bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibiogram of Clinical Isolates from Primary and Secondary Healthcare Facilities: A Step Towards Antimicrobial Stewardship
Authors: Aika Isabel Naomi , Enato Ehijie 
Published: May 2022

AbstractAntibiogram development and use is a core element of antimicrobial stewardship practice, such data is scarce in healthcare settings in developing countries. The study aims to determine the epidemiology of clinical isolates and their antibiograms in secondary healthcare (SHC) and primary healthcare (PHC) facilities in Benin City, Nigeria. This was a retrospective study in three laboratories in SHC and PHC facilities. Microbial culture and susceptibility report over the past 4 years was collated. Ethical Clearance was obtained from the Edo State Ministry of Health and Benin City. Data were entered and analyzed using SPSS version 22. Of the 819 isolates, urine, semen and vagina swab were most represented (50.7%; 16.1%; 13.2%). S.aureus (60.6%) and coliform organism (31.9%) were commonly isolated. High resistance of 75%->90% was seen with penicillin, cephalosporin, macrolide, aminoglycoside and floroquinolone against S. aureus, Ps aeruginosa, coliform and E. coli. Resistance to all antimicrobials was observed in 11.7% of the isolates, multidrug resistance (MDR) was found to be 61.4%. MDR for Ps aeruginosa, coliform, E coli, and staph aureus were 95.5%, 67.3% 25.6% and 82.8% respectively. In the SHC, 15.4% of isolates were resistant to all antibacterial compared to none in the PHC. There was consistent yearly increase in resistance to more than six agents in both centers. Gender difference in antimicrobial resistance was observed. High MDR observed in this study emphasizes the need for routine antibiogram and its use in updating treatment guidelines to reflect the current resistance pattern to available antimicrobials.
Brain injury accelerates the onset of a reversible age-related microglial phenotype associated with hyperphagocytosis and inflammatory neurodegeneration
Authors: Ritzel Rodney M. , Li Yun , Jiao Yun , Lei Zhuofan , Doran Sarah J. , He Junyun , Shahror Rami A. , Henry Rebecca J. , Liu Shaolin , Stoica Bogdan A. , Faden Alan I. , Szeto Gregory , Loane David J. , Wu Junfang 
Published: May 2022

AbstractLipofuscin is an autofluorescent (AF) pigment formed by lipids and misfolded proteins that accumulates in post-mitotic cells with advanced age. Here we immunophenotyped microglia in the brain of old C57BL/6 mice (>18 months-old) and demonstrate that in comparison to young mice, one third of old microglia are AF, characterized by profound changes in lipid and iron content, phagocytic activity, and oxidative stress. Pharmacological depletion of microglia in old mice eliminated the AF microglia following repopulation and reversed microglial dysfunction. Age-related neurological deficits and neurodegeneration after traumatic brain injury (TBI) were attenuated in old mice lacking AF microglia. Furthermore, hyperphagocytic activity and lipid accumulation in microglia persisted for up to one year after TBI, were modified by Apoe4 genotype, and chronically driven by phagocyte-mediated oxidative stress. Thus, AF may reflect a pathological state in aging microglia associated with hyperphagocytosis and inflammatory neurodegeneration that can be further accelerated by TBI.TeaserTraumatic brain injury accelerates age-related pathological phagocytosis and lipofuscin formation in microglia.
The Effects of Propofol Anaesthesia on Molecular-enriched Networks During Resting-state and Naturalistic Stimulation
Authors: Lawn Timothy , Martins Daniel , O’Daly Owen , Williams Steve , Howard Matthew , Dipasquale Ottavia 
Published: May 2022

AbstractPlacing a patient in a state of anaesthesia is crucial for modern surgical practice. However, the mechanisms by which anaesthetic drugs, such as propofol, impart their effects on consciousness remain poorly understood. Propofol potentiates GABAergic transmission, which purportedly has direct actions on cortex as well as indirect actions via ascending neuromodulatory systems. Functional imaging studies to date have been limited in their ability to unravel how these effects on neurotransmission impact system-level dynamics of the brain. Here, we leveraged advances in multi-modal imaging, Receptor-Enriched Analysis of functional Connectivity by Targets (REACT), to investigate how different levels of propofol-induced sedation alters neurotransmission-related functional connectivity (FC), both at rest and when individuals are exposed to naturalistic auditory stimulation. Propofol increased GABA-A- and noradrenaline transporter-enriched FC within occipital and somatosensory regions respectively. Additionally, during auditory stimulation, the network related to the vesicular acetylcholine transporter showed reduced FC within the right superior temporal gyrus, regardless of level of anaesthesia, and a spatial configuration correlating with a broad range of meta-analytic measures of audition- and emotion-related cognition. In bringing together these micro- and macro-scale systems, we provide support for both direct GABAergic and indirect noradrenergic-related network changes under anaesthesia and describe a cognition-related reconfiguration of the cholinergic network, highlighting the utility of REACT to explore the molecular substrates consciousness and cognition.
Influenza Virus-Induced Autophagy Is Not Always Associated with MUC1 Expressions
Authors: Ozkan Hasan Selcuk , Ozarslan Mustafa Alper , Vatansever Gokhan , Cicek Candan 
Published: May 2022

AbstractInfluenza virus-induced autophagy frequently accompanies apoptosis and results in cell death in cells infected with the virus. Autophagy has been well-known to be modulated by the mTOR/PI3K/Akt pathway, which plays an important role in response to the presence of energy sources and external stimulants. This pathway can also be modulated by MUC1, which has extracellular and intracellular components, and playing an important role in metastasis and chemotherapeutic resistance. In this study, the aim is to observe the changes in MUC1 expressions, which is known to have sialic acid residues within MUC1, therefore serving as a receptor for influenza viruses, and consequent changes in autophagy markers such as mTOR and LC3b, after inoculation of cancer cells with influenza virus.Fluorescence was detected for LC3b, mTOR and MUC1 in all influenza-positive cell lines (MCF-7, He-La, A-549) except for RD in immunofluorescence studies. In influenza-negative MCF-7, HeLa, RD and A-549 cells no fluorescence was detected. In the supernatant of all influenza-positive cells, except for RD cells, positive results were obtained for MUC1, MAP1LC3B and MTOR genes (Ct 20,01-32,04) in RT-qPCR, respectively encoding for MUC1, LC3b, and mTOR. In RT-qPCR, in cell lines without influenza inoculation, only in the A-549 cells, the gene expressions were found to be negative. In other cell lines, positive results were obtained (Ct 21,98-23,78). In RD cells, which have not been inoculated with the virus, all pathways were positive.In cells with adenocarcinoma structure, the alterations and presence of autophagy pathways and MUC1 expressions activated via influenza viruses were confirmed. However, this has not been proved using nucleic acid assays. The reason why might be the detection of only gene expressions and mRNA presence via the tests used in the study. In future studies, expressions of these genes in protein level should be detected using more advanced tests.
High-throughput single-molecule quantification of individual base stacking energies in nucleic acids
Authors: Punnoose Jibin Abraham , Thomas Kevin J. , Chandrasekaran Arun Richard , Vilcapoma Javier , Hayden Andrew , Kilpatrick Kacey , Vangaveti Sweta , Chen Alan , Banco Thomas , Halvorsen Ken 
Published: May 2022

AbstractBase stacking interactions between adjacent bases in DNA and RNA are known to be important for many biological processes, for drug development, and in other biotechnology applications. While previous work has estimated base stacking energies between pairs of bases, the individual contributions of each base to the stacking interaction has remained unknown. Here, we developed a novel methodology using a custom Centrifuge Force Microscope to perform high-throughput single molecule experiments to measure base stacking energies between individual adjacent bases. We found stacking energies strongest between purines (G|A at −2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at −0.4 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA bases had no measurable effect, but a fluorophore modification reduced stacking energy. The implications of the work are demonstrated with three applications. We experimentally show that base stacking design can influence assembly and stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and determine accuracy of force fields in molecular dynamics (MD) simulations. Our results provide new insights into fundamental DNA interactions that are critical in biology and can inform rational design in diverse biotechnology applications.
Targeted hydrolysis of native potato protein: A novel route for obtaining hydrolysates with improved interfacial properties
Authors: Echers Simon Gregersen , Jafarpour Ali , Yesiltas Betül , García-Moreno Pedro J. , Greve-Poulsen Mathias , Hansen Dennis , Jacobsen Charlotte , Overgaard Michael Toft , Hansen Egon Bech 
Published: May 2022

AbstractPeptides and protein hydrolysates are promising alternatives to substitute chemical additives as functional food ingredients. In this study, we present a novel approach for producing a potato protein hydrolysate with improved emulsifying and foaming properties by data-driven, targeted hydrolysis. Based on previous studies, we selected 15 emulsifier peptides derived from abundant potato proteins, which were clustered based on sequence identity. Through in silico analysis, we determined that from a range of industrial proteases (Neutrase (Neut), Alcalase (Alc), Flavorzyme (Flav) and Trypsin (Tryp)), Tryp was found more likely to release peptides resembling the target peptides. After applying all proteases individually, hydrolysates were assayed for in vitro emulsifying and foaming properties. No direct correlation between degree of hydrolysis and interfacial properties was found. Tryp produced a hydrolysate (DH=5.4%) with the highest (P<0.05) emulsifying and foaming abilities, good stabilities, and high aqueous solubility. Using LC-MS/MS, we identified >10,000 peptides in each hydrolysate. Through peptide mapping, we show that random overlapping with known peptide emulsifiers is not sufficient to quantitatively describe hydrolysate functionality. While Neut hydrolysates had the highest proportion of peptides with target overlap, they showed inferior interfacial activity. In contrast, Tryp was able to release specifically targeted peptides, explaining the high surface activity observed. While modest yields and residual unhydrolyzed protein indicate room for process improvement, this work shows that data-driven, targeted hydrolysis is a viable, interdisciplinary approach to facilitate hydrolysis design for production of functional hydrolysates from alternative protein sources.
Cardiac fibroblasts regulate cardiomyocyte hypertrophy through dynamic regulation of type I collagen
Authors: Meng Qinghang , Bowers Stephanie L. K. , Kuwabara Yasuhide , Huo Jiuzhou , Minerath Rachel , York Allen J. , Sargent Michelle A. , Prasad Vikram , Saviola Anthony J. , Galindo David Ceja , Hansen Kirk C. , Vagnozzi Ronald J. , Yutzey Katherine E. , Molkentin Jeffery D. 
Published: May 2022

AbstractRationaleCardiomyocytes and fibroblasts in the heart communicate through both secreted growth factors as well as through sensing the structural properties of the extracellular matrix that each helps generate. Previous studies have shown that defects in fibroblast activity during disease stimulation result in altered cardiomyocyte hypertrophy, although the role that collagen might play in this communication is unknown.ObjectiveHere we investigated how type I collagen maturation and disease-responsive matrix expansion in the heart by cardiac fibroblasts impacts cardiac fibrosis and cardiomyocyte hypertrophy.Methods and ResultsWe generated and characterized Col1a2-/- mice using standard gene-targeting. Col1a2-/- mice were viable, although by young adulthood their hearts showed alterations in extracellular matrix mechanical properties, as well as an unanticipated activation of cardiac fibroblasts and induction of a progressive fibrotic response. This included increases in fibroblast number and a progressive cardiac hypertrophy, with reduced functional performance by 9 months. Col1a2-loxP targeted mice were also generated and crossed with the tamoxifen-inducible Postn-MerCreMer knock-in mice to delete the Col1a2 gene in myofibroblasts post-pressure overload injury, to more specifically implicate fibroblasts as effectors of cardiomyocyte hypertrophy in vivo. Opposite to the gradual induction of cardiac hypertrophy observed in germline Col1a2-/- mice as they matured developmentally, adult fibroblast-specific deletion of Col1a2 during pressure overload protected these mice from cardiac hypertrophy in the first week with a delayed fibrotic response. However, this reduction in hypertrophy due to myofibroblast-specific Col1a2 deletion was gradually lost over 2 and 6 weeks of pressure overload as augmented fibrosis returned.ConclusionsDefective type I collagen in the developing heart alters the structural integrity of the extracellular matrix that leads to fibroblast expansion, activation, fibrosis and hypertrophy with progressive cardiomyopathy in adulthood. However, acute deletion of type I collagen production for the first time in the adult heart during pressure overload prevents ECM expansion and inhibits cardiomyocyte hypertrophy, while gradual restoration of fibrosis again permitted hypertrophy comparable to controls.
De novo mapping of the apicomplexan Ca2+-responsive proteome
Authors: Herneisen Alice L. , Li Zhu-Hong , Chan Alex W. , Moreno Silvia NJ , Lourido Sebastian 
Published: May 2022

ABSTRACTApicomplexan parasites cause persistent mortality and morbidity worldwide through diseases including malaria, toxoplasmosis, and cryptosporidiosis. Ca2+ signaling pathways have been repurposed in these eukaryotic pathogens to regulate parasite-specific cellular processes governing the transition between the replicative and lytic phases of the infectious cycle. Despite the presence of conserved Ca2+-responsive proteins, little is known about how specific signaling elements interact to impact pathogenesis. We mapped the Ca2+-responsive proteome of the model apicomplexan T. gondii via time-resolved phosphoproteomics and thermal proteome profiling. The waves of phosphoregulation following PKG activation and stimulated Ca2+ release corroborate known physiological changes but identify specific proteins operating in these pathways. Thermal profiling of parasite extracts identified many expected Ca2+-responsive proteins, such as parasite Ca2+-dependent protein kinases. Our approach also identified numerous Ca2+-responsive proteins that are not predicted to bind Ca2+, yet are critical components of the parasite signaling network. We characterized protein phosphatase 1 (PP1) as a Ca2+-responsive enzyme that relocalized to the parasite apex upon Ca2+ store release. Conditional depletion of PP1 revealed that the phosphatase regulates Ca2+ uptake to promote parasite motility. PP1 may thus be partly responsible for Ca2+-regulated serine/threonine phosphatase activity in apicomplexan parasites.
Large RNP granules in C. elegans oocytes have distinct phases of RNA binding proteins
Authors: Elaswad Mohamed T. , Watkins Brooklynne M. , Sharp Katherine G. , Munderloh Chloe , Schisa Jennifer A. 
Published: May 2022

ABSTRACTThe germ line provides an excellent in vivo system to study the regulation and function of RNP granules. Germ granules are conserved germ line-specific RNP granules that are positioned in the C. elegans adult gonad to function in RNA maintenance, regulation, and surveillance. In C. elegans, when oogenesis undergoes an extended meiotic arrest, germ granule proteins and other RNA binding proteins assemble into much larger RNP granules whose hypothesized function is to regulate RNA metabolism and maintain oocyte quality. To gain insight into the function of oocyte RNP granules, in this report we characterize distinct phases for four protein components of RNP granules in arrested oocytes. We find the RNA binding protein PGL-1 is dynamic and has liquid-like properties, while the intrinsically disordered protein MEG-3 has gel-like properties, similar to the properties of the two proteins in small germ granules of embryos. We find that MEX-3 exhibits several gel-like properties but is more dynamic than MEG-3, while CGH-1 is dynamic but does not consistently exhibit liquid-like characteristics and may be an intermediate phase within RNP granules. These distinct phases of RNA binding proteins correspond to, and may underlie, differential responses to stress. Interestingly, in oocyte RNP granules MEG-3 is not required for the condensation of PGL-1 or other RNA binding proteins, which differs from the role of MEG-3 in small, embryonic germ granules. Lastly, we show the PUF-5 translational repressor appears to promote MEX-3 and MEG-3 condensation into large RNP granules; however, this role may be associated with regulation of oogenesis.
PH Domain-Mediated Autoinhibition and Oncogenic Activation of Akt
Authors: Bae Hwan , Viennet Thibault , Park Eunyoung , Chu Nam , Salguero Antonieta L. , Eck Michael J. , Arthanari Haribabu , Cole Philip A. 
Published: May 2022

AbstractPreviously, we reported that the conformation of autoinhibited Akt, a Ser/Thr protein kinase that plays a central role in metabolism and cancer, may be shifted by small molecule allosteric inhibitors limiting the mechanistic insights from existing X-ray structures that have relied on such compounds (Chu, Viennet, et al, 2020). Here we discover unexpectedly that a single mutation, R86A, in Akt’s PH domain exhibits intensified autoinhibitory features with enhanced PH domain-kinase domain affinity. Structural and biochemical analysis uncovers the importance of a key interaction network involving Arg86, Glu17, and Tyr18 that controls Akt conformation and activity. Our studies also shed light on the molecular basis for E17K Akt activation as an oncogenic driver.
The leucine-rich repeat (LRR) domain of NLRP3 is required for NLRP3 inflammasome activation in macrophages
Authors: Duan Yanhui , Wang Jihong , Cai Juan , Kelley Nathan , He Yuan 
Published: May 2022

AbstractThe NLRP3 inflammasome is a critical component of innate immunity that defends the host from microbial infections. However, its aberrant activation contributes to the pathogenesis of several inflammatory diseases. Activation of the NLRP3 inflammasome induces the secretion of proinflammatory cytokines IL-1β and IL-18, and pyroptotic cell death. NLRP3 contains a leucine-rich repeat (LRR) domain at its C-terminus. Although posttranslational modifications in this LRR domain have been shown to regulate NLRP3 inflammasome activation, the role of the entire LRR domain in NLRP3 inflammasome activation remains controversial. Here, we generated mouse macrophages that express an endogenous NLRP3 mutant lacking the LRR domain. Deletion of the LRR domain destabilized endogenous NLRP3 protein and abolished NLRP3 inflammasome activation in macrophages. Furthermore, using NLRP3-deficient macrophages that are reconstituted with NLRP3 mutants lacking the LRR domain, we found that deletion of the LRR domain inhibited NLRP3 inflammasome activation. Mechanistically, deletion of the LRR domain abolished NLRP3 self-association, oligomerization, and interaction with the essential regulator NEK7. Our results demonstrate a critical role for the LRR domain in NLRP3 inflammasome activation.
Coordination of CcpA and CodY regulators in Staphylococcus aureus USA300 strains
Authors: Poudel Saugat , Hefner Ying , Szubin Richard , Sastry Anand , Gao Ye , Nizet Victor , Palsson Bernhard O. 
Published: May 2022

AbstractThe complex crosstalk between metabolism and gene regulatory networks makes it difficult to untangle individual constituents and study their precise roles and interactions. To address this issue, we modularized the transcriptional regulatory network (TRN) of the StaphylococcusaureusUSA300 strain by applying Independent Component Analysis (ICA) to 385 RNA sequencing samples. We then combined the modular TRN model with a metabolic model to study the regulation of carbon and amino acid metabolism. Our analysis showed that regulation of central carbon metabolism by CcpA and amino acid biosynthesis by CodY are closely coordinated. In general,S. aureusincreases the expression of CodY-regulated genes in the presence of preferred carbons sources such as glucose. This transcriptional coordination was corroborated by metabolic model simulations that also showed increased amino acid biosynthesis in the presence of glucose. Further, we found that CodY and CcpA cooperatively regulate the expression of ribosome hibernation promoting factor, thus linking metabolic cues with translation. In line with this hypothesis, expression of CodY-regulated genes is tightly correlated with expression of genes encoding ribosomal proteins. Together, we propose a coarse-grained model where expression ofS. aureusgenes encoding enzymes that control carbon flux and nitrogen flux through the system is coregulated with expression of translation machinery to modularly control protein synthesis. While this work focuses on three key regulators, the full TRN model we present contains 76 total independently modulated sets of genes, each with the potential to uncover other complex regulatory structures and interactions.ImportanceStaphylococcus aureusis a versatile pathogen with an expanding antibiotic resistance profile. The biology underlying its clinical success emerges from an interplay of many systems such as metabolism and gene regulatory networks. This work brings together models for these two systems to establish fundamental principles governing the regulation of S. aureus central metabolism and protein synthesis. Studies of these fundamental biological principles are often confined to model organisms such asEscherichia coli. However, expanding these models to pathogens can provide a framework from which complex and clinically important phenotypes such as virulence and antibiotic resistance can be better understood. Additionally, the expanded gene regulatory network model presented herein can deconvolute the biology underlying other important phenotypes in this pathogen.