bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opposing genetic polymorphisms of two ABC transporters contribute to the variation of nukacin resistance in
Streptococcus mutans
Authors: Sadaoka Naoki , Le Mi Nguyen-Tra , Kawada-Matsuo Miki , Eng Sopongselamuny , Zendo Takeshi , Nakanishi Jun , Takeda Katsuhiro , Shiba Hideki , Komatsuzawa Hitoshi 
Published: February 2024

ABSTRACT

Streptococcus mutans
is a cariogenic bacterium that produces a variety of bacteriocins and retains resistance to these bacteriocins. In this study, we investigated the susceptibility of 127
S
.
mutans
strains to nukacins produced by
Staphylococcus
spp., which are commensal bacteria in humans. We detected diverse susceptibilities among strains. Nineteen strains had a disrupted LctF (type I), which is responsible for nukacin susceptibility, whereas the remaining 108 strains had an intact LctF (type II) and displayed resistance to nukacins. However, the type I strains still showed resistance to nukacins to some extent. Interestingly, 18/19 (94.7%) type I strains carried a
mukA-T
locus, which is related to the synthesis of mutacin K8, and
mukFEG
, an ABC transporter. In contrast, among type II strains, only 6/108 strains (5.6%) had both the
mukA-T
locus and
mukFEG
, 19/108 strains (17.6%) carried only
mukFEG
, and 83/108 strains (76.9%) harbored neither
mukA-T
nor
mukFEG
. We also found that MukF had two variants: 305 amino acids (type α) and 302 amino acids (type β). All type I strains showed a type α (MukFα), whereas most type II strains with
mukFEG
(22/25 strains) had a type β (MukFβ). Then, we constructed a
mukFEG
-deletion mutant complemented with MukFαEG or MukFβEG and found that only MukFαEG was involved in nukacin resistance. The nukacin resistance capability of type II-LctFEG was stronger than that of MukFαEG. In conclusion, we identified a novel nukacin resistance factor, MukFEG, and either LctFEG or MukFEG was active in most strains via genetic polymorphisms depending on
mukA-T
genes.

IMPORTANCE

Streptococcus mutans
is an important pathogenic bacterium not only for dental caries but also for systemic diseases.
S. mutans
is known to produce a variety of bacteriocins and to retain resistance these bacteriocins. In this study, two ABC transporters, LctFEG and MukFEG, were implicated in nukacin resistance and each ABC transporter has two subtypes, active and inactive. Of the two ABC transporters, only one ABC transporter was always resistant, while the other ABC transporter was inactivated by genetic mutation. Interestingly, this phenomenon was defined by the presence or absence of the mutacin K8 synthesis gene region, one of the bacteriocins of
S. mutans
. This suggests that the resistance acquisition is tightly controlled in each strain. This study provides important evidence that the insertion of bacteriocin synthesis genes is involved in the induction of genetic polymorphisms and suggests that bacteriocin synthesis genes may play an important role in bacterial evolution.
Filamin B restricts vaccinia virus spread and is targeted by vaccinia virus protein C4
Authors: Georgana Iliana , Scutts Simon R. , Gao Chen , Lu Yongxu , Torres Alice A. , Ren Hongwei , Emmott Edward , Men Jinghao , Oei Keefe , Smith Geoffrey L. 
Published: February 2024

ABSTRACT

Vaccinia virus (VACV) is a large DNA virus that encodes scores of proteins that modulate the host immune response. VACV protein C4 is one such immunomodulator known to inhibit the activation of both the NF-κB signaling cascade and the DNA-PK-mediated DNA sensing pathway. Here, we show that the N-terminal region of C4, which neither inhibits NF-κB nor mediates interaction with DNA-PK, still contributes to virus virulence. Furthermore, this domain interacts directly and with high affinity to the C-terminal domain of filamin B (FLNB). FLNB is a large actin-binding protein that stabilizes the F-actin network and is implicated in other cellular processes. Deletion of FLNB from cells results in larger VACV plaques and increased infectious viral yield, indicating that FLNB restricts VACV spread. These data demonstrate that C4 has a new function that contributes to virulence and engages the cytoskeleton. Furthermore, we show that the cytoskeleton performs further previously uncharacterized functions during VACV infection.

IMPORTANCE
Vaccinia virus (VACV), the vaccine against smallpox and monkeypox, encodes many proteins to counteract the host immune response. Investigating these proteins provides insights into viral immune evasion mechanisms and thereby indicates how to engineer safer and more immunogenic VACV-based vaccines. Here, we report that the N-terminal domain of VACV protein C4 interacts directly with the cytoskeletal protein filamin B (FLNB), and this domain of C4 contributes to virus virulence. Furthermore, VACV replicates and spreads better in cells lacking FLNB, thus demonstrating that FLNB has antiviral activity. VACV utilizes the cytoskeleton for movement within and between cells; however, previous studies show no involvement of C4 in VACV replication or spread. Thus, C4 associates with FLNB for a different reason, suggesting that the cytoskeleton has further uncharacterized roles during virus infection.
Draft genome sequences of 12
Mycolicibacterium fortuitum
isolates from human pulmonary infections in Veracruz, Mexico
Authors: Mejía-Ponce Paulina M. , Chimal-Muñoz Miguel , Zenteno-Cuevas Roberto , Licona-Cassani Cuauhtémoc 
Published: February 2024

ABSTRACT

Mycolicibacterium fortuitum
, a fast-growing nontuberculous mycobacterium, is a significant pathogen in healthcare-associated infections, encompassing skin, soft tissue, and pulmonary diseases. In this study, we present draft genome sequences from 12
M
.
fortuitum
strains isolated from sputum samples from patients diagnosed with pulmonary infections in Mexico.
ProQ-dependent activation of
Salmonella
virulence genes mediated by post-transcriptional control of PhoP synthesis
Authors: Bergman Sofia , Andresen Liis , Kjellin Jonas , Martinez Burgo Yolanda , Geiser Petra , Baars Sophie , Söderbom Fredrik , Sellin Mikael E. , Holmqvist Erik 
Published: February 2024

ABSTRACT

Gastrointestinal disease caused by
Salmonella enterica
is associated with the pathogen’s ability to replicate within epithelial cells and macrophages. Upon host cell entry, the bacteria express a type-three secretion system encoded within
Salmonella
pathogenicity island 2, through which host-manipulating effector proteins are secreted to establish a stable intracellular niche. Transcription of this intracellular virulence program is activated by the PhoPQ two-component system that senses the low pH and the reduced magnesium concentration of host cell vacuoles. In addition to transcriptional control,
Salmonella
commonly employ RNA-binding proteins (RBPs) and small regulatory RNAs (sRNAs) to regulate gene expression at the post-transcriptional level. ProQ is a globally acting RBP in
Salmonella
that promotes expression of the intracellular virulence program, but its RNA repertoire has previously been characterized only under standard laboratory growth conditions. Here, we provide a high-resolution ProQ interactome during conditions mimicking the environment of the
Salmonella
-containing vacuole (SCV), revealing hundreds of previously unknown ProQ binding sites in sRNAs and mRNA 3′UTRs. ProQ positively affected both the levels and the stability of many sRNA ligands, some of which were previously shown to associate with the well-studied and infection-relevant RBP Hfq. We further show that ProQ activates the expression of PhoP at the post-transcriptional level, which, in turn, leads to upregulation of the intracellular virulence program.

IMPORTANCE

Salmonella enterica
is a major pathogen responsible for foodborne gastroenteritis, and a leading model organism for genetic and molecular studies of bacterial virulence mechanisms. One key trait of this pathogen is the ability to survive within infected host cells. During infection, the bacteria employ a type three secretion system that deliver effector proteins to target and manipulate host cell processes. The transcriptional regulation of this virulence program is well understood. By contrast, the factors and mechanisms operating at the post-transcriptional level to control virulence gene expression are less clear. In this study, we have charted the global RNA ligand repertoire of the RNA-binding protein ProQ during
in vitro
conditions mimicking the host cell environment. This identified hundreds of binding sites and revealed ProQ-dependent stabilization of intracellular-specific small RNAs. Importantly, we show that ProQ post-transcriptionally activates the expression of PhoP, a master transcriptional activator of intracellular virulence in
Salmonella
.
Toxoplasma gondii
harbors a hypoxia-responsive coproporphyrinogen dehydrogenase-like protein
Authors: Key Melanie , Baptista Carlos Gustavo , Bergmann Amy , Floyd Katherine , Blader Ira J. , Dou Zhicheng 
Published: February 2024

ABSTRACT

Toxoplasma gondii
is an apicomplexan parasite that is the cause of toxoplasmosis, a potentially lethal disease for immunocompromised individuals. During
in vivo
infection, the parasites encounter various growth environments, such as hypoxia. Therefore, the metabolic enzymes in the parasites must adapt to such changes to fulfill their nutritional requirements.
Toxoplasma
can
de novo
biosynthesize some nutrients, such as heme. The parasites heavily rely on their own heme production for intracellular survival. Notably, the antepenultimate step within this pathway is facilitated by coproporphyrinogen III oxidase (CPOX), which employs oxygen to convert coproporphyrinogen III to protoporphyrinogen IX through oxidative decarboxylation. Conversely, some bacteria can accomplish this conversion independently of oxygen through coproporphyrinogen dehydrogenase (CPDH). Genome analysis found a CPDH ortholog in
Toxoplasma
. The mutant
Toxoplasma
lacking CPOX displays significantly reduced growth, implying that
T. gondii
CPDH (TgCPDH) potentially functions as an alternative enzyme to perform the same reaction as CPOX under low-oxygen conditions. In this study, we demonstrated that TgCPDH exhibits CPDH activity by complementing it in a heme synthesis-deficient
Salmonella
mutant. Additionally, we observed an increase in TgCPDH expression in
Toxoplasma
when it grew under hypoxic conditions. However, deleting
TgCPDH
in both wild-type and heme-deficient parasites did not alter their intracellular growth under both ambient and low-oxygen conditions. This research marks the first report of a CPDH-like protein in eukaryotic cells. Although TgCPDH responds to hypoxic conditions and possesses enzymatic activity, our findings revealed that it does not directly affect acute
Toxoplasma
infections
in vitro
and
in vivo
.

IMPORTANCE

Toxoplasma gondii
is a ubiquitous parasite capable of infecting a wide range of warm-blooded hosts, including humans. During its life cycle, these parasites must adapt to varying environmental conditions, including situations with low-oxygen levels, such as intestine and spleen tissues. Our research, in conjunction with studies conducted by other laboratories, has revealed that
Toxoplasma
primarily relies on its own heme production during acute infections. Intriguingly, in addition to this classical heme biosynthetic pathway, the parasites encode a putative oxygen-independent coproporphyrinogen dehydrogenase (CPDH), suggesting its potential contribution to heme production under varying oxygen conditions, a feature typically observed in simpler organisms like bacteria. Notably, so far, CPDH has only been identified in some bacteria for heme biosynthesis. Our study discovered that
Toxoplasma
harbors a functional enzyme displaying CPDH activity, which alters its expression in the parasites when they face fluctuating oxygen levels in their surroundings.
Membrane fluidity homeostasis is required for tobramycin-enhanced biofilm in
Pseudomonas aeruginosa
Authors: David Audrey , Tahrioui Ali , Duchesne Rachel , Tareau Anne-Sophie , Maillot Olivier , Barreau Magalie , Feuilloley Marc G. J. , Lesouhaitier Olivier , Cornelis Pierre , Bouffartigues Emeline , Chevalier Sylvie 
Published: February 2024

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic pathogen, which causes chronic infections, especially in cystic fibrosis (CF) patients where it colonizes the lungs via the build-up of biofilms. Tobramycin, an aminoglycoside, is often used to treat
P. aeruginosa
infections in CF patients. Tobramycin at sub-minimal inhibitory concentrations enhances both biofilm biomass and thickness
in vitro
; however, the mechanism(s) involved are still unknown. Herein, we show that tobramycin increases the expression and activity of SigX, an extracytoplasmic sigma factor known to be involved in the biosynthesis of membrane lipids and membrane fluidity homeostasis. The biofilm enhancement by tobramycin is not observed in a
sigX
mutant, and the
sigX
mutant displays increased membrane stiffness. Remarkably, the addition of polysorbate 80 increases membrane fluidity of
sigX
-mutant cells in biofilm, restoring the tobramycin-enhanced biofilm formation. Our results suggest the involvement of membrane fluidity homeostasis in biofilm development upon tobramycin exposure.

IMPORTANCE

Previous studies have shown that sub-lethal concentrations of tobramycin led to an increase biofilm formation in the case of infections with the opportunistic pathogen
Pseudomonas aeruginosa
. We show that the mechanism involved in this phenotype relies on the cell envelope stress response, triggered by the extracytoplasmic sigma factor SigX. This phenotype was abolished in a
sigX
-mutant strain. Remarkably, we show that increasing the membrane fluidity of the mutant strain is sufficient to restore the effect of tobramycin. Altogether, our data suggest the involvement of membrane fluidity homeostasis in biofilm development upon tobramycin exposure.
Screening potential biomarkers associated with insulin resistance in high-fat diet-fed mice by integrating metagenomics and untargeted metabolomics
Authors: Zhou Yunyan , Tang Jiahui , Du Wei , Zhang Yong , Ye Bang-Ce 
Published: February 2024

ABSTRACT

Insulin resistance is the primary pathophysiological basis for metabolic syndrome and type 2 diabetes. Gut microbiota and microbiota-derived metabolites are pivotal in insulin resistance. However, identifying the specific microbes and key metabolites with causal roles is a challenging task, and the underlying mechanisms require further exploration. Here, we successfully constructed a model of insulin resistance in mice induced by a high-fat diet (HFD) and screened potential biomarkers associated with insulin resistance by integrating metagenomics and untargeted metabolomics. Our findings showed a significant increase in the abundance of 30 species of
Alistipes
in HFD mice compared to normal diet (ND) mice, while the abundance of
Desulfovibrio
and
Candidatus Amulumruptor
was significantly lower in HFD mice than in ND mice. Non-targeted metabolomics analysis identified 21 insulin resistance-associated metabolites, originating from the microbiota or co-metabolized by both the microbiota and the host. These metabolites were primarily enriched in aromatic amino acid metabolism (tryptophan metabolism, tyrosine metabolism, and phenylalanine metabolism) and arginine biosynthesis. Further analysis revealed a significant association between the three distinct genera and 21 differentiated metabolites in the HFD and ND mice. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of representative genomes from 12 species of the three distinct genera further revealed the functional potential in aromatic amino acid metabolism and arginine biosynthesis. This study lays the groundwork for future investigations into the mechanisms through which the gut microbiota and its metabolites impact insulin resistance.

IMPORTANCE
In this study, we aim to identify the microbes and metabolites linked to insulin resistance, some of which have not been previously reported in insulin resistance-related studies. This adds a complementary dimension to existing research. Furthermore, we establish a correlation between alterations in the gut microbiota and metabolite levels. These findings serve as a foundation for identifying the causal bacterial species and metabolites. They also offer insights that guide further exploration into the mechanisms through which these factors influence host insulin resistance.
The production of parallel world-class W and Cu metallogenic belts linked to an asymmetric slab window
Authors: Wu Shenghua , Mao Jingwen , Hetherington Callum J. 
Published: February 2024

Abstract
The ca. 150–135 Ma magmatic belts in the Middle–Lower Yangtze River Valley and its southern adjacent parallel northeastern Jiangnan Orogen in China experienced large-scale Cu and W metallogenesis, respectively. The magmatic belts interrupted contemporaneous magmatism along the east China continental margin and are an ideal locality to verify if Cu and W metallogenesis could be linked to a slab window. Oceanic plate subduction, intracontinental extension, lower crustal delamination, or ridge subduction models have been debated for the Cu and W belts. However, these models have weaknesses that cannot explain unique features of the belts such as the belts being coeval and intersecting with the trend of the paleo-trench, or the asymmetric distribution of the magmatic-metallogenic belts along both sides of the Middle–Lower Yangtze River Valley. Based on the configurative, compositional, and isotopic evidences, the magmatic belts record the fingerprints of the slab window generated by disassembly of the paleo-ridge between the Paleo-Pacific and Izanagi plates at ca. 150–135 Ma. During this time, the Paleo-Pacific plate rolled back beneath the eastern margin of the South China block and the Izanagi plate experienced flat-slab subduction that reached beneath the intracontinental regions of the North China block. The distinct and contrasting behaviors of the slabs produced a slab window that caused and promoted upwelling mantle to flow farther southward, inducing the asymmetric magmatic-metallogenic belts along the Middle–Lower Yangtze River Valley on both sides. The Middle–Lower Yangtze River Valley Cu-enriched magmatic belt was formed by melting of the lower crust and oceanic slab edge along the ridge by upwelling asthenospheric mantle. However, the Jiangnan Orogen W-enriched magmatic belt was induced by melting of the accretionary belt and mixing the melting of accretionary belt and the same hybrid mantle materials, during which the upwelling asthenospheric mantle tongue infiltrated southward due to the asymmetric structure of the slab window.
On the Water Striders (Heteroptera, Gerridae) of the Fauna of Russia: History of Study, Erroneous Identifications, and Features of Biology
Authors: Kanyukova E. V. 
Published: February 2024

Abstract
The history of study in Russia is reviewed and the distribution ranges are clarified for water striders of the genus Gerris: G. (s. str.) costae, G. (s. str.) thoracicus, G. (Gerriselloides) asper, G. (Gerriselloides) brachynotus, and G. (Gerriselloides) lateralis. A critical review of the faunistic literature and erroneous records of these species from Russia is given. Distribution maps with new locations are provided for G. (Gerriselloides) asper and G. (Gerriselloides) brachynotus. The preference of species of the subgenera Gerris, Gerriselloides, and Macrogerris with a brownish dorsum for the shady parts of water bodies is discussed.
Staff experiences of wearing the Rainbow Badge in a paediatric hospital setting: a mixed-methods survey
Authors: O'Dwyer Claire , Kehoe Anne , Shanahan Dee , O'Brien Warren , Hall Dani 
Published: February 2024

ObjectiveThis study aimed to assess staff’s experience of wearing the Health Service Executive (HSE) Rainbow Badge, a symbol of inclusion for LGBTQ+ (lesbian, gay, bisexual, transgender, queer/questioning; + signifying inclusivity of all sexual and gender identities) people, in a paediatric hospital setting.DesignThis was a cross-sectional multisite observational study. Participants completed an anonymous online survey, consisting of open and closed-ended questions covering domains of: responses to the badge from staff and patients; experience and impact of wearing the badge; and further training needs.SettingAll five sites (four clinical and one non-clinical) pertaining to the Children’s Health Ireland healthcare group.ParticipantsAll staff, clinical and non-clinical, who had signed up the HSE Rainbow Badge initiative were eligible to participate.ResultsA total of 151 eligible participants across a mix of disciplines participated, 29 (19.2%) of whom were members of the LGBTQ+ community. Over half (58.9%, n=89) of respondents said they learnt something new about barriers to care for LGBTQ+ young people from the initiative. Staff reported mostly positive responses to the badge; 5.1% reported mixed/negative responses from colleagues, 4.5% reported mixed/negative responses from young people and 3.7% reported mixed/negative responses from families. Open-ended questions were analysed using a thematic analysis framework. Five themes emerged: pride, a symbol of safety and inclusion, impact on workplace culture, awareness of LGBTQ+ issues and more to do for LGBTQ+ patients.ConclusionsThis study demonstrates that the Rainbow Badge initiative increases staff awareness of LGBTQ+ issues and helps to create a safe, inclusive environment for staff, young people and families.
Adult-onset mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS): a diagnostic challenge
Authors: Acquaah Jason , Ferdinand Phillip , Roffe Christine 
Published: February 2024

Rare causes of stroke-like presentations can be difficult to diagnose. We report a case of a man in his 40s who first presented with stroke symptoms, but whose clinical course was not typical for a stroke. A detailed investigation of the patient’s medical history revealed bilateral sensorineural hearing loss which prompted a wider diagnostic assessment.Furthermore, lack of vascular risk factors and a normal angiogram strengthened our suspicion of an unusual underlying condition. Raised lactic acid levels and genetic analysis confirmed a diagnosis of mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes syndrome.