bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial amino acid chemotaxis: a widespread strategy with multiple physiological and ecological roles
Authors: Matilla Miguel A. , Krell Tino 
Published: September 2024

ABSTRACT

Chemotaxis is the directed, flagellum-based movement of bacteria in chemoeffector gradients. Bacteria respond chemotactically to a wide range of chemoeffectors, including amino, organic, and fatty acids, sugars, polyamines, quaternary amines, purines, pyrimidines, aromatic hydrocarbons, oxygen, inorganic ions, or polysaccharides. Most frequent are chemotactic responses to amino acids (AAs), which were observed in numerous bacteria regardless of their phylogeny and lifestyle. Mostly chemoattraction responses are observed, although a number of bacteria are repelled from certain AAs. Chemoattraction is associated with the important metabolic value of AAs as growth substrates or building blocks of proteins. However, additional studies revealed that AAs are also sensed as environmental cues. Many chemoreceptors are specific for AAs, and signaling is typically initiated by direct ligand binding to their four-helix bundle or dCache ligand-binding domains. Frequently, bacteria possess multiple AA-responsive chemoreceptors that at times possess complementary AA ligand spectra. The identification of sequence motifs in the binding sites at dCache_1 domains has permitted to define an AA-specific family of dCache_1AA chemoreceptors. In addition, AAs are among the ligands recognized by broad ligand range chemoreceptors, and evidence was obtained for chemoreceptor activation by the binding of AA-loaded solute-binding proteins. The biological significance of AA chemotaxis is very ample including in biofilm formation, root and seed colonization by beneficial bacteria, plant entry of phytopathogens, colonization of the intestine, or different virulence-related features in human/animal pathogens. This review provides insights that may be helpful for the study of AA chemotaxis in other uncharacterized bacteria.
HCV infection activates the proteasome via PA28γ acetylation and heptamerization to facilitate the degradation of RNF2, a catalytic component of polycomb repressive complex 1
Authors: Kasai Hirotake , Yamashita Atsuya , Akaike Yasunori , Tanaka Tomohisa , Matsuura Yoshiharu , Moriishi Kohji 
Published: September 2024

ABSTRACT

We previously reported that hepatitis C virus (HCV) infection or HCV core protein expression induces HOX gene expression by impairing histone H2A monoubiquitination via a proteasome-dependent reduction in the level of RNF2, a key catalytic component of polycomb repressive complex 1 (H. Kasai, K. Mochizuki, T. Tanaka, A. Yamashita, et al., J Virol 95:e01784-20, 2021,
https://doi.org/10.1128/jvi.01784-20
). In this study, we aimed to investigate the mechanism by which HCV infection accelerates RNF2 degradation. Yeast two-hybrid screening and an immunoprecipitation assay revealed that RNF2 is a PA28γ-binding protein. The proteasome activator PA28γ destabilized the RNF2 protein in a proteasome-dependent manner, since RNF2 degradation was impaired by PA28γ knockout or MG132 treatment. HCV infection or core protein expression reduced the levels of RNF2 and histone H2A K119 monoubiquitination and induced the expression of HOX genes in the presence of PA28γ, while PA28γ knockout reversed these changes. Treatment with a lysine acetyltransferase inhibitor inhibited the acetylation of PA28γ at K195 and the degradation of the RNF2 protein, while treatment with a lysine deacetylase inhibitor accelerated these events in a PA28γ-dependent manner. RNF2 protein degradation was increased by expression of the acetylation mimetic PA28γ mutant but not by expression of the acetylation-defective mutant or the proteasome activation-defective mutant. Furthermore, HCV infection or core protein expression facilitated the interaction between PA28γ and the lysine acetyltransferase CBP/p300 and then accelerated PA28γ acetylation and heptazmerization to promote RNF2 degradation. These data suggest that HCV infection accelerates the acetylation-dependent heptamerization of PA28γ to increase the proteasomal targeting of RNF2.

IMPORTANCE
HCV is a causative agent of HCV-related liver diseases, including hepatic steatosis, cirrhosis, and hepatocellular carcinoma. PA28γ, which, in heptameric form, activates the 20S core proteasome for the degradation of PA28γ-binding proteins, is responsible for HCV-related liver diseases. HCV core protein expression or HCV infection accelerates RNF2 degradation, leading to the induction of HOX gene expression via a decrease in the level of H2Aub on HOX gene promoters. However, the mechanism of RNF2 degradation in HCV-infected cells has not been clarified. The data presented in this study suggest that PA28γ acetylation and heptamerization are promoted by HCV infection or by core protein expression to activate the proteasome for the degradation of RNF2 and are responsible for HCV propagation. This study provides novel insights valuable for the development of therapies targeting both HCV propagation and HCV-related diseases.
The feasibility of establishing a hamster model for HBV infection:
in vitro
evidence
Authors: Zhang Hu , Liu Yanan , Liu Cheng-Der , Wang Zhongde , Guo Haitao 
Published: September 2024

ABSTRACT

Chronic hepatitis B virus (HBV) infection remains a significant public health burden with no cure currently available. The research to cure HBV has long been hampered by the lack of immunocompetent small animal models capable of supporting HBV infection. Here, we set out to explore the feasibility of the golden Syrian hamster as an immunocompetent small rodent model for HBV infection. We first started with
in vitro
assessments of the HBV replication cycle in primary hamster hepatocytes (PHaHs) by adenoviral HBV (Ad-HBV) transduction. Our results demonstrated that PHaHs support HBV reverse transcription and subsequent cccDNA formation via the intracellular recycling pathway. Next, with luciferase reporter assays, we confirmed that PHaHs support the activities of all HBV major promoters. Then, we transduced PHaHs with an adenoviral vector expressing HBV receptor human Na+/taurocholate cotransporting polypeptide NTCP (Ad-huNTCP), followed by HBV inoculation. While the untransduced PHaHs did not support HBV infection, Ad-huNTCP-transduced PHaHs supported
de novo
cccDNA formation, viral mRNA transcription, and expression of viral antigens. We then humanized the amino acid (aa) residues of hamster NTCP (haNTCP) critical for HBV entry, aa84-87 and aa157-165, and transfected HepG2 cells with constructs expressing wild-type haNTCP and humanized-haNTCP, H84R/P87N and H84R/P87N/G157K/M160V/M165L, respectively, followed by HBV inoculation. The results showed that the humanization of H84R/P87N alone was sufficient to support HBV infection at a level comparable to that supported by huNTCP. Taken together, the above
in vitro
evidence supports the future direction of humanizing haNTCP for HBV infection
in vivo
.

IMPORTANCE

One of the biggest challenges in developing an HBV cure is the lack of immunocompetent animal models susceptible to HBV infection. Developing such models in mice has been unsuccessful due to the absence of a functional HBV receptor, human NTCP (huNTCP), and the defect in supporting viral cccDNA formation. In search of alternative models, we report herein multiple lines of
in vitro
evidence for developing a golden Syrian hamster model for HBV infection. We demonstrate that the primary hamster hepatocytes (PHaHs) support HBV replication, transcription, and cccDNA formation, and PHaHs are susceptible to
de novo
HBV infection in the presence of huNTCP. Furthermore, expressing hamster NTCP with two humanized residues critical for HBV entry renders HepG2 cells permissive to HBV infection. Thus, our work lays a solid foundation for establishing a gene-edited hamster model that expresses humanized NTCP for HBV infection
in vivo
.
Genome sequence of
Pseudomonas silesiensis
strain G3, a member of a bacterial consortium capable of polyethylene degradation
Authors: Schneider Beate , Pfeiffer Friedhelm , Remus Daniela , Dyall-Smith Mike , Kunte Hans-Jörg 
Published: September 2024

ABSTRACT

A consortium of landfill bacteria including strain G3 can break down polyethylene, a long-lasting plastic that accumulates in the environment. The complete genome sequence of strain G3 was determined by PacBio and Nanopore sequencing and consists of three circular replicons. Genome-based classification assigned strain G3 to the species
Pseudomonas silesiensis
.
Three endogenous pararetrovirus genomes in
Medicago sativa
Authors: Ali Raad Mohammed , Alisawi Osamah , Al Fahad Maadh 
Published: September 2024

ABSTRACT

The genome sequences of three related endogenous pararetroviruses were obtained by high-throughput genomic sequencing of
Medicago sativa
. The genomes were found to be integrated within plant genes. The phylogeny revealed that Caulimovirus-MSa3 was closely related to caulimoviruses of petunia, whereas Caulimovirus-MSa1 and Caulimovirus-MSa2 were distinct from constructed clades.
Genome sequences of seven
Mannheimia haemolytica
isolates from feedlots in Oklahoma and California
Authors: Krueger Margaret , Mani Rinosh , Sreevatsan Srinand 
Published: September 2024

ABSTRACT

This report describes the genome sequences of seven
Mannheimia haemolytica
isolates recovered from feedlot cattle. These genome sequences will enhance our understanding of
Mannheimia haemolytica
evolution and antimicrobial resistance (AMR)-associated genes they carried over a two-decade span.
Diagnosis of
Helicobacter pylori
infection: serology vs. urea breath test
Authors: Imperial Miguel , Tan Kennard , Fjell Chris , Chang Yin , Krajden Mel , Kelly Michael T. , Morshed Muhammad 
Published: September 2024

ABSTRACT

The objective of the study was to ascertain an optimal
Helicobacter pylori
diagnostic strategy using population-level laboratory data comparing the performance of serology against urea breath test (UBT).
H. pylori
diagnostic test results for serology and UBT from two laboratories over a 12-year period (2006–20017) were extracted, linked, and analyzed. A subset of this population underwent both methods of testing within days of each other, enabling a direct comparison of the two methods. The average prevalence of
H. pylor
i positivity was 21.3% by serology and 17.5% by UBT. There were 2,612 individuals who had serology performed first, followed by UBT within 14 days. For this subset, the sensitivity of serology compared with UBT was 96.5% with a specificity of 79.2%. The negative predictive value for serology was 98.4%. Contrary to various recent clinical guidelines, the data show that serology still has utility as a sensitive enough test to be used as an initial
H. pylori
screening test in a lower prevalence population. Negative serology can be used with confidence to rule out active infection, whereas a positive serology could be followed up with a UBT or a similar performing test such as stool antigen to differentiate active from past infection. For population-based diagnostic recommendations, such a strategy may be ideal since serology generally costs less than UBT and may be combined with a blood draw being done for other diagnostic tests. Continuing to offer serology increases options for patients and may provide economic benefits for single-payer health care systems or health maintenance organizations.

IMPORTANCE

This study compares the performance of serology with urea breath test in the diagnosis of
Helicobacter pylori
in a population-level data set and mimics a head-to-head direct comparison as the study population had both tests performed within 2 weeks of each other. This provides new information supporting the use of serology in a diagnostic algorithm. There are several instances where serology could be preferable to patients to rule out disease, despite some guidelines suggesting serology should not be used.
Interaction of retinal electrophysiology and novel orthokeratology lens use on myopia control efficacy in children
Authors: Choi Kai Yip , Wong Gigi Tsz King , Chan Sonia Seen Hang , Lam Thomas Chuen , Chan Henry Ho-lung 
Published: September 2024

AimsThe relationship between retinal electrophysiological function and myopia progression was evaluated in school-aged children wearing Breath-O-Correct Orthokeratology (OK) lenses compared with those wearing single vision (SV) lenses over 24 months.MethodsIn this randomised, single-blind, parallel controlled trial, children aged 8–12 years with −1.00 to −4.00 D of myopia were recruited. Retinal function was evaluated using global-flash multifocal electroretinography at baseline before OK or SV treatment. Axial length was evaluated at 6-month intervals up to 24 months. The main outcome measures were axial elongation (AE) between groups and the interactive effect of baseline retinal function.ResultsA total of 70 children (43 OK, 9.8±1.3 years; 27 SV, 9.5±1.4 years) completed the 2-year study and were included in the analysis. The 2-year normalised AE was 0.37±0.37 mm in the OK group and 0.60±0.41 mm in the SV group, respectively. For children in the SV group, the amplitude of the central inner retinal response was negatively correlated with axial length elongation (p=0.03). In contrast, this relationship between retinal electrophysiology and AE was not observed in OK group, indicating that they were independent of each other in children treated with OK (p=0.33).ConclusionA weak retinal electrophysiological response was a risk factor for rapid AE in SV controls. However, OK treatment can lower this risk factor and significantly reduce AE in school-aged children.
Presentation and characteristics of children with screen-detected type 1 diabetes: learnings from the ELSA general population pediatric screening study
Authors: Quinn Lauren M , Dias Renuka P , Bidder Christopher , Bhowmik Sudeshna , Bumke Kerstin , Ganapathi Jaikumar , Gorman Shaun , Hind Edward , Karandikar Swati , Kumar Kiran , Lipscomb Nicholas , McGovern Sheila , Puthi Vijith R , Randell Tabitha , Watts Gemma , Narendran Parth 
Published: September 2024

IntroductionWe describe the identification and management of general population screen-detected type 1 diabetes (T1D) and share learnings for best practice.Research design and methodsChildren diagnosed with T1D through a general population screening initiative, the EarLy Surveillance for Autoimmune diabetes (ELSA) study, were reviewed and described.Parents provided written, informed consent for inclusion in the case series.Results14 children with insulin requiring (stage 3) T1D are described. These cases offer unique insights into the features of screen-detected T1D. T1D is identified sooner through screening programs, characterized by absent/short symptom duration, median presenting glycated hemoglobin 6.6% (49 mmol/mol) and insulin requirements<0.5 units/kg/day. ELSA identified four children at stage 3 and another 4 progressed within 4 months of ELSA completion, including two single seropositive children. Six children developed stage 3 T1D prior to ELSA completion, including two children (14%, n=2/14) with diabetic ketoacidosis prior to confirmed antibody status.ConclusionsThere are three main learnings from this case series. First, T1D identified through screening is at an earlier stage of its natural history and requires personalized insulin regimens with lower total daily insulin doses. Second, single autoantibody seropositivity can rapidly progress to stage 3. Finally, insulin requirement can manifest at any stage of the T1D screening pathway, and therefore early education around symptom recognition is essential for families participating in screening programs.
Continuum of health equity practice and science: conceptualising health equity research and practice for injury prevention
Authors: Scheuer Hannah , Wulz Avital R , Carmichael Andrea E , Welder Laura E 
Published: September 2024

BackgroundIntegrating and advancing health equity are a core tenant of the Centers for Disease Control and Prevention’s mission. Comprehensive frameworks that clearly conceptualise equity are needed to prioritise and inform the advancement of health equity within public health.MethodsTo help meet this need, the investigative team developed The Continuum of Health Equity Practice & Science (The Continuum). The Continuum was developed in two phases: (1) an initial survey distributed to internal CDC Division of Injury Prevention investigators, and (2) a review of public health frameworks and the current health equity evidence base.ResultsThe Continuum is a framework that includes seven key components of health equity and ultimately aims to guide public health practice and research towards the advancement of health equity. To illustrate its usefulness, we provide an example using adolescent suicide for each component of The Continuum and demonstrate how this may inform efforts to advance health equity.ConclusionWith a specific focus on conceptualising health equity and addressing systemic inequities, The Continuum may be used to inform efforts to advance equity in injury prevention and beyond.
Variability in forced expiratory volume in 1 s in children with symptomatically well-controlled asthma
Authors: Filipow Nicole , Turner Stephen , Petsky Helen L , Chang Anne B , Frischer Thomas , Szefler Stanley , Vermeulen Francoise , Stanojevic Sanja 
Published: September 2024

AimsSpirometry is used by many clinicians to monitor asthma in children but relatively little is understood about its variability over time. The aim of this study was to determine the variability of forced expiratory volume in 1 s (FEV1)in children with symptomatically well-controlled asthma by applying three different methods of expressing change in FEV1over 3-month intervals.MethodsData from five longitudinal studies of children with asthma which measured FEV1at 3-month intervals over 6 or 12 months were used. We analysed paired FEV1measurements when asthma symptoms were controlled. The variability of FEV1% predicted (FEV1%), FEV1z-score (FEV1z) and conditional z score for change (Zc) in FEV1was expressed as limits of agreement.ResultsA total of 881 children had 3338 FEV1measurements on occasions when asthma was controlled; 5184 pairs of FEV1measurements made at 3-month intervals were available. Each unit change in FEV1z score was equivalent to a Zc 1.45 and an absolute change in FEV1% of 11.6%. The limits of agreement for change in FEV1% were −20 and +21, absolute change in FEV1z were −1.7 and +1.7 and Zc were −2.6 and +2.1. Regression to the mean and increased variability in younger children were present for change in FEV1% and FEV1z comparisons, but not Zc.ConclusionGiven the wide limits of agreement of paired FEV1measurements in symptomatically well-controlled children, asthma treatment should primarily be guided by symptoms and not by a change in spirometry.
Dirac stars in Anti-de Sitter spacetime
Authors: Zhang Xiao-Yu , Zhao Li , Wang Yong-Qiang 
Published: September 2024

AbstractIn this paper, we construct the Dirac stars model composed of two Dirac fields and Einstein gravity in four-dimensional Anti-de Sitter spacetime. We consider the Dirac stars with free field (no self-interacting). Our investigation focuses on understanding the relationship between Arnowitt–Deser–Misner (ADM) mass and binding energy in relation to the cosmological constant. Furthermore, we extend the study to the Dirac stars with self-interacting potentials. For the self-interacting Dirac stars, three types of interactions are examined: only quartic, only sextic, quartic and sextic interactions that is kind of Q-ball type interactions. In these three distinct scenarios, it is essential to investigate the impact of self-interaction constants on Dirac stars. Additionally, we study the Dirac solitons in the AdS background. Finally, we discussed the dependence of the spectral flow of the Dirac Hamiltonian on the model parameters.
Intermediate inflation in a generalized non-minimal derivative coupling model
Authors: Goodarzi Parviz 
Published: September 2024

AbstractIn this work, we consider intermediate inflation in the context of the generalized non-minimal derivative coupling (GNMDC) model. In the GNMDC model, inflation is driven by a canonical scalar field that is coupled not only to gravity but also to the derivative of the scalar field. The model introduces new dynamics and features during the inflationary epoch. We find inflationary solutions with a power law scalar field for the power law coupling function. Additionally, we determine the inflaton potential that generates intermediate expansion of the scale factor. We also discuss the background equations in the high friction limit and derive constraints on the parameters of our model. Furthermore, we investigate the cosmological perturbations in the slow roll approximation within the GNMDC model, and we calculate the scalar and tensor spectral index and the tensor-to-scalar ratio during intermediate inflation. We compare the results of this model with observational data that can be used to test the model using cosmic microwave background radiation data. Overall, we establish conditions for the inflaton potential that ensure the continuation of accelerated expansion during slow roll inflation. We numerically analyze the power spectrum and spectral index for scalar and tensor modes in intermediate inflation in the high friction limit, and we use Planck 2018 data to obtain constraints on the parameters of the model. We demonstrate that intermediate inflation in the GNMDC model is successful in evaluation and explanation of background and perturbation quantities using observational data.