bluuebunny/crossref_metadata_2025 huggingface dataset:
Antimicrobial susceptibility of clinical
Helicobacter pylori
isolates and its eradication by standard triple therapy: a study in west central region of Colombia
Authors: Alvarez-Aldana Adalucy , Fernandez Uribe Paula Andrea , Mejía Valencia Tatiana , Guaca-Gonzalez Yina Marcela , Santacruz-Ibarra Jorge Javier , Arturo-Arias Brenda Lucia , Castañeda-Chavez Luis Javier , Pacheco-López Robinson , Londoño-Giraldo Lina María , Moncayo-Ortiz José Ignacio
Published: June 2024

The aim of the present study was first to isolate
Helicobacter pylori
from gastric biopsy specimens and to test their antibiotic susceptibility. Second, it was to evaluate the efficacy of the standard triple therapy from patients of the west central region of Colombia.
H. pylori
positive patients received standard triple therapy with proton pump inhibitor (PPI) (40 mg b.i.d.), clarithromycin (500 mg b.i.d.), and amoxicillin (1 g b.i.d.) for 14 days. Thereafter, antibiotic susceptibility of the isolates was assessed by E-Test. From 94 patients enrolled, 67 were positive for
H. pylori
by histology or culture. Overall resistance to metronidazole, levofloxacin, rifampicin, clarithromycin, and amoxicillin was 81%, 26.2%, 23.9%, 19%, and 9.5%, respectively. No resistance was found for tetracycline. A total of 54 patients received standard triple therapy, 48 attended follow-ups testing, and of them, 30 had resistance test reports. Overall eradication rate was 81.2%. Second-line treatment was given to eight patients, four of whom were followed up with a 13C urea breath test (UBT) and remained positive for
H. pylori
. Eradication was significantly higher in patients with clarithromycin susceptible than in resistant strains (95.6% vs 42.8%
P
= 0.001). The updated percentages of resistance to clarithromycin in this geographical area had increased, so this value must be considered when choosing the treatment regimen.

IMPORTANCE

Antibiotic resistance in
Helicobacter pylori
has increased worldwide, as has resistance to multiple antimicrobials (MDRs), which seriously hampers the successful eradication of the infection. The ideal success rate in eradicating
H. pylori
infection (≥90%) was not achieved in this study (81.2%). This is the first time that MDR is reported (14.3%) in the region; the resistance to clarithromycin increased over time (3.8%–19%), and levofloxacin (26.2%) and rifampicin (23%) resistant isolates were detected for the first time. With these results, strain susceptibility testing is increasingly important, and the selection of treatment regimen should be based on local antibiotic resistance patterns.
The diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in critically ill patients with respiratory tract infections
Authors: Hu Xiaohang , Jiang Liqing , Liu Xiaowei , Chang Hong , Dong Haixin , Yan Jinyan , Zhou Xiaoya , Kong Min
Published: June 2024

Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who were admitted to the Affiliated Hospital of Jining Medical University. This study primarily aimed to determine the diagnostic performance of mNGS and conventional microbiological tests (CMTs) using bronchoalveolar lavage fluid samples for detecting pathogens. Our findings indicated that mNGS performed significantly higher sensitivity (97.54% vs 28.68%,
P
< 0.001), coincidence (90.34% vs 35.17%,
P
< 0.001), and negative predictive value (80.00% vs 13.21%,
P
< 0.001) but performed lower specificity than CMTs (52.17% vs 87.5%,
P
< 0.001).
Streptococcus pneumoniae
as the most common bacterial pathogen had the largest proportion (22.90%, 30/131) in this study. In addition to bacteria, fungi, and virus, mNGS can detect a variety of atypical pathogens such as
Mycobacterium tuberculosis
and
non-tuberculous
. Mixed infections were common in patients with severe pneumonia, and bacterial-fungal-viral-atypical pathogens were the most complicated infection. After adjustments of antibiotics based on mNGS and CMTs, the clinical manifestation improved in 139 (95.86%, 139/145) patients. Our data demonstrated that mNGS had significant advantage in diagnosing respiratory tract infections, especially atypical pathogens and fungal infections. Pathogens were detected timely and comprehensively, contributing to the adjustments of antibiotic treatments timely and accurately, improving patient prognosis and decreasing mortality potentially.

IMPORTANCE

Metagenomic next-generation sequencing using bronchoalveolar lavage fluid can provide more comprehensive and accurate pathogens for respiratory tract infections, especially when considering the previous usage of empirical antibiotics before admission or complicated clinical presentation. This technology is expected to play an important role in the precise application of antimicrobial drugs in the future.
Insights into the molecular basis of reduced vancomycin susceptibility among three prominent
Staphylococcus aureus
clonal complexes
Authors: Malachowa Natalia , Sturdevant Daniel E. , Porter Adeline R. , Martin Grant , Martens Craig , Nair Vinod , Hansen Bryan , Ricklefs Stacy , Jenkins Stephen G. , Chen Liang , Kreiswirth Barry N. , DeLeo Frank R.
Published: June 2024

Staphylococcus aureus
is a leading cause of healthcare-associated infections globally. Vancomycin-resistant
S. aureus
(VRSA), those with high-level resistance [minimum inhibitory concentration (MIC) of 16–32 µg/mL vancomycin], are uncommon, whereas vancomycin-intermediate
S. aureus
(VISA; MIC of 4–8 µg/mL), are isolated more frequently and develop during long-term and/or repeated use of the antibiotic. VISA can be difficult to eradicate and infections may persist. Our knowledge of mechanisms that underlie the development of VISA is incomplete. We used a genomics approach to investigate the VISA phenotype in three prominent
S. aureus
lineages. All VISA clinical isolates tested had increased cell wall thickness compared with vancomycin-susceptible
S. aureus
strains. Growth rates of clonal complex (CC) 5, CC8, and CC45 clinical isolates were reduced in 2 µg/mL vancomycin compared to media alone. Culture in 2 and 4 µg/mL vancomycin sequentially for two weeks reduced susceptibility to daptomycin, televancin, tigecycline, and vancomycin in a majority of CC5, CC8, and CC45 isolates tested. We identified alleles reported previously to contribute to the VISA phenotype, but unexpectedly, these alleles were unique to each CC. A subtherapeutic concentration of vancomycin elicited changes in the VISA transcriptome—common and unique—among the three CCs tested. Multiple genes, including those encoding a glycerate kinase, an M50 family metallopeptidase, and an uncharacterized membrane protein, were upregulated among all three lineages and not reported previously as associated with VISA. Although there are lineage-specific changes in DNA sequence, our findings suggest changes in the VISA transcriptome constitute a general response to stress that confers reduced susceptibility to multiple antibiotics.

IMPORTANCE

Our understanding of the mechanisms that underlie the development of vancomycin-intermediate
Staphylococcus aureus
(VISA) is incomplete. To provide a more comprehensive view of this process, we compared genome sequences of clonal complex (CC) 5, CC8, and CC45 VISA clinical isolates and measured changes in the transcriptomes of these isolates during culture with a subtherapeutic concentration of vancomycin. Notably, we identified differentially expressed genes that were lineage-specific or common to the lineages tested, including genes that have not been previously reported to contribute to a VISA phenotype. Changes in gene expression were accompanied by reduced growth rate, increased cell wall thickness, and reduced susceptibility to daptomycin, televancin, tigecycline, and vancomycin. Our results provide support to the idea that changes in gene expression contribute to the development of VISA among three CCs that are a prominent cause of human infections.
A case for implementing an HSV1/2, VZV, and syphilis lesion panel in Manitoba, Canada
Authors: Hedley Adam , Bullard Jared , Van Caeseele Paul , Shaw Souradet , Tsang Raymond , Alexander David C. , Dust Kerry , Stein Derek R.
Published: June 2024

Syphilis, caused by
Treponema pallidum
subsp.
pallidum
(TPA), is becoming a significant public health concern, with rising incidence in Manitoba exceeding the national average. The province has also seen a demographic shift leading to women representing 51.9% of cases in 2021, leading to the re-emergence of congenital syphilis. Given the similarities in lesion appearance between TPA and other pathogens such as herpesviruses, accurate diagnosis is crucial for effective management and prevention. In order to address the potential for missed TPA cases, we conducted a quality assurance study from June 2021 to March 2023, screening over 5,000 mucocutaneous lesion swabs for TPA, initially submitted for herpes simplex virus (HSV) and varicella zoster virus (VZV) testing. Positivity rates were 13% for HSV1, 13% for HSV2, 6.7% for VZV, and 6.6% for TPA. Turnaround times (TAT) for TPA testing, as a send-out to the reference laboratory, averaged 17.8 days. Of the TPA-positive specimens, 36% did not have a corresponding TPA PCR test ordered, and 19% did not have accompanying syphilis serology within 30 days of collection. Creation of a multiplex lesion panel identified high sensitivity and specificity for HSV1, HSV2, VZV, and TPA, with robust reproducibility across multiple runs. Incorporation of TPA into a lesion panel improved the TAT to 4 days. Our findings emphasize the need for improved testing strategies to combat the syphilis epidemic and enhance public health outcomes.

IMPORTANCE

Syphilis resurgence has become a significant global public health concern. In particular, the Canadian Prairies have been struggling with high incidence since 2016, exceeding the national Canadian average. We undertook a quality assurance study that highlighted significant gaps in diagnosis of acute syphilis, which led to the development of a highly sensitive and specific multiplex lesion assay for the dual detection of herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2), varicella zoster virus (VZV), and syphilis.
Quantitative analysis of the lysine acetylome reveals the role of SIRT3-mediated HSP60 deacetylation in suppressing intracellular
Mycobacterium tuberculosis
survival
Authors: Zhu Chuanzhi , Duan Yuheng , Dong Jing , Jia Hongyan , Zhang Lanyue , Xing Aiying , Li Zihui , Du Boping , Sun Qi , Huang Yinxia , Zhang Zongde , Pan Liping
Published: June 2024

Protein acetylation and deacetylation are key epigenetic modifications that regulate the initiation and development of several diseases. In the context of infection with
Mycobacterium tuberculosis
(
M. tb
), these processes are essential for host–pathogen interactions and immune responses. However, the specific effects of acetylation and deacetylation on cellular functions during
M. tb
infection are not fully understood. This study employed Tandem Mass Tag (TMT) labeling for quantitative proteomic profiling to examine the acetylproteome (acetylome) profiles of noninfected and
M. tb
-infected macrophages. We identified 715 acetylated peptides from 1,072 proteins and quantified 544 lysine acetylation sites (Kac) in 402 proteins in noninfected and
M. tb
-infected macrophages. Our research revealed a link between acetylation events and metabolic changes during
M. tb
infection. Notably, the deacetylation of heat shock protein 60 (HSP60), a key chaperone protein, was significantly associated with this process. Specifically, the deacetylation of HSP60 at K96 by sirtuin3 (SIRT3) enhances macrophage apoptosis, leading to the elimination of intracellular
M. tb
. These findings underscore the pivotal role of the SIRT3–HSP60 axis in the host immune response to
M. tb
. This study offers a new perspective on host protein acetylation and suggests that targeting host-directed therapies could be a promising approach for tuberculosis immunotherapy.

IMPORTANCE

Protein acetylation is crucial for the onset, development, and outcome of tuberculosis (TB). Our study comprehensively investigated the dynamics of lysine acetylation during
M. tb
infection, shedding light on the intricate host–pathogen interactions that underlie the pathogenesis of tuberculosis. Using an advanced quantitative lysine proteomics approach, different profiles of acetylation sites and proteins in macrophages infected with
M. tb
were identified. Functional enrichment and protein–protein network analyses revealed significant associations between acetylated proteins and key cellular pathways, highlighting their critical role in the host response to
M. tb
infection. Furthermore, the deacetylation of HSP60 and its influence on macrophage-mediated clearance of
M. tb
underscore the functional significance of acetylation in tuberculosis pathogenesis. In conclusion, this study provides valuable insights into the regulatory mechanisms governing host immune responses to
M. tb
infection and offers promising avenues for developing novel therapeutic interventions against TB.
Construction and immunogenicity of SARS-CoV-2 virus-like particle expressed by recombinant baculovirus BacMam
Authors: Nguyen Hai Trong , Falzarano Darryl , Gerdts Volker , Liu Qiang
Published: June 2024

The pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve to give rise to variants of concern that can escape vaccine-induced immunity. As such, more effective vaccines are urgently needed. In this study, we evaluated virus-like particle (VLP) as a vaccine platform for SARS-CoV-2. The spike, envelope, and membrane proteins of the SARS-CoV-2 Wuhan strain were expressed by a single recombinant baculovirus BacMam and assembled into VLPs in cell culture. The morphology and size of the SARS-CoV-2 VLP as shown by transmission electron microscopy were similar to the authentic SARS-CoV-2 virus particle. In a mouse trial, two intramuscular immunizations of the VLP BacMam with no adjuvant elicited spike-specific binding antibodies in both sera and bronchoalveolar lavage fluids. Importantly, BacMam VLP-vaccinated mouse sera showed neutralization activity against SARS-CoV-2 spike pseudotyped lentivirus. Our results indicated that the SARS-CoV-2 VLP BacMam stimulated spike-specific immune responses with neutralization activity.

IMPORTANCE

Although existing vaccines have significantly mitigated the impact of the COVID-19 pandemic, none of the vaccines can induce sterilizing immunity. The spike protein is the main component of all approved vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due primarily to its ability to induce neutralizing antibodies. The conformation of the spike protein in the vaccine formulation should be critical for the efficacy of a vaccine. By way of closely resembling the authentic virions, virus-like particles (VLPs) should render the spike protein in its natural conformation. To this end, we utilized the baculovirus vector, BacMam, to express virus-like particles consisting of the spike, membrane, and envelope proteins of SARS-CoV-2. We demonstrated the immunogenicity of our VLP vaccine with neutralizing activity. Our data warrant further evaluation of the virus-like particles as a vaccine candidate in protecting against virus challenges.
Determining the functional role of the
Gluconobacter oxydans
GOX1969 protein as a BamB homolog
Authors: Ariano Ky , Schweiger Paul
Published: June 2024

Acetic acid bacteria are used in many industrial processes such as the production of vinegar, vitamin C, the antidiabetic drug miglitol, and various artificial flavorings. These industrially important reactions are primarily carried out by an arsenal of periplasmic-facing membrane-bound dehydrogenases that incompletely oxidize their substrates and shuttle electrons directly into the respiratory chain. Among these dehydrogenases, GOX
1969
in
Gluconobacter oxydans
was predicted to be a pyrroloquinoline quinone-dependent dehydrogenase of unknown function. However, after multiple analysis by a number of labs, no dehydrogenase activity has been detected. Reanalysis of GOX1969 sequence and structure reveals similarities to
Escherichia coli
BamB, which functions as a subunit of the β-barrel assembly machinery complex that is responsible for the assembly of β-barrel outer membrane proteins in Gram-negative bacteria. To test if the physiological function of GOX1969 is similar to BamB in
E. coli
, we introduced the
gox1969
gene into an
E. coli
∆
bamB
mutant. Growth deficiencies in the ∆
bamB
mutant were restored when
gox1969
was expressed on the plasmid pGox1969. Furthermore, increased membrane permeability conferred by
bamB
deletion was restored upon
gox1969
expression, which suggests a direct link between GOX1969 and a role in maintaining outer membrane stability. Together, this evidence strongly suggests that GOX1969 is functionally acting as a BamB in
G. oxydans
. As such, functional information on uncharacterized genes will provide new insights that will allow for more accurate modeling of acetic acid bacterial metabolism and further efforts to design rational strains for industrial use.

IMPORTANCE

Gluconobacter oxydans
is an industrially important member of the acetic acid bacteria. Experimental characterization of putative genes is necessary to identify targets for further engineering of rational acetic acid bacteria strains that can be used in the production of vitamin C, antidiabetic compounds, artificial flavorings, or novel compounds. In this study, we have identified an undefined dehydrogenase GOX1969 with no known substrate and defined structural similarities to outer membrane biogenesis protein BamB in
E. coli
K12. Furthermore, we demonstrate that GOX1969 is capable of complementing
bamB
knockout phenotypes in
E. coli
K12. Taken together, these findings enhance our understanding of
G. oxydans
physiology and expand the list of potential targets for future industrial strain design.
Exploring antimicrobial resistance determinants in the Neanderthal microbiome
Authors: Sankaranarayanan Gomathinayagam , Kodiveri Muthukaliannan Gothandam
Published: June 2024

This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome’s genetic repertoire based on the taxonomy–habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history.

IMPORTANCE

The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.
A comparative cell wall analysis of
Trichoderma
spp. confirms a conserved polysaccharide scaffold and suggests an important role for chitosan in mycoparasitism
Authors: Kappel Lisa , Yu Long , Escobar Carolina , Marcianò Demetrio , Srivastava Vaibhav , Bulone Vincent , Gruber Sabine
Published: June 2024

Fungal cell walls are dynamic extracellular matrices that enable efficient adaptation to changing environments. While the cell wall compositions of yeasts, human, and plant pathogenic fungi have been studied to some extent, the cell walls of mycoparasites remain poorly characterized.
Trichoderma
species comprise a diverse group of soil fungi with different survival strategies and lifestyles. The comparative study of cell wall carbohydrate-active enzymes in 13
Trichoderma
spp. revealed that the types of enzymes involved in chitin and chitosan metabolism are phylogenetically distant between mycoparasitic and saprotrophic species. Here, we compare the carbohydrate composition and function of the cell wall of a saprotrophic strain
Trichoderma reesei
with that of the mycoparasitic, biological control agent
Trichoderma atroviride
. Monosaccharide and glycosidic linkage analyses as well as dual
in situ
interaction assays showed that the cell wall polysaccharide composition is conserved between both species, except for the amounts of chitin detected. The results suggest that the observed accumulation of chitosan during mycoparasitism may prevent host recognition. Remarkably,
Trichoderma atroviride
undergoes dynamic cell wall adaptations during both vegetative development and mycoparasitism, which appears to be confirmed by an evolutionarily expanded group of specialized enzymes. Overall, our analyses support the notion that habitat specialization is reflected in cell wall architecture and that plastic chitin remodeling may confer an advantage to mycoparasites, ultimately enabling the successful invasion and parasitism of plant pathogens. This information may potentially be exploited for the control of crop diseases using biological agents.

IMPORTANCE

Trichoderma
species are emerging model fungi for the development of biocontrol agents and are used in industrial biotechnology as efficient enzyme producers. Fungal cell walls are complex structures that differ in carbohydrate, protein, and enzyme composition across taxa. Here, we present a chemical characterization of the cell walls of two
Trichoderma
spp., namely the predominantly saprotrophic
Trichoderma reesei
and the mycoparasite
Trichoderma atroviride
. Chemical profiling revealed that
Trichoderma
spp. remodel their cell wall to adapt to particular lifestyles, with dynamic changes during vegetative development. Importantly, we found that chitosan accumulation during mycoparasitism of a fungal host emerged as a sophisticated strategy underpinning an effective attack. These insights shed light on the molecular mechanisms that allow mycoparasites to overcome host defenses and can be exploited to improve the application of
T. atroviride
in biological pest control. Moreover, our results provide valuable information for targeting the fungal cell wall for therapeutic purposes.
The microbiome compositional and functional differences between rectal mucosa and feces
Authors: Yin Xiao-Fei , Ye Taoyu , Chen Han-Lin , Liu Junyan , Mu Xue-Feng , Li Hao , Wang Jun , Hu Yuan-Jia , Cao Hongzhi , Kang Wen-Quan
Published: June 2024

In recent years, most studies on the gut microbiome have primarily focused on feces samples, leaving the microbial communities in the intestinal mucosa relatively unexplored. To address this gap, our study employed shotgun metagenomics to analyze the microbial compositions in normal rectal mucosa and matched feces from 20 patients with colonic polyps. Our findings revealed a pronounced distinction of the microbial communities between these two sample sets. Compared with feces, the mucosal microbiome contains fewer genera, with Burkholderia being the most discriminating genus between feces and mucosa, highlighting its significant influence on the mucosa. Furthermore, based on the microbial classification and KEGG Orthology (KO) annotation results, we explored the association between rectal mucosal microbiota and factors such as age, gender, BMI, and polyp risk level. Notably, we identified novel biomarkers for these phenotypes, such as
Clostridium ramosum
and
Enterobacter cloacae
in age. The mucosal microbiota showed an enrichment of KO pathways related to sugar transport and short chain fatty acid metabolism. Our comprehensive approach not only bridges the knowledge gap regarding the microbial community in the rectal mucosa but also underscores the complexity and specificity of microbial interactions within the human gut, particularly in the Chinese population.

IMPORTANCE

This study presents a system-level map of the differences between feces and rectal mucosal microbial communities in samples with colorectal cancer risk. It reveals the unique microecological characteristics of rectal mucosa and its potential influence on health. Additionally, it provides novel insights into the role of the gut microbiome in the pathogenesis of colorectal cancer and paves the way for the development of new prevention and treatment strategies.
Comparative transcriptomic insights into molecular mechanisms of the susceptibility wheat variety MX169 response to
Puccinia striiformis
f. sp.
tritici
(
Pst
) infection
Authors: Lv Xuan , Deng Jie , Zhou Congying , Abdullah Ahsan , Yang Ziqian , Wang Zhifang , Yang Lujia , Zhao Baoqiang , Li Yuchen , Ma Zhanhong
Published: June 2024

Stripe rust of wheat is caused by the fungal pathogen
Puccinia striiformis
f. sp.
tritici
(
Pst
). Breeding durably resistant wheat varieties by disrupting the susceptibility (
S
) gene has an important impact on the control of wheat stripe rust. Mingxian169 (MX169) showed strong stripe rust susceptibility to all the races of
Pst
. However, molecular mechanisms and responsive genes underlying susceptibility of the wheat variety MX169 to
Pst
have not been elucidated. Here, we utilized next-generation sequencing technology to analyze transcriptomics data of “MX169” and high-resistance wheat “Zhong4” at 24, 48, and 120 h post-inoculation (hpi) with
Pst
. Comparative transcriptome analysis revealed 3,494, 2,831, and 2,700 differentially expressed genes (DEGs) at different time points. We observed an upregulation of DEGs involved in photosynthesis, flavonoid biosynthesis, pyruvate metabolism, thiamine metabolism, and other biological processes, suggesting their involvement in MX169’s response to
Pst
. DEGs encoding transcription factors were also identified. Our study suggested the potential susceptibility gene resources in MX169 related to stripe rust response could be valuable for understanding the mechanisms involved in stripe rust susceptibility and for improving wheat resistance to
Pst
.

IMPORTANCE

Our study suggests the potential susceptibility gene resources in MX169 related to stripe rust response could be valuable for understanding the mechanisms involved in stripe rust susceptibility and for improving wheat resistance to
Pst
.
Longitudinal alterations in the urinary virome of kidney transplant recipients are influenced by BK viremia and patient sex
Authors: Maqsood Rabia , Wu Lily I. , Brennan Daniel C. , Lim Efrem S.
Published: June 2024

Little is known about the urinary virome and how it interacts with the host, particularly in renal transplant diseases. Using metagenomic sequencing, we characterized the urinary virome of 23 kidney transplant recipients longitudinally (11 BKV+ patients and 12 BKV− patients). We applied linear mixed effects models, PERMANOVA, k-means clustering, and MaAsLin2 algorithms to determine virome signatures associated with post-transplant time, BK viremia status, and patient sex. We found that the richness and alpha diversity of urinary virome were significantly different in renal transplant recipients with BKV+ over time in comparison to BKV− (richness
P
= 0.012, alpha
P
< 0.0001). Female BKV− patients had significantly higher virome richness than males (
P
= 0.0063). Virome beta diversity was significantly different between patients by BKV status (
P
< 0.001). Additionally, we identified underlying interactions between patient sex and BKV status, in terms of virome beta diversity (
P
= 0.008). BK polyomavirus infections were primarily of subtypes IA, IB1, and IB2. The non-BK dominant samples clustered into six urinary virome community states. BKV− samples had more anelloviruses than BKV+ samples though this difference was not statistically significant. Lastly, we identified specific viruses, associated with BKV+ and time in our samples. Our results indicate that dynamic alterations in the urinary virome over the post-transplant period in kidney transplant recipients can be shaped by BK viremia and patient sex. These findings advance our fundamental understanding of the urinary virome and support a new line of investigation in renal disease and transplantation.

IMPORTANCE

The urinary microbiome is increasingly implicated in renal health and disease. While most research focuses on bacteria communities of the microbiome, factors that influence the urinary virome are not understood. Here, we investigated the urinary virome of 23 adult kidney transplant recipients longitudinally over 14 weeks post-transplant. We show that alterations in the urinary virome are associated with kidney transplant recipients with BK polyomavirus viremia that can lead to BK nephropathy and allograft rejection. By modeling the temporal dynamics post-transplant, we delineated specific profiles of the urinary virome associated with patient sex and urinary community states. These findings reveal fundamental aspects of the urinary virome that can be leveraged to better manage kidney diseases.
Soil pH amendment alters the abundance, diversity, and composition of microbial communities in two contrasting agricultural soils
Authors: Xiong Ruonan , He Xinhua , Gao Nan , Li Qing , Qiu Zijian , Hou Yixin , Shen Weishou
Published: June 2024

Soil microorganisms are the most active participants in terrestrial ecosystems, and have key roles in biogeochemical cycles and ecosystem functions. Despite the extensive research on soil pH as a key predictor of microbial community and composition, a limitation of these studies lies in determining whether bacterial and/or fungal communities are directly or indirectly influenced by pH. We conducted a controlled laboratory experiment to investigate the effects of soil pH amendment (+/- 1–2 units) with six levels on soil microbial communities in two contrasting Chinese agricultural soils (pH 8.43 in Dezhou, located in the North China Plain, Shandong vs pH 6.17 in Wuxi, located in the Taihu Lake region, Jiangsu, east China). Results showed that the fungal diversity and composition were related to soil pH, but the effects were much lower than the effects of soil pH on bacterial community in two soils. The diversity and composition of bacterial communities were more closely associated with soil pH in Wuxi soils compared to Dezhou soils. The alpha diversity of bacterial communities peaked near
in situ
pH levels in both soils, displaying a quadratic fitting pattern. Redundancy analysis and variation partition analysis indicated that soil pH affected bacterial community and composition by directly imposing a physiological constraint on soil bacteria and indirectly altering soil characteristics (e.g., nutrient availability). The study also examined complete curves of taxa relative abundances at the phylum and family levels in response to soil pH, with most relationships conforming to a quadratic fitting pattern, indicating soil pH is a reliable predictor. Furthermore, soil pH amendment affected the transformation of nitrogen and the abundances of functional genes involved in the nitrogen cycle, and methane production and consumption. Overall, results from this study would enhance our comprehension of how soil microorganisms in contrasting farmlands will respond to soil pH changes, and would contribute to more effective soil management and conservation strategies.

IMPORTANCE

This study delves into the impact of soil pH on microbial communities, investigating whether pH directly or indirectly influences bacterial and fungal communities. The research involved two contrasting soils subjected to a 1–2 pH unit amendment. Results indicate bacterial community composition was shaped by soil pH through physiological constraints and nutrient limitations. We found that most taxa relative abundances at the phylum and family levels responded to pH with a quadratic fitting pattern, indicating that soil pH is a reliable predictor. Additionally, soil pH was found to significantly influence the predicted abundance of functional genes involved in the nitrogen cycle as well as in methane production and consumption processes. These insights can contribute to develop more effective soil management and conservation strategies.
Sensitivity analysis of RT-qPCR and RT-ddPCR for SARS-CoV-2 detection with mutations on N1 and E primer-probe region
Authors: Liu Shiyou , Chai Xiaoru , Liu Chao , Bai Jiaxuan , Meng Juntao , Tian Hong , Han Xu , Han Guangyue , Li Qi , Xu Xiangdong
Published: June 2024

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that undergoes rapid mutation. Based on viral whole genome sequencing analysis in Hebei Province, China, we identified several essential single nucleotide variants (SNVs) on primer-probe regions accumulating within some Omicron variants’ genomes. In this study, we focused on three SNVs, C28290T, T28297C, and C28311T emerging on 2019-nCoV-N1 (CDC-N1) primer-probe regions, recommended by CDC in 2020, and two SNVs, C26270T, A26275G emerging on E (Charité-E) primer-probe regions recommended by Charité, Germany. Our findings revealed that the presence of one or two SNVs in the primer or probe region affected the sensitivity of reverse transcription-quantitative polymerase chain reaction and droplet digital PCR to varying extents. This discovery underscores the importance of continuously monitoring the whole genome sequences of SARS-CoV-2 variants, especially the primer-probe targeting regions, and correspondingly updating commercial test kits or recommended primer-probe sequence sets.

IMPORTANCE

The emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has resulted in a growing number of mutations in its genome, presenting new challenges for the diagnosis of SARS-CoV-2 using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and droplet digital PCR (RT-ddPCR) methods. There is an urgent need to develop refined methods for modifying primers and probes to improve the detection of these emerging variants. In this study, our focus was on the SNVs that have emerged in the CDC-N1 and Charité-E primer-probe regions. Our research has confirmed that the presence of these SNVs in the primer or probe region can significantly affect the results of coronavirus disease 2019 tests. we have developed and validated a modified detection method that can provide higher sensitivity and specificity. This study emphasizes the importance of refining the primer-probe sets to ensure the diagnostic accuracy of RT-qPCR and RT-ddPCR detection.
The Problems of DNA-Barcoding the Shads of Genus Alosa (Alosidae) of the Ponto-Caspian Basin
Authors: Orlova S. Yu. , Emelyanova O. R. , Nebesikhina N. A. , Rabazanov N. I. , Orlov A. M.
Published: June 2024

Abstract—

Numerous studies show that species identification of representatives of the genus Alosa using various genetic markers is often difficult and the search for more specific biomarkers is required. For the first time we analyzed polymorphism of COI gene fragment of mitochondrial DNA of two representatives of this genus (A. tanaica and A. kessleri), supplemented with new data on A. immaculata, from the waters of the Ponto-Caspian basin in comparative aspect with other representatives of the herring (Clupeoidea) genera Alosa, Clupea, Clupeonella, Sprattus, and Sardinops. The main result was the conclusion that within the genus Alosa, it is not possible to identify species using the marker used. On the one hand, specimens collected from morphologically distinct individuals and identified as different species have the same haplotypes. On the other hand, samples belonging to different species differ from each other by an insignificant number of nucleotide substitutions and do not form independent clades on the phylogram and haplotype network. This indicates the absence of genetic differentiation between the studied samples of herrings of genus Alosa into separate species and species groups when using DNA barcoding based on the COI gene. The reasons for such a phenomenon may be the following: (1) incorrect identification of species in catches, since shads (Alosidae) have high morphological flexibility and in many species, the main external morphological characters often overlap; (2) recent time of speciation by the standards of biological evolution for shads of genus Alosa; (3) difference in proportion of interspecific hybrids, which can vary significantly between populations of the same species.
An unusual case of Pseudohypoaldosteronism coexisting with cystic fibrosis
Authors: Umapathy Navin , Thirugnana Sambanda Moorthy Balakrishnan , Azhagar Nambi Santhi Vaanmathi , Nair Lal D V
Published: June 2024

Pseudohypoaldosteronism type 1 is a rare congenital autosomal recessive disorder, characterised by failure of receptor response to aldosterone. It is caused by mutation in SCNN1A gene with clinical features like failure to thrive in infancy, hyponatraemia, hyperkalaemia and metabolic acidosis. We present a male infant with seizures, hyperkalaemia and with failure to thrive, diagnosed at day 6 of life. The baby required repeated correction for hyperkalaemia; hence, after ruling out treatable causes for hyperkalaemia, exonerated sequencing was done which showed pathogenic mutation for cystic fibrosis and recessive mutation for pseudohypoaldosteronism. But the child was clinically in favour of pseudohypoaldosteronism. Hence, features of pseudohypoaldosteronism predominate cystic fibrosis; they both may coexist.
Ovarian tumour-cutaneous fistula as a primary presentation of pelvic malakoplakia coexisting with a benign ovarian tumour mimicking advanced ovarian cancer
Authors: Aue-aungkul Apiwat , Muktabhant Chawiporn , Kleebkaow Pilaiwan
Published: June 2024

Malakoplakia is a rare granulomatous, chronic inflammatory disease generally affecting the urogenital organs, though it can arise in other organs. The clinical manifestations of malakoplakia vary depending on the affected organ. The final diagnosis is confirmed by the presence of Michaelis-Gutmann bodies on pathology. This report describes a case of pelvic malakoplakia accompanied by an ovarian tumour-cutaneous fistula, initially misdiagnosed as advanced ovarian cancer invading the anterior abdominal wall with left pleural effusion based on imaging studies and increased serum carbohydrate antigen 19-9. The patient underwent left thoracentesis and fluid collection from the fistula tract for cytology, which showed no malignancy. She underwent primary debulking surgery, including removal of the fistula tract from anterior abdominal wall. Histopathological examination revealed malakoplakia coexisting with mucinous cystadenoma of the left ovary. For postoperative management, she received prolonged oral antibiotics for 6 months. There was no evidence of disease recurrence at the 24-month follow-up.
Impact of a simulated multiday heatwave on nocturnal physiology, behavior, and sleep: a 10-day confinement study
Authors: Ioannou Leonidas G. , Tsoutsoubi Lydia , Mantzios Konstantinos , Ciuha Ursa , Kenny Glen P. , Nybo Lars , Flouris Andreas D. , Mekjavic Igor B.
Published: June 2024

This study investigated the impact of a multiday heatwave on nocturnal physiology, behavior, and sleep under controlled conditions with comprehensive monitoring of environmental factors and participant activities. Seven young healthy males were confined for 10 days in controlled conditions that ranged between hot-to-warm (day: 35.4 °C, night: 26.3 °C) during nights 4–6 and temperate (day: 25.4 °C, night: 22.3 °C) before (nights 1–3) and after (nights 7–10) the heatwave. Measurements included core and skin temperatures, heart rate, sympathovagal balance, vasomotion indicators, urine samples, blanket coverage, subjective sleep assessments, and partial polysomnography. The average nocturnal core temperature was 0.2 °C higher during and after the heatwave compared to the pre-heatwave period, with this difference being more pronounced (+0.3 °C) in the first 2 h of sleep ( p < 0.001). For every 0.1 °C rise in overnight core temperature, the total sleep time decreased by 14 min (pseudo- R2 = 0.26, p = 0.01). The elevated core temperatures occurred despite the participants exhibiting evident thermoregulatory behavior, as they covered 30% less body surface during the heatwave compared to pre- and post-heatwave periods ( p < 0.001). During the heatwave, mean skin temperature at bedtime was 1.3 °C higher than pre-heatwave and 0.8 °C higher than post-heatwave periods ( p < 0.001). No differences in other responses, including heart rate and vasomotion indicators, were observed. The paper details a 20-min sleepwalking episode that was coupled with marked changes in sleepwalker’s thermophysiological responses. In conclusion, the simulated heatwave resulted in higher overnight core temperature which was associated with reduced total sleep time. Behavioral thermoregulation during sleep may serve as a defense against these effects, though more research is needed.
Intriguing properties of transport at the microscales: Langevin equation approach
Authors: Spiechowicz J. , Łuczka J.
Published: June 2024

We present a perspective of simple models of nonequilibrium directed transport described in terms of a Langevin equation formalism. We consider a Brownian particle under various circumstances and driven by thermal (equilibrium) and non-thermal (active) fluctuations. Three examples of startling behavior are unveiled: giant transport, multiple current reversal and negative mobility.

Graphic abstract
Timelike bound orbits and pericenter precession around black hole with conformally coupled scalar hair
Authors: Qi Qi , Kuang Xiao-Mei , Li Yong-Zhuang , Sang Yu
Published: June 2024

We investigate the geodesic motions of timelike particles around a static hairy black hole with conformally coupled scalar field. We mainly focus on the effects of the scalar charge and electric charge on the marginally bound orbits (MBO), innermost stable circular orbits (ISCO) and on the precessing orbits around this black hole. Our results show that both the scalar and electric charges suppress the energy as well as the angular momentum of the particles in the bound orbits. Then, we study the relativistic periastron precessions of the particles and constrain the charge parameters by employing the observational result of the S2 star’s precession in SgrA*. It is found that the constraints on the charge parameters from S2 star’s motion are tighter than those from black hole shadow. Finally, we analyze the periodic motions of the particles and figure out samples of periodic orbits’ configurations around the hairy black hole.
The comparison of alternative spacetimes using the spherical accretion around the black hole
Authors: Donmez Orhan
Published: June 2024

In the region where the gravitational field is strong, we have examined the influence of different gravities on the accretion disk formed due to spherical accretion. To achieve this, we obtain numerical solutions of the GRH equations, utilizing Schwarzschild, Kerr, Einstein–Gauss–Bonnet, and Hartle–Thorne spacetime metrics. We investigate the impact of the rotation parameter of a black hole ([Formula: see text]), the EGB coupling constant ([Formula: see text]), and the quadrupole moment of the rotating black hole (q) on the accretion disk formed in a strong field. The formation of the disk for the slowly and rapidly rotating black hole models is separately examined, and comparisons are made. Our numerical simulations reveal that, under the specific conditions, the solution derived from Hartle–Thorne gravity converges toward solutions obtained from Kerr and other gravitational models. In the context of the slowly rotating black hole with [Formula: see text], we observe a favorable agreement between the Hartle–Thorne result and the Kerr result within the range of [Formula: see text]. Conversely, in the scenario of the rapidly rotating black hole, a more pronounced alignment with the value of [Formula: see text] is evident within the range of [Formula: see text]. Nevertheless, for [Formula: see text], it becomes apparent that the Hartle–Thorne solution diverges from solutions provided by all gravitational models. Our motivation here is to utilize the Hartle–Thorne spacetime metric for the first time in the numerical solutions of the GRH equations for the black holes, compare the results with those obtained using other gravities, and identify under which conditions the Hartle–Thorne solution is compatible with known black hole spacetime metric solutions. This may allow us to provide an alternative perspective in explaining observed X-ray data.
Refractive index profiles for a 𝒫𝒯-symmetric optical structure
Authors: Bagchi Bijan , Ghosh Rahul , Sen Sauvik
Published: June 2024

By mapping the scalar Helmholtz equation (SHE) to the Schrödinger form we investigate the behavior of [Formula: see text] optical structure when the refractive index distribution n admits variation in the longitudinal direction only. Interpreting the Schrödinger equation in terms of a superpotential we determine the supersymmetric partners for n. We also obtain new analytical solutions for the refractive index profiles and provide graphical illustrations for them.
Influence of substrate surface roughness on the adhesion of magnetron sputtered Cr coating
Authors: Liu Wenxin , Wang Chuanbin , Liu Long , Peng Jian , Li Wenjun , Shen Qiang , Xu Zhigang
Published: June 2024

Cr coatings were deposited on both the polished and rough substrate using DC magnetron sputtering. The influence of substrate surface roughness on the morphology, crystalline phase and mechanical properties of the coatings were analyzed. The results showed that surface roughness had a significant effect on the surface morphology of the coating, as the coating inherited the surface morphology of the substrate. Surface roughness before and after coating for the polished and rough surfaces were 0.054–0.046 and 0.107–0.563[Formula: see text][Formula: see text]m, respectively. The hardness and Young’s modulus of the coating deposited on the polished surface were 5.5 and 188.6[Formula: see text]GPa, respectively, while the mechanical properties of the coating deposited on the rough surface are about the same. The results showed that the adhesion of the coating can be improved by appropriately increasing the surface roughness.