bluuebunny/crossref_metadata_2025_split huggingface dataset:
Female reed warblers in social pairs with low MHC dissimilarity achieve higher MHC compatibility through random extra-pair matings
Authors: Halupka Lucyna , O’Connor Emily , Strandh Maria , Sztwiertnia Hanna , Klimczuk Ewelina , Hasselquist Dennis , Westerdahl Helena 
Published: April 2023

AbstractMajor Histocompatibility Complex (MHC) polymorphism is maintained by balancing selection through host-pathogen interactions and mate choice. MHC-based mate choice has been proposed across a wide range of vertebrates. However, the likelihood of its existence in songbirds has been questioned because of their poorly developed olfactory sense, which is a trait considered crucial in pre-copulatory mate choice to determine both own MHC and the MHC of putative partners. In this study, we show that female reed warblers,Acrocephalus scirpaceus, with extra-pair young in their nests have a lower MHC class I (MHC-I) dissimilarity with their social mate than females without extra-pair young in their nests. We also show that the MHC-I dissimilarity of successfully siring extra-pair males is not different from that of either the other males with territories surrounding the social nest (i.e.putative extra-pair males) or the pairs without extra-pair young in their nests. Taken together with the observation that extra-pair mating in reed warblers is common, we argue that these results support a scenario where extra-pair mating is more likely to lead to successful fertilisation when there is a high similarity in MHC-I between the female and her social male. Furthermore, as our data suggest that extra-pair mating at random can result in a higher MHC-I dissimilarity this scenario does not require any active female mate choice for MHC-I dissimilar males to drive this pattern.
Dynamic Entrainment: A deep learning and data-driven process approach for synchronization in the Hodgkin-Huxley model
Authors: Saghafi Soheil , Sanaei Pejman 
Published: April 2023

AbstractResonance and synchronized rhythm are important phenomena and can be either constructive or destructive in dynamical systems in the nature, specifically in biology. There are many examples showing that the human’s body organs must maintain their rhythm in order to function properly. For instance, in the brain, synchronized or desynchronized electrical activities can lead to neurodegenerative disorders such as Huntington’s disease. In this paper, we adopt a well known conductance based neuronal model known as Hodgkin-Huxley model describing the propagation of action potentials in neurons. Armed with the “data-driven” process alongside the outputs of the Hodgkin-Huxley model, we introduce a novelDynamic Entrainmenttechnique, which is able to maintain the system to be in its entrainment regime dynamically by applying deep learning approaches.
In VitroModeling of CD8 T Cell Exhaustion Enables CRISPR Screening to Reveal a Role for BHLHE40
Authors: Wu Jennifer E. , Manne Sasikanth , Ngiow Shin Foong , Baxter Amy E. , Huang Hua , Freilich Elizabeth , Clark Megan L. , Lee Joanna H. , Chen Zeyu , Khan Omar , Staupe Ryan P. , Huang Yinghui J. , Shi Junwei , Giles Josephine R. , Wherry E. John 
Published: April 2023

AbstractIdentifying novel molecular mechanisms of exhausted CD8 T cells (Tex) is a key goal of improving immunotherapy of cancer and other diseases. However, high-throughput interrogation ofin vivoTexcan be costly and inefficient.In vitromodels of Texare easily customizable and quickly generate high cellular yield, offering an opportunity to perform CRISPR screening and other high-throughput assays. We established anin vitromodel of chronic stimulation and benchmarked key phenotypic, functional, transcriptional, and epigenetic features against bona fidein vivoTex. We leveraged this model ofin vitrochronic stimulation in combination with pooled CRISPR screening to uncover transcriptional regulators of T cell exhaustion. This approach identified several transcription factors, including BHLHE40.In vitroandin vivovalidation defined a role for BHLHE40 in regulating a key differentiation checkpoint between progenitor and intermediate subsets of Tex. By developing and benchmarking anin vitromodel of Tex, we demonstrate the utility of mechanistically annotatedin vitromodels of Tex, in combination with high-throughput approaches, as a discovery pipeline to uncover novel Texbiology.
A biophysical rationale for the selective inhibition of PTP1B over TCPTP by nonpolar terpenoids
Authors: Friedman Anika J. , Padgette Hannah M. , Kramer Levi , Liechty Evan T. , Donovan Gregory W. , Fox Jerome M. , Shirts Michael R. 
Published: April 2023

AbstractProtein tyrosine phosphatases (PTPs) are emerging drug targets for many diseases, including type 2 diabetes, obesity, and cancer. However, a high degree of structural similarity between the catalytic domains of these enzymes has made the development of selective pharmacological inhibitors an enormous challenge. Our previous research uncovered two unfunctionalized terpenoid inhibitors that selectively inhibit PTP1B over TCPTP, two PTPs with high sequence conservation. Here, we use molecular modeling with experimental validation to study the molecular basis of this unusual selectivity. Molecular dynamics (MD) simulations indicate that PTP1B and TCPTP contain a conserved h-bond network that connects the active site to a distal allosteric pocket; this network stabilizes the closed conformation of the catalytically influential WPD loop, which it links to the L–11 loop andα3 andα7 helices—the C-terminal side of the catalytic domain. Terpenoid binding to either of two proximal allosteric sites—anαsite and aβsite—can disrupt the allosteric network. Interestingly, binding to theαsite forms a stable complex with only PTP1B; in TCPTP, where two charged residues disfavor binding at theαsite, the terpenoids bind to theβsite, which is conserved between the two proteins. Our findings indicate that minor amino acid differences at the poorly conservedαsite enable selective binding, a property that might be enhanced with chemical elaboration, and illustrate, more broadly, how minor differences in the conservation of neighboring—yet functionally similar—allosteric sites can have very different implications for inhibitor selectivity.
Computational design of non-porous, pH-responsive antibody nanoparticles
Authors: Yang Erin C. , Divine Robby , Miranda Marcos C. , Borst Andrew J. , Sheffler Will , Zhang Jason Z , Decarreau Justin , Saragovi Amijai , Abedi Mohamad , Goldbach Nicolas , Ahlrichs Maggie , Dobbins Craig , Hand Alexis , Cheng Suna , Lamb Mila , Levine Paul M. , Chan Sidney , Skotheim Rebecca , Fallas Jorge , Ueda George , Lubner Joshua , Somiya Masaharu , Khmelinskaia Alena , King Neil P. , Baker David 
Published: April 2023

AbstractProgramming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and important for targeted delivery of biologics. We describe the design of octahedral non-porous nanoparticles with the three symmetry axes (four-fold, three-fold, and two-fold) occupied by three distinct protein homooligomers: ade novodesigned tetramer, an antibody of interest, and a designed trimer programmed to disassemble below a tunable pH transition point. The nanoparticles assemble cooperatively from independently purified components, and a cryo-EM density map reveals that the structure is very close to the computational design model. The designed nanoparticles can package a variety of molecular payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between to 5.9-6.7. To our knowledge, these are the first designed nanoparticles with more than two structural components and with finely tunable environmental sensitivity, and they provide new routes to antibody-directed targeted delivery.
Genetic drift and genome reduction in the plant pathogenCandidatusLiberibacter solanacearum shapes a new enzyme in lysine biosynthesis
Authors: Gilkes Jenna M. , Frampton Rebekah A. , Board Amanda J. , Hudson André O. , G. Price Thomas , Crittenden Deborah L. , Muscroft-Taylor Andrew C. , Sheen Campbell R. , Smith Grant R. , Dobson Renwick C.J. 
Published: April 2023

AbstractThe effect of population bottlenecks and genome reduction on enzyme function is poorly understood. ‘CandidatusLiberibacter solanacearum’ is a bacterium with a reduced genome that is transmitted vertically to the egg of an infected psyllid—a population bottleneck that imposes genetic drift and is predicted to affect protein structure and function. Here, we define the effects of genome reduction and genetic drift on the function ofCa. L. solanacearum dihydrodipicolinate synthase (CLsoDHDPS), which catalyses the committed branchpoint reaction in diaminopimelate and lysine biosynthesis. We demonstrate thatCLsoDHDPS is expressed inCa. L. solanacearum and expression is increased ∼2-fold in the insect host compared toin planta.CLsoDHDPS has increased aggregation propensity, implying mutations have destabilised the enzyme but are compensated for through elevated chaperone expression and a stabilised oligomeric state.CLsoDHDPS uses a ternary-complex kinetic mechanism, which is unique among DHDPS enzymes, has unusually low catalytic ability, but an unusually high substrate affinity. Structural studies demonstrate that the active site is more open, and the structure ofCLsoDHDPS with both pyruvate and the substrate analogue succinic-semialdehyde reveals that the product is both structurally and energetically different and therefore evolution has in this case fashioned a new enzyme. Our study reveals the effects of genome reduction and genetic drift on the function of essential enzymes and provides insights on bacteria-host co-evolutionary association. We suggest that bacteria with endosymbiotic lifestyles present a rich vein of interesting enzymes useful for understanding enzyme function and/or informing protein engineering efforts.
Transcriptomics and Metabolomics Reveal Tomato Consumption Alters Hepatic Xenobiotic Metabolism and Induces Steroidal Alkaloid Metabolite Accumulation in Mice
Authors: Dzakovich Michael P. , Goggans Mallory L. , Thomas-Ahner Jennifer M. , Moran Nancy E. , Clinton Steven K. , Francis David M. , Cooperstone Jessica L. 
Published: April 2023

AbstractScopeTomato consumption is associated with many health benefits including lowered risk for developing certain cancers. It is hypothesized that tomato phytochemicals are transported to the liver and other tissues where they alter gene expression in ways that lead to favorable health outcomes. However, the effects of tomato consumption on mammalian liver gene expression and chemical profile are not well defined.Methods and resultsWe hypothesized that tomato consumption would alter mouse liver transcriptomes and metabolomes compared to a control diet. C57BL/6 mice (n=11-12/group) were fed a macronutrient matched diet containing either 10% red tomato, 10% tangerine tomato, or no tomato powder for 6 weeks after weaning. RNA-Seq followed by gene set enrichment analyses indicated that tomato type and consumption, in general, altered expression of phase I and II xenobiotic metabolism genes. Untargeted metabolomics experiments revealed distinct clustering between control and tomato fed animals. Nineteen molecular formulas (representing 75 chemical features) were identified or tentatively identified as steroidal alkaloids and isomers of their phase I and II metabolites; many of which are reported for the first time in mammals.ConclusionThese data together suggest tomato consumption may impart benefits partly through enhancing detoxification potential.
Normalization in mouse primary visual cortex
Authors: Zayyad Zaina A. , Maunsell John H. R. , MacLean Jason N. 
Published: April 2023

AbstractWhen multiple stimuli appear together in the receptive field of a visual cortical neuron, the response is typically close to the average of that neuron’s response to each individual stimulus. The departure from a linear sum of each individual response is referred to as normalization. In mammals, normalization has been best characterized in the visual cortex of macaques and cats. Here we study visually evoked normalization in the visual cortex of awake mice using optical imaging of calcium indicators in large populations of layer 2/3 (L2/3) V1 excitatory neurons and electrophysiological recordings across layers in V1. Regardless of recording method, mouse visual cortical neurons exhibit normalization to varying degrees. The distributions of normalization strength are similar to those described in cats and macaques, albeit slightly weaker on average.
Conserved Metabolic Regulator ArcA Responds to Oxygen Availability, Iron Limitation, and Cell Envelope Perturbations during Bacteremia
Authors: Brown Aric N. , Anderson Mark T. , Smith Sara N. , Bachman Michael A. , Mobley Harry L. T. 
Published: April 2023

ABSTRACTBacteremia, a systemic infection associated with severe clinical outcomes, is often caused by Gram-negative facultative anaerobes. ArcAB, a two-component regulatory system that represses aerobic respiration, is a key mediator of metabolic adaptation for such bacteria. Using targeted mutational analysis informed by global genetic screens, we identified thearcAgene as promoting fitness ofKlebsiella pneumoniae,Citrobacter freundii, andSerratia marcescensbut notEscherichia coliin a murine model of bacteremia. Engineered mutants lackingarcAexhibit a dysregulated response to changes in oxygen availability, iron limitation, and membrane perturbations, all of which bacterial cells experience during infection. The genetic response of thearcAmutants relative to wild-type strains to the cationic antimicrobial peptide polymyxin B demonstrates an expanded role for ArcA as an activator in response to membrane damage in addition to metabolic adaptation. ArcA function is furthermore linked to electron transport chain activity based on its response to uncoupling of proton motive force by carbonyl cyanide-m-chlorophenylhydrazone (CCCP). Differences in lactate and acetate levels as well as lactate dehydrogenase activity betweenarcAmutant and wild-type cells following CCCP treatment establish an ArcA-mediated shift to fermentation independent of oxygen availability. This study highlights the semi-conserved role of ArcA during bacteremia and consolidates infection phenotypes into a comprehensive model based on respiratory activity.AUTHOR SUMMARYInfections of the bloodstream are life-threatening and can result in sepsis, an overreaction of the host immune system that ultimately damages the body. Gram-negative bacteria are responsible for causing many cases of bloodstream infections, also referred to as bacteremia. The long-term goal of our work is to understand how these bacteria establish and maintain infection during bacteremia. We have previously identified the transcription factor ArcA, which promotes fermentation in bacteria, as a likely contributor to the growth and survival of bacteria in this environment. Here, we study ArcA in the Gram-negative speciesCitrobacter freundii,Klebsiella pneumoniae,andSerratia marcescens.Our findings aid in determining how these bacteria sense their environment, utilize nutrients, and generate energy while also countering attacks from the host immune system. This information is critical for developing better models of infection to inform future therapeutic development.
In Vivo mRNA Hacking with Staple Oligomers Prevents Myocardial Hypertrophy
Authors: Katsuda Yousuke , Kamura Takuto , Kida Tomoki , Saeki Takeru , Itsuki Yua , Kato Yuri , Nakamura Taishi , Nishida Motohiro , Kitamura Yusuke , Ihara Toshihiro , Hagihara Masaki , Sato Shin-ichi 
Published: April 2023

Summary paragraphThe elucidation of gene-silencing mechanisms by RNA interference (RNAi) and antisense oligomers has drawn increasing attention to nucleic acid medicine. However, several challenges remain to be overcome, such as in vivo stability1, target selectivity2,3, drug delivery4,5, and induced innate immunity6. Here, we report a new, versatile, and highly-selective method to hack RNA by controlling RNA structure using short oligonucleotides (RNA hacking: RNAh) in living cells. The oligonucleotide, named Staple oligomer, hybridizes specifically to a target mRNA and artificially induces an RNA higher-order structure, RNA G-quadruplex (RGq)7, on the mRNA. As a result, the RGq allows effective suppression of the target protein translation. This technology does not require cooperation with bioprocesses including enzymatic reactions as in RNAi or antisense technologies, permitting the introduction of artificial nucleic acids into Staple oligomers to increase their in vivo stability without compromising their effectiveness. The method was validated by translational regulation of the mRNAs of TPM3, MYD88, and TRPC6, in a cell-free system and in living mammalian cells. In vivo application of the technology to TRPC6 mRNA allowed us to prevent cardiac hypertrophy in transverse aortic constriction (TAC)-treated mice with no detectable off-target effects. This technology provides new insights into gene therapy after RNAi and antisense technologies.
Assembling membraneless organelles fromde novodesigned proteins
Authors: Hilditch Alexander T. , Romanyuk Andrey , Cross Stephen J. , Obexer Richard , McManus Jennifer J. , Woolfson Derek N. 
Published: April 2023

ABSTRACTRecent advances inde novoprotein design have delivered a diversity of discretede novoprotein structures and complexes. A new challenge for the field is to use these designs directly in cells to intervene in biological process and augment natural systems. The bottom-up design of self-assembled objects like microcompartments and membraneless organelles is one such challenge, which also presents opportunities for chemical and synthetic biology. Here, we describe the design of genetically encoded polypeptides that form membraneless organelles inEscherichia coli(E. coli). To do this, we combinede novoα-helical sequences, intrinsically disordered linkers, and client proteins in single-polypeptide constructs. We tailor the properties of the helical regions to shift protein assembly from diffusion-limited assemblies to dynamic condensates. The designs are characterised in cells andin vitrousing biophysical and soft-matter physics methods. Finally, we use the designed polypeptide to co-compartmentalise a functional enzyme pair inE. coli.
P2X7-dependent exchange of extracellular microparticles and mitochondria by mouse microglia
Authors: Falzoni Simonetta , Chiozzi Paola , Vultaggio-Poma Valentina , Tarantini Mario , Adinolfi Elena , Boldrini Paola , Giuliani Anna Lisa , Gorecki Dariusz C. , Virgilio Francesco Di 
Published: April 2023

AbstractMicroparticles (MPs) are ubiquitously secreted by all cells and play a fundamental role in numerous biological processes such as cell-to-cell communication, cell differentiation, inflammation, and cell energy transfer. Ligation of the P2X7 receptor (P2X7R) by extracellular ATP (eATP) is the well-known stimulus for MP release, which affects their contents in a cell-specific fashion. We investigated MP release and functional impact in mouse microglial cell lines characterized for high (N13-P2X7RHigh) or low (N13-P2X7RLow) expression of the P2X7R. Stimulation with extracellular ATP triggered a P2X7R-dependent release of a MP population enriched with naked mitochondria. Released mitochondria were taken up and incorporated into the mitochondrial network of the recipient cells in a P2X7R-dependent fashion. Other constituents of the MP cargo, e.g. NLRP3 and the P2X7R itself, were also delivered to the recipient cells. Transfer of mitochondria, NLRP3 and P2X7R increased the energy level of the recipient cells and conferred a pro-inflammatory phenotype. These data show that P2X7R-dependent exchange of MPs and mitochondria modulates energy metabolism and inflammatory responses, pointing to the P2X7R as a master regulator of intercellular organelle and MP trafficking in mouse microglia.
Measuring the perception and metacognition of time
Authors: Cropper Simon J , Little Daniel R , Xu Liheng , Bruno Aurelio M , Johnston Alan 
Published: April 2023

AbstractThe ability of humans to identify and reproduce short time intervals (in the region of a second) may be affected by many factors ranging from the gender of the individual observer, through the attentional state, to the precise spatiotemporal structure of the stimulus. The relative roles of these very different factors are a challenge to describe and define; several methodological approaches have been used to achieve this to varying degrees of success. Here we describe a new paradigm affording not only a first-order measurement of the perceived duration of an interval but also a second-order metacognitive judgement of perceived time. This approach, we argue, expands the form of the data generally collected in duration-judgements and allows more detailed comparison of psychophysical behaviour to the underlying theory. We also describe a measurement model which provides estimates of the variability of the temporal estimates and the metacognitive judgments allowing comparison to an ideal observer. We fit the model to data collected for judgements of 750ms (bisecting 1500ms) and 1500ms (bisecting 3000ms) intervals across three stimulus modalities (Visual, Audio & Audiovisual). This enhanced form of data on a given interval judgement and the ability to track its progression on a trial-by-trial basis offers a way of looking at the different roles that subject-based, task-based and stimulus-based factors have on the perception of time.
Reduction in mRNA expression of the neutrophil chemoattract factor CXCL1 inPseudomonas aeruginosatreated Barth Syndrome B lymphoblasts
Authors: Zegallai Hana M. , Duan Kangmin , Hatch Grant M. 
Published: April 2023

AbstractBarth Syndrome (BTHS) is a rare X-linked genetic disease caused by a mutation inTAFAZZIN, a cardiolipin transacylase. Approximately 70% of patients with BTHS exhibit severe infections due to neutropenia. However, neutrophils from BTHS patients have been shown to exhibit normal phagocytosis and killing activity. B lymphocytes play a crucial role in the regulation of the immune system and when activated secret cytokines known to attract neutrophils to sites of infection. We examined expression of chemokine (C-X-C motif) ligand 1 (CXCL1), a known chemotactic for neutrophils, in Epstein-Barr virus transformed control and BTHS B lymphoblasts. Age-matched control and BTHS B lymphoblasts were incubated withPseudomonas aeruginosafor 24 h and then cell viability, CD27+, CD24+, CD38+, CD138+ and PD1+ surface marker expression and CXCL1 mRNA expression determined. Cell viability was maintained in lymphoblasts incubated with a ratio of 50:1 bacteria:B cells. Surface marker expression was unaltered between control and BTHS B lymphoblasts. In contrast, CXCL1 mRNA expression was reduced approximately 90% (p<0.05) in untreated BTHS B lymphoblasts compared to control cells and approximately 70% (p<0.05) in bacterial treated BTHS B lymphoblasts compared to control cells. Thus, naïve and bacterial-activated BTHS B lymphoblasts exhibit reduced mRNA expression of the neutrophil chemoattractant factor CXCL1. We suggest that impaired bacterial activation of B cells in some BTHS patients could promote immune dysfunction, and this may contribute to infections.