bluuebunny/crossref_metadata_2025 huggingface dataset:
CXCR4 signaling determines the fate of hematopoietic multipotent progenitors by stimulating mTOR activity and mitochondrial metabolism
Authors: Rondeau Vincent , Kalogeraki Maria , Roland Lilian , Nader Zeina Abou , Gourhand Vanessa , Bonaud Amélie , Lemos Julia , Khamyath Mélanie , Moulin Clémentine , Schell Bérénice , Delord Marc , Bidaut Ghislain , Lecourt Séverine , Freitas Christelle , Anginot Adrienne , Mazure Nathalie , McDermott David H. , Parietti Véronique , Setterblad Niclas , Dulphy Nicolas , Bachelerie Françoise , Aurrand-Lions Michel , Stockholm Daniel , Lobry Camille , Murphy Philip M. , Espéli Marion , Mancini Stéphane J. C. , Balabanian Karl
Published: October 2024

Both cell-intrinsic and niche-derived, cell-extrinsic cues drive the specification of hematopoietic multipotent progenitors (MPPs) in the bone marrow, which comprise multipotent MPP1 cells and lineage-restricted MPP2, MPP3, and MPP4 subsets. Patients with WHIM syndrome, a rare congenital immunodeficiency caused by mutations that prevent desensitization of the chemokine receptor CXCR4, have an excess of myeloid cells in the bone marrow. Here, we investigated the effects of increased CXCR4 signaling on the localization and fate of MPPs. Knock-in mice bearing a WHIM syndrome–associated
CXCR4
mutation (

CXCR4
1013

) phenocopied the myeloid skewing of bone marrow in patients. Whereas MPP4 cells in wild-type mice differentiated into lymphoid cells, MPP4s in

CXCR4
1013

knock-in mice differentiated into myeloid cells. This myeloid rewiring of MPP4s in

CXCR4
1013

knock-in mice was associated with enhanced signaling mediated by the kinase mTOR and increased oxidative phosphorylation (OXPHOS). MPP4s also localized further from arterioles in the bone marrow of knock-in mice compared with wild-type mice, suggesting that the loss of extrinsic cues from the perivascular niche may also contribute to their myeloid skewing. Chronic treatment with the CXCR4 antagonist AMD3100 or the mTOR inhibitor rapamycin restored the lymphoid potential of MPP4s in knock-in mice. Thus, CXCR4 desensitization drives the lymphoid potential of MPP4 cells by dampening the mTOR-dependent metabolic changes that promote myeloid differentiation.
A novel methionyl-tRNA synthetase inhibitor targeting gram-positive bacterial pathogens
Authors: Molasky Nora M. R. , Zhang Zhongsheng , Gillespie J. Robert , Domagala John , Reyna Dawn , Lipka Elke , Fan Erkang , Buckner Frederick S.
Published: October 2024

New antibiotics are needed to treat gram-positive bacterial pathogens.
MRS-2541
is a novel inhibitor of methionyl-tRNA synthetase with selective activity against gram-positive bacteria. The minimum inhibitory concentrations (MICs) against
Staphylococcus aureus, Streptococcus pyogenes,
and
Enterococcus
species range from 0.063 to 0.5 µg/mL. Given orally to mice at 50 mg/kg every 8 hours,
MRS-2541
shows sustained plasma levels well above these MICs. In the mouse thigh infection model,
MRS-2541
decreased methicillin-resistant
Staphylococcus aureus
and
Streptococcus pyogenes
bacterial loads to the same degree as linezolid.
MRS-2541
is a promising new antibiotic for development against skin and soft tissue infections.
Effects of wildfire on soil microbial communities in karst forest ecosystems of southern Guizhou Province, China
Authors: Li Xu , Han Yanfeng , Zhang Yunlin , Shao Qiuyu , Dong Chunbo , Li Jianfeng , Ding Bo , Zhang Yanwei
Published: October 2024

Wildfires are unpredictable disturbances with profound effects on soil properties and microbial communities within forest ecosystems. However, knowledge of post-fire microbial communities in karst forests remains limited. In this study, microbial amplicon sequencing techniques were employed to investigate the impact of wildfires on the composition, diversity, function, and co-occurrence network of soil microbial communities in karst forest landscapes and to identify the key soil physicochemical factors affecting the post-fire microbial communities. The wildfire affected the fungal community to a greater extent than the bacterial community, with the former shifting from a dominance of Basidiomycota to Ascomycota at the phylum level, while the relative abundance of Actinobacteria increased significantly in the bacterial community. Moreover, the wildfire increased the α-diversity of the microbial community and changed the β-diversity. Network analysis indicated significant reductions in the complexity of microbial community networks and the hub microbiome in burned soils compared to those of unburned soils. Functional predictions indicated an increase in the highly abundant functional taxa of chemoheterotrophic and aerobic chemoheterotrophic bacteria, along with a significant rise in saprotrophic functional fungal taxa following the fire. In addition, soil organic matter, total nitrogen, total phosphorus, and soil water content emerged as key soil physicochemical factors affecting post-fire soil microbial communities in the karst forest. Overall, this study revealed the structural and functional characteristics of soil microbial communities and their key influencing factors after a fire in a karst forest, which will provide a valuable theoretical basis for ecosystem restoration after a wildfire.

IMPORTANCE

Despite the significant impacts of wildfires on forest ecosystems, most existing studies have largely focused on boreal and Mediterranean coniferous forest types, with limited research on the impacts of coniferous and broadleaf forest types in subtropical karst regions. This study reveals the effects of wildfires on soil microbial communities of coniferous and broadleaf forest types in a karst forest. The results of this study not only improve the understanding of the effects of wildfires on the composition, diversity, function, and network of soil microbial communities but also provide a meaningful theoretical basis for post-fire ecosystem restoration in the karst forest.
Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment
Authors: Somboon Kamolrat , Melling Oliver , Lejeune Maylis , Pinheiro Glaucia M. S. , Paquelin Annick , Bardiaux Benjamin , Nilges Michael , Delepelaire Phillippe , Khalid Syma , Izadi-Pruneyre Nadia
Published: October 2024

The envelope of Gram-negative bacteria is composed of two membranes separated by the periplasmic space. This organization imposes geometrical and distance constraints that are key for the mechanism of action of multicomponent systems spanning the envelope. However, consideration of all three compartments by experimental approaches is still elusive. Here, we have used the state-of-the-art molecular dynamics simulation in an
Escherichia coli
envelope model to obtain a dynamic view of molecular interactions between the outer membrane heme transporter HasR and the inner membrane TonB-like protein HasB. Their interaction allows the transfer of the inner membrane proton-motive force derived energy to the transporter for heme internalization. The simulations that incorporate both membranes show the key role of periplasmic domains of both proteins and their dynamics in complex formation and stability. They revealed a previously unidentified network of HasR-HasB protein-protein interactions in the periplasm. Experimental validation (mutations,
in vivo
phenotypic and biophysical assays) provides support for the simulation-predicted interactions. Based on structural and sequence conservation, the network of interaction revealed in this study is expected to occur in other nutrient import systems.

IMPORTANCE

Gram-negative bacteria import scarce nutrients such as metals and vitamins by an energized mechanism involving a multicomponent protein system that spans the cell envelope. It consists of an outer membrane TonB-dependent transporter (TBDT) and a TonB complex in the inner membrane that provides the proton motive force energy for the nutrient entry. Despite the intense research efforts focused on this system (a) from structural and fundamental microbiology perspectives and (b) for the interest in the development of new antibacterial strategies, the molecular mechanism of the system is not at all well understood. The lack of understanding comes from incomplete structural data and the experimental difficulties of studying an inherently flexible multicomponent complex that resides within the heterogeneous environment of the double membrane bacterial cell envelope. To address these challenges and obtain a comprehensive view of the molecular interactions at atomic level, here, we have used the combined power of advanced molecular simulations and complementary microbiology and biochemical experiments. Our results represent a significant step forward in understanding the structural and molecular bases of this vital mechanism.
Suppression of ZBP1-mediated NLRP3 inflammasome by the tegument protein VP22 facilitates pseudorabies virus infection
Authors: Ma Zicheng , Liu Depeng , Cao Wandi , Guo Lei , Liu Kesen , Bai Juan , Li Xingyi , Jiang Ping , Liu Xing
Published: October 2024

The interaction between Z-DNA binding protein 1 (ZBP1) and the NLR family pyrin domain-containing 3 (NLRP3) inflammasome has been uncovered in several viral infections. However, the role of this molecular pathway during infection with the alpha-herpesvirus pseudorabies virus (PRV) remains largely elusive. Here, we report that during PRV infection, ZBP1-mediated NLRP3 inflammasome activation is inhibited by the viral tegument protein VP22, thereby facilitating viral infection. Through a combination of RNA sequencing and genetic studies, we demonstrate that PRV VP22 functions as a virus-encoded virulence factor by evading the inhibitory effects of ZBP1 on virus infection. Importantly, the replication and pathogenicity of a recombinant PRV lacking VP22 are significantly increased in ZBP1-deficient cells and mice. Mechanistically, PRV VP22 interacts with ZBP1, impeding the recruitment of receptor-interacting protein kinase 3 and Caspase-8, thereby inhibiting NLRP3 activation. Furthermore, we show that the N-terminal 1–50 amino acid domain of VP22 dominantly destabilizes ZBP1-mediated function. Taken together, these findings identify a functional link between PRV infection and ZBP1-mediated NLRP3 inflammatory response, providing novel insights into the pathogenesis of PRV and other herpesviruses.

IMPORTANCE

Z-DNA binding protein 1 (ZBP1) functions as a pivotal innate immune sensor that regulates inflammatory cell death during viral infections. However, its role in pseudorabies virus (PRV) infection remains unknown. Here, we demonstrate that ZBP1 serves as a restrictive factor by triggering the activation of the NLR family pyrin domain-containing 3 inflammasome, a process counteracted by PRV-encoded protein VP22. Furthermore, VP22 interferes with the interaction between ZBP1 and receptor-interacting protein kinase 3/Caspase-8, particularly through its N-terminal 1–50 amino acids. Importantly, deficiency in ZBP1 enhances the replication and virulence of recombinant viruses lacking VP22 or its N-terminal 1–50 amino acids. These findings reveal how PRV escapes ZBP1-mediated inflammatory responses during infection, potentially informing the rational design of therapeutic interventions.
Elements of dissemination in cryptococcosis
Authors: Bednarek Joseph M. , Brown Jessica C. S.
Published: October 2024

As healthcare improves and our ability to support patients with compromised immune systems increases, such patients become more vulnerable to microbes in the environment. These include fungal pathogens such as
Cryptococcus neoformans
, the primary cause of fungal meningitis and a top priority pathogen on the World Health Organization fungal pathogen list. Like many other environmental pathogens,
C. neoformans
must adapt to and thrive in diverse environments in order to cause disease: (i) the environmental niche, (ii) the lungs following inhalation of infectious particles, (iii) the bloodstream and/or lymphatic system during dissemination, and (iv) the central nervous system (CNS), where it causes a deadly cryptococcal meningoencephalitis. Because CNS infection is the driver of mortality and the presenting illness, understanding the dissemination process from both host and fungal perspectives is important for treating these infections. In this review, we discuss the different stages of dissemination, how fungal cells interact with host cells during disease, and the ability to adapt to different environments within hosts.
Activation of the general stress response sigma factor SigB prevents competence development in
Bacillus subtilis
Authors: Harms Marco , Michalik Stephan , Hildebrandt Petra , Schaffer Marc , Gesell Salazar Manuela , Gerth Ulf , Mäder Ulrike , van Dijl Jan Maarten , Hecker Michael , Völker Uwe , Reder Alexander
Published: October 2024

Seemingly simple bacteria mount intricate adaptive responses when exposed to physical stress or nutrient limitation, and the activation of these responses is governed by complex signal transduction networks. Upon entry into the stationary growth phase, the soil bacterium
Bacillus subtilis
may develop natural competence, form biofilms or stress-resistant cells, or ultimately trigger a cellular differentiation program leading to spore formation. Master regulators, such as Spo0A, ComK, SinR, and SigB, constantly monitor the bacterium’s environment and then determine appropriate adaptive responses. Here, we show that exposure of
B. subtilis
to visible light and other stresses triggers a general stress response-dependent block in competence development. SigB serves as an “emergency system” to silence inappropriate expression of an alternative developmental program in the face of unfavorable conditions. In particular, we document a stress-dependent molecular mechanism that prevents accumulation of the central competence regulator ComK via expression of a SigB-driven antisense RNA (
as-comK
, S365) which is part of a noncontiguous operon.

IMPORTANCE

Bacillus subtilis
exhibits a large number of different specific and general adaptation reactions, which need to be well balanced to sustain survival under largely unfavorable conditions. Under specific conditions, natural competence develops, which enables
B. subtilis
to actively take up exogenous DNA to integrate it into its own genome. In contrast to this specific adaptation, the general stress response is induced by a variety of exogenous stress and starvation stimuli, providing comprehensive protection and enabling survival of vegetative
B. subtilis
cells. In the present work, we reveal the molecular basis for the interconnection of these two important responses in the regulatory network. We describe that the master regulator of the general stress response SigB is activated by physiological stress stimuli, including daylight and ethanol stress, leading to the inactivation of the competence master regulator ComK by transcriptional anti-sense regulation, showing a strict hierarchy of adaptational responses under severe stress.
Substrate identification of putative NCS1 and NCS2 nucleobase transporters in
Pseudomonas aeruginosa
Authors: Kennelly Corey , Prindle Arthur
Published: October 2024

Pseudomonas aeruginosa
is an opportunistic pathogen that can salvage nucleobases from the environment to conserve nutrients that would otherwise be spent on
de novo
nucleotide biosynthesis. However, little is known regarding the substrate specificity of the 13 putative nucleobase transporters in
P. aeruginosa
. Here, using a combination of genetic and chemical approaches, we report substrate identifications for 10 putative nucleobase transporters in
P. aeruginosa
. Specifically, we individually expressed each transporter in a genetic background lacking all 13 putative nucleobase transporters and quantified growth on a panel of 10 nucleobases as sole nitrogen sources. We confirmed these expression-based substrate identifications using targeted genetic knockouts. In a complementary approach, we utilized four toxic nucleobase antimetabolites to characterize antimicrobial activity in these same strains. We identified the sole allantoin transporter as well as transporters for guanine, xanthine, uric acid, cytosine, thymine, uracil, and dihydrouracil. Furthermore, we associated at least five nucleobase transporters with hypoxanthine, which has been recently reported to be an antibiofilm cue in
P. aeruginosa
. These results provide an initial characterization of the putative nucleobase transporters in
P. aeruginosa
, significantly advancing our understanding of nucleobase transport in this clinically relevant organism.

IMPORTANCE

Pseudomonas aeruginosa
is a frequently multidrug-resistant opportunistic pathogen and one of the most common causes of healthcare-acquired infections. While nucleobases are known to support growth in nutrient-limited conditions, recent work showed that adenine and hypoxanthine can also decrease
P. aeruginosa
biofilm formation by disrupting c-di-GMP metabolism. Thus, nucleobase transport may be relevant to multiple aspects of
P. aeruginosa
biology and pathogenesis. However, there is currently little known about the transport of nucleobases in
P. aeruginosa
. Our work reports initial substrate identifications for 10 putative nucleobase transporters in
P. aeruginosa
, providing new tools to address previously difficult-to-test hypotheses relating to nucleobase transport in this organism.
Metabolites augment oxidative stress to sensitize antibiotic-tolerant
Staphylococcus aureus
to fluoroquinolones
Authors: Batchelder Jonathan I. , Taylor Andrew J. , Mok Wendy W. K.
Published: October 2024

If left unchecked, infections involving antibiotic-refractory bacteria are expected to cause millions of deaths per year in the coming decades. Beyond genetically resistant bacteria, persisters, which are genetically susceptible cells that survive antibiotic doses that kill the rest of the clonal population, can potentially contribute to treatment failure and infection relapse. Stationary-phase bacterial cultures are enriched with persisters, and it has been shown that stimulating these populations with exogenous nutrients can reduce persistence to different classes of antibiotics, including topoisomerase-targeting fluoroquinolones (FQs). In this study, we show that adding glucose and amino acids to nutrient-starved
Staphylococcus aureus
cultures enhanced their sensitivity to FQs, including delafloxacin (Dela)—a drug that was recently approved for treating staphylococcal infections. We found that while the added nutrients increased nucleic acid synthesis, this increase was not required to sensitize
S. aureus
to FQs. We further demonstrate that addition of these nutrients increases membrane potential and the ability to generate harmful reactive oxygen species (ROS) during FQ treatment. Chelating iron, scavenging hydroxyl radicals, and limiting oxygenation during FQ treatment and during recovery following FQ treatment rescued nutrient-stimulated
S. aureus
. In all, our data suggest that while nutrient stimulation increases the activity of FQ targets in stationary-phase
S. aureus
, the resulting generation of ROS, presumably made possible through metabolic upregulation, is the primary driver of increased sensitivity to these drugs.

IMPORTANCE

Staphylococcus aureus
causes many chronic and relapsing infections because of its ability to endure host immunity and antibiotic therapy. While several studies have focused on the nutrient requirements for the formation and maintenance of staphylococcal infections, the effects of the nutrient environment on bacterial responses to antibiotic treatment remain understudied. Here, we show that adding nutrients to starved
S. aureus
activates biosynthetic processes, including DNA synthesis, but it is the generation of harmful reactive oxidants that sensitizes
S. aureus
to DNA topoisomerase-targeting FQs. Our results suggest that the development of approaches aimed at perturbing metabolism and increasing oxidative stress can potentiate the bactericidal activity of FQs against antibiotic-tolerant
S. aureus
.
Complete genome sequences of five bacteria isolated from rice plants in a paddy field in Sekinchan, Selangor, Malaysia
Authors: Abdul Malek Ahmad Zuhairi , Hashim Amalia Mohd , Khairil Mokhtar Nur Fadhilah , Saidi Noor Baity , Abu Bakar Mohd Faizal , Singaram Nallamai
Published: October 2024

This study examines the genome sequences of five endophytic bacterial isolates from the
Oryza sativa
microbiome to assess their potential as plant bio-inoculants. The five complete bacterial genomes from the genera
Pseudomonas, Burkholderia, Sphingobacterium, Stenotrophomonas,
and
Pantoea
were sequenced using Nanopore long-read sequencing technology.
Complete genome sequence of the saprophytic actinomycete
Rhodococcus (Prescottella) soli
DSD51W
T
, closely related to the multi-host pathogen
Rhodococcus (Prescottella) equi
Authors: Yerlikaya Zeynep , Miranda-CasoLuengo Raúl , Ó Gaora Peadar , Meijer Wim G.
Published: October 2024

Rhodococcus (Prescottella) soli
strain DSD51W
T
is an aerobic, non-spore-forming, non-motile actinomycete isolated previously from soil collected from Kyoto Park, Japan, using a resuscitative technique. Here, we report the complete, circular genome sequence of
R. soli
DSD51W
T
. We employed a hybrid approach using Illumina and Oxford Nanopore platforms.
Complete genome sequence of strain KD-1
T
, the type strain of
Sulfurisphaera javensis
, isolated from an Indonesian hot spring
Authors: Sakai Hiroyuki D. , Nur Naswandi , Suwanto Antonius , Kurosawa Norio
Published: October 2024

Sulfurisphaera javensis
KD-1
T
, originally isolated from an Indonesian acidic hot spring, is a hyperthermophilic, acidophilic, and facultatively anaerobic archaeon. Here, we report the 2.6 Mb complete genome sequence of KD-1
T
. Genes related to sulfur metabolism were found in the genome, indicating that KD-1
T
is involved in the sulfur cycle in its habitat.
Complete genome of the opportunistic pathogen
Nocardia vulneris
strain LPB4002 and its biosynthetic potential
Authors: González-Nava Janette , Salinas-Virgen Leilani I. , Sandoval-Trujillo Horacio , Torre-Hernández Ma. Eugenia de la , Ramírez-Saad Hugo
Published: October 2024

The complete genome sequence of the opportunistic pathogen
Nocardia vulneris
is reported. The strain
N. vulneris
LPB4002 was isolated from a clinical sample of a patient with actinomycetoma. The reported genome comprises a single 9,489-Kb closed chromosome, with 8,584 protein-coding genes and 68% GC content.
Kinase function of TgTKL1 is essential for its role in
Toxoplasma
propagation and pathogenesis
Authors: Ali Dima Hajj , Anandakrishnan Ramu , Carruthers Vern B. , Gaji Rajshekhar Y.
Published: October 2024

The Tyrosine Kinase-Like (TKL) family of proteins are a set of poorly studied kinases that have garnered attention in recent years for their role in
Toxoplasma
biology. The
Toxoplasma
genome contains eight TKL kinases, of which six have been predicted to be important for parasite propagation. We have previously shown that TgTKL1 is a nuclear kinase that is critical for the parasite lytic cycle and is essential for acute virulence in the animal model. However, the contribution of the kinase domain to the functioning of TgTKL1 was not known. Hence to determine the significance of its catalytic function, we first validated that TgTKL1 is a true kinase using purified recombinant protein. Furthermore, we successfully generated a TgTKL1 kinase mutant strain of
Toxoplasma
via CRISPR-Cas9 gene editing. Our studies revealed that the kinase mutant of TgTKL1 displays defects in parasite growth and host-cell invasion. Additionally, loss of kinase function alters the transcriptomic profile of the parasite, including downregulation of the invasion-related gene, TgSUB1. Importantly, this dysregulation of TgSUB1 expression leads to defects in post-exocytosis processing of micronemal proteins, an event critical for normal host-cell invasion. Furthermore, the TgTKL1 kinase mutant is completely avirulent in the mouse model of acute toxoplasmosis. Since the loss of kinase function leads to phenotypic manifestations seen previously with TgTKL1 knockout parasites, we conclude that kinase activity is important for TgTKL1 function in
Toxoplasma
propagation and virulence.

IMPORTANCE

Toxoplasma gondii
is a protozoan parasite that can cause life-threatening disease in humans. Hence, identifying key factors required for parasite growth and pathogenesis is important to develop novel therapeutics. We have previously shown that a member of the TKL protein kinase family, TgTKL1, is a plant-like kinase that is required for effective Toxoplasma growth
in vitro
and essential for virulence
in vivo
. Herein, we show that the TgTKL1 is, indeed, a
bona fide
kinase, and loss of its kinase function in the Toxoplasma leads to similar defects seen in parasites with complete loss of TgTKL1. More specifically, the TgTKL1 kinase mutant exhibits defects in parasite growth, host-cell invasion, gene expression profile, and virulence in the animal model. Together, these findings suggest that TgTKL1 is a true kinase, and loss of its kinase activity leads to disruption of TgTKL1 function in
Toxoplasma
.
Stable, multigenerational transmission of the bean seed microbiome despite abiotic stress
Authors: Sulesky-Grieb Abby , Simonin Marie , Bintarti A. Fina , Marolleau Brice , Barret Matthieu , Shade Ashley
Published: October 2024

Microbiota that originate in the seed can have consequences for the education of the plant immune system, competitive exclusion of pathogens from the host tissue, and host access to critical nutrients. Our research objective was to investigate the consequences of the environmental conditions of the parent plant for bacterial seed microbiome assembly and transmission across plant generations. Using a fully factorial, three-generational experimental design, we investigated endophytic seed bacterial communities of common bean lines (
Phaseolus vulgaris
L.) grown in the growth chamber and exposed to either control conditions, drought, or excess nutrients at each generation. We applied 16S rRNA microbiome profiling to the seed endophytes and measured plant health outcomes. We discovered stable transmission of 22 bacterial members, regardless of the parental plant condition. This study shows the maintenance of bacterial members of the plant microbiome across generations, even under environmental stress. Overall, this work provides insights into the ability of plants to safeguard microbiome members, which has implications for crop microbiome management in the face of climate change.

IMPORTANCE

Seed microbiomes initiate plant microbiome assembly and thus have critical implications for the healthy development and performance of crops. However, the consequences of environmental conditions of the parent plant for seed microbiome assembly and transmission are unknown, but this is critical information, given the intensifying stressors that crops face as the climate crisis accelerates. This study provides insights into the maintenance of plant microbiomes across generations, with implications for durable plant microbiome maintenance in agriculture on the changing planet.
Phages ZC01 and ZC03 require type-IV pilus for
Pseudomonas aeruginosa
infection and have a potential for therapeutic applications
Authors: Martins Layla Farage , dos Santos Junior Ariosvaldo Pereira , Nicastro Gianlucca Gonçalves , Scheunemann Gaby , Angeli Claudia Blanes , Rossi Fernando Pacheco Nobre , Quaggio Ronaldo Bento , Palmisano Giuseppe , Sgro Germán Gustavo , Ishida Kelly , Baldini Regina Lúcia , da Silva Aline Maria
Published: October 2024

There has been a growing interest in bacteriophages as therapeutic agents to treat multidrug-resistant bacterial infections. The present work aimed at expanding the microbiological and molecular characterization of lytic phages ZC01 and ZC03 and investigating their efficacy in the control of
Pseudomonas aeruginosa
infection in an invertebrate animal model. These two phages were previously isolated from composting using
P. aeruginosa
strain PA14 as the enrichment host and had their genomes sequenced. ZC01 and ZC03 present, respectively, siphovirus and podovirus morphotypes. ZC01 was recently classified into the genus
Abidjanvirus
, while ZC03 belongs to
Zicotriavirus
genus of the
Schitoviridae
N4-like viruses. Through proteomics analysis, we identified virion structural proteins of ZC01 and ZC03, including a large virion-associated RNA polymerase that is characteristic of N4-like viruses, some hypothetical proteins whose annotation should be changed to virion structural proteins and a putative peptidoglycan hydrolase. Phages ZC01 and ZC03 exhibit a limited yet distinct host range, with moderate to high efficiency of plating (EOP) values observed for a few
P. aeruginosa
clinical isolates. Phage susceptibility assays in PA14 mutant strains point to the type-IV pilus (T4P) as the primary receptor for phages ZC01 and ZC03, and the major pilin (PilA
PA14
) is the T4P component recognized by these phages. Moreover, both phages significantly increase survival of
Galleria mellonella
larvae infected with PA14 strain. Taken together, these results underpin the therapeutic potential of these phages to treat infections by
P. aeruginosa
and lay the groundwork for a more detailed investigation of phage-bacteria-specific recognition mechanisms.

IMPORTANCE

Phage therapy is gaining increasing interest in cases of difficult-to-treat bacterial human infections, such as carbapenem-resistant
Pseudomonas aeruginosa
. In this work, we investigated the molecular mechanism underlying the interaction of the lytic phages ZC01 and ZC03 with the highly virulent
P. aeruginosa
PA14 strain and their efficacy to treat PA14 infection in
Galleria mellonella
larvae, a commonly used invertebrate model for phage therapy. We depicted the protein composition of ZC01 and ZC03 viral particles and identified pilin A, the major component of type-4 pilus, as the receptor recognized by these phages. Our findings indicate that phages ZC01 and ZC03 may be further used for developing therapies to treat multidrug-resistant
P. aeruginosa
infections.
Distinct impacts of each anti-anti-sigma factor ortholog of the chlamydial Rsb partner switching mechanism on development in
Chlamydia trachomatis
Authors: Junker Shiomi , Singh Vandana , Al-Saadi Aamal G. M. , Wood Nicholas A. , Hamilton-Brehm Scott D. , Ouellette Scot P. , Fisher Derek J.
Published: October 2024

Partner switching mechanisms (PSMs) are signal transduction systems comprised of a sensor phosphatase (RsbU), an anti-sigma factor (RsbW, kinase), an anti-anti-sigma factor (RsbV, the RsbW substrate), and a target sigma factor.
Chlamydia
spp. are obligate intracellular bacterial pathogens of animals that undergo a developmental cycle transitioning between the infectious elementary body (EB) and replicative reticulate body (RB) within a host cell-derived vacuole (inclusion). Secondary differentiation events (RB to EB) are transcriptionally regulated, in part, by the housekeeping sigma factor (σ
66
) and two late-gene sigma factors (σ
54
and σ
28
). Prior research supports that the PSM in
Chlamydia trachomatis
regulates availability of σ
66
. Pan-genome analysis revealed that PSM components are conserved across the phylum Chlamydiota, with
Chlamydia
spp. possessing an atypical arrangement of two anti-anti-sigma factors, RsbV1 and RsbV2. Bioinformatic analyses support RsbV2 as the homolog to the pan-genome-conserved RsbV with RsbV1 as an outlier. This, combined with
in vitro
data, indicates that RsbV1 and RsbV2 are structurally and biochemically distinct. Reduced levels or overexpression of RsbV1/RsbV2 did not significantly impact
C. trachomatis
growth or development. In contrast, overexpression of a non-phosphorylatable RsbV2 S55A mutant, but not overexpression of an RsbV1 S56A mutant, resulted in a 3 log reduction in infectious EB production without reduction in genomic DNA (total bacteria) or inclusion size, suggesting a block in secondary differentiation. The block was corroborated by reduced production of σ
54/28
-regulated late proteins and via transmission electron microscopy.

IMPORTANCE

Chlamydia trachomatis
is the leading cause of reportable bacterial sexually transmitted infections (STIs) and causes the eye infection trachoma, a neglected tropical disease. Broad-spectrum antibiotics used for treatment can lead to microbiome dysbiosis and increased antibiotic resistance development in other bacteria, and treatment failure for chlamydial STIs is a recognized clinical problem. Here, we show that disruption of a partner switching mechanism (PSM) significantly reduces infectious progeny production via blockage of reticulate body to elementary body differentiation. We also reveal a novel PSM expansion largely restricted to the species infecting animals, suggesting a role in pathogen evolution. Collectively, our results highlight the chlamydial PSM as a key regulator of development that could be a potential target for novel therapeutics.
Clinical validation of an RSV neutralization assay and analysis of cross-sectional sera associated with 2021–2023 RSV outbreaks to investigate the immunity debt hypothesis
Authors: Piliper Eli A. , Reed Jonathan C. , Greninger Alexander L.
Published: October 2024

Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections and hospitalization in infants and the elderly. Newly approved vaccines and the prophylactic antibody nirsevimab have heightened interest in RSV immunologic surveillance, necessitating the development of high-throughput assays assessing anti-RSV neutralizing activity. Quantitative viral neutralization remains the best correlate of protection for RSV infection and the gold standard for RSV immunological testing. Here, we developed a high-throughput RSV strain A2 focus-reduction neutralization test validated to Clinical Laboratory Improvement Amendments (CLIA)/ Good Clinical Laboratory Practices (GCLP) standards using both clinical specimens and commercially available reference sera. The assay is highly accurate, generating reference serum neutralizing titers within twofold of established assays, with an analytical measurement range between 8 and 1,798 international units per mL (IU/mL). Neutralizing activity measured by the assay strongly correlated with antibody titer determined via indirect enzyme-linked immunosorbent assay (ELISA) (
ρ
= 1.0,
P
= 0.0014). Individuals recently having tested positive via quantitative reverse transcription polymerase chain reaction (RT-qPCR) for RSV had a 9.1-fold higher geometric mean neutralizing titer relative to RSV PCR negatives (
P
-value = 0.09). The validated assay was then used to investigate the immunity debt hypothesis for resurgent RSV outbreaks in the 2022–2023 season, using adult clinical remnant sera sent for herpes simplex virus (HSV)-1/2 antibody testing. There was no difference in geometric mean anti-RSV neutralizing titers between sera sampled before and after the 2022–2023 RSV outbreak (
P
= 0.68). These data are consistent with limited changes in RSV-neutralizing antibody levels in adults across the 2022–23 RSV outbreak.

IMPORTANCE

Population surveillance studies of serum-neutralizing activity against RSV are crucial for evaluating RSV vaccine efficacy and vulnerabilities to new strains. Here, we designed and validated a high-throughput assay for assessing anti-RSV neutralizing activity, standardized its measurements for comparison with other methodologies, and demonstrated its applicability to real-world samples. Our assay is precise, linear, and yields measurements consistent with other standardized assays, offering a methodology useful for large-scale studies of RSV immunity. We also find no significant difference in neutralizing titers among adults between those taken before and after large RSV outbreaks associated with the latter stages of the coronavirus disease of 2019 (COVID-19) public health emergency, underlining the need for a greater understanding of the dynamics of serological responses to RSV infection.
Field geology under the sea with a remotely operated vehicle: Mona Rift, Puerto Rico
Authors: Brink Uri S. ten , Bialik Or M. , Chaytor Jason D. , Flores Claudia H. , Phillips Marcie Purkey
Published: October 2024

We implemented concepts of field geology at great ocean depths by constructing virtual outcrops from a string of overlapping video frames collected by remotely operated vehicles (ROVs). This lower-cost alternative to drilling boreholes allows stratigraphic extension into the offshore and regional interpretation of marine seismic profiles. The imagery was collected along a dive transect on the western wall of Mona Rift, a deep and narrow rift northwest of Puerto Rico, between water depths of 1560 m and 3927 m. The northern coast of Puerto Rico and its large offshore area are underlain by a mid-Eocene and younger forearc basin topped by a thick carbonate platform. There are no drill holes offshore, and tying seismic lines across the shoreline there is problematic. We describe our virtual outcrop and constrain its age and stratigraphy using seven rock samples collected by ROV and compare the outcrop's stratigraphy to deep boreholes and outcrops on land. Our formation descriptions and ages agree, for the most part, with those on land, but we identified a 100-m-thick section that is represented on land by an unconformity. Our stratigraphic interpretation indicates lateral variations in formation thicknesses and establishes a cross-section for additional sampling of the Eocene–Pliocene geology. It also suggests that Mona Rift has formed since the mid-Pliocene. The presence or absence of ferromanganese (Fe-Mn) crust on rocks along the transect may be correlated with the smoothness of the rock surface.
Semiclassical Scattering by Edge Imperfections in Topological Insulators in a Magnetic Field
Authors: Dotdaev A. S. , Rodionov Ya. I. , Rozhkov A. V. , Grigoriev P. D.
Published: October 2024

We study the scattering of edge states of 2D topological insulator in the uniform external magnetic field due to edge imperfections, common in realistic 2D topological insulator samples. The external magnetic field breaks time-reversal symmetry, opening the possibility of the scattering of otherwise topologically protected fermionic edge states. The scattering happens to be always an over-barrier event, irrespective of the shape of the edge deformation and magnitude of the magnetic field. We use the advanced Pokrovsky–Khalatnikov semiclassical approach, which allows us to obtain analytically both the main exponential and pre-exponential factors of the scattering amplitude for wide classes of analytic deformation profiles.
Predictive performance of cerebrospinal fluid parameters for diagnosis of meningitis in infants: a cohort study
Authors: O'Leary Christine , Pittet Laure F , Beaumont Rachael , Constable Laura , Daley Andrew , Hodge Isabelle , Jacobs Susan E , King Arrabella , Tan Catherine , Curtis Nigel , Gwee Amanda
Published: October 2024

Background

The gold standard for diagnosis of meningitis is the isolation of a pathogen from cerebrospinal fluid (CSF) by culture or PCR. However, treatment is routinely commenced based on CSF findings prior to microbiological results. This study determined the predictive value of CSF parameters for diagnosing bacterial and viral meningitis in young infants.

Methods

Multicentre retrospective (2010–2020) cohort study of 1088 CSF results from infants aged 0–90 days. The predictive value of CSF parameters (white blood cell count (WCC), neutrophil, protein, glucose) was evaluated in 538 meningitis cases (39 bacterial, 499 viral) compared with controls with negative CSF microbiological testing and no prior antibiotics.

Results

For bacterial meningitis, the sensitivity of the commonly used CSF WCC cut-off of 20×106/L for neonates, 15×106/L for infants 1–2 months old and 5×106/L for infants 2–3 months old was 89%, 91% and 86% and the specificity was 78%, 77% and 61%, respectively. CSF protein levels ≥1 g/L in neonates and ≥0.8 g/L in infants aged 1–3 month, or CSF neutrophils ≥2×106/L, independently increased the likelihood of bacterial meningitis (positive likelihood ratios ≥5 and ≥3, respectively). 3 of 39 cases of bacterial meningitis would have been missed using the commonly used WCC cut-offs alone. However, two would have been identified using CSF protein and neutrophil thresholds. All CSF parameters were poor at identifying viral meningitis.

Conclusion

A single CSF parameter cannot reliably diagnose bacterial meningitis. For identification of bacterial meningitis, elevation of CSF WCC, neutrophil count or protein levels above threshold values improves accuracy of diagnosis.
Concurrent sarcoidosis and metastatic lung cancer in a patient with ring-enhancing brain lesions
Authors: Ardehali Mariam , Dussault Nicole , Howe John , Chudgar Saumil
Published: October 2024

This case discusses a male in his 40s with no prior medical history who presented to the emergency room with headaches and blurred vision and was found to have ring-enhancing lesions on brain MRI. Chest imaging revealed bilateral pulmonary nodules with a dominant right upper lobe nodule. On lung tissue sampling, he was found to have concurrent sarcoidosis and non-small cell lung cancer. Initial brain biopsy showed non-specific vascular lesions and inflammation which were initially thought secondary to sarcoidosis since there was no evidence of malignancy. However, given the importance of a definitive diagnosis to establish prognosis, repeat brain biopsy was pursued, which confirmed metastatic lung cancer. This case demonstrates the benefits of repeat biopsy in situations where clinical suspicion for malignancy is high, as well as the possibility for multiple concurrent diagnoses in a patient. The patient is currently undergoing stereotactic radiosurgery and chemotherapy with carboplatin, pemetrexed and pembrolizumab.
Reported side effects from hormonal contraceptives among those seeking abortion care versus contraceptive services
Authors: Jaskari Karoliina , Tekay Aydin , Saloranta Tuire Helene , Korjamo Riina , Heikinheimo Oskari , Gyllenberg Frida
Published: October 2024

Introduction

We aim to describe and compare the prevalence of subjective side effects associated with hormonal contraceptive use among reproductive healthcare users seeking either abortion care or contraceptive services.

Methods

This substudy derives from a previously reported cross-sectional survey involving 1006 users of public reproductive healthcare services in the Helsinki metropolitan area in Finland. We included all 813 respondents with a history of hormonal contraceptive use (mean age 27 years, IQR 24–33 for abortion care; 24 years, IQR 19–30 for contraceptive services). The study followed STROBE guidelines.

Results

Altogether 400 respondents sought abortion care, while 413 sought contraceptive services (counselling, prescription renewal, symptoms and/or dissatisfaction with their contraceptive method). Combined oral contraceptives and progestin-only pills were the most used methods in both groups. Respondents seeking abortion care reported contraception-associated weight changes, sex-related problems, mood changes, and acne more frequently than those seeking contraceptive services (p-value<0.05 for all). Some 52% of respondents seeking abortion care reported mood changes compared with 29% of those seeking contraceptive services, with a crude OR of 2.7 (95% CI 2.00 to 3.57). After adjustment, the OR for reporting mood changes among respondents seeking abortion care was 1.5 (95% CI 1.05 to 2.23).

Conclusions

Mood changes associated with hormonal contraceptive use were the most frequently reported side effect among all respondents. These findings suggest a need for individualised counselling on mood-related side effects as mood changes may contribute to higher discontinuation rates.
Honor ideology and private firearm ownership in US active-duty soldiers
Authors: Tucker Raymond , Bock Jarrod E , Gerner Jessica L , Albury Evan A , Osgood Jeffery , Daruwala Samantha E , Bozzay Melanie L , Dretsch Michael N , Trachik Benjamin , Anestis Michael , Bryan Craig J
Published: October 2024

Objectives

This study investigated whether honor ideology, or a belief that one’s reputation must be defended at all costs, is related to firearms ownership in soldiers.

Methods

N=301 active-duty soldiers completed online self-report measures in this cross-sectional study.

Results

Honor ideology was higher in soldiers who privately own a firearm compared with those who do not currently own and do not plan to after military separation. Higher honor ideology was correlated with a disbelief that private firearms ownership is related to soldier suicide risk. Levels of honor ideology were equal in soldiers who own a private firearm for protection versus other reasons (eg, hunting, maintaining a collection).

Conclusions

Honor ideology may be related to suicide risk through increased likelihood of owning a private firearm and disbelief in private firearm ownership being related to one’s own suicide risk in soldiers. Honor ideology could be relevant to consider when means safety initiatives are developed for active-duty military personnel.
Risk factors for suicide attempt among adolescents reporting suicidal ideation by sexual and gender minority status: Evidence from the 2022 Minnesota Student Survey
Authors: Sexton Joseph F. , Clark Kirsty A.
Published: October 2024

Background

Suicide is a leading cause of death among adolescents, yet most adolescents who report suicidal ideation do not attempt nor die by suicide. To prevent injury and death, it is thus vital to explore factors potentiating the transition from suicidal ideation to suicidal attempt, especially in high-risk groups like sexual and gender minority (SGM) adolescents. Guided by an “ideation-to-action” framework, we explored risk factors for suicide attempt (ie, “painful and provocative experiences”) among adolescents reporting suicidal ideation by SGM status.

Methods

Data were drawn from the cross-sectional 2022 Minnesota Student Survey and restricted to 10 561 adolescents reporting past-year suicidal ideation (52.3% SGM; 47.7% non-SGM). Analyses first assessed prevalence of exposure to painful and provocative experiences (ie, non-suicidal self-injury, adverse childhood experiences, bullying) by SGM status. Then, in multivariable logistic regression models, analyses probed associations between these risk factors and past-year suicide attempt.

Results

Among adolescents reporting recent suicidal ideation, a higher proportion of SGM adolescents reported past-year suicide attempt than non-SGM adolescents (26.7% vs 21.6%, respectively). All examined painful and provocative experiences were more commonly reported among SGM adolescents. In analyses restricted to SGM adolescents, non-suicidal self-injury, sexual abuse by a family member, and bullying demonstrated the largest effect sizes of associations with suicide attempt.

Discussion

Guided by an “ideation-to-action” framework, this research identifies risk factors potentiating suicide attempt in SGM adolescents reporting recent suicidal ideation. Structural and clinical interventions focused on mitigating exposure to painful and provocative experiences may help to prevent suicide among SGM adolescents.