bluuebunny/crossref_metadata_2025_split huggingface dataset:
The isoprenyl chain length of coenzyme Q mediates the nutritional resistance of fungi to amoeba predation
Authors: Saeed Nauman , Valiante Vito , Kufs Johann E. , Hillmann Falk 
Published: May 2024

ABSTRACT

Amoebae are environmental predators feeding on bacteria, fungi, and other eukaryotic microbes. Predatory interactions alter microbial communities and impose selective pressure toward phagocytic resistance or escape which may, in turn, foster virulence attributes. The ubiquitous fungivorous amoeba
Protostelium aurantium
has a wide prey spectrum in the fungal kingdom but discriminates against members of the
Saccharomyces
clade, such as
Saccharomyces cerevisiae
and
Candida glabrata
. Here, we show that this prey discrimination among fungi is solely based on the presence of ubiquinone as an essential cofactor for the predator. While the amoeba readily fed on fungi with CoQ presenting longer isoprenyl side chain variants CoQ8-10, such as those from the
Candida
clade, it failed to proliferate on those with shorter CoQ variants, specifically from the
Saccharomyces
clade (CoQ6). Supplementing non-edible yeast with CoQ9 or CoQ10 rescued the growth
of P. aurantium
, highlighting the importance of a long isoprenyl side chain. Heterologous biosynthesis of CoQ9 in
S. cerevisiae
by introducing genes responsible for CoQ9 production from the evolutionary more basic
Yarrowia lipolytica
complemented the function of the native CoQ6. The results suggest that the use of CoQ6 among members of the
Saccharomyces
clade might have originated as a predatory escape strategy in fungal lineages and could be retained in organisms that were able to thrive by fermentation.

IMPORTANCE

Ubiquinones (CoQ) are universal electron carriers in the respiratory chain of all aerobic bacteria and eukaryotes. Usually 8-10 isoprenyl units ensure their localization within the lipid bilayer. Members of the
Saccharomyces
clade among fungi are unique in using only 6. The reason for this is unclear. Here we provide evidence that the use of CoQ6 efficiently protects these fungi from predation by the ubiquitous fungivorous amoeba
Protostelium aurantium
which lacks its own biosynthetic pathway for this vitamin. The amoebae were starving on a diet of CoQ6 yeasts which could be complemented by either the addition of longer CoQs or the genetic engineering of a CoQ9 biosynthetic pathway.
Seven genome sequences of airborne, bacterial isolates from Antarctica
Authors: Dieser Markus , Smith Heidi J. , Foreman Christine M. 
Published: May 2024

ABSTRACT

Ice-covered and remote landscapes in the McMurdo Dry Valleys, Antarctica, are likely seeded by aeolian transport of biological material from ice-free local or distant environments. Here, we report the genome sequences of seven bacteria isolated from aerosols collected on top of two dry valley glaciers.
Characteristics and immune functions of the endogenous CRISPR-Cas systems in myxobacteria
Authors: Hu Wei-feng , Yang Jiang-yu , Wang Jing-jing , Yuan Shu-fei , Yue Xin-jing , Zhang Zheng , Zhang Ya-qi , Meng Jun-yan , Li Yue-zhong 
Published: May 2024

ABSTRACT

The clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) system widely occurs in prokaryotic organisms to recognize and destruct genetic invaders. Systematic collation and characterization of endogenous CRISPR-Cas systems are conducive to our understanding and potential utilization of this natural genetic machinery. In this study, we screened 39 complete and 692 incomplete genomes of myxobacteria using a combined strategy to dispose of the abridged genome information and revealed at least 19 CRISPR-Cas subtypes, which were distributed with a taxonomic difference and often lost stochastically in intraspecies strains. The
cas
genes in each subtype were evolutionarily clustered but deeply separated, while most of the CRISPRs were divided into four types based on the motif characteristics of repeat sequences. The spacers recorded in myxobacterial CRISPRs were in high G+C content, matching lots of phages, tiny amounts of plasmids, and, surprisingly, massive organismic genomes. We experimentally demonstrated the immune and self-target immune activities of three endogenous systems in
Myxococcus xanthus
DK1622 against artificial genetic invaders and revealed the microhomology-mediated end-joining mechanism for the immunity-induced DNA repair but not homology-directed repair. The panoramic view and immune activities imply potential omnipotent immune functions and applications of the endogenous CRISPR-Cas machinery.

IMPORTANCE
Serving as an adaptive immune system, clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) empower prokaryotes to fend off the intrusion of external genetic materials. Myxobacteria are a collective of swarming Gram-stain-negative predatory bacteria distinguished by intricate multicellular social behavior. An in-depth analysis of their intrinsic CRISPR-Cas systems is beneficial for our understanding of the survival strategies employed by host cells within their environmental niches. Moreover, the experimental findings presented in this study not only suggest the robust immune functions of CRISPR-Cas in myxobacteria but also their potential applications.
Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables
Authors: Junker Romane , Valence Florence , Mistou Michel-Yves , Chaillou Stéphane , Chiapello Helene 
Published: May 2024

ABSTRACT

The management of food fermentation is still largely based on empirical knowledge, as the dynamics of microbial communities and the underlying metabolic networks that produce safe and nutritious products remain beyond our understanding. Although these closed ecosystems contain relatively few taxa, they have not yet been thoroughly characterized with respect to how their microbial communities interact and dynamically evolve. However, with the increased availability of metataxonomic data sets on different fermented vegetables, it is now possible to gain a comprehensive understanding of the microbial relationships that structure plant fermentation. In this study, we applied a network-based approach to the integration of public metataxonomic 16S data sets targeting different fermented vegetables throughout time. Specifically, we aimed to explore, compare, and combine public 16S data sets to identify shared associations between amplicon sequence variants (ASVs) obtained from independent studies. The workflow includes steps for searching and selecting public time-series data sets and constructing association networks of ASVs based on co-abundance metrics. Networks for individual data sets are then integrated into a core network, highlighting significant associations. Microbial communities are identified based on the comparison and clustering of ASV networks using the “stochastic block model” method. When we applied this method to 10 public data sets (including a total of 931 samples) targeting five varieties of vegetables with different sampling times, we found that it was able to shed light on the dynamics of vegetable fermentation by characterizing the processes of community succession among different bacterial assemblages.

IMPORTANCE

Within the growing body of research on the bacterial communities involved in the fermentation of vegetables, there is particular interest in discovering the species or consortia that drive different fermentation steps. This integrative analysis demonstrates that the reuse and integration of public microbiome data sets can provide new insights into a little-known biotope. Our most important finding is the recurrent but transient appearance, at the beginning of vegetable fermentation, of amplicon sequence variants (ASVs) belonging to
Enterobacterales
and their associations with ASVs belonging to
Lactobacillales
. These findings could be applied to the design of new fermented products.
Impact of whole grain highland hull-less barley on the denaturing gradient gel electrophoresis profiles of gut microbial communities in rats fed high-fat diets
Authors: Xia Xuejuan , Lu Jing , Chen Xuanyu , Zhou Lu , Huang Yadong , Ding Shunjie , Li Guannan 
Published: May 2024

ABSTRACT

Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) is a traditional non-culture technique that can provide a fingerprint of the microbial community. In the field of gut microbiota analysis, PCR-DGGE still holds potential for development. In the present study, we utilized an improved nested PCR-DGGE approach targeting the V3 region of 16S ribosomal DNA to investigate the impact of whole grain highland hull-less barley (WHLB), a cereal known for its significant hypocholesterolemic effect, on the gut microbiota profiles of high-fat diet rats. Seventy-two male Sprague–Dawley rats were divided into four groups and fed a normal control diet, a high-fat diet, or a high-fat diet supplemented with a low or high dose of WHLB for 4 or 8 weeks. The results revealed that the dominant bands varied among different dose groups and further changed with different treatment times. The compositions of bacterial communities in feces and cecal content were similar, but the dominant bacterial bands differed. After performing double DGGE, extracting the bands, sequencing the DNA, and aligning the sequences, a total of 19 bands were classified under the Firmicutes and Bacteroidetes phyla, while two bands were identified as unclassified uncultured bacteria. The relative abundance of
Lactobacillus gasseri
, Uncultured
Prevotella
sp., and
Clostridium
sp. increased following the administration of WHLB. Illumina-based sequencing was employed to assess the reliability of DGGE, demonstrating its reliability in analyzing the dominant taxonomic composition, although it may have limitations in accurately detecting the alpha diversity of bacterial species.

IMPORTANCE
While next-generation sequencing has overshadowed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), the latter still holds promise for advancing gut microbiota analysis due to its unique advantages. In this study, we used optimized nested PCR-DGGE to investigate the gut microbiota profile of high-fat diet rats after administering whole grain highland hull-less barley. High-throughput sequencing was employed to validate the DGGE results. Our results proved the reliability of PCR-DGGE for analyzing the dominant taxonomic composition while also providing visual evidence of a notable relationship between the composition of cecal and fecal microbial communities, highlighting substantial differences in both richness and abundance.
Strontium isotopes and rare earth elements in terrestrial hot-spring deposits: Characterization and geothermal implications
Authors: Luo Lianchao , Wen Huaguo , Capezzuoli Enrico , Brogi Andrea , Liu Ruolin , Vaselli Orlando , Wang Fudong , Lu Zhipeng , You Yaxian , Kele Sándor 
Published: May 2024

Abstract
Identifying geothermal reservoir rock types is fundamental in geothermal exploration, but the absence of active surface geothermal manifestations (especially hot springs) in blind geothermal systems makes this identification difficult. Nevertheless, blind geothermal systems may develop early-formed hot-spring deposits. As (bio-)chemical precipitate, these deposits may retain geochemical signatures of spring waters and thus provide insights into reservoir rock types. To assess their geothermal implications, the 87Sr/86Sr and rare earth elements + yttrium (REE + Y) characteristics of hot-spring deposits in two geothermal systems were investigated and compared with those of their reservoir rocks. Results showed relatively uniform 87Sr/86Sr values in hot-spring deposits within each system, but occasional 87Sr/86Sr contamination induced by exogenous detritus input was also observed. The amount of detritus input relates to the potential for interaction with surrounding soils/rocks and is thus environmentally controlled. Hot-spring deposits with high Sr concentrations showed greater 87Sr/86Sr contamination resistance than those with low Sr concentrations, revealing the influence of Sr concentration in hot-spring deposits on detrital 87Sr/86Sr contamination. The detritus input also influenced the REE + Y signatures of the hot-spring deposits, underscoring the necessity of contamination assessment before geochemical interpretation. Excluding samples with significant 87Sr/86Sr and/or REE + Y contamination, the remaining samples closely mirrored their respective reservoir rocks in terms of 87Sr/86Sr, with partial overlap in REE + Y signatures. This suggests that the 87Sr/86Sr and REE + Y characteristics of hot-spring deposits provide valuable insights into reservoir rock types. However, variations in 87Sr/86Sr or REE + Y compositions between some hot-spring deposits and corresponding reservoir rocks indicate additional influencing factors beyond reservoir rock types. Therefore, a comprehensive understanding of reservoir rock types requires integrated geochemical characterization, probably including 87Sr/86Sr, REE + Y, and other parameters. These findings underscore the potential of geochemical characterization of hot-spring deposits for identifying geothermal reservoir rock types, and this geochemical approach can complement geological and geophysical data to improve exploration efficiency, especially in blind geothermal systems.
Supplemental Material: Geodetic constraints on three-component motion of the Ordos block (China) and their implications for lithospheric dynamics
Authors: Li Zhangjun , al. et 
Published: May 2024

<p>GNSS position and leveling height difference time series in the northeastern Ordos block and the Datong volcanic areas (Figs. S1 and S2). Observed and calculated vertical velocities at each continuously operating GNSS site, as well as seasonal vertical deformation signal from GNSS stations (Fig. S3). Leveling vertical velocities relative to the Ordos Block (the Suide bedrock benchmark) and geocentered ITRF2014 reference frames (Fig. S4). Rotation strain rates and median spatial smoothing distances in strain rate calculation (Fig. S5). </p>
The relative risk of fatal poisoning by methadone or buprenorphine within the wider population of England and Wales
Authors: Marteau Dave , McDonald Rebecca , Patel Kamlesh 
Published: May 2024

ObjectiveTo examine the population-wide overdose risk emerging from the prescription of methadone and buprenorphine for opioid substitution treatment in England and Wales.DesignRetrospective administrative data study.SettingNational databases for England and Wales.Participants/casesDrug-related mortality data were drawn from the Office for National Statistics, and prescription data for methadone and buprenorphine were obtained from the National Health Service for the years 2007–2012. During this 6-year period, a total of 2366 methadone-related deaths and 52 buprenorphine-related deaths were registered, corresponding to 17 333 163 methadone and 2 602 374 buprenorphine prescriptions issued. The analysis encompassed poisoning deaths among members of the wider population of England and Wales who consumed, but were not prescribed these medications, in addition to patients prescribed methadone or buprenorphine.Main outcome measuresMortality risk: substance-specific overdose rate per 1000 prescriptions issued; relative risk ratio of methadone in relation to buprenorphine.ResultsDuring the years 2007–2012, the pooled overdose death rate was 0.137/1000 prescriptions of methadone, compared to 0.022/1000 prescriptions of buprenorphine (including buprenorphine-naloxone). The analysis generated a relative risk ratio of 6.23 (95% CI 4.79 to 8.10) of methadone in relation to buprenorphine. UK Borders Agency data were taken into consideration and revealed that only negligible amounts of methadone and buprenorphine were seized on entering UK territory between 2007 and 2012, suggesting domestic diversion.ConclusionsOur analysis of the relative safety of buprenorphine and methadone for opioid substitution treatment reveals that buprenorphine is six times safer than methadone with regard to overdose risk among the general population. Clinicians should be aware of the increased risk of prescribing methadone, and tighter regulations are needed to prevent its diversion.
Practice of breast self-examination and associated factors among women of reproductive age in the North Shoa Zone, Oromia, Ethiopia, 2022: a convergent mixed-methods study
Authors: Hussein Dursa , Oyato Befekadu Tesfaye , Gashaw Ketema , Geleta Tinsae Abeya , Tufa Derara Girma , Geleta Leta Adugna 
Published: May 2024

ObjectiveTo assess practice of breast self-examination (BSE) and associated factors among women of reproductive age in the North Shoa Zone, Oromia, Ethiopia.DesignCommunity-based cross-sectional study with a convergent mixed-methods approach.SettingThe study was conducted in the North Shoa Zone of Oromia, Central Ethiopia, between 1 May 2022 and 30 June 2022.Participants1076 women of reproductive age were selected using simple random sampling technique for the quantitative study. For the qualitative part, a total of 46 women were approached purposively to elicit rich ideas and insight into the issue. The quantitative data were collected using an interviewer-administered questionnaire, and focus group discussions were used for the qualitative part. Quantitative data were analysed using SPSS V.26. An adjusted OR with a 95% CI was employed. Thematic analysis approach was applied for the qualitative data analysis.Outcome measuresParticipants were interviewed to respond whether they practised BSE.ResultsOverall, 192 (18.2%; 15.7%–20.5%) of the participants had ever performed BSE. Having a family history of breast cancer (BC) (adjusted OR (AOR)=6.9, 95% CI 4.6 to 10.3), being knowledgeable on BSE (AOR=3, 95% CI 1.9 to 4.3), having high perceived susceptibility (AOR=1.7, 95% CI 1.2 to 2.5), having high self-efficacy (AOR=1.5, 95% CI 1.1 to 2.3) and having a high perceived benefit to BSE (AOR=1.5, 95% CI 1.1 to 2.3) were significantly associated with increased odds of BSE practice.Four main themes emerged from the qualitative analysis: BC and BSE-related knowledge, perceived benefits of treatment, barriers to BSE practice and enablers of BSE practice.ConclusionThe practice of BSE in this area was considerably low. The North Shoa Zonal Health Office and other stakeholders should disseminate instructional materials that cover the techniques and benefits of regularly performing BSE. Healthcare professionals should engage in the community to address the obstacles women face in practising BSE.
Predicting the association of different levels of physical activity on postoperative pulmonary complications using the international physical activity questionnaire in patients undergoing thoracoscopic lung surgery under general anaesthesia: protocol for a prospective cohort study
Authors: Qiu Lei , Zhao Liang , Wang Bailun , Yang Li , Cao Cuicui , Lv Meng , Xu Mengchao , Hou Ming , Wang Xiaofei , Wang Yuelan , Gu Chang Ping 
Published: May 2024

IntroductionPostoperative pulmonary complications (PPCs) occur frequently in patients undergoing lung surgery under general anaesthesia and are strongly associated with longer postoperative hospital stays and increased mortality. The existing literature has shown that a higher level of preoperative physical activity (PA) plays a positive role in the low incidence of postoperative complications and the quality of life in patients undergoing lung surgery. However, the association between preoperative PA levels and the incidence of PPCs has rarely been studied, particularly in thoracoscopic lung surgery. This study aims to evaluate PA levels in patients undergoing thoracoscopic lung surgery using the International Physical Activity Questionnaire and to investigate the association between PA levels and the incidence of PPCs.Methods and analysisA total of 204 participants aged 18–80 years undergoing thoracoscopic lung surgery (thoracoscopic wedge resection, thoracoscopic segmentectomy and thoracoscopic lobectomy) will be included in the study. The primary outcome is the incidence of PPCs within the first 5 postoperative days. The secondary outcomes include the number of PPCs, the incidence of PPCs 1 month postoperatively, the arterial blood levels of inflammatory markers, the incidence of postoperative adverse events within the first 5 postoperative days, extubation time, unplanned admission to the intensive care unit, postoperative length of stay and mortality 1 month postoperatively.Ethics and disseminationThe study was reviewed and approved by the Research Ethics Committee of the First Affiliated Hospital of Shandong First Medical University on 31 March 2022 (YXLL-KY-2022(014)) and is registered at ClinicalTrials.gov. We plan to disseminate the data and findings of this study in international and peer-reviewed journals.Trial registration numberThe trial has been prospectively registered at the clinicaltrials.gov registry (NCT05401253).
Body mass index and all-cause mortality in HUNT and UK biobank studies: revised non-linear Mendelian randomisation analyses
Authors: Burgess Stephen , Sun Yi-Qian , Zhou Ang , Buck Christopher , Mason Amy M , Mai Xiao-Mei 
Published: May 2024

ObjectivesTo estimate the shape of the causal relationship between body mass index (BMI) and mortality risk in a Mendelian randomisation framework.DesignMendelian randomisation analyses of two prospective population-based cohorts.SettingIndividuals of European ancestries living in Norway or the UK.Participants56 150 participants from the Trøndelag Health Study (HUNT) in Norway and 366 385 participants from UK Biobank recruited by postal invitation.OutcomesAll-cause mortality and cause-specific mortality (cardiovascular, cancer, non-cardiovascular non-cancer).ResultsA previously published non-linear Mendelian randomisation analysis of these data using the residual stratification method suggested a J-shaped association between genetically predicted BMI and mortality outcomes with the lowest mortality risk at a BMI of around 25 kg/m2. However, the ‘constant genetic effect’ assumption required by this method is violated. The reanalysis of these data using the more reliable doubly-ranked stratification method provided some indication of a J-shaped relationship, but with much less certainty as there was less precision in estimates at the lower end of the BMI distribution. Evidence for a harmful effect of reducing BMI at low BMI levels was only present in some analyses, and where present, only below 20 kg/m2. A harmful effect of increasing BMI for all-cause mortality was evident above 25 kg/m2, for cardiovascular mortality above 24 kg/m2, for cancer mortality above 30 kg/m2and for non-cardiovascular non-cancer mortality above 26 kg/m2. In UK Biobank, the association between genetically predicted BMI and mortality at high BMI levels was stronger in women than in men.ConclusionThis research challenges findings from previous conventional observational epidemiology and Mendelian randomisation investigations that the lowest level of mortality risk is at a BMI level of around 25 kg/m2. Our results provide some evidence that reductions in BMI will increase mortality risk for a small proportion of the population, and clear evidence that increases in BMI will increase mortality risk for those with BMI above 25 kg/m2.