bluuebunny/crossref_metadata_2025_split huggingface dataset:
Live cell imaging of ATP levels reveals metabolic compartmentalization within motoneurons and early metabolic changes inFUSALS motoneurons
Authors: Zimyanin Vitaly , Pielka Anne-Marie , Glaß Hannes , Japtok Julia , Martin Melanie , Deussen Andreas , Szewczyk Barbara , Deppmann Chris , Zunder Eli , Andersen Peter M. , Boeckers Tobias M. , Sterneckert Jared , Redemann Stefanie , Storch Alexander , Hermann Andreas 
Published: March 2023

AbstractMotoneurons are one of the highest energy demanding cell types and a primary target in Amyotrophic lateral sclerosis (ALS), a debilitating and lethal neurodegenerative disorder without currently available effective treatments. Disruption of mitochondrial ultra-structure, transport and metabolism is a commonly reported phenotype in ALS models and can critically affect survival and proper function of motor neurons. However, how changes in metabolic rates contribute to ALS progression are not fully understood yet. Here we utilize hiPCS derived motoneuron cultures and live imaging quantitative techniques to evaluate metabolic rates in Fused in Sarcoma (FUS)-ALS model cells. We show that differentiation and maturation of motoneurons is accompanied by an overall upregulation of mitochondrial components and significant increase in metabolic rates that corresponds to their high energy-demanding state. Detailed compartment-specific live measurements using a fluorescent ATP sensor and FLIM imaging show significantly lower levels of ATP in the somas of cells carrying FUS-ALS mutations. These changes lead to the increased vulnerability of disease motoneurons to further metabolic challenges with mitochondrial inhibitors and could be due to the disruption of mitochondrial inner membrane integrity and an increase in its proton leakage. Furthermore, our measurements demonstrate heterogeneity between axonal and somatic compartments with lower relative levels of ATP in axons. Our observations strongly support the hypothesis that mutated FUS impacts metabolic states of motoneurons and makes them more susceptible to further neurodegenerative mechanisms.
Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA
Authors: Inlow Koe , Tenenbaum Debora , Friedman Larry J. , Kondev Jane , Gelles Jeff 
Published: March 2023

ABSTRACTFree-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryote Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so is unclear. We used multi-wavelength single-molecule fluorescence microscopy in vitro to examine RapA function in theE. colitranscription cycle. In our experiments, RapA at < 5 nM concentration did not appear to alter transcription initiation, elongation, or intrinsic termination. Instead, we directly observed a single RapA molecule bind specifically to the kinetically stable post-termination complex (PTC) -- consisting of core RNA polymerase (RNAP) bound to dsDNA -- and efficiently remove RNAP from DNA within seconds in an ATP-hydrolysis-dependent reaction. Kinetic analysis elucidates the process through which RapA locates the PTC and the key mechanistic intermediates that bind and hydrolyze ATP. This study defines how RapA participates in the transcription cycle between termination and initiation and suggests that RapA helps set the balance between global RNAP recycling and local transcription re-initiation in proteobacterial genomes.SIGNIFICANCERNA synthesis is an essential conduit of genetic information in all organisms. After transcribing an RNA, the bacterial RNA polymerase (RNAP) must be reused to make subsequent RNAs, but the steps that enable RNAP reuse are unclear. We directly observed the dynamics of individual molecules of fluorescently labeled RNAP and the enzyme RapA as they colocalized with DNA during and after RNA synthesis. Our studies show that RapA uses ATP hydrolysis to remove RNAP from DNA after the RNA is released from RNAP and reveal essential features of the mechanism by which this removal occurs. These studies fill in key missing pieces in our current understanding of the events that occur after RNA is released and that enable RNAP reuse.
Profiles of bacteria isolates and their antimicrobial resistance pattern among housemaids working in communal living residences in Jimma City, Ethiopia
Authors: Ango Tadele Shiwito , Teshome Tizita , Getahun Tesfalem , Mamo Girma , Byadgie Negalgn 
Published: March 2023

AbstractBackgroundBacterial pathogens continued to be the major causes of foodborne gastroenteritis in humans and remained public health important pathogens across the globe. As regards, housemaids operating inside a kitchen could be the source of infection and may transmit disease-inflicting pathogens through infected hands. Profiles of bacteria isolates and their antimicrobial resistance patterns among housemaids employed in dwellings in Ethiopia; particularly in the study area haven’t been underexplored yet.ObjectiveA study aimed to assess the profiles of bacteria isolates and antimicrobial resistance patterns among housemaids working in communal living residences in Jimma City, Ethiopia.MethodsLaboratory-based cross-sectional study design was employed among 230 housemaids from April-June 2022. Hand swabs samples from the dominant hand of the study participants were collected under sterile conditions for the segregation of commensal microbes following standard operating procedures. Then in the laboratory, the swabs were inoculated aseptically using streak-plating methods on mannitol salt agar, MacConkey agar, Salmonella-shigella agar, and Eosin Methylene Blue Agar. Then inoculated samples were incubated at 37°C for 24 hours for bacterial isolation. In addition, a set of biochemical tests was applied to examine bacterial species. Data was entered into Epidata version 3.1. All statistics were performed using SPSS®statistics version 26. Descriptive analyses were summarized using frequency and percentage.ResultsThe response rate of respondents was 97.8%. The prevalence of bacterial contaminants in the hands of housemaids who tested positive was 72% (95%CI: 66.2-77.8%). The isolated bacterial wereStaphylococcus aureus(31.8%),Coagulase-Negative Staphylococci(0.9%),Escherichia coli(21.5%),Salmonella(1.3%),Shigella(6.7%),Klebsiella species(23.3%) andProteus species(14.8%). The isolation rate of bacteria was significantly associated with the removal watch, ring, and bracelet during hand washing. Most isolated bacteria were sensitive to Chloramphenicol while the majority of them were resistant to Tetracycline, Gentamycin, Vancomycin, and Ceftazidime.ConclusionsHands of housemaids are important potential sources of disease-causing bacterial pathogens that would result in the potential risk of foodborne diseases. Most isolated bacteria were resistant to tested antimicrobial drugs. Everybody responsible should work practice of good hand hygiene.
Obesity and Smoking: A Tale of 2 Risk Factors with Implications for the Next Pandemic
Authors: Adams Mary L. 
Published: March 2023

AbstractBackgroundIn 1990, two risk factors that would figure prominently in the COVID-19 pandemic were on divergent paths in the US. The smoking rate was 23.5% and dropped to 13.5% in 2021, while the obesity rate was 11.5% and increased 186% to 33.0%.ObjectiveThe study objective was to compare the global impact of those risk factors on COVID deaths to help prepare the US for future pandemics.MethodsStata and Excel were used to regress global COVID deaths on obesity and smoking before and after vaccines were available, and US deaths/day were compared pre-and post-vaccines.ResultsObesity was associated with global COVID deaths, with R2as high as 0.87 for cumulative data with slightly lower R2and coefficients for post-vaccines. For 9 regressions of deaths on obesity, all P values (overall and coefficients) were <0.05 while for regressions on smoking, no P values were < 0.05. Of the 1.1 million US deaths, the death rate/day post-vaccines was 59% of that pre-vaccines. If the US obesity rate had remained 11.5%, estimates suggest 800,000+ lives could have been saved. US smoking rate was reduced 42% by multiple strategies using support from a 1998 multi-billion-dollar settlement between states and tobacco companies.ConclusionVaccines have limited ability to reduce total COVID deaths, with obesity remaining a key factor in death rates. Results suggest that lower obesity rates are needed to further reduce US COVID deaths, potentially saving thousands of lives in future pandemics. Lessons from reducing smoking rates might prove useful.
Targeted and selective knockout of the TLQP-21 neuropeptide unmasks its unique role in energy homeostasis
Authors: Sahu Bhavani S. , Razzoli Maria , McGonigle Seth , Pallais Jean Pierre , Nguyen Megin E. , Sadahiro Masato , Jiang Cheng , Lin Wei-Jye , Kelley Kevin A. , Rodriguez Pedro , Mansk Rachel , Cero Cheryl , Caviola Giada , Palanza Paola , Rao Loredana , Beetch Megan , Alejandro Emilyn , Sham Yuk Y. , Frontini Andrea , Salton Stephen R. , Bartolomucci Alessandro 
Published: March 2023

AbstractPro-peptide precursors are processed into biologically active peptide hormones or neurotransmitters, each playing an essential role in physiology and disease. Genetic loss of function of a pro-peptide precursor results in the simultaneous ablation of all biologically-active peptides within that precursor, often leading to a composite phenotype that can be difficult to align with the loss of specific peptide components. Due to this biological constraint and technical limitations, mice carrying the selective ablation of individual peptides encoded by pro-peptide precursor genes, while leaving the other peptides unaffected, have remained largely unaddressed. Here, we developed and characterized a mouse model carrying the selective knockout of the TLQP-21 neuropeptide (ΔTLQP-21) encoded by theVgfgene. To achieve this goal, we used a knowledge-based approach by mutating a codon in theVgfsequence leading to the substitution of the C-terminal Arginine of TLQP-21, which is the pharmacophore as well as an essential cleavage site from its precursor, into Alanine (R21→A). We provide several independent validations of this mouse, including a novel in-gel digestion targeted mass spectrometry identification of the unnatural mutant sequence, exclusive to the mutant mouse. ΔTLQP-21 mice do not manifest gross behavioral and metabolic abnormalities and reproduce well, yet they have a unique metabolic phenotype characterized by a temperature-dependent resistance to diet-induced obesity and activation of the brown adipose tissue.
IpaA reveals distinct modes of vinculin activation duringShigellainvasion and cell-matrix adhesion
Authors: Cocom-Chan Benjamin , Khakzad Hamed , Konate Mahamadou , Aguilar Daniel Isui , Bello Chakir , Valencia-Gallardo Cesar , Zarrouk Yosra , Fattaccioli Jacques , Mauviel Alain , Javelaud Delphine , Tran Van Nhieu Guy 
Published: March 2023

AbstractVinculin is a cytoskeletal linker strengthening cell adhesion. TheShigellaIpaA invasion effector binds to vinculin to promote vinculin supra-activation associated with head-domain mediated oligomerization. Our study investigates the impact of mutations of vinculin D1D2 subdomains’ residues predicted to interact with IpaA VBS3. These mutations affected the rate of D1D2 trimer formation with distinct effects on monomer disappearance, consistent with structural modeling of a “closed” and “open” D1D2 conformer induced by IpaA. Notably, mutations targeting the closed D1D2 conformer significantly reducedShigellainvasion of host cells as opposed to mutations targeting the open D1D2 conformer and later stages of vinculin head-domain oligomerization. In contrast, all mutations affected the formation of focal adhesions (FAs), supporting the involvement of vinculin supra-activation in this process. Our findings suggest that IpaA-induced vinculin supra-activation primarily reinforces matrix adhesion in infected cells, rather than promoting bacterial invasion. Consistently, shear stress studies pointed to a key role for IpaA-induced vinculin supra-activation in accelerating and strengthening cell matrix adhesion.
Selective bioelectronic sensing of quinone pharmaceuticals using extracellular electron transfer inLactiplantibacillus plantarum
Authors: Li Siliang , Tavares Caroline De Groote , Tolar Joe G. , Ajo-Franklin Caroline M. 
Published: March 2023

AbstractRedox-active small molecules containing quinone functional groups play important roles as pharmaceuticals, but can be toxic if overdosed. Despite the need for a fast and quantitative method to detect quinone and its derivatives, current sensing strategies are often slow and struggle to differentiate between structural analogs. Leveraging the discovery that microorganisms use certain quinones to perform extracellular electron transfer (EET), we investigated the use ofLactiplantibacillus plantarumas a whole-cell bioelectronic sensor to selectively sense quinone analogs. By tailoring the native EET pathway inL. plantarum, we enabled quantitative quinone sensing of 1,4-dihydroxy-2-naphthoic acid (DHNA) - a gut bifidogenic growth stimulator. We found thatL. plantarumcould respond to environmental DHNA within seconds, producing electronic signals that cover a 106concentration range. This sensing capacity was robust in different assay media and allowed for continuous monitoring of DHNA concentrations. In a simulated gut environment containing a mixed pool of quinone derivatives, this tailored EET pathway can selectively sense pharmacologically relevant quinone analogs, such as DHNA and menadione, amongst other structurally similar quinone derivatives. We also developed a multivariate model to describe the mechanism behind this selectivity and found a predictable correlation between quinone physiochemical properties and the corresponding electronic signals. Our work presents a new strategy to selectively sense redox-active molecules using whole-cell bioelectronic sensors and opens the possibility of using probioticL. plantarumfor bioelectronic applications in human health.Significant StatementQuinone-containing pharmaceuticals show toxicity at high concentrations, making it important to quickly and accurately measure their concentration while distinguishing between analogs. To address this problem, we leveraged recent discoveries in electroactive bacteria to develop a novel concept for whole-cell sensing. This concept combines selectivity and specificity, enabling differentiation between analogs based on the temporal dynamic of electron transfer in living cells. With this strategy, we achieved selective detection of pharmacologically relevant quinones with distinct electronic signals for each analog. These signals were deciphered by a multivariate model to provide insight into the specific physiochemical properties of each analog. We envision that this new concept can be applied to other analytes for faster and more efficient sensing using electroactive whole cells.
TAp73 regulates mitochondrial dynamics and multiciliated cell homeostasis through an OPA1 axis
Authors: Buckley Niall , Craxton Andrew , Sun Xiao-Ming , Panatta Emanuele , Pinon Lucia , Llodrá Jaime , Morone Nobuhiro , Amelio Ivano , Melino Gerry , Martins L. Miguel , MacFarlane Marion 
Published: March 2023

ABSTRACTDysregulated mitochondrial fusion and fission has been implicated in the pathogenesis of numerous diseases. We have identified a novel function of the p53 family protein TAp73 in regulating mitochondrial dynamics. TAp73 regulates the expression of Optic atrophy 1, a protein responsible for controlling mitochondrial fusion, cristae biogenesis and electron transport chain function. Disruption of this axis results in a fragmented mitochondrial network and an impaired capacity for energy productionviaoxidative phosphorylation. Owing to the role of OPA1 in modulating cytochromecrelease, TAp73-/-cells also display an increased sensitivity to apoptotic cell death, e.g.,viaBH3-mimetics. We also show that the TAp73/OPA1 axis has functional relevance in the upper airway, where TAp73 expression is essential for multiciliated cell differentiation and function. Consistently, ciliated epithelial cells ofTrp73-/-(global p73 KO) mice display decreased expression of OPA1 and perturbations of the mitochondrial network, which may drive multiciliated cell loss. In support of this,Trp73andOPA1gene expression is decreased in COPD patients, a disease characterised by alterations in mitochondrial dynamics. We therefore highlight a potential mechanism involving the loss of p73 in COPD pathogenesis. This work also adds to the growing body of evidence for growth-promoting roles of TAp73 isoforms.
Contribution and functional connectivity between cerebrum and cerebellum on sub-lexical and lexical-semantic processing of verbs
Authors: Reyes-Aguilar Azalea , Licea-Haquet Giovanna , Arce Brenda I. , Giordano Magda 
Published: March 2023

AbstractLanguage comprehension requires sub-lexical (e.g., phonological) and lexical-semantic processing. We designed a task to compare the sub-lexical and lexical-semantic processing of verbs during functional magnetic resonance imaging (fMRI). Likewise, we were interested in the dichotomous representation of concrete-motor versus abstract-non-motor concepts, so two semantic categories of verbs were included: motor and mental. The findings support the involvement of the left dorsal stream of the perisylvian network for sub-lexical processing during the reading of pseudo-verbs and the ventral stream for lexical-semantic representation during the reading of verbs. According to the embodied or grounded cognition approach, modality-specific mechanisms, i.e.,, sensory-motor systems, and the well-established multimodal left perisylvian network contribute to semantic representation for concrete and abstract verbs. The present study detected a preferential modality-specific system for abstract-mental verbs. The visual system was recruited by mental verbs and showed functional connectivity with the right crus I/lobule VI from the cerebellum, suggesting the existence of this network to support the semantic representation of abstract concepts. These results confirm the dissociation between sub-lexical and lexical-semantic processing and provide evidence about the neurobiological basis of semantic representations for abstract verbs.
Haplotype-resolved assembly of the African catfish (Clarias gariepinus) provides insights for semi-terrestrial adaptation of airbreathing catfishes
Authors: Nguinkal Julien A. , Zoclanclounon Yedomon A. B. , Brunner Ronald M. , Goldammer Tom 
Published: March 2023

ABSTRACTAirbreathing catfishes are a group of stenohaline freshwater fish that can withstand various environmental conditions and farming practices, including the ability to breathe atmospheric oxygen. This unique ability has allowed them to thrive in semi-terrestrial habitats. However, the genomic mechanisms underlying their adaptation to adverse ecological conditions remain poorly understood. Here, we sequenced the genome of the African catfishClarias gariepinus, one of the most commonly farmed clariids. By integrating different long reads sequencing technologies, we generated a chromosome-level assembly with high-resolution haplotypes, including the male-specific haplotype. The diploid assembly yielded 58 contigs spanning 969.72 Mb with a contig N50 of 33.71 Mb. We report 25,655 predicted protein-coding genes and 49.94% repetitive elements in the African catfish genome. Several gene families involved in ion transport, osmoregulation, oxidative stress response, and muscle metabolism were expanded or positively selected in clariids, suggesting a potential role in their transition to terrestrial life. The reported findings expand our understanding of the genomic mechanisms underpinning the resilience and adaptive mechanisms of C. gariepinus to adverse environments. These insights will serve as a valuable resource for future studies in elucidating these unique biological traits in related teleosts and leverage these insights for aquaculture improvement.
Staphylococcus aureusDelta Toxin Modulates both Extracellular Membrane Vesicle Biogenesis and Amyloid Formation
Authors: Wang Xiaogang , Uppu Divakara SSM , Dickey Seth W. , Burgin Dylan J. , Otto Michael , Lee Jean C. 
Published: March 2023

AbstractStaphylococcus aureussecretes phenol-soluble modulins (PSMs), a family of small, amphipathic, secreted peptides with multiple biologic activities. Community-acquiredS. aureusstrains produce high levels of PSMs in planktonic cultures, and PSM alpha peptides have been shown to augment the release of extracellular membrane vesicles (MVs). We observed that amyloids, aggregates of proteins characterized by a fibrillar morphology and stained with specific dyes, co-purified with MVs harvested from cell-free culture supernatants of community-acquiredS. aureusstrains. δ-toxin was a major component of amyloid fibrils that co-purified with strain LAC MVs, and δ-toxin promoted the production of MVs and amyloid fibrils in a dose-dependent manner. To determine whether MVs and amyloid fibrils were generated under in vivo conditions, we inoculated mice withS. aureusharvested from planktonic cultures. Bacterial MVs could be isolated and purified from lavage fluids recovered from infected animals. Although δ-toxin was the most abundant PSM in lavage fluids, amyloid fibrils could not be detected in these samples. Our findings expand our understanding of amyloid fibril formation inS. aureuscultures, reveal important roles of δ-toxin in amyloid fibril formation and MV biogenesis, and demonstrate that MVs are generated in vivo in a staphylococcal infection model.ImportanceExtracellular membrane vesicles (MVs) produced byStaphylococcus aureusin planktonic cultures encapsulate a diverse cargo of bacterial proteins, nucleic acids, and glycopolymers that are protected from destruction by external factors. δ-toxin, a member of the phenol soluble modulin family, was shown to be critical for MV biogenesis. Amyloid fibrils co-purified with MVs generated by virulent, community-acquiredS. aureusstrains, and fibril formation was dependent on expression of theS. aureusδ-toxin gene (hld). Mass spectrometry data confirmed that the amyloid fibrils were comprised of δ-toxin. AlthoughS. aureusMVs were produced in vivo in a localized murine infection model, amyloid fibrils were not observed in the in vivo setting. Our findings provide critical insights into staphylococcal factors involved in MV biogenesis and amyloid formation.
Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B12delivery and repair
Authors: Mascarenhas Romila , Ruetz Markus , Gouda Harsha , Heitman Natalie , Yaw Madeline , Banerjee Ruma 
Published: March 2023

AbstractG-proteins function as molecular switches to power cofactor translocation and confer fidelity in metal trafficking. MMAA, a G-protein motor, together with MMAB, an adenosyltransferase, orchestrate cofactor delivery and repair of B12-dependent human methylmalonyl-CoA mutase (MMUT). The mechanism by which the motor assembles and moves a >1300 Da cargo, or fails in disease, are poorly understood. Herein, we report the crystal structure of the human MMUT-MMAA nanomotor assembly, which reveals a dramatic 180° rotation of the B12domain, exposing it to solvent. The nanomotor complex, stabilized by MMAA wedging between two MMUT domains, leads to ordering of the switch I and III loops, revealing the molecular basis of mutase-dependent GTPase activation. The structure explains the biochemical penalties incurred by methylmalonic aciduria-causing mutations that reside at the newly identified MMAA-MMUT interfaces.