bluuebunny/crossref_metadata_2025_split huggingface dataset:
A DNase T6SS effector requires its MIX domain for secretion
Authors: Fridman Chaya Mushka , Jana Biswanath , Ben-Yaakov Rotem , Bosis Eran , Salomon Dor 
Published: May 2022

ABTRACTGram-negative bacteria often employ the type VI secretion system (T6SS) to deliver diverse cocktails of antibacterial effectors into rival bacteria. In many cases, even when the identity of the delivered effectors is known, their toxic activity and mechanism of secretion are not. Here, we investigate VPA1263, aVibrio parahaemolyticusT6SS effector that belongs to a widespread class of polymorphic effectors containing a MIX domain. We reveal a C-terminal DNase toxin domain belonging to the HNH nuclease superfamily, and we show that it mediates the antibacterial toxicity of this effector during bacterial competition. Furthermore, we demonstrate that the VPA1263 MIX domain is necessary for T6SS-mediated secretion and intoxication of recipient bacteria. These results are the first indication of a functional role for MIX domains in T6SS secretion.IMPORTANCESpecialized protein delivery systems are used during bacterial competition to deploy cocktails of toxins that target conserved cellular components. Although numerous toxins have been revealed, the activity of many remains unknown. In this study, we investigated such a toxin from the pathogenVibrio parahaemolyticus. Our findings indicated that the toxin employs a DNase domain to intoxicate competitors. We also showed that a domain used as a marker for secreted toxins is required for secretion of the toxin via a type VI secretion system.
Human papilloma virus E6 regulates therapy responses in oropharyngeal cancer by repressing the PGC-1α/ERRα axis
Authors: Sannigrahi Malay K. , Rajagopalan Pavithra , Lai Ling , Liu Xinyi , Sahu Varun , Nakagawa Hiroshi , Jalaly Jalal , Brody Robert M. , Morgan Iain M. , Windle Bradford E. , Wang Xiaowei , Gimotty Phyllis A. , Kelly Daniel P. , White Elizabeth A. , Basu Devraj 
Published: May 2022

ABSTRACTTherapy with radiation plus cisplatin kills human papilloma virus-related (HPV+) oropharyngeal squamous cell carcinomas (OPSCCs) by increasing reactive oxygen species beyond cellular antioxidant capacity. To explore why some patients fail these standard treatments, we evaluated whether the variation in HPV oncoprotein levels among HPV+ OPSCCs impacts mitochondrial metabolism, a source of antioxidant capacity. In cell line and patient-derived xenograft models, levels of HPV full-length E6 (fl-E6) inversely correlated with oxidative phosphorylation, antioxidant capacity, and therapy resistance, and fl-E6 was the only HPV oncoprotein to display such correlation. Ectopically expressing fl-E6 in models with low levels reduced mitochondrial mass, depleted antioxidant capacity, and sensitized to therapy. In this setting, fl-E6 repressed the PGC-1α/ERRα pathway for mitochondrial biogenesis by reducing p53-dependent PGC-1α transcription. Concordant observations were made in three clinical cohorts, where expression of mitochondrial components was higher in tumors of patients with reduced survival. These tumors contained the lowest fl-E6 levels, highest p53 target gene expression, and an activated PGC-1α/ERRα pathway. Our findings demonstrate that E6 can potentiate treatment responses by depleting mitochondrial antioxidant capacity and provide evidence for low E6 negatively impacting patient survival. E6’s interaction with the PGC-1α/ERRα axis has implications for predicting and targeting treatment resistance in OPSCC.
A heterogeneous pool of tumor precursor cells with self-replenishing and tumor-originating properties in early pathogenesis of Chronic Lymphocytic Leukemia
Authors: Budeus Bettina , Dampmann Maria , Kibler Artur , Faßbender Bianca , Brauser Martina , Bronischewski Kevin , Homp Ekaterina , Taudien Sarah , Johansson Patricia , Bloehdorn Johannes , Stilgenbauer Stephan , von Tresckow Julia , Dürig Jan , Reinhardt Hans Christian , Küppers Ralf , Dietrich Sascha , Seifert Marc 
Published: May 2022

AbstractIntratumor heterogeneity (ITH) refers to the coexistence of distinct cancer cell subpopulations within a single tumor, each with unique molecular and functional properties. Understanding the dynamics and evolution of ITH is crucial for predicting tumor progression and the development of therapy resistance.Here, we conducted a comprehensive investigation of ITH in Chronic Lymphocytic Leukemia (CLL) and identified a subpopulation that carried the CLL B-cell receptor rearrangement but contrasted from the CLL main population by low CD5 and high CD20 expression and highly mutated Ig-genes. This CLL-related memory B-cell population shared somatic driver mutations with the main CLL population but also exhibited exclusive somatic mutations. Phylogenetic analysis suggested a pathogenically early generation of these CLL-related B cells before monoclonal B lymphocytosis or CLL manifestation. Our data indicated that CLL-related B cells have self-replenishing potential, as they diminish upon treatment but recover indistinguishably on relapse. This contrasts with the main CLL population, which mostly represents a selective and novel expansion of the CLL-related B cells. This differentiation capacity into conventional CLL cells, and the expression of leukemic stem cell signatures further supported their tumorigenic capacity.We propose that these CLL-related B cells represent a pool of highly diversified, early-stage CLL precursor cells, which persist in the shape of “malignant memory B cells”. Longitudinal analyses of these CLL precursor cells suggested that they form a reservoir of malignant, leukemia-originating cells which contribute during disease progression to CLL outgrowth and clonal evolution.
Behavioral and brain responses to verbal stimuli reveal transient periods of cognitive integration of external world in all sleep stages
Authors: Türker Başak , Musat Esteban Munoz , Chabani Emma , Fonteix-Galet Alexandrine , Maranci Jean-Baptiste , Wattiez Nicolas , Pouget Pierre , Sitt Jacobo , Naccache Lionel , Arnulf Isabelle , Oudiette Delphine 
Published: May 2022

AbstractSleep has long been considered as a state of disconnection from the environment, with absent reactivity to external stimuli. Here, we questioned this sleep disconnection dogma by directly investigating behavioral responsiveness in 49 napping subjects (27 with narcolepsy and 22 healthy volunteers) engaged in a lexical decision task. Participants were instructed to frown or smile depending on the stimulus type (words vs pseudo-words). We found accurate behavioral responses, visible via contractions of the corrugator or zygomatic muscles, in all sleep stages in both groups (except slow-wave sleep for healthy volunteers). Stimuli presented during states with high (vs. low) values of neural markers indexing rich cognitive states more often yielded responses. Our findings suggest that transient windows of reactivity to external stimuli exist in all sleep stages, even in healthy individuals. Such windows of reactivity could be used to probe sleep-related mental and cognitive processes in real-time across all sleep stages.
Cardiopulmonary bypass activates classical monocytes via shear-mediated activation of Store-Operated Calcium Entry
Authors: Li Weiming , Tu Lan N. , Hsieh Lance , Smith Julian R. , Yeh Yi-Ting , Sinyagin Anthony , Ghassemian Majid , Timms Andrew , Charette Kevin , Mauchley David , McMullan Michael , Bohuta Lyubomyr , Greene Christina , Regier Mary C. , del Alamo Juan Carlos , Savan Ram , Nigam Vishal 
Published: May 2022

AbstractPatients undergoing cardiac surgery face significant inflammatory induced by exposure to cardiopulmonary bypass (CPB), contributing to heightened morbidity and mortality. The molecular and cellular mechanisms that underpin this inflammatory process remain unknown. To address this knowledge gap, we performed snRNA/ATAC-Sequencing on leukocytes from neonatal CPB patients. Classical monocytes become more prevalent and have dysregulation of inflammatory genes after CPB, indicating their role in CPB-associated inflammation. A genome-wide CRISPR screen andin vitroexperiments in non-adherent monocytic cells identified two novel genes, SPTAN1 and RAF1, as effectors of hemodynamic stress. SPTAN1 and RAF1 activate store-operated calcium entry that results inflammation and cell death. snATAC-Seq revealed dynamically changing patterns of chromatin accessibility and AP-1 transcription factor binding after CPB exposure. These findings provide novel insights into the pathogenesis of CPB-associated inflammation, with broad implications for understanding the early stages of sterile inflammation and how non-adherent cells sense shear stress.
Retinoic acid-gated BDNF synthesis in neuronal dendrites drives presynaptic homeostatic plasticity
Authors: Thapliyal Shruti , Arendt Kristin L. , Lau Anthony G. , Chen Lu 
Published: May 2022

AbstractHomeostatic synaptic plasticity is a non-Hebbian synaptic mechanism that adjusts synaptic strength to maintain network stability while achieving optimal information processing. Among the molecular mediators shown to regulate this form of plasticity, synaptic signaling through retinoic acid (RA) and its receptor, RARα, has been shown to be critically involved in the homeostatic adjustment of synaptic transmission in both hippocampus and sensory cortices. In this study, we explore the molecular mechanism through which postsynaptic RA and RARα regulates presynaptic neurotransmitter release during prolonged synaptic inactivity at excitatory synapses. We show that RARα binds to a subset of dendritically sorted brain-derived neurotrophic factor (BDNF) mRNA splice isoforms and represses their translation. The RA-mediated translational de-repression of postsynaptic BDNF results in the retrograde activation of presynaptic Tropomyosin receptor kinase B (TrkB) receptors, facilitating presynaptic homeostatic compensation through enhanced presynaptic release. Together, our study illustrates a RA-mediated retrograde synaptic signaling pathway through which postsynaptic protein synthesis during synaptic inactivity drives compensatory changes at presynaptic site.
A comprehensive map of human glucokinase variant activity
Authors: Gersing Sarah , Cagiada Matteo , Gebbia Marinella , Gjesing Anette P. , Coté Atina G. , Seesankar Gireesh , Li Roujia , Tabet Daniel , Stein Amelie , Gloyn Anna L. , Hansen Torben , Roth Frederick P. , Lindorff-Larsen Kresten , Hartmann-Petersen Rasmus 
Published: May 2022

AbstractGlucokinase (GCK) regulates insulin secretion to maintain appropriate blood glucose levels. Sequence variants can alter GCK activity to cause hyperinsulinemic hypoglycemia (HH) or hyperglycemia associated with GCK-maturity-onset diabetes of the young (GCK-MODY), collectively affecting up to 10 million people worldwide. Patients with GCK-MODY are frequently misdiagnosed and treated unnecessarily. Genetic testing can prevent this but is hampered by the challenge of interpreting novel missense variants. Here we exploited a multiplexed yeast complementation assay to measure both hyper- and hypoactive GCK variation, capturing 97% of all possible missense and nonsense variants. Activity scores correlated with in vitro catalytic efficiency, fasting glucose levels in carriers of GCK variants and with evolutionary conservation. Hypoactive variants were concentrated at buried positions, near the active site, and at a region of known importance for GCK conformational dynamics. Some hyperactive variants shifted the conformational equilibrium towards the active state through a relative destabilization of the inactive conformation. Our comprehensive assessment of GCK variant activity promises to facilitate variant interpretation and diagnosis, expand our mechanistic understanding of hyperactive variants, and inform development of therapeutics targeting GCK.
Impact of Salmonella genome rearrangement on gene expression
Authors: Waters Emma V. , Tucker Liam A. , Ahmed Jana K. , Wain John , Langridge Gemma C. 
Published: May 2022

AbstractIn addition to nucleotide variation, many bacteria also undergo changes at a much larger scale via rearrangement of their genome structure around long repeat sequences. These rearrangements result in genome fragments shifting position and/or orientation in the genome without necessarily affecting the underlying nucleotide sequence. To date, scalable techniques have not been applied to genome structure (GS) identification, so it remains unclear how extensive this variation is and the extent of its impact upon gene expression. However, the emergence of multiplexed, long-read sequencing overcomes the scale problem, as reads of several thousand bases are routinely produced that can span long repeat sequences to identify the flanking chromosomal DNA, allowing GS identification. Genome rearrangements were generated in Salmonella enterica serovar Typhi through long-term culture at ambient temperature. Colonies with rearrangements were identified via long-range PCR and subjected to long-read nanopore sequencing to confirm genome variation. Four rearrangements were investigated for differential gene expression using transcriptomics. All isolates with changes in genome arrangement relative to the parent strain were accompanied by changes in gene expression. Rearrangements with similar fragment movements demonstrated similar changes in gene expression. The most extreme rearrangement caused a large imbalance between the origin and terminus of replication and was associated with differential gene expression as a factor of distance moved towards or away from the origin of replication. Genome structure variation may provide a mechanism through which bacteria can quickly adapt to new environments and warrants routine assessment alongside traditional nucleotide level measures of variation.
Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples
Authors: Ana Baricevic , Cécile Chardon , Maria Kahlert , Maaria Karjalainen Satu , Daniela Maric Pfannkuchen , Martin Pfannkuchen , Frédéric Rimet , Mirta Smodlaka Tankovic , Rosa Trobajo , Valentin Vasselon , Jonas Zimmermann , Agnès Bouchez 
Published: May 2022

AbstractThe development of DNA metabarcoding and High-Throughput Sequencing for diatoms is nowadays offering an interesting approach to assess their communities in freshwater and marine ecosystems. In the context of the implementation of these genomic methods to environmental monitoring, protocol constraints are moving from scientific to operational applications, requiring operational guidelines and standards. In particular, the first steps of the diatom metabarcoding process, which consist of sampling and storage, have been addressed in various ways in scientific and pilot studies.The objective of this study was to compare three currently applied preservation protocols through different storage durations (ranging from one day to one year) for phytobenthos and phytoplankton samples intended for diatom DNA metabarcoding analysis. The experimental design included four freshwater and two marine samples from sites of diverse ecological characteristics. The impact of the preservation and storage was assessed through diatom metabarcoding endpoints: DNA quality and quantity, diversity and richness, community composition and ecological index values (for freshwater samples). The yield and quality of extracted DNA only decreased for freshwater phytobenthos samples preserved with ethanol. Diatom diversity was not affected and their taxonomic composition predominantly reflects the site origin. Only rare taxa (below 100 reads) differed among methods and durations. Thus, importance of preservation method choice is important for low-density species (rare, invasive, threatened or toxic species). However, for biomonitoring purposes, freshwater ecological index values were not affected whatever the preservation method and duration considered (including ethanol preservation), reflecting the site ecological status.This study proved that diatom metabarcoding is robust enough to replace or complement the current approach based on morphotaxonomy, paving the way to new possibilities for biomonitoring. Thus, accompanied by operational standards, the method will be ready to be confidently deployed and prescribed in future regulatory monitoring.
A systematic approach to study protein-substrate specificity enables the identification of Ssh1 substrate range
Authors: Cohen Nir , Aviram Naama , Schuldiner Maya 
Published: May 2022

AbstractMany cellular functions are carried out by protein pairs, or families, providing robustness alongside functional diversity. For such processes, it remains a challenge to map the degree of specificity versus promiscuity. Protein-protein interactions (PPIs) can be used to inform on these matters as they highlight cellular locals, regulation and, in cases where proteins affect other proteins – substrate range. However, methods to study transient PPIs systematically are underutilized. In this study we create a novel approach to study stable as well as transient PPIs in yeast. Our approach, Cel-lctiv (CELlular biotin-Ligation forCapturingTransientInteractionsinVivo), uses high- throughput pairwise proximity biotin ligation for uncovering PPIs systematically andin vivo. As a proof of concept we study the homologous translocation pores Sec61 and Ssh1. We show how Cel-lctiv can uncover the unique substrate range for each translocon allowing us to pinpoint a specificity determinator driving interaction preference. More generally this demonstrates how CEl-lctiv can provide direct information on substrate specificity even for highly homologous proteins.
Plasticity facilitates rapid evolution
Authors: Burtsev Mikhail , Anokhin Konstantin , Bateson Patrick 
Published: May 2022

AbstractDevelopmental plasticity enables organisms to cope with new environmental challenges. If deploying such plasticity is costly in terms of time or energy, the same adaptive behavior could subsequently evolve through piecemeal genomic reorganisation that replaces the requirement to acquire that adaptation by individual plasticity. Here we report a new dimension to the way in which plasticity can drive evolutionary change leading to ever greater complexity in biological organization. Our model deploys the concept of partially overlapping functional systems. We found that plasticity accelerated dramatically the evolutionary accumulation of adaptive systems in model organisms with relatively low rates of mutation. The effect of plasticity on the evolutionary growth of complexity was even greater when the number of elements needed to construct a functional system was increased. These results suggest that as the difficulty of challenges from the environment become greater, so plasticity exerts an ever more powerful role in meeting those challenges and in opening up new avenues for the subsequent evolution of complex adaptations.
The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs
Authors: Herchenröther Andreas , Gossen Stefanie , Friedrich Tobias , Reim Alexander , Daus Nadine , Diegmüller Felix , Leers Jörg , Sani Hakimeh Moghaddas , Gerstner Sarah , Schwarz Leah , Stellmacher Inga , Szymkowiak Laura Victoria , Nist Andrea , Stiewe Thorsten , Borggrefe Tilman , Mann Matthias , Mackay Joel P. , Bartkuhn Marek , Borchers Annette , Lan Jie , Hake Sandra B. 
Published: May 2022

Abstract/SummarySpecialized chromatin-binding proteins are required for DNA-based processes during development. We recently established PWWP2A as direct histone variant H2A.Z interactor involved in mitosis and cranial-facial development. Here, we identify the H2A.Z/PWWP2A-associated protein HMG20A as part of several chromatin-modifying complexes including NuRD, and show that it localizes to genomic regulatory regions. Hmg20a depletion causes severe head and heart developmental defects inXenopus laevis.Our data indicate that craniofacial malformations are caused by defects in neural crest cell (NCC) migration and cartilage formation. These developmental defects are pheno-copied in HMG20A-depleted mESCs, which show inefficient differentiation into NCCs and cardiomyocytes (CMs). Accordingly, loss of HMG20A caused striking deregulation of transcription programs involved in epithelial- mesenchymal transition (EMT) and cardiac differentiation, thereby providing insights into the regulatory circuits controlled by HMG20A. Collectively, our findings implicate HMG20A as part of the H2A.Z/PWWP2A/NuRD-axis and reveal it as a key modulator of the intricate developmental transcription programs that guide NCC and cardiomyocyte differentiation.
Adsorption of Pulmonary and Exogeneous Surfactants on SARS-CoV-2 Spike Protein
Authors: Santo Kolattukudy P. , Neimark Alexander V. 
Published: May 2022

ABSTRACTCOVID-19 is transmitted by inhaling SARS-CoV-2 virions, which are enveloped by a lipid bilayer decorated by a “crown” of Spike protein protrusions. In the respiratory tract, virions interact with surfactant films composed of phospholipids and cholesterol that coat lung airways. Here, we explore by using coarse-grained molecular dynamics simulations the physico-chemical mechanisms of surfactant adsorption on Spike proteins. With examples of zwitterionic dipalmitoyl phosphatidyl choline, cholesterol, and anionic sodium dodecyl sulphate, we show that surfactants form micellar aggregates that selectively adhere to the specific regions of S1 domain of the Spike protein that are responsible for binding with ACE2 receptors and virus transmission into the cells. We find high cholesterol adsorption and preferential affinity of anionic surfactants to Arginine and Lysine residues within S1 receptor binding motif. These findings have important implications for informing the search for extraneous therapeutic surfactants for curing and preventing COVID-19 by SARS-CoV-2 and its variants.
Mapping the T cell repertoire to a complex gut bacterial community
Authors: Nagashima Kazuki , Zhao Aishan , Atabakhsh Katayoon , Weakley Allison , Jain Sunit , Meng Xiandong , Cheng Alice G. , Wang Min , Higginbottom Steven , Dimas Alex , Murugkar Pallavi , Fischbach Michael A. 
Published: May 2022

ABSTRACTCertain bacterial strains from the microbiome induce a potent, antigen-specific T cell response1–5. However, the specificity of microbiome-induced T cells has not been explored at the strain level across the gut community. Here, we colonize germ-free mice with a complex defined community (97 or 112 bacterial strains) and profile T cell responses to each strain individually. Unexpectedly, the pattern of T cell responses suggests that many T cells in the gut repertoire recognize multiple bacterial strains from the community. We constructed T cell hybridomas from 92 T cell receptor (TCR) clonotypes; by screening every strain in the community against each hybridoma, we find that nearly all of the bacteria-specific TCRs exhibit a one-to-many TCR-to-strain relationship, including 13 abundant TCR clonotypes that are polyspecific for 18 Firmicutes in the community. By screening three pooled bacterial genomic libraries against 13 pooled hybridomas, we discover that they share a single target: a conserved substrate-binding protein (SBP) from an ABC transport system. Treg and Th17 cells specific for an epitope from this protein are abundant in community-colonized and specific-pathogen-free mice. Our work reveals that T cell recognition of Firmicutes is focused on a widely conserved cell-surface antigen, opening the door to new therapeutic strategies in which colonist-specific immune responses are rationally altered or redirected.