bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp
Authors: Pinto Renan Terassi , Freitas Natália Chagas , Máximo Wesley Pires Flausino , Cardoso Thiago Bergamo , Prudente Débora de Oliveira , Paiva Luciano Vilela 
Published: November 2019

AbstractBackgroundCoffee production relies on plantations with varieties fromCoffea arabicaandCoffea canephoraspecies. The first, the most representative in terms of coffee consumption, is mostly propagated by seeds, which leads to management problems regarding the plantations maintenance, harvest and processing of grains. Therefore, an efficient clonal propagation process is required for this species cultivation, which is possible by reaching a scalable and cost-effective somatic embryogenesis protocol. A key process on somatic embryogenesis induction is the auxin homeostasis performed by Gretchen Hagen 3 (GH3) proteins through amino acid conjugation. In this study, theGH3family members were identified onC. canephoragenome, and by performing analysis related to gene and protein structure and transcriptomic profile on embryogenic tissues, we point aGH3gene as a potential regulator of auxin homeostasis during early somatic embryogenesis inC. arabicaplants.ResultsWe have searched within the publishedC. canephoragenome and found 17GH3family members. We checked the conserved domains for GH3 proteins and clustered the members in three main groups according to phylogenetic relationships. We identified amino acids sets in four GH3 proteins that are related to acidic amino acid conjugation to auxin, and using a transcription factor (TF) network approach followed by RT-qPCR we analyzed their possible transcriptional regulators and expression profiles in cells with contrasting embryogenic potential inC. arabica. TheCaGH3.15expression pattern is the most correlated with embryogenic potential and withCaBBM, aC. arabicaortholog of a major somatic embryogenesis regulator.ConclusionTherefore, one out of theGH3members may be influencing on coffee somatic embryogenesis by auxin conjugation with acidic amino acids, which leads to the phytohormone degradation. It is an indicative that this gene can serve as a molecular marker for coffee cells with embryogenic potential and needs to be further studied on how much determinant it is for this process. This work, together with future studies, can support the improvement of coffee clonal propagation through in vitro derived somatic embryos.
Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale
Authors: Vila Nova Meryl , Durimel Kévin , La Kévin , Felten Arnaud , Bessières Philippe , Mistou Michel-Yves , Mariadassou Mahendra , Radomski Nicolas 
Published: November 2019

AbstractBackgroundSalmonella entericasubsp.enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440Salmonellagenomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv).ResultsBased on a genome dataset includingSalmonellaserovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively.ConclusionsOur results suggest that the genetic and metabolic determinants ofSalmonellaadaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.
Transcriptome analysis reveals a positive effect of brassinosteroids on the photosynthetic capacity of wucai under low temperature
Authors: Zhao Mengru , Yuan Lingyun , Wang Jie , Xie Shilei , Zheng Yushan , Nie Libing , Zhu Shidong , Hou Jinfeng , Chen Guohu , Wang Chenggang 
Published: November 2019

Abstract

Background
Brassinosteroids (BRs) have a positive effect on many processes during plant growth and development, and in response to various abiotic stressors. Low-temperature (LT) stress constricts the geographic distribution, growth, and development of wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen). However, there is little information on the global gene expression of BRs under LT stress in wucai. In this study, the molecular roles of 24-epibrassinolide (EBR) after exogenously application, were explored by RNA sequencing under LT conditions.

Results
According to the Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, photosynthesis was significantly enriched after spraying EBR under LT. The transcripts encoding the photosystem II (PSII) oxygen-evolving enhancer protein, photosystem I (PSI) subunit, light-harvesting chlorophyll protein complexes I and II, and ferredoxin were up-regulated after the application of EBR. Transcripts encoding several key enzymes involved in chlorophyll biosynthesis were also up-regulated, accompanied by significant differences in the contents of 5-aminolevulinic acid (ALA), porphobilinogen (PBG), protoporphyrin IX (Proto IX), Mg-protoporphyrin IX (Mg-proto IX), protochlorophyllide (Pchl), and photosynthetic pigments. Notably, transcriptional and physiological analyses revealed that under LT stress, plant responses to EBR involved a major reorientation of photosynthesis, as well as porphyrin and chlorophyll metabolism.

Conclusion
This study explored the role of EBR as an LT stress tolerance mechanism in wucai. At the transcription level, LT tolerance manifests as an enhancement of photosynthesis, and the amelioration of porphyrin and chlorophyll metabolism.
Sex- and tissue-specific transcriptome analyses and expression profiling of olfactory-related genes in Ceracris nigricornis Walker (Orthoptera: Acrididae)
Authors: Yuan Hao , Chang Huihui , Zhao Lina , Yang Chao , Huang Yuan 
Published: November 2019

Abstract

Background
The sophisticated insect olfactory system plays an important role in recognizing external odors and enabling insects to adapt to environment. Foraging, host seeking, mating, ovipositing and other forms of chemical communication are based on olfaction, which requires the participation of multiple olfactory genes. The exclusive evolutionary trend of the olfactory system in Orthoptera insects is an excellent model for studying olfactory evolution, but limited olfaction research is available for these species. The olfactory-related genes of Ceracris nigricornis Walker (Orthoptera: Acrididae), a severe pest of bamboos, have not yet been reported.

Results
We sequenced and analyzed the transcriptomes from different tissues of C. nigricornis and obtained 223.76 Gb clean data that were assembled into 43,603 unigenes with an N50 length of 2235 bp. Among the transcripts, 66.79% of unigenes were annotated. Based on annotation and tBLASTn results, 112 candidate olfactory-related genes were identified for the first time, including 20 odorant-binding proteins (OBPs), 10 chemosensory-binding proteins (CSPs), 71 odorant receptors (ORs), eight ionotropic receptors (IRs) and three sensory neuron membrane proteins (SNMPs). The fragments per kilobase per million mapped fragments (FPKM) values showed that most olfactory-related differentially expressed genes (DEGs) were enriched in the antennae, and these results were confirmed by detecting the expression of olfactory-related genes with quantitative real-time PCR (qRT-PCR). Among these antennae-enriched genes, some were sex-biased, indicating their different roles in the olfactory system of C. nigricornis.

Conclusions
This study provides the first comprehensive list and expression profiles of olfactory-related genes in C. nigricornis and a foundation for functional studies of these olfactory-related genes at the molecular level.
Saccharomyces boulardii alleviates ulcerative colitis carcinogenesis in mice by reducing TNF-α and IL-6 levels and functions and by rebalancing intestinal microbiota
Authors: Wang Chunsaier , Li Wenbin , Wang Hongying , Ma Yiming , Zhao Xinhua , Zhang Xudong , Yang Hong , Qian Jiaming , Li Jingnan 
Published: November 2019

Abstract

Background and Aims
To explore the inhibition mechanism of Saccharomyces boulardii (S. boulardii) on ulcerative colitis (UC) carcinogenesis.

Methods
C57BL/6 mice were treated with azoxymethane and dextran sulfate sodium (AOM/DSS) to develop a UC carcinogenesis model. The treatment group was lavaged with S. boulardii (5 × 107 CFU/d) for 12 weeks. The mice were sacrificed and the tumor load in the treatment group was compared with that of a control group. The levels of TNF-α and IL-6 in colon tissue were measured by enzyme-linked immunosorbent assays. The influence of S. boulardii on TNF-α and IL-6 regulation was also investigated using different colon cell lines. Differences in intestinal microbiota in both stool and intestinal mucosa samples were assessed using 16S rDNA sequencing.

Results
S. boulardii treatment reduced AOM/DSS-induced UC carcinogenesis in mice, as indicated by the reduced tumor load and reduced TNF-α and IL-6 levels in vivo, as well its effects on TNF-α and IL-6 activities in vitro. Significant changes in both fecal and mucosal microbiota were observed among the control, the AOM/DSS treated, and AOM/DSS plus S. boulardii treated groups. For fecal microbiota, the AOM/DSS treated group was lower in Lactobacillus, but higher in Oscillibacter and Lachnoclostridium than the control group. After intervention with S. boulardii, the percentage of Bacillus and Lactococcus increased, but Lachnoclostridium, Oscillibacter, Bacteroides, and Pseudomonas decreased. For the intestinal mucosal microbiota, the AOM/DSS treated group was lower in Bifidobacterium and Ruminococcaceae_UCG-014 and higher in Alloprevotella than the control group. After S. boulardii exposure, the percentage contributions of Lachnoclostridium and Lachnospiraceae_NK4A136 increased.

Conclusions
S. boulardii effectively reduced UC carcinogenesis in an AOM/DSS induced mice model. This positive result can likely be attributed to the reduction of TNF-α and IL-6 levels or the blockade of their function combined with alterations to the intestinal microbiota.
Elucidating the role of shikimate dehydrogenase in controlling the production of anthocyanins and hydrolysable tannins in the outer peels of pomegranate
Authors: Habashi Rida , Hacham Yael , Dhakarey Rohit , Matityahu Ifat , Holland Doron , Tian Li , Amir Rachel 
Published: November 2019

Abstract

Background
The outer peels of pomegranate (Punica granatum L.) possess two groups of polyphenols that have health beneficial properties: anthocyanins (ATs, which also affect peel color); and hydrolysable tannins (HTs). Their biosynthesis intersects at 3-dehydroshikimate (3-DHS) in the shikimate pathway by the activity of shikimate dehydrogenase (SDH), which converts 3-DHS to shikimate (providing the precursor for AT biosynthesis) or to gallic acid (the precursor for HTs biosynthesis) using NADPH or NADP+ as a cofactor. The aim of this study is to gain more knowledge about the factors that regulate the levels of HTs and ATs, and the role of SDH.

Results
The results have shown that the levels of ATs and HTs are negatively correlated in the outer fruit peels of 33 pomegranate accessions, in the outer peels of two fruits exposed to sunlight, and in those covered by paper bags. When calli obtained from the outer fruit peel were subjected to light/dark treatment and osmotic stresses (imposed by different sucrose concentrations), it was shown that light with high sucrose promotes the synthesis of ATs, while dark at the same sucrose concentration promotes the synthesis of HTs. To verify the role of SDH, six PgSDHs (PgSDH1, PgSDH3–1,2, PgSDH3a-1,2 and PgSDH4) were identified in pomegranate. The expression of PgSDH1, which presumably contributes to shikimate biosynthesis, was relatively constant at different sucrose concentrations. However, the transcript levels of PgSDH3s and PgSDH4 increased with the accumulation of gallic acid and HTs under osmotic stress, which apparently accumulates to protect the cells from the stress.

Conclusions
The results strongly suggest that the biosynthesis of HTs and ATs competes for the same substrate, 3-DHS, and that SDH activity is regulated not only by the NADPH/NADP+ ratio, but also by the expression of the PgSDHs. Since the outer peel affects the customer’s decision regarding fruit consumption, such knowledge could be utilized for the development of new genetic markers for breeding pomegranates having higher levels of both ATs and HTs.
Studies on genome size estimation, chromosome number, gametophyte development and plant morphology of salt-tolerant halophyte Suaeda salsa
Authors: Cheng Yan , Yang Pan , Zhao Lihua , Priyadarshani S. V. G. N. , Zhou Qiao , Li Zeyun , Li Weimin , Xiong Junjie , Lin Zhibin , Li Li , Huang Xinyu , Liu Jindian , Aslam Mohammad , Zhao Heming , Li Gang , Ma Jinbiao , Li Lei , Qin Yuan 
Published: November 2019

Abstract

Background
Soil salinization and alkalization are among the major agricultural threats that affect crop productivity worldwide, which are increasing day by day with an alarming rate. In recent years, several halophytes have been investigated for their utilization in soil remediation and to decipher the mechanism of salt-tolerance in these high salt tolerant genetic repositories. Suaeda salsa is an annual halophytic herb in the family Amaranthaceae, displaying high salt and alkali-resistance and having nutritive value. However, the fundamental biological characteristics of this valuable plant remain to be elucidated until today.

Results
In this study, we observed the morphology and development of Suaeda salsa, including seed morphology, seed germination, plant morphology, and flower development. Using microscopy, we observed the male and female gametophyte developments of Suaeda salsa. Also, chromosome behaviour during the meiosis of male gametophyte was studied. Eventually, the genome size of Suaeda salsa was estimated through flow cytometry using Arabidopsis as reference.

Conclusions
Our findings suggest that the male and female gametophyte developments of Suaeda salsa are similar to those of the model plant Arabidopsis, and the diploid Suaeda salsa contains nine pairs of chromosomes. The findings also indicate that the haploid genome of Suaeda salsa is approximately 437.5 MB. The observations and results discussed in this study will provide an insight into future research on Suaeda salsa.
WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat
Authors: Cram Dustin , Kulkarni Manoj , Buchwaldt Miles , Rajagopalan Nandhakishore , Bhowmik Pankaj , Rozwadowski Kevin , Parkin Isobel A. P. , Sharpe Andrew G. , Kagale Sateesh 
Published: November 2019

Abstract

Background
CRISPR/Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement.

Description
We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat. A collaborative study between the Broad Institute and Microsoft Research used large-scale empirical evidence to devise algorithms (Doech et al., 2016, Nature Biotechnology 34, 184–191) for predicting the on-target activity and off-target potential of CRISPR/SpCas9 (Streptococcus pyogenes Cas9). We applied these prediction models to determine on-target specificity and potential off-target activity for individual gRNAs targeting specific loci in the wheat genome. The genome-wide gRNA mappings and the corresponding Doench scores predictive of the on-target and off-target activities were used to create a gRNA database which was used as a data source for the web application termed WheatCRISPR.

Conclusion
The WheatCRISPR tool allows researchers to browse all possible gRNAs targeting a gene or sequence of interest and select effective gRNAs based on their predicted high on-target and low off-target activity scores, as well as other characteristics such as position within the targeted gene. It is publicly available at https://crispr.bioinfo.nrc.ca/WheatCrispr/.
Induction techniques that reduce redistribution hypothermia: a prospective, randomized, controlled, single blind effectiveness study
Authors: Roth Jonathan V. , Braitman Leonard E. , Hunt Lacy H. 
Published: November 2019

AbstractBackgroundWhile much effort has been devoted to correcting intraoperative hypothermia, less attention has been directed to preventing redistribution hypothermia. In this study, we compared three different anesthetic induction techniques to standard IV propofol inductions (control) in their effect on reducing redistribution hypothermia.MethodsElective, afebrile patients, age 18 to 55 years, were randomly assigned to one of four groups (n = 50 each). Group “INH/100” was induced with 8% sevoflurane in 100% oxygen, Group “INH/50” with 8% sevoflurane in 50% oxygen and 50% nitrous oxide, Group “PROP” with 2.2 mg/kg propofol, and Group “Phnl/PROP” with 2.2 mg/kg propofol immediately preceded by 160 mcg phenylephrine. Patients were maintained with sevoflurane in 50% nitrous oxide and 50% oxygen in addition to opioid narcotic. Forced air warming was used. Core temperatures were recorded every 15 min after induction for 1 h.ResultsCompared to control group PROP, the mean temperatures in groups INH/100, INH/50, and Phnl/PROP were higher 15, 30, 45 and 60 min after induction (p < 0.001 for all comparisons), averaging between 0.39 °C and 0.54 °C higher. In group PROP, 60% of patients had at least one temperature below 36.0 °C in the first hour whereas only 16% did in each of groups INH/100, INH/50, and Phnl/PROP (p < 0.0001 in each group compared to PROP).ConclusionsIn this effectiveness trial, inhalation inductions with sevoflurane or with prophylactic phenylephrine bolus prior to propofol induction reduced the magnitude of redistribution hypothermia by an average of 0.4 to 0.5 °C in patients aged 18 to 55 years.Trial registrationRetrospectively registered on clinical-trials.gov asNCT02331108, November 20, 2014.
Thrombelastometry guided blood-component therapy after cardiac surgery: a randomized study
Authors: Haensig Martin , Kempfert Joerg , Kempfert Pia-Maria , Girdauskas Evaldas , Borger Michael Andrew , Lehmann Sven 
Published: November 2019

AbstractBackgroundSignificant bleeding is a well known complication after cardiac surgical procedures and is associated with worse outcome. Thrombelastometry (ROTEM®) allows point-of-care testing of the coagulation status but only limited data is available yet. The aim was to evaluate the ROTEM®-guided blood component therapy in a randomized trial.MethodsIn case of significant postoperative bleeding (> 200 ml/h) following elective isolated or combined cardiac surgical procedures (including 14% re-do procedures and 4% requiring circulatory arrest) patients were randomized to either a 4-chamber ROTEM®-guided blood-component transfusion protocol or received treatment guided by an algorithm based on standard coagulation testing (control). One hundred four patients (mean age: 67.2 ± 10.4 years, mean log. EuroSCORE 7.0 ± 8.8%) met the inclusion criteria. Mean CPB-time was 112.1 ± 55.1 min., mean cross-clamp time 72.5 ± 39.9 min.ResultsBaseline demographics were comparable in both groups. Overall there was no significant difference in transfusion requirements regarding red blood cells, platelets, plasma, fibrinogen or pooled factors and the re-thoracotomy rate was comparable (ROTEM®: 29% vs. control: 25%). However, there was a trend towards less 24-h drainage loss visible in the ROTEM®-group (ROTEM®: 1599.1 ± 834.3 ml vs. control: 1867.4 ± 827.4 ml;p = 0.066). In the subgroup of patients with long CPB-times (> 115 min.;n = 55) known to exhibit an increased risk for diffuse coagulopathy ROTEM®-guided treatment resulted in a significantly lower 24-h drainage loss (ROTEM®: 1538.2 ± 806.4 ml vs. control: 2056.8 ± 974.5 ml;p = 0.032) and reduced 5-year mortality (ROTEM®: 0% vs. control: 15%;p = 0.03).ConclusionIn case of postoperative bleeding following cardiac surgical procedures a treatment algorithm based on “point-of-care” 4-chamber ROTEM® seems to be at least as effective as standard therapy. In patients with long CPB-times ROTEM®-guided treatment may result in less bleeding, a marked reduction in costs and long-term mortality.Trial registrationGerman Clinical Trials Register, TRN:DRKS00017367, date of registration: 05.06.2019, ‘retrospectively registered’.
A case report: a giant cardiac atypical lipoma associated with pericardium and right atrium
Authors: Wang Xin , Yu Xiaona , Ren Weidong , Li Dongyu 
Published: November 2019

Abstract

Background
Among primary cardiac tumors, atypical lipoma is very rare. In particular, cases with lipomas in both the pericardium and the atria are even rare.

Case presentation
We report the case of a 49-year-old male patient presented to our department because of chest pain. Echocardiography revealed two large masses in both the pericardium and the right atrium. Then the tumors were completely resected and the histopathological examination revealed atypical lipoma. The patient recovered well without any complication and discharged from hospital.

Conclusions
We report a very rare case of a huge atypical lipomas located on the pericardium and right atrium. These tumors were easily detected by echocardiography and final diagnosed after surgical resection and pathological examination.