bluuebunny/crossref_metadata_2025_split huggingface dataset:
A role for the Gram-negative outer membrane in bacterial shape determination
Authors: Fivenson Elayne M. , Rohs Patricia D.A. , Vettiger Andrea , Sardis Marios F. , Torres Grasiela , Forchoh Alison , Bernhardt Thomas G. 
Published: February 2023

ABSTRACTThe cell envelope of Gram-negative bacteria consists of three distinct layers: the cytoplasmic membrane, a cell wall made of peptidoglycan (PG), and an asymmetric outer membrane (OM) composed of phospholipid in the inner leaflet and lipopolysaccharide (LPS) glycolipid in the outer leaflet. The PG layer has long been thought to be the major structural component of the envelope protecting cells from osmotic lysis and providing them with their characteristic shape. In recent years, the OM has also been shown to be a load-bearing layer of the cell surface that fortifies cells against internal turgor pressure. However, whether the OM also plays a role in morphogenesis has remained unclear. Here, we report that changes in LPS synthesis or modification predicted to strengthen the OM can suppress the growth and shape defects ofEscherichia colimutants with reduced activity in a conserved PG synthesis machine called the Rod system (elongasome) that is responsible for cell elongation and shape determination. Evidence is presented that OM fortification in the shape mutants restores the ability of MreB cytoskeletal filaments to properly orient the synthesis of new cell wall material by the Rod system. Our results are therefore consistent with a role for the OM in the propagation of rod shape during growth in addition to its well-known function as a diffusion barrier promoting the intrinsic antibiotic resistance of Gram-negative bacteria.SIGNIFICANCEThe cell wall has traditionally been thought to be the main structural determinant of the bacterial cell envelope that resists internal turgor and determines cell shape. However, the outer membrane (OM) has recently been shown to contribute to the mechanical strength of Gram-negative bacterial envelopes. Here, we demonstrate that changes to OM composition predicted to increase its load bearing capacity rescue the growth and shape defects ofEscherichia colimutants defective in the major cell wall synthesis machinery that determines rod shape. Our results therefore reveal a previously unappreciated role for the OM in bacterial shape determination in addition to its well-known function as a diffusion barrier that protects Gram-negative bacteria from external insults like antibiotics.
Automated Agnostic Designation of Pathogen Lineages
Authors: McBroome Jakob , de Bernardi Schneider Adriano , Roemer Cornelius , Wolfinger Michael T. , Hinrichs Angie S. , O’Toole Aine Niamh , Ruis Christopher , Turakhia Yatish , Rambaut Andrew , Corbett-Detig Russell 
Published: February 2023

AbstractPathogen nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were added to a growing global dataset. This approach to dynamic lineage designation is dependent on a large and active epidemiological community identifying and curating each new lineage. This is vulnerable to time-critical delays as well as regional and personal bias. To address these issues, we developed a simple heuristic approach that divides a phylogenetic tree into lineages based on shared ancestral genotypes. We additionally provide a framework that automatically prioritizes the lineages by growth rate and association with key mutations or locations, extensible to any pathogen. Our implementation is efficient on extremely large phylogenetic trees and produces similar results to existing Pango lineage designations when applied to SARS-CoV-2. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever increasing genomic datasets.
Gene panel selection for targeted spatial transcriptomics
Authors: Zhang Yida , Petukhov Viktor , Biederstedt Evan , Que Richard , Zhang Kun , Kharchenko Peter V. 
Published: February 2023

AbstractTargeted spatial transcriptomics hold particular promise in analysis of complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes being studied. A limitation of existing gene selection methods is that they rely on scRNA-seq data, ignoring platform effects between technologies. Here we describe gpsFISH, a computational method to perform gene selection through optimizing detection of known cell types. By modeling and adjusting for platform effects, gpsFISH outperforms other methods. Furthermore, gpsFISH can incorporate cell type hierarchies and custom gene preferences to accommodate diverse design requirements.
Lung microenvironments harborMycobacterium tuberculosisphenotypes with distinct treatment responses
Authors: Walter Nicholas D. , Ernest Jackie P. , Dide-Agossou Christian , Bauman Allison A. , Ramey Michelle E. , Rossmassler Karen , Massoudi Lisa M. , Pauly Samantha , Al Mubarak Reem , Voskuil Martin I. , Kaya Firat , Sarathy Jansy P. , Zimmerman Matthew D. , Dartois Véronique , Podell Brendan K. , Savic Radojka M. , Robertson Gregory T. 
Published: February 2023

ABSTRACTTuberculosis lung lesions are complex and harbor heterogeneous microenvironments that influence antibiotic effectiveness. Major strides have been made recently in understanding drug pharmacokinetics in pulmonary lesions, but the bacterial phenotypes that arise under these conditions and their contribution to drug tolerance is poorly understood. A pharmacodynamic marker called the RS ratio quantifies ongoing rRNA synthesis based on the abundance of newly-synthesized precursor rRNA relative to mature structural rRNA. Application of the RS ratio in the C3HeB/FeJ mouse model demonstrated thatMycobacterium tuberculosispopulations residing in different tissue microenvironments are phenotypically distinct and respond differently to drug treatment with rifampin, isoniazid or bedaquiline. This work provides a foundational basis required to address how anatomic and pathologic microenvironmental niches may contribute to the long treatment duration and drug tolerance during treatment of human tuberculosis.
ncBAF, a chromatin remodeler, enhances PXR-mediated transcriptional activation in the human and mouse liver
Authors: Kurosawa Kiamu , Nakano Masataka , Yokoseki Itsuki , Nagaoka Mai , Takemoto Seiya , Sakai Yoshiyuki , Kobayashi Kaoru , Kazuki Yasuhiro , Fukami Tatsuki , Nakajima Miki 
Published: February 2023

AbstractPregnane X receptor (PXR) is one of the key regulators of drug metabolism, gluconeogenesis, and lipid synthesis in the human liver. Activation of PXR by drugs such as rifampicin, simvastatin, and efavirenz causes adverse reactions such as drug□drug interaction, hyperglycemia, and dyslipidemia. The inhibition of PXR activation has merit in preventing such adverse events. Here, we demonstrated that bromodomain containing protein 9 (BRD9), a component of non-canonical brahma-related gene 1-associated factor (ncBAF), one of the chromatin remodelers, interacts with PXR. Rifampicin-mediated induction of CYP3A4 expression was attenuated by iBRD9, an inhibitor of BRD9, in human primary hepatocytes and CYP3A/PXR-humanized mice, indicating that BRD9 enhances the transcriptional activation of PXRin vitroandin vivo. Chromatin immunoprecipitation assay reveled that iBRD9 treatment resulted in attenuation of the rifampicin-mediated binding of PXR to theCYP3A4promoter region, suggesting that ncBAF functions to facilitate the binding of PXR to its response elements. Efavirenz-induced hepatic lipid accumulation was attenuated by iBRD9 in C57BL/6J mice, suggesting that the inhibition of BRD9 would be useful to reduce the risk of efavirenz-induced hepatic steatosis. Collectively, we found that inhibitors of BRD9, a component of ncBAF that plays a role in assisting transactivation by PXR, would be useful to reduce the risk of PXR-mediated adverse reactions.
Fecal virome transplantation is sufficient to alter fecal microbiota and drive lean and obese body phenotypes in mice
Authors: Borin Joshua M. , Liu Roland , Wang Yanhan , Wu Tsung-Chin , Chopyk Jessica , Huang Lina , Kuo Peiting , Ghose Chandrabali , Meyer Justin R. , Tu Xin M. , Schnabl Bernd , Pride David T. 
Published: February 2023

AbstractBackgroundThe gastrointestinal microbiome plays a significant role in numerous host processes and has an especially large impact on modulating the host metabolism. Prior studies have shown that when mice receive fecal transplants from obese donors that were fed high-fat diets (HFD) (even when recipient mice are fed normal diets after transplantation), they develop obese phenotypes. These studies demonstrate the prominent role that the gut microbiota play in determining lean and obese phenotypes. While much of the credit has been given to gut bacteria, studies have not measured the impact of gut viruses on these phenotypes. To address this shortcoming, we gavaged mice with viromes isolated from donors fed HFD or normal chow. By characterizing the mice’s gut bacterial biota and weight-gain phenotypes over time, we demonstrate that viruses can shape the gut bacterial community and affect weight gain or loss.ResultsWe gavaged mice longitudinally over 4 weeks while measuring their body weights and collecting fecal samples for 16S rRNA amplicon sequencing. We evaluated mice that were fed normal chow or high-fat diets, and gavaged each group with either chow-derived fecal viromes, HFD-derived fecal viromes, or phosphate buffered saline controls. We found a significant effect of gavage type, where mice fed chow but gavaged with HFD-derived viromes gained significantly more weight than their counterparts receiving chow-derived viromes. The converse was also true: mice fed HFD but gavaged with chow-derived viromes gained significantly less weight than their counterparts receiving HFD-derived viromes. These results were replicated in two separate experiments and the phenotypic changes were accompanied by significant and identifiable differences in the fecal bacterial biota. Notably, there were differences in Lachnospirales and Clostridia in mice fed chow but gavaged with HFD-derived fecal viromes, and in Peptostreptococcales, Oscillospirales, and Lachnospirales in mice fed HFD but gavaged with chow-derived fecal viromes. Due to methodological limitations, we were unable to identify specific bacterial species or strains that were responsible for respective phenotypic changes.ConclusionsThis study confirms that virome-mediated perturbations can alter the fecal microbiome in anin vivomodel and indicates that such perturbations are sufficient to drive lean and obese phenotypes in mice.
Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts
Authors: Zhou Weichen , Karan Kalpita R. , Gu Wenjin , Klein Hans-Ulrich , Sturm Gabriel , De Jager Philip L. , Bennett David A. , Hirano Michio , Picard Martin , Mills Ryan E 
Published: February 2023

AbstractThe transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non-human species1–3and recently demonstrated to occur in rare instances from one human generation to the next4. Here we investigated numtogenesis dynamics in humans in two ways. First, we quantified Numts in 1,187 post-mortem brain and blood samples from different individuals. Compared to circulating immune cells (n=389), post-mitotic brain tissue (n=798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, more brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures WGS design in a human fibroblast model that recapitulates several molecular hallmarks of aging5. These longitudinal experiments revealed a gradual accumulation of one Numt every ∼13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derivedSURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7- fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human post-mitotic tissues produce functionally-relevant human Numts over timescales shorter than previously assumed.
High-level ceftazidime-avibactam resistance inEscherichia coliconferred by the novel plasmid-mediated beta-lactamase CMY-185 variant
Authors: Shropshire William C. , Endres Bradley T. , Borjan Jovan , Aitken Samuel L. , Bachman William C. , McElheny Christi L. , Khan Ayesha , Bhatti Micah M. , Saharasbhojane Pranoti , Kawai Akito , Shields Ryan K. , Shelburne Samuel A. , Doi Yohei 
Published: February 2023

AbstractObjectivesTo characterize ablaCMYvariant associated with ceftazidime-avibactam (CZA) resistance from a serially collectedEscherichia coliisolate.MethodsA patient with an intra-abdominal infection due to recurrentE. coliwas treated with CZA. On day 48 of CZA therapy,E. coliwith a CZA MIC of >256 mg/L was identified from abdominal drainage. Illumina WGS was performed on all isolates to identify potential resistance mechanisms. Site-directed mutants of CMY β-lactamase were constructed to identify amino acid residues responsible for CZA resistance.ResultsWGS revealed that all three isolates wereE. coliST410. The CZA-resistant strain uniquely acquired a novel CMY β-lactamase gene, herein calledblaCMY-185, harbored on an IncIγ-type conjugative plasmid. The CMY-185 enzyme possessed four amino acid substitutions relative to CMY-2 including A114E, Q120K, V211S, and N346Y and conferred high-level CZA resistance with an MIC of 32 mg/L. Single CMY-2 mutants did not confer reduced CZA susceptibility. However, double and triple mutants containing N346Y previously associated with CZA resistance in other AmpC enzymes, conferred CZA MICs ranging between 4 and 32 mg/L as well as reduced susceptibility to the newly developed cephalosporin, cefiderocol. Molecular modelling suggested that the N346Y substitution confers the reduction of avibactam inhibition due to the steric hindrance between the side chain of Y346 and the sulfate group of avibactam.ConclusionWe identified CZA resistance inE. coliassociated with a novel CMY variant. Unlike other AmpC enzymes, CMY-185 appears to require an additional substitution on top of N346Y to confer CZA resistance.
Conditioning electrical stimulation fails to enhance sympathetic axon regeneration
Authors: Tian Tina , Patel Kevin , Kim David , SiMa HaoMin , Harris Alandrea R. , Owyoung Jordan N. , Ward Patricia J. 
Published: February 2023

ABSTRACTPeripheral nerve injuries are common, and there is a critical need for the development of novel treatments to complement surgical repair. Conditioning electrical stimulation (CES) is a novel variation of the well-studied perioperative electrical stimulation treatment paradigm. CES is a clinically attractive alternative because of its ability to be performed at the bedside prior to a scheduled nerve repair surgery. Although 60 minutes of CES has been shown to enhance motor and sensory axon regeneration, the effects of CES on sympathetic regeneration are unknown. We investigated how two clinically relevant CES paradigms (10 minutes and 60 minutes) impact sympathetic axon regeneration and distal target reinnervation. Our results indicate that the growth of sympathetic axons is inhibited by CES at acute time points, and at a longer survival time point post-injury, there is no difference between sham CES and the CES groups.We conclude sympathetic axons may retain some regenerative ability, but no enhancement is exhibited after CES, which may be accounted for by the inability of the electrical stimulation paradigm to recruit the small-caliber sympathetic axons into activity. Furthermore, 10-minute CES did not enhance motor and sensory regeneration with a direct repair, and neither 60-minute nor 10-minute CES enhanced motor and sensory regeneration through a graft. Further studies will be needed to optimize electrical stimulation parameters to enhance the regeneration of all neuron types.
Targeting fungal BET bromodomains as apan-Candidaantifungal strategy
Authors: Wei Kaiyao , Overhulse Justin M. , Arlotto Marie , Zhou Yingsheng , Dupper Nathan J. , Kashemirov Boris A. , Garnaud Cécile , Bourgine Gaëlle , Cornet Muriel , Rabut Gwenaël , McKenna Charles E. , Petosa Carlo , Govin Jérôme 
Published: February 2023

AbstractSmall molecules that target one or both bromodomains (BDs) of human BET proteins are intensely studied as potential new therapeutics against cancer, diabetes and other diseases. The BDs of the fungal BET protein Bdf1 are essential for the human fungal pathogenCandida albicans, suggesting BET inhibition as a potential antifungal strategy. However, while the inactivation of both Bdf1 BDs is lethal, that of a single BD only modestly affects viability, implying the need to develop antifungal compounds that selectively target both Bdf1 BDs without inhibiting human BDs. Here, we investigate Bdf1 as a potential antifungal target inCandida glabrata, an invasiveCandidaspecies phylogenetically distant fromC. albicansand of increasing medical concern. We show that Bdf1 BD functionality is essential inC. glabrataand identify a phenyltriazine derivative that targets both Bdf1 BDs with selectivity over human BET BDs. We show that human BET BDs can functionally replace Bdf1 BDs inC. glabrataand we use the humanized strains to demonstrate on-target antifungal activity of the phenyltriazine compound. Moreover, by exploiting the humanized and parental fungal strains we identified BET inhibitor I-BET726 to have potent antifungal activity against a broad spectrum ofCandidaspecies, including azole- and echinocandin-resistant clinicalC. albicansandC. glabrataisolates. Crystal structures suggest how to improve the potency and selectivity of these compounds. Taken together, our findings provide compelling support for the development of BET inhibitors as potential pan-Candidaantifungal therapeutics.
Too hot or too disturbed? Temperatures more than hikers affect circadian activity of females in northern chamois
Authors: Thel Lucie , Garel Mathieu , Marchand Pascal , Bourgoin Gilles , Loison Anne 
Published: February 2023

ABSTRACTRecreational activities often result in a spatial and/or temporal activity shift in wildlife. With the concurrent development of outdoor activities and increase in temperatures due to climate change, mountain species face increasing pressures in terms of managing their activity pattern to limit both risk exposure and thermal discomfort. Using more than 15 years of long-term GPS and activity sensor data, we investigated how female northern chamois,Rupicapra rupicapra rupicapra, adjust their summer circadian activity to spatiotemporal variation in both temperatures and hikers’ presence. Chamois behaviour was more affected by high temperatures than by hikers’ presence. During the hottest days, they shifted their activity peak earlier in the morning, were more active at night, less active during daytime and had longer morning and evening peaks compared to the coldest days. Global activity was only slightly different during the hottest than the coldest days. Conversely, hikers’ disturbance had weak effects on activity levels and on the timing of activity peaks. This is especially true for temporal disturbance (weekdays versus weekends and public holidays), possibly because most weekdays in summer fell during school holidays. During the hottest conditions, the morning activity peak was shorter and the evening peak longer in females living in the most exposed areas compared to females living in the least exposed areas. One possible explanation for the overall low effect of hikers’ disturbance may be that behavioural changes buffering animals from high temperatures and hikers’ presence (e.g. moving away from trails) allow them to just marginally modify their activity pattern. In the context of ongoing socioenvironmental changes, it is critical to conserve habitats providing thermal refuges against summer heat and protection from disturbance to mitigate potential detrimental consequences.
A panel of TDP-43-regulated splicing events verify loss of TDP-43 function in amyotrophic lateral sclerosis brain tissue
Authors: Cao Maize C. , Ryan Brigid , Wu Jane , Curtis Maurice , Faull Richard , Dragunow Mike , Scotter Emma L. 
Published: February 2023

AbstractTDP-43 dysfunction is a molecular hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A major hypothesis of TDP-43 dysfunction in disease is the loss of normal nuclear function, resulting in impaired RNA regulation and the emergence of cryptic exons. Cryptic exons and exon changes are emerging as promising markers of lost TDP-43 function in addition to revealing biological pathways involved in neurodegeneration in ALS/FTD. In this brief report, we identified markers of TDP-43 loss of function by depletingTARDBPfrom post-mortem human brain pericytes, a manipulablein vitroprimary human brain cell model, and identifying differential exon usage events with bulk RNA-sequencing analysis. We present these data in an interactive database (https://www.scotterlab.auckland.ac.nz/research-themes/tdp43-lof-db-v2/) together with seven other TDP-43-depletion datasets we meta-analysed previously, for user analysis of differential expression and splicing signatures. Differential exon usage events that were validated by qPCR were then compiled into a ‘differential exon usage panel’ with other well-established TDP-43 loss-of-function exon markers. This differential exon usage panel was investigated in ALS and control motor cortex tissue to verify whether, and to what extent, TDP-43 loss of function occurs in ALS. We find that profiles of TDP-43-regulated cryptic exons and changed exon usage discriminate ALS brain tissue from controls, verifying TDP-43 loss of function as a pathomechanism in ALS. We propose that TDP-43-regulated splicing markers with most predictive value for therapeutic intervention will be those based on splicing events that occur both in tissues/biofluids amenable to sampling, and in brain tissue susceptible to disease.