bluuebunny/crossref_metadata_2025_split huggingface dataset:
The expression of the acarbose biosynthesis gene cluster in Actinoplanes sp. SE50/110 is dependent on the growth phase
Authors: Droste Julian , Ortseifen Vera , Schaffert Lena , Persicke Marcus , Schneiker-Bekel Susanne , Pühler Alfred , Kalinowski Jörn 
Published: November 2020

Abstract
Background
Actinoplanes sp. SE50/110 is the natural producer of the diabetes mellitus drug acarbose, which is highly produced during the growth phase and ceases during the stationary phase. In previous works, the growth-dependency of acarbose formation was assumed to be caused by a decreasing transcription of the acarbose biosynthesis genes during transition and stationary growth phase.

Results
In this study, transcriptomic data using RNA-seq and state-of-the-art proteomic data from seven time points of controlled bioreactor cultivations were used to analyze expression dynamics during growth of Actinoplanes sp. SE50/110. A hierarchical cluster analysis revealed co-regulated genes, which display similar transcription dynamics over the cultivation time. Aside from an expected metabolic switch from primary to secondary metabolism during transition phase, we observed a continuously decreasing transcript abundance of all acarbose biosynthetic genes from the early growth phase until stationary phase, with the strongest decrease for the monocistronically transcribed genes acbA, acbB, acbD and acbE. Our data confirm a similar trend for acb gene transcription and acarbose formation rate.
Surprisingly, the proteome dynamics does not follow the respective transcription for all acb genes. This suggests different protein stabilities or post-transcriptional regulation of the Acb proteins, which in turn could indicate bottlenecks in the acarbose biosynthesis. Furthermore, several genes are co-expressed with the acb gene cluster over the course of the cultivation, including eleven transcriptional regulators (e.g. ACSP50_0424), two sigma factors (ACSP50_0644, ACSP50_6006) and further genes, which have not previously been in focus of acarbose research in Actinoplanes sp. SE50/110.

Conclusion
In conclusion, we have demonstrated, that a genome wide transcriptome and proteome analysis in a high temporal resolution is well suited to study the acarbose biosynthesis and the transcriptional and post-transcriptional regulation thereof.
In silico identification of effector proteins from generalist herbivore Spodoptera litura
Authors: Prajapati Vinod Kumar , Varma Mahendra , Vadassery Jyothilakshmi 
Published: November 2020

Abstract
Background
The common cutworm, Spodoptera litura Fabricius is a leaf and fruit feeding generalist insect of the order Lepidoptera and a destructive agriculture pest. The broad host range of the herbivore is due to its ability to downregulate plant defense across different plants. The identity of Spodoptera litura released effectors that downregulate plant defense are largely unknown. The current study aims to identify genes encoding effector proteins from salivary glands of S. litura (Fab.).

Results
Head and salivary glands of Spodoptera litura were used for de-novo transcriptome analysis and effector prediction. Eight hundred ninety-nine proteins from the head and 330 from salivary gland were identified as secretory proteins. Eight hundred eight proteins from the head and 267 from salivary gland proteins were predicted to be potential effector proteins.

Conclusions
This study is the first report on identification of potential effectors from Spodoptera litura salivary glands.
jouvence, a new human snoRNA involved in the control of cell proliferation
Authors: El-Khoury Flaria , Bignon Jérôme , Martin Jean-René 
Published: November 2020

Abstract
Background
Small nucleolar RNAs (snoRNAs) are non-coding RNAs that are conserved from archaebacteria to mammals. They are associated in the nucleolus, with proteins to form small nucleolar ribonucleoprotein (snoRNPs). They modify ribosomal RNAs, for example, the H/ACA box that converts uridine to pseudouridine. In humans, various pathologies have been associated with snoRNAs, and several snoRNAs have been reported to participate in many cancer processes. Recently, a new H/ACA box snoRNA named jouvence has been identified in Drosophila and has been shown to be involved in lifespan determination in relation to gut homeostasis. Because snoRNAs are conserved through evolution, both structurally and functionally, a jouvence orthologue has been identified in humans. RT-PCR has revealed that jouvence is expressed, suggesting that it might be functional. These results suggest the hypothesis that jouvence may display similar functions, including increasing the healthy lifespan in humans.

Results
Here, we report the characterization of the human snoRNA jouvence, which has not yet been annotated in the genome. We show that its overexpression significantly stimulates cell proliferation, both in various stable cancerous cell lines as well as in primary cells. By contrast, its knockdown by siRNA leads to the opposite phenotype, a rapid decrease in cell proliferation. Transcriptomic analysis (RNA-Seq) revealed that the overexpression of jouvence leads to a dedifferentiation signature of the cells. Conversely, the knockdown of jouvence led to a striking decrease in the expression levels of genes involved in ribosome biogenesis and the spliceosome.

Conclusion
The overexpression of a single and short non-coding RNA of 159 nucleotides, the snoRNA-jouvence, seems to be sufficient to reorient cells toward stemness, while its depletion blocks cell proliferation. In this context, we speculate that the overexpression of jouvence, which appears to be a non-canonical H/ACA snoRNA, could represent a new tool to fight against the deleterious effects of aging, while inversely, its knockdown by siRNA could represent a new approach in cancer therapy.
Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout
Authors: Chapagain Pratima , Walker Donald , Leeds Tim , Cleveland Beth M. , Salem Mohamed 
Published: November 2020

AbstractBackgroundFish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 fish representing an F2 high-muscle genetic line (ARS-FY-H) and 20 fish representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota profiling using the 16S rRNA gene. Significant differences in microbial assemblages between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host.ResultsTukey’s transformed inverse Simpson indices indicated that high muscle yield genetic line (ARS-FY-H) samples have higher microbial diversity compared to those of the low muscle yield genetic line (ARS-FY-L) (LMM, χ2(1) =14.11,p < 0.05). The fecal samples showed statistically distinct structure in microbial assemblages between the genetic lines (F1,36 = 4.7, p < 0.05, R2 = 11.9%). Functional profiling of bacterial operational taxonomic units predicted characteristic functional capabilities of the microbial communities in the high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic line samples.ConclusionThe significant differences of the microbial assemblages between high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic lines indicate a possible effect of genetic selection on the microbial diversity of the host. The functional composition of taxa demonstrates a correlation between bacteria and improving the muscle accretion in the host, probably, by producing various metabolites and enzymes that might aid in digestion. Further research is required to elucidate the mechanisms involved in shaping the microbial community through host genetic selection.
GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data
Authors: Wilkey Andrew P. , Brown Anne V. , Cannon Steven B. , Cannon Ethalinda K. S. 
Published: November 2020

Abstract
Background
Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to thousands of accessions. There is a need for tools to help rapidly explore such datasets, to assess characteristics such as overall differences between accessions and regional anomalies across the genome.

Results
We present GCViT (Genotype Comparison Visualization Tool), for visualizing and exploring large genotyping datasets. GCViT can be used to identify introgressions, conserved or divergent genomic regions, pedigrees, and other features for more detailed exploration. The program can be used online or as a local instance for whole genome visualization of resequencing or SNP array data. The program performs comparisons of variants among user-selected accessions to identify allele differences and similarities between accessions and a user-selected reference, providing visualizations through histogram, heatmap, or haplotype views. The resulting analyses and images can be exported in various formats.

Conclusions
GCViT provides methods for interactively visualizing SNP data on a whole genome scale, and can produce publication-ready figures. It can be used in online or local installations. GCViT enables users to confirm or identify genomics regions of interest associated with particular traits.
GCViT is freely available at https://github.com/LegumeFederation/gcvit. The 1.0 version described here is available at 10.5281/zenodo.4008713.
Genomic analysis of Helicobacter himalayensis sp. nov. isolated from Marmota himalayana
Authors: Hu Shoukui , Niu Lina , Wu Lei , Zhu Xiaoxue , Cai Yu , Jin Dong , Yan Linlin , Zhao Fan 
Published: November 2020

Abstract
Background
Helicobacter himalayensis was isolated from Marmota himalayana in the Qinghai-Tibet Plateau, China, and is a new non-H. pylori species, with unclear taxonomy, phylogeny, and pathogenicity.

Results
A comparative genomic analysis was performed between the H. himalayensis type strain 80(YS1)T and other the genomes of Helicobacter species present in the National Center for Biotechnology Information (NCBI) database to explore the molecular evolution and potential pathogenicity of H. himalayensis. H. himalayensis 80(YS1)T formed a clade with H. cinaedi and H. hepaticus that was phylogenetically distant from H. pylori. The H. himalayensis genome showed extensive collinearity with H. hepaticus and H. cinaedi. However, it also revealed a low degree of genome collinearity with H. pylori. The genome of 80(YS1)T comprised 1,829,936 bp, with a 39.89% GC content, a predicted genomic island, and 1769 genes. Comparatively, H. himalayensis has more genes for functions in “cell wall/membrane/envelope biogenesis” and “coenzyme transport and metabolism” sub-branches than the other compared helicobacters, and its genome contained 42 virulence factors genes, including that encoding cytolethal distending toxin (CDT).

Conclusions
We characterized the H. himalayensis 80(YS1)T genome, its phylogenetic position, and its potential pathogenicity. However, further understanding of the pathogenesis of this potentially pathogenic bacterium is required, which might help to manage H. himalayensis-induced diseases.
Rhamnolipids and surfactin inhibit the growth or formation of oral bacterial biofilm
Authors: Yamasaki Ryota , Kawano Aki , Yoshioka Yoshie , Ariyoshi Wataru 
Published: November 2020

AbstractBackgroundBacteria survive in various environments by forming biofilms. Bacterial biofilms often cause significant problems to medical instruments and industrial processes. Techniques to inhibit biofilm formation are essential and have wide applications. In this study, we evaluated the ability of two types of biosurfactants (rhamnolipids and surfactin) to inhibit growth and biofilm formation ability of oral pathogenic bacteria such asAggregatibacter actinomycetemcomitans,Streptococcus mutans, andStreptococcus sanguinis.ResultsRhamnolipids inhibited the growth and biofilm formation ability of all examined oral bacteria. Surfactin showed effective inhibition againstS. sanguinisATCC10556, but lower effects towardA. actinomycetemcomitansY4 andS. mutansUA159. To corroborate these results, biofilms were observed by scanning electron microscopy (SEM) and confocal microscopy. The observations were largely in concordance with the biofilm assay results. We also attempted to determine the step in the biofilm formation process that was inhibited by biosurfactants. The results clearly demonstrated that rhamnolipids inhibit biofilm formation after the initiation process, however, they do not affect attachment or maturation.ConclusionsRhamnolipids inhibit oral bacterial growth and biofilm formation byA. actinomycetemcomitansY4, and may serve as novel oral drug against localized invasive periodontitis.
Enriched environment ameliorates adult hippocampal neurogenesis deficits in Tcf4 haploinsufficient mice
Authors: Braun Katharina , Häberle Benjamin M. , Wittmann Marie-Theres , Lie D. Chichung 
Published: November 2020

Abstract
Background
Transcription factor 4 (TCF4) has been linked to human neurodevelopmental disorders such as intellectual disability, Pitt-Hopkins Syndrome (PTHS), autism, and schizophrenia. Recent work demonstrated that TCF4 participates in the control of a wide range of neurodevelopmental processes in mammalian nervous system development including neural precursor proliferation, timing of differentiation, migration, dendritogenesis and synapse formation. TCF4 is highly expressed in the adult hippocampal dentate gyrus – one of the few brain regions where neural stem / progenitor cells generate new functional neurons throughout life.

Results
We here investigated whether TCF4 haploinsufficiency, which in humans causes non-syndromic forms of intellectual disability and PTHS, affects adult hippocampal neurogenesis, a process that is essential for hippocampal plasticity in rodents and potentially in humans. Young adult Tcf4 heterozygote knockout mice showed a major reduction in the level of adult hippocampal neurogenesis, which was at least in part caused by lower stem/progenitor cell numbers and impaired maturation and survival of adult-generated neurons. Interestingly, housing in an enriched environment was sufficient to enhance maturation and survival of new neurons and to substantially augment neurogenesis levels in Tcf4 heterozygote knockout mice.

Conclusion
The present findings indicate that haploinsufficiency for the intellectual disability- and PTHS-linked transcription factor TCF4 not only affects embryonic neurodevelopment but impedes neurogenesis in the hippocampus of adult mice. These findings suggest that TCF4 haploinsufficiency may have a negative impact on hippocampal function throughout adulthood by impeding hippocampal neurogenesis.
Autistic traits are associated with the functional connectivity of between—but not within—attention systems in the general population
Authors: Yoshimura Sayaka , Kobayashi Kei , Ueno Tsukasa , Miyagi Takashi , Oishi Naoya , Murai Toshiya , Fujiwara Hironobu 
Published: November 2020

AbstractBackgroundPrevious studies have demonstrated that individuals with autism spectrum disorder (ASD) exhibit dysfunction in the three attention systems (i.e., alerting, orienting, and executive control) as well as atypical relationships among these systems. Additionally, other studies have reported that individuals with subclinical but high levels of autistic traits show similar attentional tendencies to those observed in ASD. Based on these findings, it was hypothesized that autistic traits would affect the functions and relationships of the three attention systems in a general population. Resting-state functional magnetic resonance imaging (fMRI) was performed in 119 healthy adults to investigate relationships between autistic traits and within- and between-system functional connectivity (FC) among the three attention systems. Twenty-six regions of interest that were defined as components of the three attention systems by a previous task-based fMRI study were examined in terms of within- and between-system FC. We assessed autistic traits using the Autism-Spectrum Quotient.ResultsCorrelational analyses revealed that autistic traits were significantly correlated with between-system FC, but not with within-system FC.ConclusionsOur results imply that a high autistic trait level, even when subclinical, is associated with the way the three attention systems interact.
Identification and validation of quantitative trait loci for kernel traits in common wheat (Triticum aestivum L.)
Authors: Liu Hong , Zhang Xiaotao , Xu Yunfeng , Ma Feifei , Zhang Jinpeng , Cao Yanwei , Li Lihui , An Diaoguo 
Published: November 2020

AbstractBackgroundKernel weight and morphology are important traits affecting cereal yields and quality. Dissecting the genetic basis of thousand kernel weight (TKW) and its related traits is an effective method to improve wheat yield.ResultsIn this study, we performed quantitative trait loci (QTL) analysis using recombinant inbred lines derived from the cross ‘PuBing3228 × Gao8901’ (PG-RIL) to dissect the genetic basis of kernel traits. A total of 17 stable QTLs related to kernel traits were identified, notably, two stable QTLsQTkw.cas-1A.2andQTkw.cas-4Aexplained the largest portion of the phenotypic variance for TKW and kernel length (KL), and the other two stable QTLsQTkw.cas-6A.1andQTkw.cas-7D.2contributed more effects on kernel width (KW). Conditional QTL analysis revealed that the stable QTLs for TKW were mainly affected by KW. The QTLsQTkw.cas-7D.2andQKw.cas-7D.1associated with TKW and KW were delimited to the physical interval of approximately 3.82 Mb harboring 47 candidate genes. Among them, the candidate geneTaFT-D1had a 1 bp insertions/deletion (InDel) within the third exon, which might be the reason for diversity in TKW and KW between the two parents. A Kompetitive Allele-Specific PCR (KASP) marker ofTaFT-D1allele was developed and verified by PG-RIL and a natural population consisted of 141 cultivar/lines. It was found that the favorableTaFT-D1 (G)-allelehas been positively selected during Chinese wheat breeding. Thus, these results can be used for further positional cloning and marker-assisted selection in wheat breeding programs.ConclusionsSeventeen stable QTLs related to kernel traits were identified. The stable QTLs for thousand kernel weight were mainly affected by kernel width.TaFT-D1could be the candidate gene for QTLsQTkw.cas-7D.2andQKw.cas-7D.1.
What is the role of locoregional anesthesia in breast surgery? A systematic literature review focused on pain intensity, opioid consumption, adverse events, and patient satisfaction
Authors: Sansone Pasquale , Giaccari Luca Gregorio , Faenza Mario , Di Costanzo Pasquale , Izzo Sara , Aurilio Caterina , Coppolino Francesco , Passavanti Maria Beatrice , Pota Vincenzo , Pace Maria Caterina 
Published: November 2020

AbstractBackgroundBreast surgery in the United States is common. Pain affects up to 50% of women undergoing breast surgery and can interfere with postoperative outcomes. General anesthesia is the conventional, most frequently used anaesthetic technique. Various locoregional anesthetic techniques are also used for breast surgeries. A systematic review of the use of locoregional anesthesia for postoperative pain in breast surgery is needed to clarify its role in pain management.ObjectivesTo systematically review literature to establish the efficacy and the safety of locoregional anesthesia used in the treatment of pain after breast surgery.MethodsEmbase, MEDLINE, Google Scholar and Cochrane Central Trials Register were systematically searched in Mars 2020 for studies examining locoregional anesthesia for management of pain in adults after breast surgery. The methodological quality of the studies and their results were appraised using the Consensus-based Standards for the Selection of Health Measurement Instruments (COSMIN) checklist and specific measurement properties criteria, respectively.ResultsNineteen studies evaluating locoregional anesthesia were included: 1058 patients underwent lumpectomy/mastectomy, 142 breast augmentation and 79 breast reduction. Locoregional anesthesia provides effective anesthesia and analgesia in the perioperative setting, however no statistically significant difference emerged if compared to other techniques. For mastectomy only, the use of locoregional techniques reduces pain in the first hour after the end of the surgery if compared to other procedures (p = 0.02). Other potentially beneficial effects of locoregional anesthesia include decreased need for opioids, decreased postoperative nausea and vomiting, fewer complications and increased patient satisfaction. All this improves postoperative recovery and shortens hospitalization stay. In none of these cases, locoregional anesthesia was statistically superior to other techniques.ConclusionThe results of our review showed no differences between locoregional anesthesia and other techniques in the management of breast surgery. Locoregional techniques are superior in reducing pain in the first hour after mastectomy.
C-reactive protein concentration as a risk predictor of mortality in intensive care unit: a multicenter, prospective, observational study
Authors: Qu Rong , Hu Linhui , Ling Yun , Hou Yating , Fang Heng , Zhang Huidan , Liang Silin , He Zhimei , Fang Miaoxian , Li Jiaxin , Li Xu , Chen Chunbo 
Published: November 2020

AbstractBackgroundIt is not clear whether there are valuable inflammatory markers for prognosis judgment in the intensive care unit (ICU). We therefore conducted a multicenter, prospective, observational study to evaluate the prognostic role of inflammatory markers.MethodsThe clinical and laboratory data of patients at admission, including C-reactive protein (CRP), were collected in four general ICUs from September 1, 2018, to August 1, 2019. Multivariate logistic regression was used to identify factors independently associated with nonsurvival. The area under the receiver operating characteristic curve (AUC-ROC), net reclassification improvement (NRI), and integrated discrimination improvement (IDI) were used to evaluate the effect size of different factors in predicting mortality during ICU stay. 3 -knots were used to assess whether alternative cut points for these biomarkers were more appropriate.ResultsA total of 813 patients were recruited, among whom 121 patients (14.88%) died during the ICU stay. The AUC-ROC values of PCT and CRP for discriminating ICU mortality were 0.696 (95% confidence interval [CI], 0.650–0.743) and 0.684 (95% CI, 0.633–0.735), respectively. In the multivariable analysis, only APACHE II score (odds ratio, 1.166; 95% CI, 1.129–1.203;P = 0.000) and CRP concentration > 62.8 mg/L (odds ratio, 2.145; 95% CI, 1.343–3.427;P = 0.001), were significantly associated with an increased risk of ICU mortality. Moreover, the combination of APACHE II score and CRP > 62.8 mg/L significantly improved risk reclassification over the APACHE II score alone, with NRI (0.556) and IDI (0.013). Restricted cubic spline analysis confirmed that CRP concentration > 62.8 mg/L was the optimal cut-off value for differentiating between surviving and nonsurviving patients.ConclusionCRP markedly improved risk reclassification for prognosis prediction.