bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted syndromic next-generation sequencing panel for simultaneous detection of pathogens associated with bovine reproductive failure
Authors: Periyasamy Dhinesh , Huang Yanyun , Hill Janet E. 
Published: December 2024

ABSTRACT

Bovine reproductive failure, which includes infertility, abortion, and stillbirth in cattle, leads to significant economic losses for beef and milk producers. Diagnosing the infectious causes of bovine reproductive failure is challenging as there are multiple pathogens associated with it. The traditional stepwise approach to diagnostic testing is time-consuming and can cause significant delays. In this study, we have developed a syndromic next-generation sequencing panel (BovReproSeq) for the simultaneous detection of 17 pathogens (bacteria, virus, and protozoa) associated with bovine reproductive failure. This targeted approach involves amplifying multiple pathogen-specific targets using ultra-multiplex PCR, followed by sequencing with the Oxford Nanopore platform and subsequent analysis of the data using a custom bioinformatic pipeline to determine the presence or absence of pathogens. We tested 116 clinical samples and found that BovReproSeq results matched with current diagnostic methods for 93% of the samples, and most of the disagreements occurring in samples with very low pathogen loads (Ct >35). At the optimal read-count threshold of 10 reads (minimum number of reads to classify the sample as positive), the clinical sensitivity of the assay was approximately 82%, while clinical specificity was 100%. The overall accuracy of the assay was 98.8%. Matthews correlation coefficient (correlation coefficient of binary classification) was approximately 0.90 and F1 score (harmonic mean of precision and recall) was 0.90, indicating excellent overall performance. Our study presents a significant advancement in detecting the infectious agents associated with bovine reproductive failure and the BovReproSeq panel’s ability to detect 17 pathogens makes it a promising tool for veterinary diagnostics.

IMPORTANCE
Bovine reproductive failure causes substantial economic losses to beef and milk producers, and infectious disease contributes significantly to this syndrome. Etiologic diagnosis is complicated since multiple pathogens can be involved and infections with some pathogens are asymptomatic or cause similar clinical signs. A stepwise approach to diagnostic testing is time-consuming and increases the risk of missing the correct diagnosis. BovReproSeq is a next-generation sequencing-based diagnostic panel that allows detection of 17 reproductive failure pathogens simultaneously.
Deubiquitinase USP37 enhances the anti-HIV-2/SIV ability of the host restriction factor SAMHD1
Authors: Cui Wenzhe , Wang Hongfei , Gao Yuan , Zhang Xue , Xin Jingguo , Li Zhaolong , Li Guangquan , Gao Wenying , Zhang Wenyan 
Published: December 2024

ABSTRACT

The Vpx protein encoded by HIV-2/simian immunodeficiency virus (SIV) can antagonize the restriction of the host intrinsic restriction factor, SAMHD1, in nondividing cells by promoting its polyubiquitination and subsequent degradation, thereby facilitating viral replication and immune evasion. However, the role of deubiquitinating enzymes (DUBs) in the dynamics of virus and host remains poorly understood. Here, we demonstrate that DUB USP37 significantly reverses the Vpx-mediated degradation of SAMHD1 in various HIV-2/SIV subtypes by interacting with SAMHD1 and removing its ubiquitin chains. Notably, USP37 deubiquitinates SAMHD1 by directly recognizing SAMHD1 rather than by targeting the E3 ubiquitin ligase. The deubiquitinase activity of USP37 and its ubiquitin interacting motifs are essential for the deubiquitination of SAMHD1, whereas the phosphorylation state of USP37 does not influence its activity. Additionally, USP37 enhances the suppression of the retrotransposition of LINE-1 elements by SAMHD1 via stabilizing SAMHD1. Our findings provide important evidence that enhancing the deubiquitinating activity of some DUBs results in the stability of the host restriction factor and might be a viable strategy against HIV/SIV infections.

IMPORTANCE
SAMHD1 is a multifunctional protein, including restricting virus replication, maintaining genomic integrity through DNA repair, modulating the immune response by influencing the production of type I interferons and other cytokines, and affecting cancer cell proliferation and sensitivity to chemotherapy. However, HIV-2/simian immunodeficiency virus (SIV)-encoded Vpx and the host E3 ligase TRIM21 can induce the degradation of SAMHD1 via the ubiquitin–proteasome pathway. Therefore, it is necessary to find the strategy to stabilize SAMHD1. Our study demonstrates that the deubiquitinase USP37 reverses Vpx- and TRIM21-mediated degradation of SAMHD1, thereby inhibiting SIV replication and LINE-1 activity by stabilizing SAMHD1. Thus, we report a novel role of USP37, which represents a potentially useful target for the development of new drugs.
The
Trypanosoma brucei
tRNA methylome
Authors: Militello Kevin T. 
Published: December 2024

ABSTRACT

Herein, the
Trypanosoma brucei
procyclic form and bloodstream form tRNA methylome is reported as revealed by small RNA bisulfite sequencing. 5-Methylcytosines were identified at six unique positions with 54 total 5-methylcytosines revealed. The main hot spot for 5-methylcytosine in tRNA is the junction between the variable region and the T-arm.
Draft genome sequences of
Flagellimonas
sp. MMG031 and
Marinobacter
sp. MMG032 isolated from the dinoflagellate
Symbiodinium pilosum
Authors: Farrell Morgan V. , Aljaber Aya M. , Amoruso Madison , Chan Wyman F. , Dael Jiellen R. , De Tomas Mathieu L. , Delavega Emily G. , Eslava Jacob M. , Holdbrook-Smith Benjamin J. , Lee Precilla , Mai Van , Michael Laith R. , Moreno Stephanie V. , Quevedo Jose F. , Roberts Aaron G. , Villanueva Jorge , Westin Carl , Zazueta Daniela M. , Shikuma Nicholas J. 
Published: December 2024

ABSTRACT

Here, we report the draft genome sequences of
Flagellimonas
sp. MMG031 and
Marinobacter
sp. MMG032, isolated from coral-associated dinoflagellate
Symbiodinium pilosum
, assembled and analyzed by undergraduate students participating in a Marine Microbial Genomics (MMG) course. A genomic comparison suggests MMG031 and MMG032 are novel species and a resource for restoration and biotechnology.
Characterization of the microbial communities in paddy soils in Lajas, Puerto Rico using 16S rRNA gene
Authors: Rivera-Lopez Edwin Omar , Huertas-Miranda Javier , Rios-Velazquez Carlos 
Published: December 2024

ABSTRACT

The microbiota in the paddy soils of the Lajas Agricultural Experimental Station at the University of Puerto Rico (LAES-UPR) plays a crucial role in agricultural ecosystems. Despite being at an experimental station, these soils represent natural environments supporting rice cultivation. Microbial diversity was evaluated during pre-harvest and post-harvest periods.
Draft genome sequences of two distinct
Clostridioides difficile
isolates coinfecting a patient
Authors: Lu Xin , Feng Yu , Wang Xiaohui 
Published: December 2024

ABSTRACT

Clostridioides difficile
is a spore-forming anaerobic Gram-positive bacillus. In this study, two distinct strains of
C. difficile
causing coinfection were isolated from the same fecal sample. Whole-genome sequencing was performed on these two strains to elucidate their genomic characteristics.
Dysbiosis of gut microbiota in COVID-19 is associated with intestinal DNA phage dynamics of lysogenic and lytic infection
Authors: Ishizaka Aya , Tamura Azumi , Koga Michiko , Mizutani Taketoshi , Yamayoshi Seiya , Iwatsuki-Horimoto Kiyoko , Yasuhara Atsuhiro , Yamamoto Shinya , Nagai Hiroyuki , Adachi Eisuke , Suzuki Yutaka , Kawaoka Yoshihiro , Yotsuyanagi Hiroshi 
Published: December 2024

ABSTRACT

This study compared intestinal DNA phage dynamics and gut microbiota changes observed at the onset of coronavirus disease 2019 (COVID-19). The study participants included 19 healthy individuals and 19 patients with severe acute respiratory syndrome coronavirus 2 infection. Significant differences were observed in the diversity of the intestinal DNA virome after the onset of COVID-19 compared with that in healthy individuals. Classification by their tail morphology resulted in the order Caudovirales, a double-stranded DNA phage, accounting for >95% of all participants. In classifying phages based on host bacteria, a decreased number of phages infecting mainly the Clostridia class was observed immediately after the onset of COVID-19 and recovered over time. After the onset of COVID-19, two distinct movement patterns of intestinal phages and their host bacteria were observed: phage- and bacteria-predominant. The abundance of obligate anaerobes, such as
Clostridium_sense_strict_1
,
Fusicatenibacter
, and
Romboutsia
, and the phages hosting these bacteria decreased immediately after the onset of COVID-19, and faster phage recovery was observed compared with bacterial recovery. In contrast, the genus
Staphylococcus
, a facultative anaerobic bacterium, increased immediately after the onset of COVID-19, whereas the phages infecting
Staphylococcus
decreased. Furthermore, immediately after the onset of COVID-19, the percentage of lytic phages increased, whereas that of temperate phages decreased. These observations suggest that the gut microbiota dysbiosis observed immediately after the onset of COVID-19 may be linked to phage dynamics that control gut microbiota and may also affect the recovery from dysbiosis.

IMPORTANCE
Bacteriophages infect and replicate with bacteria and archaea and are closely associated with intestinal bacteria. The symbiotic relationship between gut microbiota and bacteriophages is of interest, but it is challenging to study their dynamics in the human body over time. SARS-CoV-2 infection has been reported to alter the gut microbiota, which is involved in gut immune regulation and pathophysiology, although changes in the intestinal phages of patients with SARS-CoV-2 and their dynamic relationship with the gut microbiota remain unclear. SARS-CoV-2 infection, which follows a transient pathological course from disease onset to cure, may provide a reliable model to investigate these interactions in the gut environment. Therefore, this study aimed to elucidate the correlation between gut microbiota and intestinal DNA virome dynamics in COVID-19 pathogenesis. This study found that the dysbiosis observed in SARS-CoV-2 infection involves a growth strategy that depends on the phage or bacterial dominance.
Establishment and application of a rapid new detection method for antimicrobial susceptibility testing of
Klebsiella pneumoniae
based on MALDI-TOF MS
Authors: Zhang Yapei , Fan Fanghua , Wang Xuan , Zhu Jie , Dong Shilei 
Published: December 2024

ABSTRACT

The earlier appropriate treatment of
Klebsiella pneumoniae
infections according to the antimicrobial susceptibility profile based on the minimum inhibitory concentration (MIC) has a great clinical benefit. Our objective was to establish a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based antimicrobial susceptibility test (AST) for
K. pneumoniae
that produces reliable results within a few hours. Our rapid method is similar to the classical turbidity-based microdilution method. We confirmed, theoretically and experimentally, that MALDI-TOF MS can replace the naked eye in judging the results (MIC
MS
) by “seeing” the bacterial growth in the presence of different concentrations of antibiotics, including determination of the lower limit of bacterial count detection (4 × 10
5
cfu), the optimal period of incubation (2 h), and bacterial growth curve assay. Based on the study mentioned above, we determined the susceptibility of
K. pneumoniae
to imipenem. The MIC
MS
and MIC data agreed over 85% (40/46) within 1 dilution range. Susceptibility profiles determined with our rapid method and the reference broth microdilution method were also compared. MIC
MS
resulted in 97.9% (45/46) category agreement, 2.2% minor discrepancies, no major discrepancies, and no very major discrepancies. The summarized category agreement resulted in a kappa coefficient of almost 1 for weighted Cohen’s kappa, which could be considered a nearly perfect agreement. It took just 2 h to produce a susceptibility profile with a low failure rate using our new rapid AST method, a work day earlier than the broth microdilution method.

IMPORTANCE

Empirical antimicrobial use before antimicrobial susceptibility test (AST) is necessary but risks patient harm and excess costs. It is particularly worrying that the inappropriate use of carbapenems has allowed carbapenem-resistant
Klebsiella pneumoniae
to become the commonest transmissible carbapenem-resistant Enterobacterales worldwide. Guidelines recommend targeted therapy based on minimum inhibitory concentration results, which directly reflect the effectiveness of antibacterial drugs. The gold standard method of AST relies on visible bacterial growth, causing long turnaround times. Current rapid AST techniques are hampered by factors such as high costs, technological complexities, and limited detection capabilities. We present a novel rapid method and applied to the determination of the susceptibility of
K. pneumoniae
to imipenem. It took just 2 h to produce a susceptibility profile with a low failure rate, a work day earlier than the standard method. Our method is potentially a faster, more precise, cost-efficient, and user-friendly AST method that can enhance the effectiveness of treatment strategies.
Microhabitat accessibility determines peptide substrate degradation by soil microbial community
Authors: Arellano-Caicedo Carlos , Ohlsson Pelle , Moradi Saleh , Hammer Edith C. 
Published: December 2024

ABSTRACT

Soil pore space, considered the most complex biomaterial that exists, generates a complex environment, that gives rise to a wide variety of properties, such as microbial diversity and carbon storage. Soils contain, at the same time, the largest carbon reservoir on earth and an immense amount of nutrient-limited microbial biomass. The reason why this carbon is not consumed by soil microbes is attributed to the complex nature of soil, which forms a labyrinth where carbon and microbes cannot be in direct contact. In the present study, by using microfluidics, we tested the effect of labyrinth-like structures of decreasing accessibility on the decomposing activity of soil microbial communities from a soil inoculum. The two parameters used to study the effect of microhabitat accessibility were either the turning angle in an array of channel-like pore structures or the fractal order in an array of maze-like pore structures. We found that in both cases, channels and mazes, decreasing accessibility produced a higher peptide substrate degradation. When we analyzed the degradation within the structures, we found that most of the activity is concentrated in the regions of intermediate accessibility. We think that the increased degradation activity in low accessibility mazes might be due to the reduced interactions within the microbial communities which leads to a reduction in competition. Lowered competition allows different communities with a wide range of metabolic strategies to cohabit in the structures, which resulted in a bulk increase of the peptide substrate degradation.

IMPORTANCE
The role microbes have in the environment is highly influenced by the characteristics of their habitat. Here, we show that a complex habitat enhances the enzymatic activity of a soil microbial inoculum. This might occur due to a reduced competition in complex habitats, which allows a more diverse community to coexist and explore a wider variety of metabolic strategies. The different rates of enzymatic activity in different levels of complexity suggest emergent properties of microbial communities in complex microhabitats which could have important implication for microbial processes, such as soil carbon storage and nutrient cycling.
Predictive validity of interleukin 6 (IL-6) for the mortality in critically ill COVID-19 patients with the B.1.617.2 (Delta) variant in Vietnam: a single-centre, cross-sectional study
Authors: Nguyen Chi Van , Luong Chinh Quoc , Dao Co Xuan , Nguyen My Ha , Pham Dung Thi , Khuat Nhung Hong , Pham Quynh Thi , Hoang Dat Tien , Nguyen Anh Diep , Nguyen Phuong Minh , Cao Duong Dai , Pham Dung Thuy , Nguyen Thai Quoc , Nong Vuong Minh , Dang Dung Tuan , Nguyen Dat Tuan , Nguyen Vinh Duc , Le Thuan Quang , Nguyen Viet Khoi , Ngo Hung Duc , Nguyen Dung Van , Pham Thach The , Nguyen Dung Tien , Nguyen Nguyen Trung , Do Tan Dang , Huynh Nhung Thi , Phan Nga Thu , Nguyen Cuong Duy , Vo Khoi Hong , Vu Thom Thi , Do Cuong Duy , Dang Tuan Quoc , Vu Giap Van , Nguyen Tan Cong , Do Son Ngoc 
Published: December 2024

ObjectivesTo investigate the serum IL-6 levels and their rate of change in predicting the mortality of critically ill patients with COVID-19 in Vietnam.DesignA single-centre, cross-sectional study.SettingAn Intensive Care Centre for the Treatment of Critically Ill Patients with COVID-19 in Ho Chi Minh City, Vietnam.ParticipantsWe included patients aged 18 years or older who were critically ill with COVID-19 and presented to the study centre from 30 July 2021 to 15 October 2021. We excluded patients who did not have serum IL-6 measurements between admission and the end of the first day.Primary outcome measuresThe primary outcome was hospital all-cause mortality.ResultsOf 90 patients, 41.1% were men, the median age was 60.5 years (Q1–Q3: 52.0–71.0), and 76.7% of patients died in the hospital. Elevated IL-6 levels were observed on admission (41.79 pg/mL; Q1–Q3: 20.68–106.27) and on the third day after admission (72.00 pg/mL; Q1–Q3: 26.98–186.50), along with a significant rate of change in IL-6 during that period (839.5%; SD: 2753.2). While admission IL-6 level (areas under the receiver operator characteristic curve (AUROC): 0.610 (95% CI: 0.459 to 0.761); cut-off value ≥15.8 pg/mL) and rate of change in IL-6 on the third day of admission (AUROC: 0.586 (95% CI: 0.420 to 0.751); cut-off value ≥−58.7%) demonstrated poor discriminatory ability in predicting hospital mortality, the third day IL-6 rate of change from admission ≥−58.7% (adjusted OR: 12.812; 95% CI: 2.104 to 78.005) emerged as an independent predictor of hospital mortality.ConclusionsThis study focused on a highly selected cohort of critically ill COVID-19 patients with a high IL-6 level and mortality rate. Despite the poor discriminatory value of admission IL-6 levels, the rate of change in IL-6 proved valuable in predicting mortality. To identify critically ill COVID-19 patients with the highest risk for mortality, monitoring the serial serum IL-6 measurements and observing the rate of change in serum IL-6 levels over time are needed.
Biopsychosocial factors associated with physical activity among Resettlers of the former Soviet Union in Germany: a cross-sectional analysis
Authors: Ouma Mary Achieng , Juma Kenneth , Meisinger Christa , Stolpe Susanne , Becher Heiko , Winkler Volker Franz , Deckert Andreas 
Published: December 2024

ObjectivePrevious research suggests an overall lower cardiovascular disease mortality among ethnic German Resettlers from the Former Soviet Union. However, evidence points to a high burden of metabolic risk factors and chronic conditions among Resettlers, factors which are correlated to lower levels of physical activity. Thus, this study aims to assess factors associated with physical activity among Resettlers, by investigating the interplay between biopsychosocial factors and physical activity between men and women.DesignWe conducted a cross-sectional study by administering questionnaires between 2011 and 2012. Data from 595 individuals were analysed, and total and extracurricular physical activity scores were generated. A backward stepwise linear regression was run to investigate the effect of various predictors on various physical activity domains.SettingAugsburg, Germany.ParticipantsWe targeted Resettlers who had moved to Augsburg, Germany between 1990 and 1999.ResultsDisease and psychological distress were linked to decreasing physical activity in men. Higher socioeconomic status was correlated with increasing physical activity except for work-related physical activity for both men and women. Single women were less likely to report extracurricular activity, and so did women who reported a shorter duration of stay and men who smoked.ConclusionsMigration experience and culture account for gender-related sex differences in physical activity alongwith other interlocking social factors such as psychological stressors and health status among Resettlers. Individual psychological stressors may hinder or motivate physical activity, but physical activity can reverse the influence of such stressors on Resettlers. Understanding migrant health and experiences is crucial due to the migration influx and health disparities. However, data on this topic are scarce in Germany.
Effects of core training based on respiratory therapy on elderly stable COPD patients in the rehabilitation hospital: a study protocol for a randomised controlled trial
Authors: Su Jianqing , Qu Yan , Wei Yingjun , Wang Shanshan , Zhou Jingjing , Gao Bingyang , Niu Chunlai , Zhang Zinan , Feng Wei 
Published: December 2024

IntroductionElderly stable chronic obstructive pulmonary disease (COPD) patients frequently experience walking dysfunction. Research indicates that balance training holds promise for enhancing walking stability in these individuals, whereas respiratory therapy (RT) can enhance walking endurance effectively. However, existing balance training regimens tailored for COPD are intricate and lack specificity, and the impact of combined RT on patients’ walking function remains uncertain. This study aims to assess the influence of core training (CT) integrated with RT on walking function among elderly stable COPD patients.Methods and analysisThis randomised, assessment-blinded, routine rehabilitation-controlled trial will be carried out at the Department of Respiratory and Critical Care Rehabilitation, the Second Rehabilitation Hospital of Shanghai. A total of 42 elderly patients diagnosed with stable COPD will be randomly allocated to either the study group (SG) or the control group in a 1:1 ratio. Both groups will undergo 6 weeks of standard rehabilitation training. Additionally, patients in the SG will receive CT based on RT. The primary outcome of the study is the 6 min walk test. Secondary outcomes encompass ultrasound indicators of the diaphragm and multifidus, pulmonary function tests, Berg balance scale test, trunk impairment scale test, COPD assessment test and St. George’s Respiratory Questionnaire.Ethics and disseminationEthical approval was obtained from the Ethics Committee of the Second Rehabilitation Hospital of Shanghai (2023-01-01, see online supplemental file 1). All patients will provide written informed consent before participation. The results of the trial are intended for publication in a peer-reviewed journal.Trial registration numberChiCTR2400080276.