bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shifting the Energy Toward Los Angeles: Comparing the Energetic Contribution and Pacing Approach Between 2000- and 1500-m Maximal Ergometer Rowing
Authors: Astridge Daniel J. , Peeling Peter , Goods Paul S.R. , Girard Olivier , Watts Sophie P. , Dennis Myles C. , Binnie Martyn J. 
Published: November 2023

Purpose: To compare the energetic contribution and pacing in 2000- and 1500-m maximal rowing-ergometer performances. Methods: On separate visits (>48 h apart, random order), 18 trained junior (16.7 [0.4] y) male rowers completed 3 trials: a 7 × 4-minute graded exercise test, a 2000-m time trial (TT2000), and a 1500-m TT (TT1500). Respiratory gases were continuously measured throughout each trial. The submaximal power-to-oxygen-consumption relationship from the graded exercise test was used to determine the accumulated oxygen deficit for each TT. Differences in mean power output (MPO), relative anaerobic contribution, percentage of peak oxygen uptake, pacing index, maximum heart rate, rating of perceived exertion, and blood lactate concentration were assessed using linear mixed modeling. Results: Compared to TT2000 (324 [24] W), MPO was 5.2% (3.3%) higher in TT1500 (341 [29 W]; P < .001, ). There was a 4.9% (3.3%) increase (P < .001, ) in anaerobic contribution from 17.3% (3.3%) (TT2000) to 22.2% (4.3%) (TT1500). Compared to TT1500, maximum heart rate, rating of perceived exertion, and blood lactate concentration were all greater (P < .05) in TT2000. The pacing index was not different between trials. Percentage increase in MPO from TT2000 to TT1500 was negatively associated with pacing variance in TT1500 (R2 = .269, P = .027). Conclusions: Maximal ergometer performance over 1500 m requires a significantly greater anaerobic contribution compared with 2000 m. Junior male athletes adopt a consistent pacing strategy across both distances. However, those who experienced greater percentage increases in MPO over the shorter test adopted a more even pacing strategy. To prepare for 1500-m performance, greater emphasis should be placed on developing capacity for work in the severe domain and completing race simulations with a more even pacing strategy.
Effect of a Customized Physical Activity Promotion Program on Visceral Fat and Glycemic Parameters in Individuals With Prediabetes: A Randomized Controlled Trial
Authors: Jadhav Radhika A. , Maiya G. Arun , Umakanth Shashikiran , Shivashankara K.N. 
Published: November 2023

Background: Physical activity of any amount results in substantial health benefits. However, public awareness of physical activity benefits in chronic diseases is inadequate in India. Prediabetes is a significant health issue on a global scale. Visceral fat (VF) is considered as an early predictor of prediabetes. Ethnicity and race have a substantial impact on VF. Hence, this study intended to evaluate the effect of a customized physical activity promotion program on VF and glycemic parameters in individuals with prediabetes. Methods: In the current, parallel group randomized controlled trial, a total of 158 participants were recruited: 79 in intervention and 79 in control group. The study included the prediabetes individuals based on American Diabetes Association criteria. Participants from the intervention group received the customized physical activity promotion program for 24 weeks. The primary outcome measures of the study were VF level and glycemic parameters that included fasting blood sugar and glycosylated hemoglobin. Two-way mixed analysis of variance was used to study the mean difference of an outcome between 2 groups over time. Results: The study found a statistically significant interaction between the intervention and times on VF level, F1,136 = 23.564, fasting blood sugar levels, F1,136 = 8.762, and glycosylated hemoglobin levels, F1,136 = 64.582 at the end of 24 weeks (P < .05). Conclusions: This study concluded that a customized physical activity promotion program was effective in reducing VF in individuals with prediabetes as compared with controls. It improved glycemic control by reducing fasting blood sugar and glycosylated hemoglobin levels.
Introducing an environmental microbiome to axenic
Aedes aegypti
mosquitoes documents bacterial responses to a blood meal
Authors: LaReau Jacquelyn C. , Hyde Josephine , Brackney Doug E. , Steven Blaire 
Published: November 2023

ABSTRACT

Axenic
Aedes aegypti
mosquitoes were colonized with bacteria from an environmental water source to compare the midgut microbiota acquired from the wild to the microbiome of insectary-reared mosquitoes, specifically over the course of blood meal digestion. 16S rRNA gene sequencing revealed that diversity, composition, and community turnover of the midgut microbiomes were distinct between the insectary and environmental groups, with the environmental microbiomes having a greater diversity and larger temporal shifts over the course of the blood meal. Metagenomic prediction from the 16S rRNA gene sequence data pointed to metabolic processes such as vitamin biosynthesis, fatty acid recycling, and fermentation pathways differentiating the functional potential of the two different microbiomes. To further test if we could identify functional traits that distinguished the two microbiomes, we performed a culture-based assay. Culturable bacteria were more abundant in the insectary microbiomes and there was very little overlap in the taxonomy of bacteria recovered from the insectary or environmental groups. The ability of the isolates to lyse blood cells was determined on blood agar plates, and only isolates from the environmental microbiome harbored the ability to perform hemolysis in culture. These data support that the differences in taxonomy observed between the two different microbiomes also result in differences in the functional potential of the community. Thus, this study demonstrates the power of the axenic mosquito model to shed light on the community ecology of the mosquito microbiome, and the potential to better represent the microbiomes of wild mosquitoes in a laboratory setting.

IMPORTANCE
The blood meal of the female mosquito serves as a nutrition source to support egg development, so is an important aspect of its biology. Yet, the roles the microbiome may play in blood digestion are poorly characterized. We employed axenic mosquitoes to investigate how the microbiome differs between mosquitoes reared in the insectary versus mosquitoes that acquire their microbiome from the environment. Environmental microbiomes were more diverse and showed larger temporal shifts over the course of blood digestion. Importantly, only bacteria from the environmental microbiome performed hemolysis in culture, pointing to functional differences between bacterial populations. These data highlight that taxonomic differences between the microbiomes of insectary-reared and wild mosquitoes are potentially also related to their functional ecology. Thus, axenic mosquitoes colonized with environmental bacteria offer a way to investigate the role of bacteria from the wild in mosquito processes such as blood digestion, under controlled laboratory conditions.
Identification of an operon and its regulator required for autoaggregation in
Tetragenococcus halophilus
Authors: Endo Ryuhei , Hotta Shiori , Wakinaka Takura , Mogi Yoshinobu , Watanabe Jun 
Published: November 2023

ABSTRACT

Bacterial autoaggregation is associated with self- and non-self-recognition, surface colonization, and biofilm formation. Numerous aggregation factors have been cloned for basic and applied purposes. Snowflake Forming Collagen Binding Aggregation Factor (SFCBAF) is one such aggregation factor isolated from a few lactic acid bacteria species; however, the regulatory mechanisms of SFCBAF remain poorly understood. Here, we report the
aggR
and
aggABC
genes associated with autoaggregation in the halophilic lactic acid bacterium
Tetragenococcus halophilus
. A draft genome sequence analysis of five aggregating strains and subsequent comparative genomic analysis revealed that all of them have
aggR
and
aggABC
genes, which are possibly involved in autoaggregation. SFCBAF, a sortase, and a hypothetical protein are encoded by
aggABC
, which constitutes the
agg
operon. To analyze the function of these genes, phenotype- and genotype-based mutant screening was carried out. Mutants of either
aggR
or
aggA
lack autoaggregation and collagen binding abilities, indicating that they are both essential for these phenotypes.
aggR
was considered a positive regulator for the
agg
operon because
aggR
encodes a helix-turn-helix protein and
aggR
mutation resulted in diminished
agg
operon expression. Our results provide genetic bases underlying the mechanisms of aggregation and its regulation in
T. halophilus
.

IMPORTANCE

Tetragenococcus halophilus
is a halophilic lactic acid bacterium generally used as a starter culture in fermenting soy and fish sauces. Aggregating strains can be useful in fermenting and obtaining clear soy sauce because cell clumps are trapped by the filter cake when the soy sauce mash is pressed. However, the genetic mechanisms of aggregation in
T. halophilus
are unknown. In this study, we identified genes encoding aggregation factor and its regulator. These findings may provide a foundation for developing improved
T. halophilus
starter cultures for soy sauce fermentation, leading to more efficient and consistent clear soy sauce production.
Angucyclinones rescue PhLOPS
A
antibiotic activity by inhibiting Cfr-dependent antibiotic resistance
Authors: Schaenzer Adam J. , Rodriguez Hernandez Annia , Tsai Kaitlyn , Hobson Christian , Fujimori Danica Galonić , Wright Gerard D. 
Published: November 2023

ABSTRACT

Methylation of the ribosome is a prevalent strategy conferring resistance to antibiotics that inhibit protein synthesis. Methylation is catalyzed by several distinct enzymes, many encoded on mobile genetic elements widespread in bacteria. One enzyme that is increasingly common in Gram-positive pathogens is Cfr. This radical S-adenosyl-L-methionine rRNA methylase confers resistance to the antibiotics
ph
enicols,
l
incosamides,
o
xazolidinones,
p
leuromutilins, and
s
treptogramin
A
(PhLOPS
A
)
via methylation of A2503 of the 23S rRNA of the large ribosomal subunit. One strategy to safeguard the utility of these antibiotics is to identify inhibitors of Cfr-dependent methylation that may rescue antibiotic activity. We screened our in-house library of microbial natural product extracts against Cfr
+
Escherichia coli
and identified an extract from
Streptomyces
WAC01849 that potentiated the PhLOPS
A
antibiotic linezolid in a Cfr-dependent manner. We isolated the active angucyclinones 8-
O
-methyltetrangomycin (MTN) and 8-
O
-methyltetrangulol (MTL) from this extract. Both compounds selectively potentiated representatives of the PhLOPS
A
antibiotics in
Escherichia coli
and methicillin-resistant
Staphylococcus aureus
in a Cfr-dependent manner. Finally, we observed inhibition of Cfr-mediated ribosome methylation in cells treated with MTN and MTL. Our findings suggest that MTN and MTL interfere with Cfr-dependent methylation to protect the efficacy of the PhLOPS
A
antibiotics and offer a unique chemical scaffold that may be applied in developing clinically useful Cfr inhibitors.

IMPORTANCE

Cfr is an antibiotic resistance enzyme that inhibits five clinically important antibiotic classes, is genetically mobile, and has a minimal fitness cost, making Cfr a serious threat to antibiotic efficacy. The significance of our work is in discovering molecules that inhibit Cfr-dependent methylation of the ribosome, thus protecting the efficacy of the PhLOPS
A
antibiotics. These molecules are the first reported inhibitors of Cfr-mediated ribosome methylation and, as such, will guide the further discovery of chemical scaffolds against Cfr-mediated antibiotic resistance. Our work acts as a foundation for further development of molecules that safeguard the PhLOPS
A
antibiotics from Cfr.
Draft genome sequence of
Streptomyces murinus
strain SPC1 with antimicrobial potential against fungal pathogens of palms
Authors: Dhillon Braham , Chakrabarti Seemanti 
Published: November 2023

ABSTRACT

Streptomyces murinus
strain SPC1, isolated from foxtail palm seeds, exhibited antimicrobial activity against fungal pathogens of palms. The assembled genome was 8.3 Mb, with 71.96% GC content, and contained 37 secondary metabolite clusters (SMCs). A complete SMC for antifungal metabolite pentamycin (fungichromin) biosynthesis was identified in SPC1 genome.
Insights into virulence: structure classification of the
Vibrio parahaemolyticus
RIMD mobilome
Authors: Kinch Lisa N. , Schaeffer R. Dustin , Zhang Jing , Cong Qian , Orth Kim , Grishin Nick 
Published: November 2023

ABSTRACT

Vibrio parahaemolyticus
(
Vpar
) is a major cause of seafood-related gastroenteritis. A pandemic strain, RIMD2210633 (RIMD), has emerged from ancestors due to virulence mechanisms acquired through horizontal gene transfer (HGT). Mobile genetic elements play an essential role in RIMD pathogenicity, but they evolve rapidly and are challenging for sequence-based homology detection and functional inference. Guided by the Evolutionary Classification of protein Domains (ECOD), we utilized structure-assisted homology detection of high-quality AlphaFold models for RIMD proteins to augment their functional interpretation. This approach detected 7,107 domains from 3,970 RIMD proteins and classified them into the ECOD hierarchy, providing functional insights into 80% of the proteome. RIMD proteins originating from HGT were identified by comparison against 86 complete proteomes of other
Vpar
strains. The resulting RIMD mobilome is enriched with phage markers and bacterial defense domains. Evolutionary classification of known HGT proteins suggests they provide selective advantages against the human host, phage, and other stresses. Compared to a pre-pandemic strain, we found fast-evolving proteins with potential involvement in RIMD virulence and phage avoidance. These findings provide vital insights into bacterial evolution, pathogenic mechanisms, and adaptation strategies while offering testable hypotheses for experimental studies and an online resource for future investigation of the RIMD proteome.

IMPORTANCE

The pandemic
Vpar
strain RIMD causes seafood-borne illness worldwide. Previous comparative genomic studies have revealed pathogenicity islands in RIMD that contribute to the success of the strain in infection. However, not all virulence determinants have been identified, and many of the proteins encoded in known pathogenicity islands are of unknown function. Based on the EOCD database, we used evolution-based classification of structure models for the RIMD proteome to improve our functional understanding of virulence determinants acquired by the pandemic strain. We further identify and classify previously unknown mobile protein domains as well as fast evolving residue positions in structure models that contribute to virulence and adaptation with respect to a pre-pandemic strain. Our work highlights key contributions of phage in mediating seafood born illness, suggesting this strain balances its avoidance of phage predators with its successful colonization of human hosts.
Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer
Authors: Zhuang Yimin , Guo Wei , Cui Kai , Tu Yan , Diao Qiyu , Zhang Naifeng , Bi Yanliang , Ma Tao 
Published: November 2023

ABSTRACT

The use of milk replacer (MR) is a modern strategy to ensure the health and growth of neonatal ruminants. Some studies have confirmed that dietary factors have significant effects on ruminal antimicrobial resistance genes (ARGs), which, as a potential threat to livestock, have received more attention. However, the effect of different milk sources (milk or MR) on the rumen resistome of yaks is still largely unknown. Here, using metagenome technology, we investigated the occurrence of ruminal ARGs in yaks and their relationship with rumen bacteria in response to different milk sources. The metagenomic result showed that MR feeding significantly increased the abundance of
Prevotella
members compared to milk feeding. A total of 138 rumen resistome-conveying ARGs to 17 different classes of antimicrobials were detected, of which tetracycline resistance was the predominant. MR feeding also drove the changes in the rumen resistome, and the predicted bacterial origins of ARGs had complex and various manifestations. Moreover, enzymes of butyrate metabolism and carbohydrate-active enzymes encoding carbohydrate and cellulose degradation were increased. This study revealed that MR feeding increased the abundance of beneficial bacteria
Prevotella
members, changed the microbial resistome, and promoted the metabolic function of volatile fatty acid biosynthesis in the rumen of yaks, which could provide beneficial evidence for the regulation of the rumen microbiome and the intervention of antimicrobial resistance in ruminants by dietary or nutritional methods.

IMPORTANCE

Yaks, as ruminants inhabiting high-altitude environments, possess a distinct rumen microbiome and are resistant to extreme living conditions. This study investigated the microbiota, resistome, and functional gene profiles in the rumen of yaks fed milk or milk replacer (MR), providing insights into the regulation of the rumen microbiome and the intervention of antimicrobial resistance in yaks through dietary methods. The abundance of
Prevotella
members increased significantly in response to MR. Tetracycline resistance was the most predominant. The rumen of yaks contained multiple antimicrobial resistance genes (ARGs) originating from different bacteria, which could be driven by MR, and these ARGs displayed intricate and complex interactions. MR also induced changes in functional genes. The enzymes associated with fiber degradation and butyrate metabolism were activated and showed close correlations with
Prevotella
members and butyrate concentration. This study allows us to deeply understand the ruminal microbiome and ARGs of yaks and their relationship with rumen bacteria in response to different milk sources.
SalivaDirect: an alternative to a conventional RNA extraction protocol for molecular detection of SARS-CoV-2 in a clinical setting
Authors: Uddin Mohammad Khaja Mafij , Hossain Mohammad Enayet , Ami Jenifar Quaiyum , Hasan Rashedul , Hasan Md. Mahmudul , Islam Ashabul , Hasan Md. Jahid , Shaly Nusrat Jahan , Ahmed Shahriar , Samina Pushpita , Rahman Mohammed Ziaur , Rahman Mustafizur , Banu Sayera 
Published: November 2023

ABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) continues to spread and evolve, giving rise to new surges in cases and deaths. Although nasopharyngeal swab (NPS) samples are the gold standard for diagnosing SARS-CoV2, NPS sampling is invasive and requires skilled staff, specialized transport medium, and nucleic acid extraction. The SalivaDirect method uses saliva samples and a simplified, flexible approach to overcome these drawbacks. In our study conducted at the COVID-19 Screening Unit of the Dhaka Hospital of icddr,b (International Centre for Diarrheal Disease Research, Bangladesh), the diagnostic performance of SalivaDirect and NPS was compared using paired samples. SARS-CoV2 was detected by performing RT-qPCR using RNA extracted from saliva samples with the SalivaDirect method and from the NPS with extracted RNA. A total of 200 participants were enrolled from February to March 2021, among whom 78 (39.0%) tested positive for SAR-CoV2 from at least one sample. Among the 78 participants testing positive, 65 (83.3%) tested positive in both specimens, eight (10.3%) tested positive only in NPS, and five (6.4%) tested positive only in saliva. SalivaDirect had a sensitivity of 89.0% and specificity of 96.1%, with NPS as the reference test. The sensitivity of NPS and SalivaDirect was 93.6% and 89.7% respectively, with a composite reference standard (where patients are defined as positive if tested positive in either method) as the reference. Our findings demonstrated that the SalivaDirect method can be used as an alternative to NPS in our clinical setting and also supports the use of SalivaDirect in other settings.

IMPORTANCE
Affordable and accessible tests for COVID-19 allow for timely disease treatment and pandemic management. SalivaDirect is a faster and easier method to implement than NPS sampling. Patients can self-collect saliva samples at home or in other non-clinical settings without the help of a healthcare professional. Sample processing in SalivaDirect is less complex and more adaptable than in conventional nucleic acid extraction methods. We found that SalivaDirect has good diagnostic performance and is ideal for large-scale testing in settings where supplies may be limited or trained healthcare professionals are unavailable.
MDSCs-derived GPR84 induces CD8+T-cell senescence via p53 activation to suppress the antitumor response
Authors: Liu Jinyan , Liu Jiayin , Qin Guohui , Li Jiahui , Fu Ziyi , Li Jieyao , Li Miaomiao , Guo Caijuan , Zhao Ming , Zhang Zhen , Li Feng , Zhao Xuan , Wang Liping , Zhang Yi 
Published: November 2023

BackgroundsG-protein-coupled receptor 84 (GPR84) marks a subset of myeloid-derived suppressor cells (MDSCs) with stronger immunosuppression in the tumor microenvironment. Yet, how GPR84 endowed the stronger inhibition of MDSCs to CD8+T cells function is not well established. In this study, we aimed to identify the underlying mechanism behind the immunosuppression of CD8+T cells by GPR84+MDSCs.MethodsThe role and underlying mechanism that MDSCs or exosomes (Exo) regulates the function of CD8+T cells were investigated using immunofluorescence, fluorescence activating cell sorter (FACS), quantitative real-time PCR, western blot, ELISA, Confocal, RNA-sequencing (RNA-seq), etc. In vivo efficacy and mechanistic studies were conducted with wild type, GPR84 and p53 knockout C57/BL6 mice.ResultsHere, we showed that the transfer of GPR84 from MDSCs to CD8+T cells via the Exo attenuated the antitumor response. This inhibitory effect was also observed in GPR84-overexpressed CD8+T cells, whereas depleting GPR84 elevated CD8+T cells proliferation and function in vitro and in vivo. RNA-seq analysis of CD8+T cells demonstrated the activation of the p53 signaling pathway in CD8+T cells treated with GPR84+MDSCs culture medium. While knockout p53 did not induce senescence in CD8+T cells treated with GPR84+MDSCs. The per cent of GPR84+CD8+T cells work as a negative indicator for patients’ prognosis and response to chemotherapy.ConclusionsThese data demonstrated that the transfer of GPR84 from MDSCs to CD8+T cells induces T-cell senescence via the p53 signaling pathway, which could explain the strong immunosuppression of GPR84 endowed to MDSCs.