phase diagram with a transition from non-wetting to partial to complete wetting over a biologically realistic parameter range. This work provides a quantitative framework for characterizing condensate-membrane interactions, uncovering potential mechanisms by which membranes mediate cellular organization and function.
Single-Cell full-length Isoform Sequencing Unveils Transcriptional Dysregulation in Autism Spectrum Disorder During Cerebral Cortex Development
Authors: Xu Xiaoyi , Wang Jun , Hu Kunhua , Su Dan , Huang Qingpei , Fan Xiaotang , Fan Xiaoying 
Published: December 2024

ABSTRACTRegulation of RNA splicing is pivotal in neural development, with established gene isoform expression patterns (1, 2). However, the specific roles of isoform diversity across cell types in both healthy and diseased brains warrant further investigation. Here, we employed a combination of metabolic RNA labeling using 4-thiouridine (4sU) and long-read sequencing based single-cell full-length transcriptome sequencing to capture newly synthesized transcripts within the developing mouse cortices. This approach allowed us to identify predetermined cell states supported by new RNAs and the driving isoforms of transcription factors that regulate the development of deep-and upper-layer neurons. Through detailed single-cell isoform expression analysis, we discovered novel cell type-specific isoforms and uncovered isoform switch events that modulate neuron differentiation. Additionally, we investigated isoform regulation associated with Autism Spectrum Disorder (ASD) during embryonic development of BTBRT+Itpr3tf(BTBR) mice. Notably, our findings indicate a premature emergence of cortical projection neurons (CPNs) with an immature identity in ASD-affected cortices. These CPNs exhibit the highest degree of differential transcript usage (DTU), significantly overlapping with their cell type markers and being enriched in RNA splicing processes. Exon inclusion was significantly enriched in ASD and the related RNA binding proteins (RBPs) were extracted, nearly 60% of which have been reported as ASD risk genes. Lastly, we revealed a reduction in isoform diversity in ASD, potentially linked to H3K27ac dysregulation in the associated genes. Collectively, our study marks a substantial advancement in understanding the molecular basis of cortical development and function, paving the way for future studies on neurodevelopmental disorders.
Bridging molecular to cellular scales for models of membrane receptor signaling
Authors: Peterson Kelvin J. , Slepchenko Boris M. , Loew Leslie M. 
Published: December 2024

ABSTRACTBiochemical interactions at membranes are the starting points for cell signaling networks. But bimolecular reaction kinetics are difficult to experimentally measure on 2-dimensional membranes and are usually measured in volumetricin vitroassays. Membrane tethering produces confinement and steric effects that will significantly impact binding rates in ways that are not readily estimated from volumetric measurements. Also, there are situations when 2D reactions do not conform to simple kinetics. Here we show how highly coarse-grained molecular simulations using the SpringSaLaD software can be used to estimate membrane-tethered rate constants from experimentally determined volumetric kinetics. The approach is validated using an analytical solution for dimerization of binding sites anchored via stiff linkers. This approach can provide 2-dimensional bimolecular rate constants to parameterize cell-scale models of receptor-mediated signaling. We explore how factors such as molecular reach, steric effects, disordered domains, local concentration and diffusion affect the kinetics of binding. We find that for reaction-limited cases, the key determinant in converting 3D to 2D rate constant is the distance of the binding sites from the membrane. On the other hand, the mass action rate law may no longer be obeyed for diffusion-limited reaction on surfaces; the simulations reveal when this situation pertains. We then apply our approach to epidermal growth factor receptor (EGFR) mediated activation of the membrane-bound small GTPase Ras. The analysis reveals how prior binding of Ras to the allosteric site of SOS, a guanine nucleotide exchange factor (GEF) that is recruited to EGFR, significantly accelerates its catalytic activity.SIGNIFICANCE STATEMENTIn cell signaling, the activation of a surface receptor leads to a cascade of intracellular biochemical events. Many of these occur near the inner plasma membrane surface. However, accurate rate parameters for these initial steps in models of signaling are rarely available because membrane-tethered reaction kinetics are difficult to experimentally measure. Here, we use a highly coarse-grained molecular simulator to model the kinetics of reactions between binding sites that are tethered to a membrane. We can fit these simulation outputs to 2-dimensional rate laws to obtain rate constants that can be used to build complex models of cell signaling. These rate constants can also be compared to understand the key biophysical features controlling the kinetics of bimolecular membrane reactions.