bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pentameric assembly of glycine receptor intracellular domains provides insights into gephyrin clustering
Authors: Macha Arthur , Grünewald Nora , Havarushka Nastassia , Burdina Nele , Toelzer Christine , Merkler Yvonne , Cabrera-Orefice Alfredo , Brandt Ulrich , Pauly Thomas , Nagel-Steger Luitgard , Niefind Karsten , Schwarz Guenter 
Published: November 2022

AbstractPentameric ligand-gated ion channels represent a large family of receptors comprising an extracellular domain, four transmembrane helices and a cytosolic intracellular domain (ICD). ICDs play important roles in receptor localization and trafficking, thus regulating synaptic activity and plasticity. Glycine and GABA type A receptor ICDs bind to the scaffolding protein gephyrin, a master regulator of inhibitory synapses. Here we report the use of yeast lumazine synthase as soluble pentameric protein scaffold for the study of receptor ICDs derived from GlyR α1− and β-subunits. We were able to create ICDs assemblies in a homo- (LS-βICD) and hetero-pentameric state (LS-αβICD) and provide first-in-class structural insights on their high structural flexibility using small angle X-ray scattering. We report a high-affinity interaction between the LS-αβICD and gephyrin leading to thein vitroformation of high-molecular mega-Dalton complexes composed of three gephyrin trimers and three pentamers as basic building block. Depending on the stoichiometric ratios between gephyrin and LS-ICDs the formed complexes grow or shrink in size. In cells, LS-ICDs efficiently recruited gephyrin and were able to accumulate gephyrin at GABAergic synapses in neurons. Our findings collectively propose a new, potentially general, mechanistic concept for a gephyrin-dependent bridging of GlyRs at the inhibitory synapse.
A tracheal aspirate-derived airway basal cell model reveals a proinflammatory epithelial defect in congenital diaphragmatic hernia
Authors: Wagner Richard , Amonkar Gaurang M. , Wang Wei , Shui Jessica E. , Bankoti Kamakshi , Tse Wai Hei , High Frances A. , Zalieckas Jill M. , Buchmiller Terry L. , Zani Augusto , Keijzer Richard , Donahoe Patricia K. , Lerou Paul H. , Ai Xingbin 
Published: November 2022

ABSTRACTRationaleCongenital diaphragmatic hernia (CDH) is characterized by incomplete closure of the diaphragm and lung hypoplasia. The pathophysiology of lung defects in CDH is poorly understood.ObjectivesTo establish a translational model of human airway epithelium in CDH for pathogenic investigation and therapeutic testing.MethodsWe developed a robust methodology of epithelial progenitor derivation from tracheal aspirates of newborns. Basal stem cells (BSCs) from CDH patients and preterm and term, non-CDH controls were derived and analyzed by bulk RNA-sequencing, ATAC-sequencing, and air-liquidinterface differentiation. Lung sections from fetal human CDH samples and the nitrofen rat model of CDH were subjected to histological assessment of epithelial defects. Therapeutics to restore epithelial differentiation were evaluated in human epithelial cell culture and the nitrofen rat model of CDH.Measurements and Main ResultsTranscriptomic and epigenetic profiling of CDH and non-CDH basal stem cells reveals a disease-specific, proinflammatory signature independent of severity or hernia size. In addition, CDH basal stem cells exhibit defective epithelial differentiationin vitrothat recapitulates epithelial phenotypes found in fetal human CDH lung samples and fetal tracheas of the nitrofen rat model of CDH. Furthermore, steroid treatment normalizes epithelial differentiation phenotypes of human CDH basal stem cellsin vitroand in nitrofen rat tracheasin vivo.ConclusionsOur findings have identified an underlying proinflammatory signature and BSC differentiation defects as a potential therapeutic target for airway epithelial defects in CDH.
Investigating vaccine uptake dynamics of neutrophils using HIV-1 Envelope glycoprotein trimer
Authors: Ngo Philip Y.X. 
Published: November 2022

ABSTRACTRhesus macaques were previously immunized with two distinct subunit vaccine candidates, to monitor antigen trafficking by immune cells infiltrating the site of injection. The first, a formulation based on the HIV-1 envelope glycoprotein (Env) and the other based on the RSV-fusion (F) protein. Neutrophil and monocyte uptake profiles were vastly different between the vaccine candidates despite similar cell infiltration numbers, hinting that antigen characteristics could orchestrate different innate responses. Notably, the Env trimer is significantly more glycosylated than RSV-F.Recapitulating thesein vivoobservations under reliablein vitroconditions is thus of importance in exploring uptake dynamics and insights into the manipulation of innate responses. The study later demonstrated a complement component, Mannose Binding Lectin (MBL), to be resistant to heat-inactivation and binds Env in a CRDdependent manner. Interestingly, the data suggests a heat-labile component of the serum hinders MBL from binding to Env, which corresponded to a weaker uptake profile. Also, the generation of 3 differentially glycosylated Env variants to study glycan-mediated uptake by neutrophils derived contrary observations. In all, modulation of MBL interactions could potentially target specific innate immune cells, particularly neutrophils, and the later development of adaptive immune responses after immunization.
Nucleus accumbens dopamine release reflects the selective nature of pair bonds
Authors: Pierce Anne F. , Protter David S.W. , Chapel Gabriel D. , Cameron Ryan T. , Donaldson Zoe R. 
Published: November 2022

ABSTRACTIn monogamous species, prosocial behaviors directed towards partners are dramatically different from those directed towards unknown individuals and potential threats. Dopamine release in the nucleus accumbens plays an important role in guiding social behavior, however, its role in real time social decision making in a monogamous species remains largely unknown. We used monogamous prairie voles to investigate how dopamine release differs in voles when seeking and interacting with a pair bonded partner or a novel vole. Employing the sub-second temporal resolution of the fluorescent biosensor, GRABDA, during a social operant task, we found that partner seeking, anticipation, and interaction resulted in more dopamine release than the same events directed towards a novel vole. Furthermore, partner-elicited dopamine release decreases after prolonged partner separation. Thus, differences in partner- and novel-elicited dopamine release reflect the selective nature of pair bonds and may drive the social behaviors that reinforce and cement bonds over time, eroding after partner loss to facilitate new bond formation.
Transcriptome dynamics ofPseudomonas aeruginosaduring transition from replication-uncoupled to -coupled growth
Authors: Alpers Kathrin , Vatareck Elisabeth , Gröbe Lothar , Müsken Mathias , Scharfe Maren , Häussler Susanne , Tomasch Jürgen 
Published: November 2022

AbstractIn bacteria, either chromosome duplication is coupled to cell division with only one replication round per cell cycle or DNA is replicated faster than the cells divide thus both processes are uncoupled. Here, we show that the opportunistic pathogenPseudomonas aeruginosaswitches from fast uncoupled to sustained coupled growth when cultivated under standard laboratory conditions. The transition was characterized by fast-paced, sequential changes in transcriptional activity along theori-teraxis of the chromosome reflecting adaptation to the metabolic needs during both growth phases. Quorum sensing (QS) activity was highest at the onset of the coupled growth phase during which only a quarter of the cells keeps replicating. RNA sequencing of subpopulations of these cultures sorted based on their DNA content, revealed a strong gene dosage effect as well as specific expression patterns for replicating and non-replicating cells. Expression of flagella andmexE, involved in multi drug efflux was restricted to cells that did not replicate, while those that did showed a high activity of the cell division locus and recombination genes. A possible role of QS in the formation of these subpopulations upon switching to coupled growth could be a subject of further research.Significance statementThe coordination of gene expression with the cell cycle has so far been studied only in a handful of bacteria, the bottleneck being the need for synchronized cultures. Here, we determined replication-associated effects on transcription by comparingPseudomonas aeruginosacultures that differ in their growth mode and number of replicating chromosomes. We further show that cell cycle-specific gene regulation can be principally identified by RNA sequencing of subpopulations from cultures that replicate only once per cell division and that are sorted according to their DNA content. Our approach opens the possibility to study asynchronously growing bacteria from a wide phylogenetic range and thereby enhance our understanding of the evolution of cell-cycle control on the transcriptional level.
The Nature of Race in Germany: A systematic literature review of human classifications in German life sciences
Authors: Bartram Isabelle , Schnieder Laura , Ellebrecht Nils , Ruland Florian , Plümecke Tino , Nieden Andrea zur 
Published: November 2022

AbstractThe use of human diversity classifications like race, ethnicity, ancestry, or migration background entails a range of scientific as well as social consequences, therefore, a careful application is vital. In this article, we present results from a systematic literature review and subsequent quantitative content analysis based on 546 papers focusing on classifications applied in life sciences studies at German research institutions. Our aim is to capture a snap-shot of current classification practices applied to categorize humans across various disciplines and fields in a specific national context that remains underexposed in this regard. The review substantiates a) the results from earlier studies that point to heterogeneity, inconsistency and vagueness of human classifications used in the life sciences, and b) underlines the presumed specificity of the German science context, where the term “race” is comparatively little used. Our findings stress the need for German researchers to partake in the ongoing international debate on the practice of human classification in the life sciences to advance the international and interdisciplinary transferability of scientific results and, first and foremost, to avoid unintended effects such as overgeneralization, racialization, and stigmatization.
Male mammalian meiosis and spermiogenesis is critically dependent on the shared functions of the katanins KATNA1 and KATNAL1
Authors: Dunleavy Jessica EM , Graffeo Maddison , Wozniak Kathryn , O’Connor Anne E , Merriner D. Jo , Nguyen Joseph , Schittenhelm Ralf B , Houston Brendan J , O’Bryan Moira K 
Published: November 2022

SummaryKatanin microtubule severing enzymes are potent M-phase regulators in oocytes and somatic cells. How the complex, and evolutionarily critical, male mammalian meiotic spindle is sculpted remains unknown. Here, using multiple single and double gene knockout mice, we reveal that the canonical katanin A-subunit, KATNA1, and its close paralogue, KATNAL1, together execute multiple aspects of meiosis. We show KATNA1 and KATNAL1 collectively regulate the male meiotic spindle, cytokinesis and midbody abscission, in addition to diverse spermatid remodelling events, including Golgi organisation, and acrosome and manchette formation. We also define KATNAL1-specific roles in sperm flagella development, manchette regulation, and sperm-epithelial disengagement. Finally, using proteomic approaches we define the KATNA1, KATNAL1, and KATNB1 mammalian testis interactome, which includes a network of cytoskeletal and vesicle trafficking proteins. Collectively, we reveal the presence of multiple katanin A-subunit paralogs in mammalian spermatogenesis allows for ‘customized cutting’ via neofunctionalization and protective buffering via gene redundancy.
Microbial and Viral Genome and Proteome Nitrogen Demand Varies Across Multiple Spatial Scales Within a Marine Oxygen Minimum Zone
Authors: Muratore Daniel , Bertagnolli Anthony D. , Bristow Laura A. , Thamdrup Bo , Weitz Joshua S. , Stewart Frank J. 
Published: November 2022

ABSTRACTNutrient availability can significantly influence microbial genomic and proteomic streamlining, for example by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter- and even micron-level spatial scales. It is unclear if such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions distinguishing free-living versus particle-associated microbes. We find a substantial increase in nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size-fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in modulating the C:N ratio of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers.IMPORTANCEThe genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses using metagenomes from the nitracline of the eastern tropical North Pacific OMZ including both particle-associated and non-associated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micro- to millimeter scale associated with particle-associated versus free-living lifestyles.
Structural Assessment of the Full-Length Wild-Type Tumor Suppressor Protein p53 by Mass Spectrometry-Guided Computational Modeling
Authors: Di Ianni Alessio , Tüting Christian , Kipping Marc , Ihling Christian H. , Köppen Janett , Iacobucci Claudio , Arlt Christian , Kastritis Panagiotis L. , Sinz Andrea 
Published: November 2022

AbstractThe tetrameric tumor suppressor p53 represents a great challenge for 3D-structural analysis due to its high degree of intrinsic disorder (ca. 40%). We aim to shed light on the structural and functional roles of p53’s C-terminal region in full-length, wild-type human p53 tetramer and their importance for DNA binding. For this, we employed complementary techniques of structural mass spectrometry (MS) in an integrated approach with AI-based computational modeling. Our results show no major conformational differences in p53 between DNA-bound and DNA-free states, but reveal a substantial compaction of p53’s C-terminal region. This supports the proposed mechanism of unspecific DNA binding to the C-terminal region of p53 prior to transcription initiation by specific DNA binding to the core domain of p53. The synergies between complementary structural MS techniques and computational modeling as pursued in our integrative approach is envisioned to serve as general strategy for studying intrinsically disordered proteins (IDPs) and intrinsically disordered region (IDRs).
Fluid flow structures gut microbiota biofilm communities by distributing public goods
Authors: Wong Jeremy P. H. , Fischer-Stettler Michaela , Zeeman Samuel C. , Battin Tom J. , Persat Alexandre 
Published: November 2022

AbstractBacterial gut commensals experience a biologically and physically complex mucosal environment. While many chemical factors mediate the composition and structure of these microbial communities, less is known about the role of mechanics. Here, we demonstrate that fluid flow impacts the spatial organization and composition of gut biofilm communities by shaping how different species interact metabolically. We first demonstrate that a model community composed ofBacteroides thetaiotaomicron(Bt) andBacteroides fragilis(Bf), two representative human commensals, can form robust biofilms in flow. We identified dextran as a polysaccharide readily metabolized byBtbut notBf, but whose fermentation generates a public good enablingBfgrowth. We demonstrate that in flow,Btbiofilms share dextran metabolic by-products, promotingBfbiofilm formation. By transporting this public good, flow structures the spatial organization of the community, positioning theBfpopulation downstream fromBt. We show that sufficiently strong flows abolishBfbiofilm formation by limiting the effective public good concentration at the surface. Physical factors such as flow may therefore contribute to the composition of intestinal microbial communities, potentially impacting host health.
Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless
Authors: Jagtap Pravin Kumar Ankush , Müller Marisa , Kiss Anna E. , Thomae Andreas W. , Lapouge Karine , Beck Martin , Becker Peter B. , Hennig Janosch 
Published: November 2022

SummaryUnwinding RNA secondary structures by RNA helicases is essential for RNA metabolism. How the basic unwinding reaction of DExH-type helicases is regulated by their accessory domains is unresolved. Here, we combine structural and functional analyses to address this challenge for the prototypic DExH RNA helicase maleless (MLE) fromDrosophila.We captured the helicase cycle of MLE with multiple structural snapshots. We discovered that initially, dsRBD2 flexibly samples substrate dsRNA and aligns it with the open helicase tunnel. Subsequently, dsRBD2 releases RNA and associates with the helicase core, leading to closure of the tunnel around ssRNA. Structure-based MLE mutations confirm the functional relevance of the structural model in cells. We propose a molecular model in which the dsRBD2 domain of MLE orchestrates large structural transitions that depend on substrate RNA but are independent of ATP.Our findings reveal the fundamental mechanics of dsRNA unwinding by DExH helicases with high general relevance for dosage compensation and specific implications for MLE’s human orthologue DHX9/RHA mechanisms in disease.
Attenuated humoral responses in HIV infection after SARS-CoV-2 vaccination are linked to global B cell defects and cellular immune profiles
Authors: Touizer Emma , Alrubbayi Aljawharah , Ford Rosemarie , Hussain Noshin , Gerber Pehuén Pereyra , Shum Hiu-Long , Rees-Spear Chloe , Muir Luke , Gea-Mallorquí Ester , Kopycinski Jakub , Jankovic Dylan , Pinder Christopher , Fox Thomas A , Williams Ian , Mullender Claire , Maan Irfaan , Waters Laura , Johnson Margaret , Madge Sara , Youle Michael , Barber Tristan , Burns Fiona , Kinloch Sabine , Rowland-Jones Sarah , Gilson Richard , Matheson Nicholas J , Morris Emma , Peppa Dimitra , McCoy Laura E 
Published: November 2022

ABSTRACTPeople living with HIV (PLWH) on suppressive antiretroviral therapy (ART) can have residual immune dysfunction and often display poorer responses to vaccination. We assessed in a cohort of PLWH (n=110) and HIV negative controls (n=64) the humoral and spike-specific B-cell responses following 1, 2 or 3 SARS-CoV-2 vaccine doses. PLWH had significantly lower neutralizing antibody (nAb) titers than HIV-negative controls at all studied timepoints. Moreover, their neutralization breadth was reduced with fewer individuals developing a neutralizing response against the Omicron variant (BA.1) relative to controls. We also observed a delayed development of neutralization in PLWH that was underpinned by a reduced frequency of spike-specific memory B cells (MBCs) and pronounced B cell dysfunction. Improved neutralization breadth was seen after the third vaccine dose in PLWH but lower nAb responses persisted and were associated with global, but not spike-specific, MBC dysfunction. In contrast to the inferior antibody responses, SARS-CoV-2 vaccination induced robust T cell responses that cross-recognized variants in PLWH. Strikingly, a subset of PLWH with low or absent neutralization had detectable functional T cell responses. These individuals had reduced numbers of circulating T follicular helper cells and an enriched population of CXCR3+CD127+CD8+T cells after two doses of SARS-CoV-2 vaccination, which may compensate for sub-optimal serological responses in the event of infection. Therefore, normalisation of B cell homeostasis could improve serological responses to vaccines in PLWH and evaluating T cell immunity could provide a more comprehensive immune status profile in these individuals and others with B cell imbalances.
Modeling multiphage-bacteria kinetics to predict phage therapy potency and longevity
Authors: Yu Zhiyuan , Luong Tiffany , Banuelos Selenne , Sue Andrew , Horn Mary Ann , Ryu Hwayeon , Roach Dwayne , Segal Rebecca , Huang Qimin 
Published: November 2022

AbstractPseudomonas aeruginosais a frequent cause of life-threatening opportunistic infections in the critically ill and immunocompromised. Its treatment is challenging due to the increasing prevalence of resistance to most conventional antibiotics. Although numerous alternative therapies are currently under investigation, bacteriophage (phage) cocktail therapy appears poised for long-term success. Here, we investigate potency and longevity of individualPseudomonasphages in cocktail to determine viral co-factors that promote optimal treatment efficacy. We combinedin vitroandin silicomodels to predict sixty-eight treatment permutations with three phages that adsorb symmetrically and asymmetrically when administered singly, double simultaneously, or double sequentially. We showed that simultaneously administering two asymmetrically binding phages with high cell lysis efficiencies improved cocktail potency. Use of a higher-potency cocktail, along with a reduction in the net probability of independent gene mutations was associated with prolonged bacterial suppression. Nevertheless,in vitrowe almost always observed evolution of multiphage resistance. Simulations also predict that when combining phages with polar potencies, susceptible host cells are monopolized by the more efficiently replicating phage. Thus, further perpetuating the growth demise of the weaker phage in cocktail. Our mathematical model was used to explore and predict changes in phage and bacterial populations that were difficult to measure experimentally. This framework has many inferential and exploratory uses for clinical investigation such as identifying the most sensitive parameters for phage selection and exploring different treatment regimens. Collectively, our findings attempt to dissect the mechanisms of phage cocktails combatingP. aeruginosainfections and highlight the viral co-factors necessary for treatment efficacy.