bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disease-specific loss of microbial cross-feeding interactions in the human gut
Authors: Marcelino Vanessa R. , Welsh Caitlin , Diener Christian , Gulliver Emily L. , Rutten Emily L. , Young Remy B. , Giles Edward M. , Gibbons Sean M. , Greening Chris , Forster Samuel C. 
Published: February 2023

AbstractMany gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feeding interactions are still challenging to quantify and remain poorly characterized. Here we introduce a Metabolite Exchange Score (MES) to quantify those interactions. Using metagenome-wide metabolic models from over 1600 individuals, the MES allowed us to identify and rank metabolic interactions that were significantly affected by a loss of cross-feeding partners in 10 out of 11 diseases. When applied to a Crohn’s disease case-control study, our approach identified a lack of species with the ability to consume hydrogen sulphide as the main distinguishing microbiome feature of disease. We propose that our conceptual framework will help prioritize in-depth analyses, experiments and clinical targets, and that targeting the restoration of microbial cross-feeding interactions is a promising mechanism-informed strategy to reconstruct a healthy gut ecosystem.
New RoxS sRNA targets identified inB. subtilisby pulsed SILAC
Authors: Allouche Delphine , Kostova Gergana , Hamon Marion , Marchand Christophe H. , Caron Mathias , Belhocine Sihem , Christol Ninon , Charteau Violette , Condon Ciarán , Durand Sylvain 
Published: February 2023

Non-coding RNAs (sRNA) play a key role in controlling gene expression in bacteria, typically by base-pairing with ribosome binding sites to block translation. The modification of ribosome traffic along the mRNA generally affects its stability. However, a few cases have been described in bacteria where sRNAs can affect translation without a major impact on mRNA stability. To identify new sRNA targets inB. subtilispotentially belonging to this class of mRNAs, we used pulsed-SILAC (stable isotope labeling by amino acids in cell culture) to label newly synthesized proteins after short expression of the RoxS sRNA, the best characterized sRNA in this bacterium. RoxS sRNA was previously shown to interfere with the expression of genes involved in central metabolism, permitting control of the NAD+/NADH ratio inB. subtilis. In this study, we confirmed most of the known targets of RoxS, showing the efficiency of the method. We further expanded the number of mRNA targets encoding enzymes of the TCA cycle and identified new targets primarily regulated at the translational level. One of these is YcsA, a tartrate dehydrogenase that uses NAD+ as co-factor, in excellent agreement with the proposed role of RoxS in Firmicutes.ImportanceNon-coding RNA (sRNA) play an important role in bacterial adaptation and virulence. The identification of the most complete set of targets for these regulatory RNAs is key to fully identify the perimeter of its function(s). Most sRNAs modify both the translation (directly) and mRNA stability (indirectly) of their targets. However, sRNAs can also influence the translation efficiency of the target primarily, with little or no impact on mRNA stability. The characterization of these targets is challenging. We describe here the application of the pulsed SILAC method to identify these targets and obtain the most complete list of targets for a defined sRNA.
An engineered electroosmotic flow transports unravelled proteins across nanopores
Authors: Sauciuc Adina , Morozzo Blasco , Tadema Matthijs , Chinappi Mauro , Maglia Giovanni 
Published: February 2023

AbstractThe development of a technology capable of sequencing single proteins holds promise to unravel new biological information hidden in ensemble analysis. However, new techniques must be first developed. In one approach, proteins are unfolded and translocate across a nanopore under an external bias. Unlike DNA, however, proteins do not have a uniform charge, and the electrophoretic force cannot be used to translocate proteins. Here, we show that by introducing sets of charges spaced by ~1 nm an otherwise neutral nanopore an electroosmotic force is created that induces the unidirectional transport of polypeptides, even against relatively strong electrophoretic forces. Unstructured polypeptides and native proteins unfolded with urea produce current signatures as they traversed the nanopore, which could lead to quick protein identifcation. This approach can be used to translocate and stretch proteins in non-enzymatic protein identification and enzymatic protein sequencing approaches.
The dynamics of hinge flexibility in receptor bound immunoglobulin E revealed by electron microscopy
Authors: Jensen Rasmus K , Miehe Michaela , Gandini Rosaria , Jørgensen Martin H , Spillner Edzard , Andersen Gregers R 
Published: February 2023

AbstractImmunoglobulin E is a mammal specific antibody isotype supporting the immune response against parasites and venoms, but also a driver of allergic responses. Prior studies have defined the conformation of the IgE Fc fragment bound to the cell surface receptor FcεRIα and the dynamic properties of the IgE Fc. It remains unknown, how these prior studies translate to the complex of a full antibody including the Fab arms with the receptor. Here we show that in a cryo-EM structure of the IgE FcεRIα complex, IgE adopts a T-like conformation where the antigen binding Fab arms may be parallel to the cell membrane. Two additional conformations are captured in negative stain EM (ns-EM) where the arrangements of the Fab arms differ from the cryo-EM conformation. Small angle scattering data favors the FcεRIα bound IgE conformation observed by cryo-EM, but the major IgE conformation observed by ns-EM possibly may also occur. In all observed conformations of FcεRIα bound IgE, one Fab arm is fixed relative to the IgE Fc moiety whereas the second Fab may alternate its position. Introduction of flexibility in the Fab-Fc hinge diminishes the biological activity of IgE demonstrating a functional role for the observed defined Fab-Fc hinge conformations. Our data show the organization of a full size antibody on its receptor and reveal a new layer of dynamics in FcεRIα bound IgE on top of the well established spectrum of IgE Fc conformations. Development of novel anti-IgE therapeutics may take into account these distinct FcεRIα bound IgE conformations.Significance statementIgE represents a canonical antibody isotype and is a key molecule for the allergic immune response to environmental triggers driven by mast cells and basophils. The requirements for efficient mediation of IgE’s effects are not fully understood. Here we elucidate the structure of the entire IgE in complex with its high affinity receptor and identify two clearly distinct and dominant conformations, in which one of the Fab arms is fixed relative to the Fc domains. Enforcing IgE flexibility impacts the biological function with potential consequences for the allergic response. This unique behavior makes IgE different from all other isotypes and its understanding sheds light on the allergenic activation of the immune response.
Reversal of drug resistance by disruption of a Gain-of-Function mutant p53 and transcriptional co-activator PC4 interaction
Authors: Mondal Priya , Roy Kumar Singha , Kundu Tapas K. , Roychoudhury Susanta , Roy Siddhartha 
Published: February 2023

SummaryThe positive coactivator 4 or PC4 is a chromatin-associated protein whose role in gene regulation by wild-type p53 is now well-known. During tumorigenesis, p53 is often mutated resulting in its loss of function. A sub-class of these mutants gain new pro-proliferation properties which occur largely due to the upregulation of many pro-proliferation genes. Little is known about the roles of PC4 in tumor cells bearing mutant p53 genes. In this article, we show that PC4 associates with one of the tumor-associated gain-of-function p53 mutants, R273H. This association drives its recruitment to two promoters, UBE2C, and MDR1, known to be responsible for imparting aggressive growth and resistance to many drugs. A previously reported peptide that disrupts PC4-wild-type p53 interaction also disrupts the PC4-R273Hp53 protein-protein interaction. The introduction of this peptide to tumor cells bearing the R273HTP53 gene resulted in a lowering of MDR1 expression and abrogation of drug resistance. Interestingly, cells bearing another gain-of-function mutant R248W do not show the same type of response, suggesting that the action of PC4 on mutant p53s may differ for different GOF mutants. The results presented here suggest that PC4-R273H interaction may be a promising target for reducing proliferation and tumor drug resistance.
Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background
Authors: Evangelista C. , Kamenova S. , Pauli B. Diaz , Sandkjenn J. , Vøllestad L.A. , Edeline E. , Trosvik P. , de Muinck EJ. 
Published: February 2023

AbstractUnravelling evolution-by-environment interactions on the gut microbiome is particularly relevant considering the unprecedented level of human-driven disruption of the ecological and evolutionary trajectories of species. Here, we aimed to evaluate whether an evolutionary response to size-selective mortality influences the gut microbiome of medaka (Oryzias latipes), how environmental conditions interact with the genetic background of medaka on their microbiota, and the association between microbiome diversity and medaka growth-related traits. To do so, we studied two lineages of medaka with known divergence in foraging efficiency and life history raised under antagonistic size-selective regimes for 10 generations (i.e. the largest or the smallest breeders were removed to mimic fishing-like or natural mortality). In pond mesocosms, the two lineages were subjected to contrasting population density and light intensity (used as proxies of resource availability). We observed significant differences in the gut microbiome composition and richness between the two lines, and this effect was mediated by light intensity. The bacterial richness of fishing-like medaka (small-breeder line) was reduced by 34% under low-light conditions compared to high-light conditions, while it remained unchanged in natural mortality-selected medaka (large-breeder line). However, the observed changes in bacterial richness did not correlate with changes in adult growth rate or body condition. Given the growing evidence about the gut microbiomes importance to host health, more in-depth studies are required to fully understand the role of the microbiome in size-selected organisms and the possible ecosystem-level consequences.
Predictive learning rules generate a cortical-like replay of probabilistic sensory experiences
Authors: Asabuki Toshitake , Fukai Tomoki 
Published: February 2023

AbstractThe brain is thought to construct an optimal internal model representing the probabilistic structure of the environment accurately. Evidence suggests that spontaneous brain activity gives such a model by cycling through activity patterns evoked by previous sensory experiences with the experienced probabilities. The brain’s spontaneous activity emerges from internally-driven neural population dynamics. However, how cortical neural networks encode internal models into spontaneous activity is poorly understood. Recent computational and experimental studies suggest that a cortical neuron can implement complex computations, including predictive responses, through soma-dendrite interactions. Here, we show that a recurrent network of spiking neurons subject to the same predictive learning principle provides a novel mechanism to learn the spontaneous replay of probabilistic sensory experiences. In this network, the learning rules minimize probability mismatches between stimulus-evoked and internally driven activities in all excitatory and inhibitory neurons. This learning paradigm generates stimulus-specific cell assemblies that internally remember their activation probabilities using within-assembly recurrent connections. Our model contrasts previous models that encode the statistical structure of sensory experiences into Markovian transition patterns among cell assemblies. We demonstrate that the spontaneous activity of our model well replicates the behavioral biases of monkeys performing perceptual decision making. Our results suggest that interactions between intracellular processes and recurrent network dynamics are more crucial for learning cognitive behaviors than previously thought.
Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity
Authors: Rohban Sara , Rafiee Mahmoud-Reza , Ule Jernej , Luscombe Nicholas M. 
Published: February 2023

AbstractIntegrator is a multi-subunit complex that directly interacts with the C-terminal domain (CTD) of RNA polymerase II (RNAPII). Through its RNA endonuclease activity, Integrator is required for 3′-end processing of both non-coding and coding transcripts. Here we demonstrate that depleting Integrator subunit 11 (INTS11), the main catalytic subunit of the Integrator complex, leads to a global elongation defect as a result of decreased polymerase processivity. We observe this defect in the region approximately 12 to 35 kb downstream of the transcription start site (TSS), where RNAPII normally transitions to its maximum processivity. We also identify an important role for INTS11, possibly in association with RNAPII CTD phospho-Tyr1, in repressing antisense transcription upstream of active promoters, as well as repressing transcription of genic regions near AsiSI-induced double-strand breaks.Altogether, this study points toward a novel function of Integrator in promoting termination of incompetent RNAPII molecules while facilitating the transition to fully processive polymerase in order to enable efficient elongation.
NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons
Authors: Hamagami Nicole , Wu Dennis Y. , Clemens Adam W. , Nettles Sabin A. , Gabel Harrison W. 
Published: February 2023

SummaryDuring postnatal development the DNA methyltransferase DNMT3A deposits high levels of non-CG cytosine methylation in neurons. This unique methylation is critical for transcriptional regulation in the mature mammalian brain, and loss of this mark is implicated in DNMT3A-associated neurodevelopmental disorders (NDDs). The mechanisms determining genomic non-CG methylation profiles are not well defined however, and it is unknown if this pathway is disrupted in additional NDDs. Here we show that genome topology and gene expression converge to shape histone H3 lysine 36 dimethylation (H3K36me2) profiles, which in turn recruit DNMT3A and pattern neuronal non-CG methylation. We show that NSD1, the H3K36 methyltransferase mutated in the NDD, Sotos syndrome, is required for megabase-scale patterning of H3K36me2 and non-CG methylation in neurons. We find that brain-specific deletion of NSD1 causes alterations in DNA methylation that overlap with models of DNMT3A disorders and define convergent disruption in the expression of key neuronal genes in these models that may contribute to shared phenotypes in NSD1- and DNMT3A-associated NDD. Our findings indicate that H3K36me2 deposited by NSD1 is an important determinant of neuronal non-CG DNA methylation and implicates disruption of this methylation in Sotos syndrome.HighlightsTopology-associated DNA methylation and gene expression independently contribute to neuronal gene body and enhancer non-CG DNA methylation patterns.Topology-associated H3K36me2 patterns and local enrichment of H3K4 methylation impact deposition of non-CG methylation by DNMT3A.Disruption of NSD1in vivoleads to alterations in H3K36me2, DNA methylation, and gene expression that overlap with models of DNMT3A disorders.
Ergosterol distribution controls surface structure formation and fungal pathogenicity
Authors: Choy Hau Lam , Gaylord Elizabeth A. , Doering Tamara L. 
Published: February 2023

ABSTRACTErgosterol, the major sterol in fungal membranes, is critical for defining membrane fluidity and regulating cellular processes. Although ergosterol synthesis has been well defined in model yeast, little is known about sterol organization in the context of fungal pathogenesis. We identified a retrograde sterol transporter, Ysp2, in the opportunistic fungal pathogenCryptococcus neoformans. We found that the lack of Ysp2 under host-mimicking conditions leads to abnormal accumulation of ergosterol at the plasma membrane, invagination of the plasma membrane, and malformation of the cell wall, which can be functionally rescued by inhibiting ergosterol synthesis with the antifungal drug fluconazole. We also observed that cells lacking Ysp2 mislocalize the cell surface protein Pma1 and have thinner and more permeable capsules. As a result of perturbed ergosterol distribution and its consequences,ysp2Δ cells cannot survive in physiologically-rele-vant environments such as host phagocytes and are dramatically attenuated in virulence. These findings expand our knowledge of cryptococcal biology and underscore the importance of sterol homeostasis in fungal pathogenesis.IMPORTANCECryptococcus neoformansis an opportunistic fungal pathogen that kills over 100,000 people worldwide each year. Only three drugs are available to treat cryptococcosis, and these are variously limited by toxicity, availability, cost, and resistance. Ergosterol is the most abundant sterol in fungi and a key component in modulating membrane behavior. Two of the drugs used for cryptococcal infection, amphotericin B and fluconazole, target this lipid and its synthesis, highlighting its importance as a therapeutic target. We discovered a cryptococcal ergosterol transporter, Ysp2, and demonstrated its key roles in multiple aspects of cryptococcal biology and pathogenesis. These studies demonstrate the role of ergosterol homeostasis inC. neoformansvirulence, deepen our understanding of a pathway with proven therapeutic importance, and open a new area of study.
Pathology of naturally acquired high pathogenicity avian influenza virus H5N1 infection in seabirds
Authors: Lean Fabian ZX , Falchieri Marco , Furman Natalia , Tyler Glen , Robinson Caroline , Holmes Paul , Reid Scott M , Banyard Ashley C , Brown Ian H , Man Catherine , Núñez Alejandro 
Published: February 2023

AbstractThe re-emergence of the high pathogenicity avian influenza virus (HPAIV) subtype H5N1 in the United Kingdom in 2021-2022 has caused unprecedented epizootic events in wild birds and poultry. During the summer of 2022 there was a shift in virus transmission dynamics resulting in increased HPAIV infection in seabirds and consequently a profound impact on seabird populations. To understand the pathological impact of HPAIV in seabirds, we have evaluated the virus distribution and associated pathological changes in the tissues of great skua (Stercorarius skua, n=8), long tailed skua (Stercorarius longicaudus, n=1), European herring gull (Larus argentatus, n=5), and black-headed gull (Chroicocephalus ridibundus, n=4). Grossly there was gizzard ulceration in one great skua and pancreatic necrosis in four herring gulls, which were confirmed for virus infectionin situby immunohistochemistry. Microscopical analysis revealed neuro-, pneumo-, lymphoidand cardiotropism of HPAIV H5N1, with the most common virus-associated pathological changes being pancreatic and splenic necrosis. Examination of the reproductive tract of the great skua revealed HPAIV-associated oophoritis and salpingitis, and virus replication within the oviductal epithelium. Across the birds, epitheliotropism was evident in the intestine, nasal turbinate, and trachea. This was, in contrast, not observed in the 2021 summer mortality event in great skuas and may be significant for the disease epidemiology observed in 2022. The emergence of HPAIV in seabirds, particularly during summer 2022, has challenged the dogma of HPAIV dynamics, posing a significant threat to wild bird life with potential implications to the reproductive performance of seabirds of conservation importance.
A Single Cell Time Course of Senescence Uncovers Discrete Cell Trajectories and Transcriptional Heterogeneity
Authors: Ciotlos Serban , Wimer Lauren , Campisi Judy , Melov Simon 
Published: February 2023

AbstractSenescent cells (SnCs) are typically studied as endpoints of a complex transformational process, owing to their frequent maladaptive effects on surrounding tissue and cells. SnCs accumulate with age, and while they ultimately comprise a small percentage of cells in tissues, they have important roles in age associated pathologies. Several obstacles remain in understanding the heterogeneous nature of senescence, and formulating potent beneficial intervention strategies. One approach targets senescent cells and kills them (“senolytic” approach), and is often driven by a low resolution understanding of SnC identity, which risks both incomplete clearance and off-target effects. Cellular senescence is not a singular binary response, but a suite of response trajectories that vary by multiple parameters including inducer and initial cell state. In order to elucidate the developmental trajectories of SnCs, we performed single-cell RNA sequencing on IMR90 lung fibroblasts senescencing across a 12 day time period. Our analysis reveals substantial heterogeneity in gene expression within timepoints and across the full time-course. We uncovered unique markers and differentially regulated pathways in cell populations within each timepoint. Supervised trajectory inference of the time-course data uncovered the root-origin and fates of distinct SnC lineages over 3 stages of senescence induction. Altogether our data provide a novel approach to stud SnC development, identifying cell states of interest, and differentiating between SnCs and quiescent cells. This will aid in identifying key targets for therapeutic intervention in senescence.
Distinct genomic contexts predict gene presence-absence variation in different pathotypes of a fungal plant pathogen
Authors: Joubert Pierre M. , Krasileva Ksenia V. 
Published: February 2023

AbstractBackgroundFungi use the accessory segments of their pan-genomes to adapt to their environments. While gene presence-absence variation (PAV) contributes to shaping these accessory gene reservoirs, whether these events happen in specific genomic contexts remains unclear. Additionally, since pan-genome studies often group together all members of the same species, it is uncertain whether genomic or epigenomic features shaping pan-genome evolution are consistent across populations within the same species. Fungal plant pathogens are useful models for answering these questions because members of the same species often infect distinct hosts, and they frequently rely on gene PAV to adapt to these hosts.ResultsWe analyzed gene PAV in the rice and wheat blast fungus,Magnaporthe oryzae, and found that PAV of disease-causing effectors, antibiotic production, and non-self-recognition genes may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features and data from available datasets for patterns that might help explain these PAV events. We observed that proximity to transposable elements (TEs), gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between PAV genes and conserved genes, among other features. We used these features to construct a random forest classifier that was able to predict whether a gene is likely to experience PAV with high precision (86.06%) and recall (92.88%) in rice-infectingM. oryzae. Finally, we found that PAV in wheat- and rice-infecting pathotypes ofM. oryzaediffered in their number and their genomic context.ConclusionsOur results suggest that genomic and epigenomic features of gene PAV can be used to better understand and even predict fungal pan-genome evolution. We also show that substantial intra-species variation can exist in these features.