bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ubiquitination of Sec22b by a novel
Legionella pneumophila
ubiquitin E3 ligase
Authors: Ma Kelong , Shu Rundong , Liu Hongtao , Fu Jiaqi , Luo Zhao-Qing , Qiu Jiazhang 
Published: October 2023

ABSTRACT

Legionella pneumophila
is a facultative intracellular pathogen that causes legionellosis. The key to its virulence is the delivery of hundreds of effector proteins into host cells via the
d
efective in
o
rganelle
t
rafficking/
i
ntra
c
ellular
m
ultiplication type IV secretion system. These effectors modulate numerous host signaling pathways to create a niche called the

L
egionella

-
c
ontaining
v
acuole (LCV) permissive for its intracellular replication. Previous investigation revealed that exploitation of the host ubiquitin system is among the most important strategies used by
L. pneumophila
to coopt host processes for its benefit. Here, we show that the effector
Legionella
ubiquitin ligase gene 15 (Lug15) (Lpg2327), which has no detectable homology with any enzyme involved in ubiquitin signaling, is an E3 ligase. In
L. pneumophila
-infected cells, Lug15 is localized on the LCV and impacts its association with polyubiquitinated proteins. We also demonstrate that Sec22b is ubiquitinated and recruited to the LCV by Lug15. Thus, our results establish Lug15 as a novel E3 ligase that functions to recruit a SNARE protein to remodel the
L. pneumophila
phagosome.

IMPORTANCE

Protein ubiquitination is one of the most important post-translational modifications that plays critical roles in the regulation of a wide range of eukaryotic signaling pathways. Many successful intracellular bacterial pathogens can hijack host ubiquitination machinery through the action of effector proteins that are injected into host cells by secretion systems.
Legionella pneumophila
is the etiological agent of legionellosis that is able to survive and replicate in various host cells. The
d
efective in
o
rganelle
t
rafficking (Dot)/
i
ntra
c
ellular
m
ultiplication (Icm) type IV secretion system of
L. pneumophila
injects over 330 effectors into infected cells to create an optimal environment permissive for its intracellular proliferation. To date, at least 26 Dot/Icm substrates have been shown to manipulate ubiquitin signaling via diverse mechanisms. Among these, 14 are E3 ligases that either cooperate with host E1 and E2 enzymes or adopt E1/E2-independent catalytic mechanisms. In the present study, we demonstrate that the
L. pneumophila
effector
Legionella
ubiquitin ligase gene 15 (Lug15) is a novel ubiquitin E3 ligase. Lug15 is involved in the remodeling of LCV with polyubiquitinated species. Moreover, Lug15 catalyzes the ubiquitination of host SNARE protein Sec22b and mediates its recruitment to the LCV. Ubiquitination of Sec22b by Lug15 promotes its noncanonical pairing with plasma membrane-derived syntaxins (e.g., Stx3). Our study further reveals the complexity of strategies utilized by
L. pneumophila
to interfere with host functions by hijacking host ubiquitin signaling.
An isothermal CRISPR-based diagnostic assay for
Neisseria gonorrhoeae
and
Chlamydia trachomatis
detection
Authors: Luo Hao , Zeng Lihong , Yin Xiaona , Pan Yuying , Yang Jianjiang , Liu Mingjing , Qin Xiaolin , Feng Zhanqin , Chen Wentao , Zheng Heping 
Published: October 2023

ABSTRACT

The occurrence of
Chlamydia trachomatis
(CT) and
Neisseria gonorrhoeae
(NG) is increasing worldwide, particularly in low- and middle-income countries. In cases where most infections are asymptomatic and remain in a coinfection condition. It may cause missed detections or the severe subsequent symptoms. Accurate diagnosis and convenient screening are essential for disease control. However, molecular diagnostics for CT/NG predominantly rely on polymerase chain reaction (PCR)-based detection, which requires special devices and conditions. Here, we developed an isothermal CRISPR-based CT/NG dual-target detection system by pairing recombinase polymerase amplification (RPA) and CRISPR-Cas12a/13a detection. Multiplex RPA can amplify NG and CT simultaneously, and a single-pot reaction with the Cas12a/13a can be performed for further recognizing the amplified target, driving the cleavage of the corresponding fluorescence reporter separately; thus, the signal can be monitored in different channels. This CRISPR-based CT/NG detection system achieved analytical sensitivities of 10° copies/μL for both synthetic CT/NG dsDNA and exhibited no cross-reaction with other species. In tests on 88 clinical samples, our CRISPR-based assay showed excellent agreement with the commercial assay Roche Cobas 4800 (100% accuracy for NG, 94.32% accuracy for CT, and 97.73% accuracy for CT/NG coinfection) and showed higher positive percent agreement, negative percent agreement, and accuracy than those reported for TaqMan PCR in a previous study. In addition, the results of this CRISPR-based system could be acquired within 75 min. Our isothermal diagnostic method with promising performance provides more convenience than PCR-based methods for detection and screening.

IMPORTANCE

A method for
Neisseria gonorrhoeae
(NG)/
Chlamydia trachomatis
(CT) detection is developed using multiplex-recombinase polymerase amplification and Cas12a/Cas13a. This method can detect NG and CT simultaneously with high sensitivity and specificity. This method has great potential to be further developed into larger-scale screening and point-of-care testing (POCT).
Identification and production of novel potential pathogen-specific biomarkers for diagnosis of histoplasmosis
Authors: Puerta-Arias Juan David , Isaza Agudelo Juan Pablo , Naranjo Preciado Tonny Williams 
Published: October 2023

ABSTRACT

Immunological assays based on the detection of circulating fungal biomarkers are helpful in clinical practice for diagnosing invasive fungal infections. Some of these targeting antigenic components are common to several different fungi. Histoplasmosis is a mycosis caused by the dimorphic fungus
Histoplasma capsulatum
, which in recent years has gained significant relevance due to the increase in the population susceptible to developing severe clinical forms, including those living with HIV/AIDS. Immunological tests that detect cell wall polysaccharide antigens are among the most used laboratory techniques for diagnosing this mycosis. However, none have shown adequate performance, and cross-reactivity with other fungal pathogens may be observed. Considering that there is a real need to improve the sensitivity and specificity of current diagnostic methods, we explored a novel strategy for the identification of
H. capsulatum-
specific antigens (
Hc_Ags
) that could be detected in clinical samples during infection based on a computational analysis model that included the application of bioinformatics tools and the analysis of experimental data from transcriptomics and proteomics. The
Hc_Ags
identified were expressed and purified by eukaryotic and prokaryotic systems. First, the
Hc_Ags
were used in an in-house immunization model in mice (BALB/c) to obtain
Hc_Ag
-specific polyclonal antibodies (
Hc_Ag_PAb
). Then, the presence of these antigens in
H. capsulatum
-yeast culture extracts and the specificity of
Hc_Ag_PAb
against culture extracts of
Candida albicans
,
Aspergillus fumigatus
,
Cryptococcus neoformans
,
Fusarium
spp., and
Paracoccidioides brasiliensis
were confirmed. Finally, we demonstrated the immunoreactivity of these
Hc_Ag
-specific polyclonal antibodies with urine samples from patients previously diagnosed with histoplasmosis.

IMPORTANCE
Histoplasmosis is considered one of the most important mycoses due to the increasing number of individuals susceptible to develop severe clinical forms, particularly those with HIV/AIDS or receiving immunosuppressive biological therapies, the high mortality rates reported when antifungal treatment is not initiated in a timely manner, and the limitations of conventional diagnostic methods. In this context, there is a clear need to improve the capacity of diagnostic tools to specifically detect the fungal pathogen, regardless of the patient’s clinical condition or the presence of other co-infections. The proposed novel pathogen-specific biomarkers have the potential to be used in immunodiagnostic platforms and antifungal treatment monitoring in histoplasmosis. In addition, the bioinformatics strategy used in this study could be applied to identify potential diagnostic biomarkers in other models of fungal infection of public health importance.
Longitudinal analysis of vaginal microbiota during IVF fresh embryo transfer and in early pregnancy
Authors: Väinämö Sofia , Saqib Schahzad , Kalliala Ilkka , Kervinen Kaisa , Luiro Kaisu , Niinimäki Maarit , Halttunen-Nieminen Mervi , Virtanen Seppo , Nieminen Pekka , Salonen Anne , Holster Tiina 
Published: October 2023

ABSTRACT

Non-
Lactobacillus
-dominated vaginal microbiota has been associated with poor gynecologic health and complications during pregnancy. Lactobacilli and especially
Lactobacillus crispatus
associate with good reproductive health and dominate the microbiota during healthy pregnancy. We examined whether the composition of vaginal microbiota at the time of fresh embryo transfer (ET) has an impact on the success of
in vitro
fertilization (IVF) and whether vaginal microbiota changes from IVF-ET to early pregnancy within individuals. Vaginal swab samples were collected from subfertile women at the time of IVF-ET (
n
= 76) and at the eighth gestational week (
n
= 21) from those who achieved clinical pregnancy. The microbiota composition was analyzed using 16S rRNA gene amplicon sequencing.
L. crispatus
was more abundant among the 30 women who achieved clinical pregnancy (46.9% vs. 19.1%,
q
= 0.039) and the 26 women who had live birth (43.3% vs. 23.1%,
q
= 0.32) compared to those who did not. Lactobacilli, mainly
L. crispatus
(76.2%), dominated all early pregnancy samples. Microbiota remained the same, i.e.,
Lactobacillus
-dominated type in 52% (11/21), shifted from one
Lactobacillus-
dominated type to another in 24% (5/21), or shifted from mixed community to
Lactobacillus
-dominated type in 24% (5/21) women, but never from
Lactobacillus
dominance to non-lactobacilli dominance. Our results emphasize the role of
L. crispatus
in the success of IVF-ET and in early pregnancy. During pregnancy, the microbiota shifted toward
L. crispatus
dominance even if it was undetectable before pregnancy, indicating that most women hold a reservoir of this beneficial
Lactobacillus
in their reproductive tract.

IMPORTANCE

Infertility is a global public health issue which leads many couples to seek fertility treatments, of which
in vitro
fertilization (IVF) is considered to be the most effective. Still, only about one-third of the women achieve live birth after the first IVF embryo transfer (IVF-ET). Factors affecting embryo implantation are poorly known, but the female reproductive tract microbiota may play a key role. Our study confirms the beneficial role of vaginal lactobacilli, especially
Lactobacillus crispatus,
in the probability of achieving clinical pregnancy and live birth following IVF-ET. Our findings regarding the intra-individual shift of vaginal microbiota between non-pregnancy and pregnancy states are novel and provide new information about the dynamics of microbiota in the early steps of human reproduction. These findings may help clinicians in their attempts to optimize the conditions for ET by microbiota screening or modulation and timing the ET when the microbiota is the most favorable.
Phylogenomic analysis of the understudied
Neisseriaceae
species reveals a poly- and paraphyletic
Kingella
genus
Authors: Morreale Daniel P. , St Geme III Joseph W. , Planet Paul J. 
Published: October 2023

ABSTRACT

Taxonomic classification and phylogenetic analysis of the
Neisseriaceae
family have focused on the pathogens
Neisseria meningitidis
and
Neisseria gonorrhoeae
. Less is known about the relationships of commensal
Neisseria
species and other
Neisseriaceae
genera, raising the possibility that the phylogeny of this family may not agree with current taxonomy. In this study, we used available nucleotide sequences and a phylogenetic approach to assess the
Kingella
genus and its relatives. We found that this genus is both paraphyletic and polyphyletic.
Kingella potus
is more closely related to
Neisseria bacilliformis
than to other
Kingella
species. The
Alysiella
and
Simonsiella
genera form a distinct clade within the
Kingella
genus that is closely related to the pathogens
K. kingae
and
K. negevensis
. We find a phylogenetic relationship between
Conchiformibius
,
Alysiella
,
Simonsiella
, and
Kingella
, which we name the CASK clade. Finally, we define the gene sets that differentiate each genus of the CASK clade from one another and from the rest of the
Neisseriaceae
family.

IMPORTANCE

Understanding the evolutionary relationships between the species in the
Neisseriaceae
family has been a persistent challenge in bacterial systematics due to high recombination rates in these species. Previous studies of this family have focused on
Neisseria meningitidis
and
N. gonorrhoeae
. However, previously understudied
Neisseriaceae
species are gaining new attention, with
Kingella kingae
now recognized as a common human pathogen and with
Alysiella
and
Simonsiella
being unique in the bacterial world as multicellular organisms. A better understanding of the genomic evolution of the
Neisseriaceae
can lead to the identification of specific genes and traits that underlie the remarkable diversity of this family.
Comparison of phage-derived recombinases for genetic manipulation of
Pseudomonas
species
Authors: Kalb Madison J. , Grenfell Andrew W. , Jain Abhiney , Fenske-Newbart Jane , Gralnick Jeffrey A. 
Published: October 2023

ABSTRACT

Several strains in the
Pseudomonas
genus are categorized as plant growth-promoting rhizobacteria (PGPR). Although several of these strains are strong candidates for applications as biofertilizers or biopesticides, genome editing approaches are generally limited and require further development. Editing genomes in PGPR could enable more robust agricultural applications, persistence, and biosafety measures. In this study, we investigate the use of five phage-encoded recombinases to develop a recombineering workflow in three PGPR strains:
Pseudomonas protegens
Pf-5,
Pseudomonas protegens
CHA0, and
Pseudomonas putida
KT2440. Using point mutations in the
rpoB
gene, we reach maximum recombineering efficiencies of 1.5 × 10
−4
, 3 × 10
−4
, and 5 × 10
−5
, respectively, in these strains using λ-Red Beta recombinase from
Escherichia coli
. We further examine recombineering efficiencies across these strains as a function of selected mutation, editing template concentration, and phosphorothiolate bond protection. This work validates the use of these tools across several environmentally and biotechnologically relevant strains to expand the possibilities of genetic manipulation in the
Pseudomonas
genus.

IMPORTANCE

The
Pseudomonas
genus contains many members currently being investigated for applications in biodegradation, biopesticides, biocontrol, and synthetic biology. Though several strains have been identified with beneficial properties, chromosomal manipulations to further improve these strains for commercial applications have been limited due to the lack of efficient genetic tools that have been tested across this genus. Here, we test the recombineering efficiencies of five phage-derived recombinases across three biotechnologically relevant
Pseudomonas
strains:
P. putida
KT2440,
P. protegens
Pf-5, and
P. protegens
CHA0. These results demonstrate a method to generate targeted mutations quickly and efficiently across these strains, ideally introducing a method that can be implemented across the
Pseudomonas
genus and a strategy that may be applied to develop analogous systems in other nonmodel bacteria.
Virulence factors and antimicrobial resistance profiles of
Campylobacter
isolates recovered from consecutively reused broiler litter
Authors: Woyda Reed , Oladeinde Adelumola , Endale Dinku , Strickland Timothy , Plumblee Lawrence Jodie , Abdo Zaid 
Published: October 2023

ABSTRACT

Campylobacter
infections are a leading cause of bacterial diarrhea in humans globally. Infections are due to consumption of contaminated food products and are highly associated with chicken meat, with chickens being an important reservoir for
Campylobacter
. Here, we characterized the genetic diversity of
Campylobacter jejuni
(
C. jejuni
) and
Campylobacter coli
(
C. coli
) detected in broiler chicken litter over three consecutive flocks and determined their antimicrobial resistance (ARM) and virulence factor (VF) profiles.
Campylobacter
was detected in 9.38% (27/288) of litter samples collected. Antimicrobial susceptibility testing and whole genome sequencing were performed on
C. jejuni
(
n
= 39) and
C. coli
(
n
= 5) isolates.
Campylobacter
virulence factors differed within and across broiler houses but were explained by the broiler flock cohort raised on litter,
Campylobacter
species and
Campylobacter
multilocus sequence type (MLST). Virulence factors involved in the ability to invade and colonize host tissues and evade host defenses were present in
C. jejuni
isolates (ST-464) from flock cohorts 1 and 2 but absent in
C. jejuni
isolates (ST-48) from flock cohort 3.
C. jejuni
isolates from house three harbored a significantly higher proportion of virulence genes with functions related to glycosylation and immune evasion than
C. jejuni
isolates from houses 1 and 2 (
P
< 0.01). All
C. jejuni
isolates were susceptible to all antibiotics tested while
C. coli
(
n
= 4) were resistant to tetracycline and harbored the tetracycline resistant ribosomal protection protein (TetO). Our results suggest that house environment and broiler management practices imposed selective pressures on virulence factors and antimicrobial resistance genes of
Campylobacter
.

IMPORTANCE

Campylobacter
is a leading cause of foodborne illness in the United States due to consumption of contaminated or mishandled food products, often associated with chicken meat.
Campylobacter
is common in the microbiota of avian and mammalian gut; however, acquisition of antimicrobial resistance genes (ARGs) and virulence factors (VFs) may result in strains that pose significant threat to public health. Although there are studies investigating the genetic diversity of
Campylobacter
strains isolated from post-harvest chicken samples, there are limited data on the genome characteristics of isolates recovered from preharvest broiler production. Here, we show that
Campylobacter jejuni
and
Campylobacter coli
differ in their carriage of antimicrobial resistance and virulence factors may also differ in their ability to persist in litter during consecutive grow-out of broiler flocks. We found that presence/absence of virulence factors needed for evasion of host defense mechanisms and gut colonization played an integral role in differentiating
Campylobacter
strains.
A structural foundation for studying chlamydial polymorphic membrane proteins
Authors: Debrine Abigail M. , Karplus P. Andrew , Rockey Daniel D. 
Published: October 2023

ABSTRACT
Polymorphic membrane proteins (Pmps) are chlamydial cell surface proteins with signature repeating FxxN and GGA (I, V, L) tetrapeptide motifs. These autotransporter proteins are key immune targets and mediators of host-microbe interactions but by unknown mechanisms. AlphaFold predictions reveal that Pmp passenger domains have two distinct β-helical parts: a C-terminal globular “Pmp middle region” that forms six β-helical rungs, and an N-terminal highly-regular “Pmp repeat region” that is from 9 to 25 rungs long. In the repeat region, paired FxxN and GGA (I, V, L) motifs – or close variants – are fully buried and packed together to form novel β-helical rungs from which variable-length loops extend out from one face. Similar motifs in proteins from diverse organisms are predicted to form analogous structures. In Pmps, the structures imply that the tetrapeptide motifs are not directly involved in host-cell adhesion, but position protein loops on a common face where they can interact with ligands important for infection. These structural descriptions provide a guide for mutagenesis studies to identify those parts of Pmps involved in infection.

IMPORTANCE

Infections by bacteria in the genus
Chlamydia
cause a range of widespread and potentially debilitating conditions in humans and other animals. We analyzed predicted structures of a family of proteins that are potential vaccine targets found in all
Chlamydia
spp. Our findings deepen the understanding of protein structure, provide a descriptive framework for discussion of the protein structure, and outline regions of the proteins that may be key targets in host-microbe interactions and anti-chlamydial immunity.
Supplemental Material: Precursors to a continental-arc ignimbrite flare-up: Early central volcanoes of the San Juan Mountains, Colorado, USA
Authors: Lipman Peter , al. et 
Published: October 2023

<p>Table S1: Summary of <sup>40</sup>Ar/<sup>39</sup>Ar and U-Pb zircon age determinations, pre-ignimbrite volcanoes of the eastern San Juan region. Table S2: New and published X-ray fluorescence (XRF) rock analyses, pre-ignimbrite volcanoes of the San Juan region. Table S3 and figures: Analytical data—new <sup>40</sup>Ar/<sup>39</sup>Ar age determinations. Table S4: Analytical data—new U-Pb zircon age determinations. Table S5: Multimineral age comparisons—single samples and multiple samples from the same locality. Table S6: Groundmass-mineral age comparisons. </p>
Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins
Authors: Ostrovsky Mikhail A. , Smitienko Olga A. , Bochenkova Anastasia V. , Feldman Tatiana B. 
Published: October 2023

Abstract
The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.
The Electronic Structure, Thermoelectric, and Optical Properties of Heusler Alloys Mn2MeAl (Me = Ti, V, Cr)
Authors: Shreder E. I. , Filanovich A. N. , Chernov E. D. , Lukoyanov A. V. , Marchenkov V. V. , Stashkova L. A. 
Published: October 2023

Abstract
The results of calculations of the electronic structure, thermoelectric characteristics, and experimental study of the thermoelectric, electrical, and optical properties of Mn2MeAl Heusler alloys (Me = Ti, V, Cr) are presented. The agreement between theory and experiment in the sign of the Seebeck coefficient is shown. The obtained pattern of the band spectrum allows us to qualitatively explain the peculiarities of the temperature dependences of the electrical resistance and the permittivity dispersion.