bluuebunny/crossref_metadata_2025_split huggingface dataset:
VapC12 ribonuclease toxin modulates host immune response duringMycobacterium tuberculosisinfection
Authors: Tyagi Shaifali , Sadhu Srikanth , Sharma Taruna , Paul Abhijit , Pandey Manitosh , Nain Vaibhav , Rathore Deepak , Chatterjee Samrat , Awasthi Amit , Pandey Amit Kumar 
Published: August 2023

AbstractMechanistic understanding of antibiotic persistence is a prerequisite in controlling the emergence of MDR cases in Tuberculosis (TB). We have reported that the cholesterol-induced activation of VapC12 ribonuclease is critical for disease persistence in TB. In this study, we observed that relative to the wild type, mice infected with ΔvapC12induced a proinflammatory response, had a higher pathogen load, and responded better to the anti-TB treatment. In a high-dose infection model, all the mice infected with ΔvapC12succumbed early to the disease. Finally, we reported that the above phenotype of ΔvapC12was dependent on the presence of the TLR4 receptor. Overall, the data suggest that the inability of ΔvapC12to resolve neutrophil-mediated inflammation reduced bacterial killing by altering the T-cell response. In conclusion, our findings suggest the role of the VapC12 toxin in modulating the host’s innate immune response in ways that favor the long-term survival of the pathogen inside the host.
Remote sensing of emperor penguin abundance and breeding success
Authors: Winterl Alexander , Richter Sebastian , Houstin Aymeric , Barracho Téo , Boureau Matthieu , Cornec Clément , Couet Douglas , Cristofari Robin , Eiselt Claire , Fabry Ben , Krellenstein Adélie , Mark Christoph , Mainka Astrid , Ménard Delphine , Morinay Jennifer , Pottier Susie , Schloesing Elodie , Bohec Céline Le , Zitterbart Daniel P. 
Published: August 2023

AbstractEmperor penguins (Aptenodytes forsteri) are under increasing environmental pressure. Monitoring colony size and trends of this Antarctic seabird relies primarily on satellite imagery recorded near the end of the breeding season, when illumination levels are sufficient to capture images, but colony occupancy is highly variable. To correct population estimates for this variability, we develop a phenological model that accurately predicts the number of breeding pairs and fledging chicks, as well as key phenological events such as arrival, hatching and foraging times, from as few as six data points from a single season. The ability to extrapolate occupancy from sparse data makes the model particularly useful for monitoring remotely sensed animal colonies where ground-based population estimates are very rare or unavailable.TeaserThe Emperor penguin becomes the Southern Ocean’s canary in a coal mine through remote sensing its annual breeding success.
Role of protonation states in stability of molecular dynamics simulations of high-resolution membrane protein structures
Authors: Lasham Jonathan , Djurabekova Amina , Zickermann Volker , Vonck Janet , Sharma Vivek 
Published: August 2023

AbstractClassical molecular dynamics (MD) simulations provide unmatched spatial and time resolution of protein structure and function. However, accuracy of MD simulations often depends on the quality of force field parameters and the time scale of sampling. Another limitation of conventional MD simulations is that the protonation states of titratable amino acid residues remain fixed during simulations, even though protonation state changes coupled to conformational dynamics are central to protein function. Due to the uncertainty in selecting protonation states, classical MD simulations are sometimes performed with all amino acids modeled in their standard charged states at pH 7. Here we performed and analyzed classical MD simulations on high-resolution cryo-EM structures of two membrane proteins that transfer protons by catalyzing protonation/deprotonation reactions. In simulations performed with amino acids modeled in their standard protonation state the structure diverges far from its starting conformation. In comparison, MD simulations performed with pre-determined protonation states of amino acid residues reproduce the structural conformation, protein hydration, and protein-water and protein-protein interactions of the structure much better. The results suggest it is crucial to perform basic protonation state calculations, especially on structures where protonation changes play an important functional role, prior to launching any MD simulations. Furthermore, the combined approach of protonation state prediction and MD simulations can provide valuable information on the charge states of amino acids in the cryo-EM sample. Even though accurate prediction of protonation states currently remains a challenge, we introduce an approach of combining pKa prediction with cryo-EM density map analysis that helps in improving not only the protonation state predictions, but also the atomic modeling of density data.
Understanding Author Choices in the Current Conservation Publishing Landscape
Authors: Yoh Natalie , Holle Mukhlish Jamal Musa , Willis Jasmin , Rudd Lauren F , Fraser Iain M , Verissimo Diogo 
Published: August 2023

AbstractConservation literature addresses a broad spectrum of interdisciplinary questions and benefits most by representing a diverse range of authors, particularly those from countries where much conservation work is focused. In other disciplines, it is well known that barriers and biases exist in the academic publishing sphere, which can impact research dissemination and an author’s career development. Here, we used a Discrete Choice Experiment to determine how different journal attributes impact authors’ choices of where to publish in conservation. We identified three demographic groups across 1038 respondents who have previously published in conservation journals, each exhibiting different publishing preferences. Only two attributes showed a consistent response across groups: cost to publish negatively impacted journal choice, including for those in high-income countries, and authors had a consistent preference for double-blind review. Authors from middle-income countries were willing to pay more for society-owned journals, unlike authors from higher-income countries. Journals with a broad geographical scope, which were Open Access, and which had higher impact factors were preferable to two of the three demographic groups. However, we found journal scope and Open Access were more important in dictating journal choice than impact factor. Overall, our findings demonstrate that different demographics experience different preferences or limitations depending on attributes such as a journal’s Open Access policy. However, the scarcity of published authors from low-income countries highlights further, pervasive barriers to representation in conservation research. Based on our findings, we provide recommendations to conservation-related journals to reduce barriers to publishing and ultimately benefit conservation science.
A General Framework to Interpret Hydrogen-Deuterium Exchange Native Mass Spectrometry of G-Quadruplex DNA
Authors: Largy Eric , Ranz Matthieu , Gabelica Valérie 
Published: August 2023

AbstractG-quadruplexes (G4s) are secondary structures formed by guanine-rich oligonucleotides involved in various biological processes. However, characterizing G4s is challenging because of their structural polymorphism. Here, we establish how hydrogen-deuterium exchange native mass spectrometry (HDX/MS) can help to characterize G4 structures and dynamics in solution. We correlated the time range of G4 exchange to the number of guanines involved in inner and outer tetrads. We also established relationships between exchange rates, number of tetrads, bound cations, and stability. The use of HDX/native MS allows for the determination of tetrads formed and assessment of G4 stability at a constant temperature. A key finding is that stable G4s exchange through local fluctuations (EX2 exchange), whereas less stable G4s also undergo exchange through partial or complete unfolding (EX1 exchange). Deconvolution of the bimodal isotope distributions resulting from EX1 exchange provides valuable insight into the kinetics of folding and unfolding processes, and allows one to detect and characterize transiently unfolded intermediates, even if scarcely populated. HDX/native MS thus represents a powerful tool for a more comprehensive exploration of the folding landscapes of G4s.TOC graphic
Targeted lipid A modification ofShigellavaccine strains reduced endotoxicity without compromising immunogenicity or invasiveness
Authors: Sherman Matthew E , Michalski Jane , Das Sayan , Yang Hyojik , Barnoy Shoshana , Chandrasekaran Lakshmi , Venkatesan Malabi , Ernst Robert K 
Published: August 2023

AbstractShigellainfection contributes significantly to the global disease burden, especially affecting young children in developing countries. Currently, a vaccine againstShigellais unavailable and the prevalence of antibiotic resistance amongstShigellaspecies is continually rising. Live-attenuatedShigellavaccine candidates developed at Walter Reed Army Institute of Research have shown remarkable immunogenicity but exhibit adverse reactogenicity, most likely due to the highly toxic lipid A moiety present on the bacterial membrane. Previous attempts at reducing the endotoxicity have focused on deletion of intrinsic lipid A biosynthesis enzymes. In this study, we instead introduce exogenous lipid A modifying enzymes, generating targeted modifications in the lipid A structure, leading to a dampened TLR4 response within the host. In doing so, we generated vaccine candidates with detoxified lipid A and unaltered O-antigen structure thereby preserving the serotype-specific immunity while reducing endotoxicity.
Prolonging the Delivery of Influenza Virus Vaccine Improves the Quantity and Quality of the Induced Immune Responses in Mice
Authors: Beukema M. , Gong S. , Al-Jaawni K. , de Vries-Idema J. J. , Krammer F. , Zhou F. , Cox R. J. , Huckriede A. L. W. 
Published: August 2023

AbstractInfluenza vaccines play a vital role in protecting individuals from influenza virus infection and severe illness. However, current influenza vaccines have suboptimal efficacy, which is further reduced in cases where the vaccine strains do not match the circulating strains. One strategy to enhance the efficacy of influenza vaccines is by extended antigen delivery, thereby mimicking the antigen kinetics of a natural infection. Prolonging antigen availability was shown to quantitatively enhance influenza virus-specific immune responses but how it affects the quality of the induced immune response is unknown. Therefore, the current study aimed to investigate whether prolongation of the delivery of influenza vaccine improves the quality of the induced immune responses over that induced by prime-boost immunization. To study this, mice were given daily doses of whole inactivated influenza virus vaccine for periods of 14, 21, or 28 days; the control group received prime-boost immunization with a 28 days interval. Our data show that the highest levels of cellular and humoral immune responses were induced by 28 days of extended antigen delivery, followed by 21, and 14 days of delivery, and prime-boost immunization. Moreover, prolonging vaccine delivery also improved the quality of the induced antibody response, as indicated by higher level of high avidity antibodies, a balanced IgG subclass profile, and a higher level of cross-reactive antibodies. Overall, our findings contribute to a better understanding of the immune response to influenza vaccination and have important implications for the design and development of future slow-release influenza vaccines.
Lineage tracing of newly accrued nuclei in skeletal myofibers uncovers distinct transcripts and interplay between nuclear populations
Authors: Sun Chengyi , Swoboda Casey O. , Petrany Michael J. , Parameswaran Sreeja , VonHandorf Andrew , Weirauch Matthew T. , Lepper Christoph , Millay Douglas P. 
Published: August 2023

SummaryMultinucleated skeletal muscle cells have an obligatory need to acquire additional nuclei through fusion with activated skeletal muscle stem cells when responding to both developmental and adaptive growth stimuli. A fundamental question in skeletal muscle biology has been the reason underlying this need for new nuclei in syncytial cells that already harbor hundreds of nuclei. To begin to answer this long-standing question, we utilized nuclear RNA-sequencing approaches and developed a lineage tracing strategy capable of defining the transcriptional state of recently fused nuclei and distinguishing this state from that of pre-existing nuclei. Our findings reveal the presence of conserved markers of newly fused nuclei both during development and after a hypertrophic stimulus in the adult. However, newly fused nuclei also exhibit divergent gene expression that is determined by the myogenic environment to which they fuse. Moreover, accrual of new nuclei through fusion is required for nuclei already resident in adult myofibers to mount a normal transcriptional response to a load-inducing stimulus. We propose a model of mutual regulation in the control of skeletal muscle development and adaptations, where newly fused and pre-existing myonuclear populations influence each other to maintain optimal functional growth.
Conservation of affinity rather than sequence underlies a dynamic evolution of the motif-mediated p53/MDM2 interaction in teleosts
Authors: Mihalič Filip , Arcila Dahiana , Pettersson Mats E. , Farkhondehkish Pouria , Andersson Eva , Andersson Leif , Betancur-R Ricardo , Jemth Per 
Published: August 2023

ABSTRACTThe transcription factor and cell cycle regulator p53 is marked for degradation by the ubiquitin ligase MDM2. The interaction between these two proteins is mediated by a conserved binding motif in the disordered p53 transactivation domain (p53TAD) and the folded SWIB domain in MDM2. The conserved motif in p53TAD from zebrafish displays a 20-fold weaker interaction with MDM2, compared to the interaction in human and chicken. To investigate this apparent difference, we tracked the molecular evolution of the p53TAD/MDM2 interaction among ray- finned fishes (Actinopterygii), the largest vertebrate clade. Intriguingly, phylogenetic analyses, ancestral sequence reconstructions, and binding experiments showed that different loss-of- affinity changes in the canonical binding motif within p53TAD have occurred repeatedly and convergently in different fish lineages, resulting in relatively low extant affinities (KD= 0.5-5 μM). However, for eleven different fish p53TAD/MDM2 interactions, non-conserved regions flanking the canonical motif increased the affinity 4 to 73-fold to be on par with the human interaction. Our findings suggest that compensating changes at conserved and non-conserved positions within the motif, as well as in flanking regions of low conservation, underlie a stabilizing selection of “functional affinity” in the p53TAD/MDM2 interaction. Such interplay complicates bioinformatic prediction of binding and call for experimental validation. Motif- mediated protein-protein interactions involving short binding motifs and folded interaction domains are very common across multicellular life. It is likely that evolution of affinity in motif- mediated interactions often involves an interplay between specific interactions made by conserved motif residues and non-specific interactions by non-conserved disordered regions.
iATPSnFR2: a high dynamic range fluorescent sensor for monitoring intracellular ATP
Authors: Marvin Jonathan S. , Kokotos Alexandros C. , Kumar Mukesh , Pulido Camila , Tkachuk Ariana N. , Yao Jocelyn Shuxin , Brown Timothy A. , Ryan Timothy A. 
Published: August 2023

AbstractWe developed a significantly improved genetically encoded quantitative adenosine triphosphate (ATP) sensor to provide real-time dynamics of ATP levels in subcellular compartments. iATPSnFR2 is a variant of iATPSnFR1, a previously developed sensor that has circularly permuted super-folder GFP inserted between the ATP-binding helices of theε-subunit of a bacterial F0-F1ATPase. Optimizing the linkers joining the two domains resulted in a ∼ 5-6 fold improvement in the dynamic range compared to the previous generation sensor, with excellent discrimination against other analytes and affinity variants varying from 4 μM to 500 μM. A chimeric version of this sensor fused to either the HaloTag protein or a suitably spectrally separated fluorescent protein, provides a ratiometric readout allowing comparisons of ATP across cellular regions. Subcellular targeting of the sensor to nerve terminals reveals previously uncharacterized single synapse metabolic signatures, while targeting to the mitochondrial matrix allowed direct quantitative probing of oxidative phosphorylation dynamics.Significance StatementAdenosine triphosphate (ATP) is a key metabolite necessary for cellular life. Here we develop a next-generation genetically encoded ratiometric fluorescent ATP sensor that allows subcellular tracking of ATP levels in living cells. The large dynamic range makes it possible to follow the dynamics of this metabolite across cells and subcellular regions under different metabolic stressors. We expect that iATPSnFR2 will provide researchers with exciting new opportunities to study ATP dynamics with temporal and spatial resolution that has, until now, been unavailable.
Neither alpha-synuclein-preformed fibrils derived from patients withGBA1mutations nor the host murine genotype significantly influence seeding efficacy in the mouse olfactory bulb
Authors: Walton Sara , Fenyi Alexis , Tittle Tyler , Sidransky Ellen , Pal Gian , Choi Solji , Melki Ronald , Killinger Bryan A. , Kordower Jeffrey H. 
Published: August 2023

AbstractParkinson’s disease (PD) is a neurodegenerative disease characterized by progressive motor symptoms and alpha-synuclein (αsyn) aggregation in the nervous system. For unclear reasons, PD patients with certain GBA mutations (GBA-PD) have a more aggressive clinical progression. Two testable hypotheses that can potentially account for this phenomenon are thatGBA1mutations promote αsyn spread or drive the generation of highly pathogenic αsyn polymorphs (i.e., strains). We tested these hypotheses by treating homozygousGBA1D409V knockin (KI) mice with human α-syn-preformed fibrils (PFFs) and treating wild-type mice (WT) with several αsyn-PFF polymorphs amplified from brain autopsy samples collected from patients with idiopathic PD and GBA-PD patients with either homozygous or heterozygousGBA1mutations. Robust phosphorylated-αsyn (PSER129) positive pathology was observed at the injection site (i.e., the olfactory bulb granular layer) and throughout the brain six months following PFF injection. The PFF seeding efficiency and degree of spread were similar regardless of the mouse genotype or PFF polymorphs. We found that PFFs amplified from the human brain, regardless of patient genotype, were generally more effective seeders than wholly synthetic PFFs (i.e., non-amplified); however, PFF concentration differed between these two studies, and this might also account for the observed differences. To investigate whether the molecular composition of pathology differed between different seeding conditions, we permed Biotinylation by Antibody Recognition on PSER129 (BAR-PSER129). We found that for BAR-PSER129, the endogenous PSER129 pool dominated identified interactions, and thus, very few potential interactions were explicitly identified for seeded pathology. However, we found Dctn2 interaction was shared across all PFF conditions, and Nckap1 and Ap3b2 were unique to PFFs amplified from GBA-PD brains of heterozygous mutation carriers. In conclusion, both the genotype and αsyn strain had little effect on overall seeding efficacy and global PSER129-interactions.
The genome of the Wollemi pine, a critically endangered “living fossil” unchanged since the Cretaceous, reveals extensive ancient transposon activity
Authors: Stevenson Dennis Wm. , Ramakrishnan Srividya , Alves Cristiane de Santis , Coelho Laís Araujo , Kramer Melissa , Goodwin Sara , Ramos Olivia Mendevil , Eshel Gil , Sondervan Veronica M. , Frangos Samantha , Zumajo-Cardona Cecilia , Jenike Katherine , Ou Shujun , Wang Xiaojin , Lee Yin Peng , Loke Stella , Rossetto Maurizio , McPherson Hannah , Nigris Sebastiano , Moschin Silvia , Little Damon P. , Katari Manpreet S. , Varala Kranthi , Kolokotronis Sergios-Orestis , Ambrose Barbara , Croft Larry J. , Coruzzi Gloria M. , Schatz Michael , McCombie W. Richard , Martienssen Robert A. 
Published: August 2023

AbstractWe present the genome of the living fossil,Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity.Wollemia, like other conifers, is susceptible toPhytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.
Cell-extrinsic effects ofIrf2on cDC2 development
Authors: O’Connor Kevin W. , Liu Tiantian , Kim Sunkyung , Murphy Theresa L. , Murphy Kenneth M. 
Published: August 2023

AbstractCharacterization of the functional effects of cDC2s in vivo requires model systems in which cDC2s are depleted. Previous literature has reported a loss of cDC2s in mice lacking the transcription factor IRF21,2. We sought to further characterize the cDC2 defect in these animals. Here, we find that the requirement for IRF2 in cDC2 development and survival is cell-extrinsic and correlated to the development of dermatitis in theIrf2-/-model system. We also find that Flt3L-mediated in vitro development of cDC1s and cDC2s, but not pDCs, is abrogated inIrf2-/-bone marrow, as well as in wild-type bone marrow cultured with IFNα. Loss of interferon α (IFNα) signaling inIrf2-/-mice restored cDC2 development in vivo and cDC1 and cDC2 development in vitro. We therefore conclude that IRF2 is required for cDC2 development in a cell-extrinsic manner dependent on IFNα signaling.