bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of pleiotropic
ompR
and
envZ
alleles of
Escherichia coli
on envelope stress and antibiotic sensitivity
Authors: Gerken Henri , Shetty Dasvit , Kern Brea , Kenney Linda J. , Misra Rajeev 
Published: May 2024

ABSTRACT

The EnvZ-OmpR two-component system of
Escherichia coli
regulates the expression of the
ompF
and
ompC
porin genes in response to medium osmolarity. However, certain mutations in
envZ
confer pleiotropy by affecting the expression of genes of the iron and maltose regulons not normally controlled by EnvZ-OmpR. In this study, we obtained two novel
envZ
and
ompR
pleiotropic alleles,
envZT15P
and
ompRL19Q
, among revertants of a mutant with heightened envelope stress and an outer membrane (OM) permeability defect. Unlike
envZ
, pleiotropic mutations in
ompR
have not been described previously. The mutant alleles reduced the expression of several outer membrane proteins (OMPs), overcame the temperature-sensitive growth defect of a protease-deficient (Δ
degP
) strain, and lowered envelope stress and OM permeability defects in a background lacking the BamB protein of an essential β-barrel assembly machinery complex. Biochemical analysis showed OmpRL19Q, like wild-type OmpR, is readily phosphorylated by EnvZ, but the EnvZ-dependent dephosphorylation of OmpRL19Q~P was drastically impaired compared to wild-type OmpR. This defect would lead to a prolonged half-life for OmpRL19Q~P, an outcome remarkably similar to what we had previously described for EnvZR397L, resulting in pleiotropy. By employing null alleles of the OMP genes, it was determined that the three pleiotropic alleles lowered envelope stress by reducing OmpF and LamB levels. The absence of LamB was principally responsible for lowering the OM permeability defect, as assessed by the reduced sensitivity of a Δ
bamB
mutant to vancomycin and rifampin. Possible mechanisms by which novel EnvZ and OmpR mutants influence EnvZ-OmpR interactions and activities are discussed.

IMPORTANCE

Maintenance of the outer membrane (OM) integrity is critical for the survival of Gram-negative bacteria. Several envelope homeostasis systems are activated when OM integrity is perturbed. Through the isolation and characterization of novel pleiotropic
ompR
/
envZ
alleles, this study highlights the involvement of the EnvZ-OmpR two-component system in lowering envelope stress and the OM permeability defect caused by the loss of proteins that are involved in OM biogenesis, envelope homeostasis, and structural integrity.
The chaperone PrsA2 regulates the secretion, stability, and folding of listeriolysin O during
Listeria monocytogenes
infection
Authors: Agbavor Charles , Zimnicka Adriana , Kumar Allison , George Jada L. , Torres Madeline , Prehna Gerd , Alonzo Francis , Durrant Jacob D. , Freitag Nancy E. , Cahoon Laty A. 
Published: May 2024

ABSTRACT

Pathogenic bacteria rely on secreted virulence factors to cause disease in susceptible hosts. However, in Gram-positive bacteria, the mechanisms underlying secreted protein activation and regulation post-membrane translocation remain largely unknown. Using proteomics, we identified several proteins that are dependent on the secreted chaperone PrsA2. We followed with phenotypic, biochemical, and biophysical assays and computational analyses to examine the regulation of a detected key secreted virulence factor, listeriolysin O (LLO), and its interaction with PrsA2 from the bacterial pathogen
Listeria monocytogenes
(
Lm
). Critical to
Lm
virulence is internalization by host cells and the subsequent action of the cholesterol-dependent pore-forming toxin, LLO, which enables bacterial escape from the host cell phagosome. Since
Lm
is a Gram-positive organism, the space between the cell membrane and wall is solvent exposed. Therefore, we hypothesized that the drop from neutral to acidic pH as the pathogen is internalized into a phagosome is critical to regulating the interaction of PrsA2 with LLO. Here, we demonstrate that PrsA2 directly interacts with LLO in a pH-dependent manner. We show that PrsA2 protects and sequesters LLO under neutral pH conditions where LLO can be observed to aggregate. In addition, we identify molecular features of PrsA2 that are required for interaction and ultimately the folding and activity of LLO. Moreover, protein-complex modeling suggests that PrsA2 interacts with LLO via its cholesterol-binding domain. These findings highlight a mechanism by which a Gram-positive secretion chaperone regulates the secretion, stability, and folding of a pore-forming toxin under conditions relevant to host cell infection.

IMPORTANCE

Lm
is a ubiquitous food-borne pathogen that can cause severe disease to vulnerable populations. During infection,
Lm
relies on a wide repertoire of secreted virulence factors including the LLO that enables the bacterium to invade the host and spread from cell to cell. After membrane translocation, secreted factors must become active in the challenging bacterial cell membrane-wall interface. However, the mechanisms required for secreted protein folding and function are largely unknown.
Lm
encodes a chaperone, PrsA2, that is critical for the activity of secreted factors. Here, we show that PrsA2 directly associates and protects the major
Lm
virulence factor, LLO, under conditions corresponding to the host cytosol, where LLO undergoes irreversible denaturation. Additionally, we identify molecular features of PrsA2 that enable its interaction with LLO. Together, our results suggest that
Lm
and perhaps other Gram-positive bacteria utilize secreted chaperones to regulate the activity of pore-forming toxins during infection.
Draft genome sequences of multiple bacterial strains isolated from human feces
Authors: Selma-Royo Marta , Ricci Liviana , Golzato Davide , Servais Charlotte , Nabinejad Amir , Armanini Federica , Asnicar Francesco , Pinto Federica , Tamburini Sabrina , Segata Nicola 
Published: May 2024

ABSTRACT

Bacterial isolation is necessary for functional and mechanistic analyses, and the increased human microbiome diversity revealed by metagenomic sequencing is expanding the relevant cultivation targets. Here, we report 46 draft genome sequences of bacterial isolates obtained from fecal samples of healthy adults in Trento and Milan (Italy), including strains from seven taxonomically uncharacterized species.
Draft genome sequences of three
Lactobacillus crispatus
strains, isolated from the female urinary tract
Authors: Sedano Cerena , Stegman Natalie , Steiling Maria , Jackson Briana , Putonti Catherine 
Published: May 2024

ABSTRACT

Lactobacillus crispatus is
a frequent member of the female urogenital microbiota. Here, we present the draft genome assemblies of three
L. crispatus
strains: UMB4356, UMB5661, and UMB6244. All strains were isolated from voided urine samples from females with type 2 diabetes.
Salmonella enterica
subsp.
enterica
serovar Paratyphi B from mute swan (
Cygnus olor
): complete genome sequence features point towards invasive variant potential
Authors: Lamparter Marina C. , Borowiak Maria , Kutzer Peter , Schlieben Patricia , Szabo Istvan , Fischer Jennie 
Published: May 2024

ABSTRACT

A subgroup of Salmonella (S.) enterica subsp. enterica serovar Paratyphi B is significantly associated with invasive infections in humans. We report the complete genome sequence of a potentially invasive.
S.
Paratyphi B isolated from a mute swan (
Cygnus olor
) found dead at an urban recreation park in Berlin, Germany.
Genomic characterization of circulating human respiratory syncytial viruses A and B in Kuwait using whole-genome sequencing
Authors: Madi Nada , Safar Hussain A. , Al-Adwani Anfal , Sadeq Mohammed , Al-Turab Mariam 
Published: May 2024

ABSTRACT

The human respiratory syncytial virus (RSV) is considered one of the most common viruses that infect children globally. The virus is known to have extensive gene sequence variability within and between RSV groups A and B globally; however, there is no information on the whole-genome characterization and diversity of RSV in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with acute respiratory tract infection (ARTI) in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with ARTI in Kuwait. Between January 2020 and September 2022, 7,093 respiratory samples were collected from hospitalized infants, children, and adults and were analyzed for respiratory viruses by multiplex real-time PCR. Whole-genome sequencing using the Oxford Nanopore sequencing technology was performed on 84 RSV-positive samples. The results revealed a higher prevalence of group A (76%) than group B (24%) RSV isolates. Phylogenetic analysis showed that RSV-A strains clustered with the GA2.3.5 sub-genotype and RSV-B strains clustered with the GB5.0.5a sub-genotype; however, forming new lineages of RSV-A and RSV-B circulated in Kuwait during this period. Genetic variability was higher among the group A viruses than group B viruses, and the rate of synonymous and missense mutations was high in genes other than the G protein-coding gene. We also detected several known and unique molecular markers in different protein-coding genes. This is the first study in Kuwait to characterize the whole genomes of RSV A and B to identify the circulating genotypes, comprehend the genetic diversity and the evolution of the virus, and identify important genetic markers associated with specific genotypes.

IMPORTANCE
Whole-genome sequencing of respiratory syncytial virus (RSV) strains in Kuwait using MinION Nanopore technology was used to characterize and analyze the genotypes and sub-genotypes of the RSV circulating among patients with acute respiratory tract infections in Kuwait. This study also identified known and unknown gene mutations and imported genetic markers associated with specific genotypes. These results will assist in establishing a framework for RSV classification and allow for a better consideration of the mechanisms leading to the generation of diversity of RSV. In addition, these data will allow a comparison of vaccine viruses with those in Kuwait, providing useful insights into future vaccine and therapy strategies for RSV in Kuwait.
An observational study investigating soluble immune checkpoints as indicators of severe COVID-19
Authors: Cortés-Vieyra Ricarda , Gutiérrez-Castellanos Sergio , Gómez-García Anel , Bravo-Patiño Alejandro , Calderón-Rico Fernando , Martínez-Sepúlveda José Daniel , Ortega-Flores Roberto , Perez-Duran Francisco , Franco-Correa Luis Enrique , Zamora-Avilés Alicia Gabriela , Nuñez-Anita Rosa Elvira 
Published: May 2024

ABSTRACT

This study aimed to investigate the immunomodulatory behavior of soluble immune checkpoints (sICPs) and other biomarkers in the pathophysiology of SARS-CoV-2 infection. The study included 59 adult participants, 43 of whom tested positive for SARS-CoV-2. Patients were divided into three cohorts: those with moderate disease (
n
= 16), recovered patients with severe disease (
n
= 13), and deceased patients with severe disease (
n
= 16). In addition, 16 participants were pre-pandemic subjects negative for SARS-CoV-2. The relative activity of neutralizing antibodies (rNAbs) against SARS-CoV-2 and the values of 14 sICPs in peripheral blood were compared between the four groups. Because the increase of markers values of inflammation [NLR > 12; CRP > 150 mg/L] and venous thromboembolism [D-dimer > 0.5 mg/L] has been associated with mortality from COVID-19, the total and differential leukocyte counts, the NLR, and CRP and D-dimer values were obtained in patients with severe disease. No differences in rNAbs were observed between the cohorts. Only the levels of five sICPs, sCD27, sHVEM sTIM-3, sPD-1, and sPDL-1, were significantly higher in patients with severe rather than moderate disease. The sPDL-2 level and NLR were higher in deceased patients than in recovered patients. However, there was no difference in CRP and D-dimer values between the two groups. Of the five soluble biomarkers compared among patients with severe disease, only sPDL-2 was higher in deceased patients than in recovered patients. This suggests that immuno-inhibitory sICPs might be used as indicators for severe COVID-19, with sPDL-2 used to assess individual risk for fatality.

IMPORTANCE
COVID-19, the disease caused by a SARS-CoV-2 infection, generates a broad spectrum of clinical symptoms, progressing to multiorgan failure in the most severe cases. As activation of the immune system is pivotal to eradicating the virus, future research should focus on identifying reliable biomarkers to efficiently predict the outcome in severe COVID-19 cases. Soluble immune checkpoints represent the function of the immune system and are easily determined in peripheral blood. This research could lead to implementing more effective severity biomarkers for COVID-19, which could increase patients’ survival rate and quality of life.
Recombinant
Beauveria bassiana
expressing
Bacillus thuringiensis
toxin Cyt1Aa: a promising approach for enhancing
Aedes
mosquito control
Authors: Deng Sheng-Qun , Li Ni , Yang Xu-Ke , Lu Hong-Zheng , Liu Jia-Hua , Peng Zhe-Yu , Wang Lin-Min , Zhang Mao , Zhang Chao , Chen Chen 
Published: May 2024

ABSTRACT

The entomopathogenic fungus
Beauveria bassiana
provides an eco-friendly substitute to chemical insecticides for mosquito control. Nevertheless, its widespread application has been hindered by its comparatively slow efficacy in eliminating mosquitoes. To augment the potency of
B. bassiana
against
Aedes
mosquitoes, a novel recombinant strain,
Bb
-Cyt1Aa, was developed by incorporating the
Bacillus thuringiensis
toxin gene
Cyt1Aa
into
B. bassiana
. The virulence of
Bb
-Cyt1Aa was evaluated against
Aedes aegypti
and
Aedes albopictus
using insect bioassays. Compared to the wild-type (WT) strain, the median lethal time (LT
50
) for
A. aegypti
larvae infected with
Bb
-Cyt1Aa decreased by 33.3% at a concentration of 1 × 10
8
conidia/mL and by 22.2% at 1 × 10
7
conidia/mL. The LT
50
for
A. aegypti
adults infected with
Bb
-Cyt1Aa through conidia ingestion was reduced by 37.5% at 1 × 10
8
conidia/mL and by 33.3% at 1 × 10
7
conidia/mL. Likewise, the LT
50
for
A. aegypti
adults infected with
Bb
-Cyt1Aa through cuticle contact decreased by 33.3% and 30.8% at the same concentrations, respectively. Furthermore, the
Bb
-Cyt1Aa strain also demonstrated increased toxicity against both larval and adult
A. albopictus
, when compared to the WT strain. In conclusion, our study demonstrated that the expression of
B. thuringiensis
toxin Cyt1Aa in
B. bassiana
enhanced its virulence against
Aedes
mosquitoes. This suggests that
B. bassiana
expressing Cyt1Aa has potential value for use in mosquito control.

IMPORTANCE

Beauveria bassiana
is a naturally occurring fungus that can be utilized as a bioinsecticide against mosquitoes. Cyt1Aa is a delta-endotoxin protein produced by
Bacillus thuringiensis
that exhibits specific and potent insecticidal activity against mosquitoes. In our study, the expression of this toxin Cyt1Aa in
B. bassiana
enhances the virulence of
B. bassiana
against
Aedes aegypti
and
Aedes albopictus
, thereby increasing their effectiveness in killing mosquitoes. This novel strain can be used alongside chemical insecticides to reduce dependence on harmful chemicals, thereby minimizing negative impacts on the environment and human health. Additionally, the potential resistance of
B. bassiana
against mosquitoes in the future could be overcome by acquiring novel combinations of exogenous toxin genes. The presence of
B. bassiana
that expresses Cyt1Aa is of significant importance in mosquito control as it enhances genetic diversity, creates novel virulent strains, and contributes to the development of safer and more sustainable methods of mosquito control.
Microbiome of lovebug (
Plecia longiforceps
) in Seoul, South Korea
Authors: Yi Myung-hee , Choi Jun Ho , Kim Myungjun , Chavarria Xavier , Yun Sohyeon , Oh Singeun , Kang Dongjun , Yong Tai-Soon , Kim Ju Yeong 
Published: May 2024

ABSTRACT

Lovebugs appeared in large numbers across a wide area in Seoul, South Korea, in June 2023. The sudden appearance of exotic insects not only discomforts people but also fosters anxiety, as their potential for pathogen transmission would be unknown. In this study, targeted next-generation sequencing (NGS) of the 16S rRNA gene V4 region was performed using iSeq 100 to screen for bacteria in lovebugs. Forty-one lovebugs (20 females and 21 males) collected in Seoul, Korea, were identified as
Plecia longiforceps
based on mitochondrial cytochrome oxidase subunit 1 sequencing data using PCR. We analyzed the microbiome of the lovebugs and detected 453 species of bacteria. Among all bacteria screened based on NGS,
Rickettsia
was detected in all samples with an average relative abundance of 80.40%, followed by
Pandoraea
and
Ewingella
. Diversity (alpha and beta) between females and males did not differ; however, only
Tumebacillus
showed a higher relative abundance in females. Sequencing analysis of
Rickettsia
using a
gltA
gene-specific primer by PCR showed that it had higher sequence similarity to the
Rickettsia
symbiont of arthropods than to the spotted fever group rickettsiae. Eleven samples in which
Pandoraea
was detected by iSeq 100 were confirmed by PCR and exhibited 100% sequence identity to
Pandoraea oxalativorans
strain DSM 23570. Consequently, the likelihood of pathogen transmission to humans is low. The applied method may play a crucial role in swiftly identifying bacterial species in the event of future outbreaks of exotic insects that may be harmful to humans.

IMPORTANCE

Lovebugs have recently emerged in large numbers in Seoul, causing major concern regarding potential health risks. By performing the next-generation sequencing of the 16S rRNA gene V4 region, we comprehensively examined the microbiome of these insects. We identified the presence of numerous bacteria, including
Rickettsia
and
Pandoraea
. Reassuringly, subsequent tests confirmed that these detected bacteria were not pathogenic. The present study addresses health concerns related to lovebugs and shows the accuracy and efficiency of our detection technique. Such methods prove invaluable for rapidly identifying bacterial species during potential outbreaks of unfamiliar insects, thereby ensuring public safety.
Career Reflections from a Chinese American Geology Professor
Authors: Chan Marjorie A. 
Published: May 2024

ABSTRACT
I’ve enjoyed a rich career of four decades in academia as a Chinese American sedimentary geology professor. From the start, I was a clear minority, being nonwhite and a woman, but somehow with strong mentors and good fortune, I survived, persevered, and flourished. Despite discrimination and marginalization, there have been many positives, and the superb students and colleagues I have met on my journey have enriched my life immensely.
I want to see geoscience change to become one of the most inclusive sciences because it is really a capstone science that needs broad and diverse perspectives. I hope my story can encourage others and also highlight how we should continue to create opportunities for inclusive participation. The future of our Earth and the balance of nature and society depend on it!
Choroidal neovascularisation secondary toX-linked retinoschisis
Authors: Zhang Linyan , Liu Xinyu , Sun Limei , Zhou Xiaodi , Ke Shuya , Ding Xiaoyan 
Published: May 2024

Aims
Choroidal neovascularisation (CNV) in patients with X-linked retinoschisis (XLRS) has been poorly documented. This study aims to investigate the prevalence and clinical characteristics of CNV in patients with XLRS, as well as analyse the preliminary genotype–phenotype correlation.

Methods
A retrospective case series of patients with genetically confirmed XLRS was included. Demographic, clinical and genetic features were analysed, with a comparison between CNV and non-CNV eyes.

Results
Among 185 eyes of 129 patients with XLRS, the prevalence of CNV was 8.1% (15/185). The mean diagnostic age of all patients with CNV is 5.1±2.56 years. CNV eyes exhibited a mean best-corrected visual acuity (BCVA) (logarithm of the minimal angle of resolution) of 1.37±0.74. All CNVs were classified as subretinal and active. Peripapillary CNVs accounted for 80.0% (12/15), while subfoveal CNVs accounted for 20.0% (3/15). In CNV eyes, the prevalence of macular atrophy (5/15, 33.3%, p=0.013) and bullous peripheral schisis (14/15, 93.3%, p=0.000) was higher compared with non-CNV eyes. Additionally, CNV eyes exhibited poorer integrity of the outer retina and BCVA (p=0.007) compared with non-CNV eyes. All 15 eyes with CNV underwent anti-vascular endothelial growth factor (anti-VEGF) therapy. Genotype analysis revealed that 7 of 10 patients (70.0%, 10 eyes) were predicted to have missense variants, while 3 of 10 patients (30.0%, 5 eyes) exhibited severe variants.

Conclusions
The prevalence of CNV in XLRS eyes was found to be 8.1%. All CNVs secondary to XLRS were active and classified as type 2. CNV eyes demonstrated poorer visual function and compromised retinal structures. Anti-VEGF therapy demonstrated effectiveness in treating XLRS-CNVs. No significant genotype–phenotype correlation was established.
First and second-generation endometrial ablation devices: A network meta-analysis
Authors: Marchand Greg J , Masoud Ahmed , Grover Sandeep , King Alexa , Brazil Giovanna , Ulibarri Hollie , Parise Julia , Arroyo Amanda , Coriell Catherine , Moir Carmen , Govindan Malini 
Published: May 2024

ObjectiveFirst-generation and second-generation endometrial ablation (EA) techniques, along with medical treatment and invasive surgery, are considered successful lines of management for abnormal uterine bleeding (AUB). We set out to determine the efficacy of first and second-generation ablation techniques compared with medical treatment, invasive surgery and different modalities of the EA techniques themselves.DesignSystematic review and network meta-analysis using a frequentist network.Data sourcesWe searched Medline (Ovid), PubMed, ClinicalTrials.gov, Cochrane CENTRAL, Web of Science, EBSCO and Scopus for all published studies up to 1 March 2021 using relevant keywords.Eligibility criteriaWe included all randomised controlled trials (RCTs) that compared premenopausal women with AUB receiving the intervention of second-generation EA techniques.Data extraction and synthesis49 high-quality RCTs with 8038 women were included. We extracted and pooled the data and then analysed to estimate the network meta-analysis models within a frequentist framework. We used the random-effects model of the netmeta package in R (V.3.6.1) and the ‘Meta-Insight’ website.ResultsOur network meta-analysis showed many varying results according to specific outcomes. The uterine balloon ablation had significantly higher amenorrhoea rates than other techniques in both short (hydrothermal ablation (risk ratio (RR)=0.51, 95% CI 0.37; 0.72), microwave ablation (RR=0.43, 95% CI 0.31; 0.59), first-generation techniques (RR=0.44, 95% CI 0.33; 0.59), endometrial laser intrauterine therapy (RR=0.18, 95% CI 0.10; 0.32) and bipolar radio frequency treatments (RR=0.22, 95% CI 0.15; 0.31)) and long-term follow-up (microwave ablation (RR=0.11, 95% CI 0.01; 0.86), bipolar radio frequency ablation (RR=0.12, 95% CI 0.02; 0.90), first generation (RR=0.12, 95% CI 0.02; 0.90) and endometrial laser intrauterine thermal therapy (RR=0.04, 95% CI 0.01; 0.36)). When calculating efficacy based only on calculated bleeding scores, the highest scores were achieved by cryoablation systems (p-score=0.98).ConclusionMost second-generation EA systems were superior to first-generation systems, and statistical superiority between devices depended on which characteristic was measured (secondary amenorrhoea rate, treatment of AUB, patient satisfaction or treatment of dysmenorrhoea). Although our study was limited by a paucity of data comparing large numbers of devices, we conclude that there is no evidence at this time that any one of the examined second-generation systems is clearly superior to all others.