bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel bacterial sulfite dehydrogenase that requires three
c
-type cytochromes for electron transfer
Authors: Sun Weining , Xu Yuanyou , Liang Yawen , Yu Qingzi , Gao Haichun 
Published: September 2023

ABSTRACT

c
-type Cytochromes (
c
-Cyts), primarily as electron carriers and oxidoreductases, play a key role in energy transduction processes in virtually all living organisms. Many bacteria, such as
Shewanella oneidensis
, are particularly rich in
c
-Cyts, supporting respiratory versatility not seen in eukaryotes. Unfortunately, a large number of
c
-Cyts are underexplored, and their biological functions remain unknown. In this study, we identify SorCABD of
S. oneidensis
as a novel sulfite dehydrogenase (SDH), which catalyzes the oxidation of sulfite to sulfate. In addition to catalytic subunit SorA, this enzymatic complex includes three
c
-Cyt subunits, which all together carry out electron transfer. The electrons extracted from sulfite oxidation are ultimately delivered to oxygen, leading to oxygen reduction, a process relying on terminal oxidase cyt
cbb
3
. Genomic analysis suggests that the homologs of this SDH are present in a small number of bacterial genera,
Shewanella
and
Vibrio
in particular. Because these bacteria are generally capable of reducing sulfite under anaerobic conditions, the co-existence of a sulfite oxidation system implies that they may play especially important roles in the transformation of sulfur species in natural environments.

Importance

c
-type Cytochromes (
c
-Cyts) endow bacteria with high flexibility in their oxidative/respiratory systems, allowing them to extracellularly transform diverse inorganic and organic compounds for survival and growth. However, a large portion of the bacterial
c
-Cyts remain functionally unknown. Here, we identify three
c
-Cyts that work together as essential electron transfer partners for the catalytic subunit of a novel SDH in sulfite oxidation in
Shewanella oneidensis
. This characteristic makes
S. oneidensis
the first organism known to be capable of oxidizing and reducing sulfite. The findings suggest that
Shewanella
, along with a small number of other aquatic bacteria, would serve as a particular driving force in the biogeochemical sulfur cycle in nature.
Proteomic survey of the DNA damage response in
Caulobacter crescentus
Authors: Tashjian Tommy F. , Zeinert Rilee D. , Eyles Stephen J. , Chien Peter 
Published: September 2023

ABSTRACT

The bacterial DNA damage response is a critical, coordinated response to endogenous and exogenous sources of DNA damage. Response dynamics are dependent on coordinated synthesis and loss of relevant proteins. While much is known about its global transcriptional control, changes in protein abundance that occur upon DNA damage are less well characterized at the system level. Here, we perform a proteome-wide survey of the DNA damage response in
Caulobacter crescentus
. We find that while most protein abundance changes upon DNA damage are readily explained by changes in transcription, there are exceptions. The survey also allowed us to identify the novel DNA damage response factor, YaaA, which has been overlooked by previously published, transcription-focused studies. A similar survey in a ∆
lon
strain was performed to explore
lon’s
role in DNA damage survival. The ∆
lon
strain had a smaller dynamic range of protein abundance changes in general upon DNA damage compared to the wild-type strain. This system-wide change to the dynamics of the response may explain this strain’s sensitivity to DNA damage. Our proteome survey of the DNA damage response provides additional insight into the complex regulation of stress response and nominates a novel response factor that was overlooked in prior studies.

IMPORTANCE

The DNA damage response helps bacteria to react to and potentially survive DNA damage. The mutagenesis induced during this stress response contributes to the development of antibiotic resistance. Understanding how bacteria coordinate their response to DNA damage could help us to combat this growing threat to human health. While the transcriptional regulation of the bacterial DNA damage response has been characterized, this study is the first to our knowledge to assess the proteomic response to DNA damage in
Caulobacter
.
Representative measles virus infection requires appropriate airway epithelia culture conditions
Authors: Kaufman Justin W. , Singh Brajesh K. , Durnell Lorellin A. , Sinn Patrick L. 
Published: September 2023

ABSTRACT

Despite an effective vaccine, measles virus (MeV) remains a critical health burden worldwide. Many fundamental questions remain about its unique biology. Because MeV is a human specific pathogen, research has largely relied on immortalized human cell lines with confirmatory studies in non-human primates or humanized mice. A critical challenge for MeV research is identification of representative
in vitro
model systems. To study infection, spread, and release in the airways, we utilize primary cultures of airway epithelia cells collected from human donor lungs. This cell culture model recapitulates the pseudostratified columnar epithelial structure and multiple cell types of the conducting airways. In this model, direct cell-to-cell spread of MeV results in well-defined foci termed infectious centers. Here, we demonstrate that infectious center formation following basolateral MeV infection is consistent between two primate species (human and macaque), between two university core facilities that provide primary human airway cultures, and between human primary cells and fresh human tracheal explants. Canine distemper virus infection of differentiated primary cultures of ferret airway epithelial cells also results in infectious center formation suggesting that this mechanism of infection and spread is shared between morbilliviruses. Importantly, the well-defined morphology of the pseudostratified columnar epithelial layer is lost when fetal bovine serum is included in the culture media or when primary cells are passaged twice. Both conditions lead to apical infection by MeV and loss of defined infectious centers. These results suggest that MeV-induced infectious center formation depends on appropriate differentiation, maintenance, and morphology of primary cultures.

Importance

For many years, measles virus (MeV) was assumed to first enter the host via the apical surface of airway epithelial cells and subsequently spread systemically. We and others reported that MeV has an overwhelming preference for entry at the basolateral surface of airway epithelial cells, which led to a fundamental new understanding of how MeV enters a human host. This unexpected observation using well-differentiated primary cultures of airway epithelia from human donors contradicted previous studies using immortalized cultured cells. Here, we show that appropriate differentiation and cell morphology of primary human airway epithelial cells are critical to recapitulate MeV infection patterns and pathogenesis of the
in vivo
airways. By simply culturing primary cells in media containing serum or passaging primary cultures, erroneous results quickly emerge. These results have broad implications for data interpretation related to respiratory virus infection, spread, and release from human airway epithelial cells.
Development of Cas13a-based assays for
Neisseria gonorrhoeae
detection and gyrase A determination
Authors: Allan-Blitz Lao-Tzu , Shah Palak , Adams Gordon , Branda John A. , Klausner Jeffrey D. , Goldstein Robert , Sabeti Pardis C. , Lemieux Jacob E. 
Published: September 2023

ABSTRACT

Neisseria gonorrhoeae
is one of the most common bacterial sexually transmitted infections. The emergence of antimicrobial-resistant
N. gonorrhoeae
is an urgent public health threat. Currently, the diagnosis of
N. gonorrhoeae
infection requires expensive laboratory infrastructure, while antimicrobial susceptibility determination requires bacterial culture, both of which are infeasible in low-resource areas where the prevalence of infection is highest. Recent advances in molecular diagnostics, such as
s
pecific
h
igh-sensitivity
e
nzymatic
r
eporter un
lock
ing (SHERLOCK) using CRISPR-Cas13a and isothermal amplification, have the potential to provide low-cost detection of pathogen and antimicrobial resistance. We designed and optimized RNA guides and primer sets for SHERLOCK assays capable of detecting
N. gonorrhoeae
via the
por
A gene and of predicting ciprofloxacin susceptibility via a single mutation in the gyrase A (
gyr
A) gene. We evaluated their performance using both synthetic DNA and purified
N. gonorrhoeae
isolates. For
por
A
,
we created both a fluorescence-based assay and lateral flow assay using a biotinylated fluorescein reporter. Both methods demonstrated sensitive detection of 14
N
.
gonorrhoeae
isolates and no cross-reactivity with 3 non-gonococcal
Neisseria
isolates. For
gyr
A, we created a fluorescence-based assay that correctly distinguished between 20 purified
N. gonorrhoeae
isolates with phenotypic ciprofloxacin resistance and 3 with phenotypic susceptibility. We confirmed the
gyr
A genotype predictions from the fluorescence-based assay with DNA sequencing, which showed 100% concordance for the isolates studied. We report the development of Cas13a-based SHERLOCK assays that detect
N. gonorrhoeae
and differentiate ciprofloxacin-resistant isolates from ciprofloxacin-susceptible isolates.

IMPORTANCE

Neisseria gonorrhoeae,
the cause of gonorrhea, disproportionately affects resource-limited settings. Such areas, however, lack the technical capabilities for diagnosing the infection. The consequences of poor or absent diagnostics include increased disease morbidity, which, for gonorrhea, includes an increased risk for HIV infection, infertility, and neonatal blindness, as well as an overuse of antibiotics that contributes to the emergence of antibiotic resistance. We used a novel CRISPR-based technology to develop a rapid test that does not require laboratory infrastructure for both diagnosing gonorrhea and predicting whether ciprofloxacin can be used in its treatment, a one-time oral pill. With further development, that diagnostic test may be of use in low-resource settings.
Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota
Authors: Mujakić Izabela , Cabello-Yeves Pedro J. , Villena-Alemany Cristian , Piwosz Kasia , Rodriguez-Valera Francisco , Picazo Antonio , Camacho Antonio , Koblížek Michal 
Published: September 2023

ABSTRACT

Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the
nosZ
gene, involved in the reduction of N
2
O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments.

IMPORTANCE
Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.
The role of integration host factor in biofilm and virulence of high-alcohol-producing
Klebsiella pneumoniae
Authors: Fan Zheng , Fu Tongtong , Li Zhoufei , Du Bing , Cui Xiaohu , Zhang Rui , Feng Yanling , Zhao Hanqing , Xue Guanhua , Cui Jinghua , Yan Chao , Gan Lin , Feng Junxia , Xu Ziying , Yu Zihui , Tian Ziyan , Ding Zanbo , Chen Jinfeng , Chen Yujie , Yuan Jing 
Published: September 2023

ABSTRACT

Klebsiella pneumoniae
is a well-known human nosocomial pathogen with an arsenal of virulence factors, including capsular polysaccharides (CPS), fimbriae, flagella, and lipopolysaccharides (LPS). Our previous study found that alcohol acted as an essential virulence factor for high-alcohol-producing
K. pneumoniae
(HiAlc
Kpn
). Integration host factor (IHF) is a nucleoid-associated protein that functions as a global virulence regulator in
Escherichia coli
. However, the regulatory role of IHF in
K. pneumoniae
remains unknown. In the present study, we found that deletion of
ihfA
or
ihfB
resulted in a slight defect in bacterial growth, a severe absence of biofilm formation and cytotoxicity, and a significant reduction in alcohol production. RNA sequencing differential gene expression analysis showed that compared with the wild-type control, the expression of many virulence factor genes was downregulated in Δ
ihfA
and Δ
ihfB
strains, such as those related to CPS (
rcsA
,
galF
,
wzi
, and
iscR
), LPS (
rfbABCD
), type I and type III fimbriae (
fim
and
mrk
operon), cellulose (
bcs
operon), iron transporter (
feoABC
,
fhuA
,
fhuF
,
tonB
,
exbB
, and
exbD
), quorum sensing (
lsr
operon and
sdiA
), type II secretion system (T2SS) and type VI secretion system (T6SS) (
tssG
,
hcp
, and
gspE
). Of these virulence factors, CPS, LPS, fimbriae, and cellulose are involved in biofilm formation. In addition, IHF could affect the alcohol production by regulating genes related to glucose intake (
ptsG
), pyruvate formate-lyase, alcohol dehydrogenase, and the tricarboxylic acid (TCA) cycle. Our data provided new insights into the importance of IHF in regulating the virulence of HiAlc
Kpn
.

IMPORTANCE

Klebsiella pneumoniae
is a well-known human nosocomial pathogen that causes various infectious diseases, including urinary tract infections, hospital-acquired pneumonia, bacteremia, and liver abscesses. Our previous studies demonstrated that HiAlc
Kpn
mediated the development of nonalcoholic fatty liver disease by producing excess endogenous alcohol
in vivo
. However, the regulators regulating the expression of genes related to metabolism, biofilm formation, and virulence of HiAlc
Kpn
remain unclear. In this study, the regulator IHF was found to positively regulate biofilm formation and many virulence factors including CPS, LPS, type I and type III fimbriae, cellulose, iron transporter, AI-2 quorum sensing, T2SS, and T6SS in HiAlc
Kpn
. Furthermore, IHF positively regulated alcohol production in HiAlc
Kpn
. Our results suggested that IHF could be a potential drug target for treating various infectious diseases caused by
K. pneumoniae
. Hence, the regulation of different virulence factors by IHF in
K. pneumoniae
requires further investigation.
PeAP1-mediated oxidative stress response plays an important role in the growth and pathogenicity of
Penicillium expansum
Authors: Chen Yong , Zhang Yichen , Xu Dongying , Zhang Zhanquan , Li Boqiang , Tian Shiping 
Published: September 2023

ABSTRACT

Penicillium expansum
is the causal agent of post-harvest blue mold in various fruits and serves as a model for understanding fungal pathogenicity and mycotoxin production. The relevance of oxidative stress response in the growth and virulence of
P. expansum
has been largely unexplored. Here, we identify the transcriptional factor PeAP1 as a regulator of oxidative stress response in
P. expansum
. Gene expression and protein abundance of PeAP1, as well as its nuclear localization, are specifically induced by H
2
O
2
. Deletion of
PeAP1
results in increased sensitivity to H
2
O
2
, and
PeAP1
mutants exhibit a variety of defects in hyphal growth and virulence. PeAP1 prevents the accumulation of both intracellular H
2
O
2
during vegetative growth and host-derived H
2
O
2
during biotrophic growth. Application of an antioxidant glutathione and a NADPH oxidase inhibitor, diphenylene iodonium, to the
PeAP1
mutant partially restored fungal growth and virulence. RNA sequencing analysis revealed 144 H
2
O
2
-induced PeAP1 target genes, including four antioxidant-related genes,
PeGST1
,
PePrx1
,
PePrx2
, and
PeTRX2
, that were also demonstrated to be involved in oxidative stress response and/or virulence. Collectively, our results demonstrate the global regulatory role of PeAP1 in response to oxidative stress and provide insights into the critical role of the PeAP1-mediated oxidative stress response to regulate growth and virulence of
P. expansum
.

IMPORTANCE

Reactive oxygen species are the core of host plant defense and also play a vital role in the successful invasion of host plants by pathogenic fungi. Despite its importance, the relevance of oxidative stress response in fungal growth and virulence is poorly understood in
P. expansum
. In this study, we reveal that the transcription factor PeAP1 acts as a central regulator of oxidative stress response in
P. expansum
and that there is a major link between PeAP1-mediated oxidative stress response and fungal growth and virulence. To explore the underlying mechanisms, we performed comparative transcriptomic studies and identified a number of H
2
O
2
-induced PeAP1 target genes, including four novel ones,
PePrx1
,
PePrx2
,
PeGST1
, and
PeTRX2
, whose functions were linked to PeAP1 and pathogenicity. These findings provide novel insights into the regulation mechanism of PeAP1 on growth and virulence, which might offer promising targets for control of blue mold and patulin contamination.
Formation of lower arc crust by magmatic underplating revealed by high-precision geochronology
Authors: Stirling Jack E. , Denyszyn Steven W. , Loucks Robert R. , Kemp Anthony I.S. , Hammerli Johannes , Fiorentini Marco L. , Vervoort Jeffrey D. 
Published: September 2023

Abstract
In modern plate tectonic regimes, continental crust is generated above subduction zones in magmatic island arcs. Models for continental growth—largely based on the modeling of geochemical processes that can transform mantle melts into the intermediate composition of bulk continental crust—have been hampered by a lack of definitive geochronology, which could clarify the temporal emplacement of igneous rocks at the base of island arc crust. The Kohistan Arc Complex (KAC) of Pakistan is a rare window into a nearly complete section of lower arc crust, revealing a sequence of igneous rocks representing discrete batches of magma underplated along the base of the arc crust. We present high-precision isotope dilution–thermal ionization mass spectrometry U-Pb geochronological data from zircon, and Lu-Hf and Sm-Nd isochron data from several mafic lower crustal cumulates within the KAC. These data establish a clear downward-younging age trend throughout this succession of cumulate complexes, demonstrating a total magmatic duration of ~20 m.y., corresponding to a rate of lower crust formation of up to 200–260 km3 km–1 Ma–1. These results provide the first direct evidence of a sequential process of underplating, revealing a fundamental mechanism responsible for building the root of island arc crust.
Endophthalmitis rates and risk factors following intraocular surgeries in the medicare population from 2016 to 2019
Authors: Chen Ariel , Dun Chen , Schein Oliver D , Srikumaran Divya , Zafar Sidra , Makary Martin , Woreta Fasika 
Published: September 2023

AimsTo determine endophthalmitis rates and risk factors following intraocular surgeries in the Medicare population.MethodsRetrospective, cross-sectional study from 2016 to 2019 in Medicare fee-for-service and Medicare Advantage beneficiaries. 100% Medicare claims were used to identify eyes that underwent intraocular surgery. Exclusion criteria included eyes that had intraocular surgery 42 days before or after and eyes in patients with a history of endophthalmitis within 12 months.Results9 744 400 intraocular surgeries were performed among Medicare beneficiaries from 2016 to 2019. A 42-day postoperative endophthalmitis rate was 0.09%. Endophthalmitis rate by surgery type was 0.43% for corneal transplant, 0.36% for secondary intraocular lens (IOL), 0.24% for retina, 0.16% for glaucoma, 0.11% for cataract combined with other procedures and 0.08% for cataract surgeries alone. On multivariable analysis, the risk of endophthalmitis was increased for all intraocular surgery types when compared with cataract surgeries; adjusted OR (aOR) 5.30 (p<0.01) for corneal transplant, aOR 4.50 (p<0.01) for secondary IOL, aOR 3.00 (p<0.01) for retina, aOR 1.93 (p<0.01) for glaucoma, aOR 1.45 (p<0.01) for combined cataract surgeries. Increased risk of developing endophthalmitis was associated with older age (≥85 vs 65–75 years: aOR 1.36; p<0.01), male sex (aOR 1.20; p<0.001) and greater Charlson Comorbidity Index (≥7 vs 0: aOR 1.79; p<0.01).ConclusionsPostoperative endophthalmitis rate after intraocular surgeries was 0.09% between 2016 and 2019 for Medicare beneficiaries. Endophthalmitis rates were highest for corneal transplant surgeries followed by secondary IOL surgeries and lowest for cataract surgeries. Older age, male gender and higher comorbidity index were associated with risk of endophthalmitis.