bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

Abstract
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.
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

BackgroundThe 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.MethodsMulticentre 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.ResultsFor 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.ConclusionA 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.
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

IntroductionWe 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.MethodsThis 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.ResultsAltogether 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).ConclusionsMood 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

ObjectivesThis 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.MethodsN=301 active-duty soldiers completed online self-report measures in this cross-sectional study.ResultsHonor 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).ConclusionsHonor 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

BackgroundSuicide 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.MethodsData 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.ResultsAmong 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.DiscussionGuided 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.