bluuebunny/crossref_metadata_2025_split huggingface dataset:
iPseU-NCP: Identifying RNA pseudouridine sites using random forest and NCP-encoded features
Authors: Nguyen-Vo Thanh-Hoang , Nguyen Quang H. , Do Trang T.T. , Nguyen Thien-Ngan , Rahardja Susanto , Nguyen Binh P. 
Published: December 2019

Abstract
Background
Pseudouridine modification is most commonly found among various kinds of RNA modification occurred in both prokaryotes and eukaryotes. This biochemical event has been proved to occur in multiple types of RNAs, including rRNA, mRNA, tRNA, and nuclear/nucleolar RNA. Hence, gaining a holistic understanding of pseudouridine modification can contribute to the development of drug discovery and gene therapies. Although some laboratory techniques have come up with moderately good outcomes in pseudouridine identification, they are costly and required skilled work experience. We propose iPseU-NCP – an efficient computational framework to predict pseudouridine sites using the Random Forest (RF) algorithm combined with nucleotide chemical properties (NCP) generated from RNA sequences. The benchmark dataset collected from Chen et al. (2016) was used to develop iPseU-NCP and fairly compare its performances with other methods.

Results
Under the same experimental settings, comparing with three state-of-the-art methods including iPseU-CNN, PseUI, and iRNA-PseU, the Matthew’s correlation coefficient (MCC) of our model increased by about 20.0%, 55.0%, and 109.0% when tested on the H. sapiens (H_200) dataset and by about 6.5%, 35.0%, and 150.0% when tested on the S. cerevisiae (S_200) dataset, respectively. This significant growth in MCC is very important since it ensures the stability and performance of our model. With those two independent test datasets, our model also presented higher accuracy with a success rate boosted by 7.0%, 13.0%, and 20.0% and 2.0%, 9.5%, and 25.0% when compared to iPseU-CNN, PseUI, and iRNA-PseU, respectively. For majority of other evaluation metrics, iPseU-NCP demonstrated superior performance as well.

Conclusions
iPseU-NCP combining the RF and NPC-encoded features showed better performances than other existing state-of-the-art methods in the identification of pseudouridine sites. This also shows an optimistic view in addressing biological issues related to human diseases.
Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens)
Authors: Silva-Pereira Taiana T. , Ikuta Cássia Y. , Zimpel Cristina K. , Camargo Naila C. S. , de Souza Filho Antônio F. , Ferreira Neto José S. , Heinemann Marcos B. , Guimarães Ana M. S. 
Published: December 2019

Abstract
Background
Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization.

Results
We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 indels, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation analyses indicate that genes of the VapBC family, a toxin-antitoxin system, and genes related to cell wall remodeling are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations were only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamate, respectively) gene families. We also detected large deletions in ancient and modern M. pinnipedii strains, including a few occurring only in modern strains, indicating a process of genome reduction occurring over the past one thousand years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 deletions may have occurred independently, twice, over the evolutionary course of the MTBC.

Conclusion
The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. Mycobacterium pinnipedii proteomes of the studied isolates showed a high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.
Proximal femoral head transcriptome reveals novel candidate genes related to epiphysiolysis in broiler chickens
Authors: de Oliveira Peixoto Jane , Savoldi Igor Ricardo , Ibelli Adriana Mércia Guaratini , Cantão Maurício Egídio , Jaenisch Fátima Regina Ferreira , Giachetto Poliana Fernanda , Settles Matthew Lee , Zanella Ricardo , Marchesi Jorge Augusto Petroli , Pandolfi José Rodrigo , Coutinho Luiz Lehmann , Ledur Mônica Corrêa 
Published: December 2019

AbstractBackgroundThe proximal femoral head separation (FHS) or epiphysiolysis is a prevalent disorder affecting the chicken femur epiphysis, being considered a risk factor to infection which can cause bacterial chondronecrosis with osteomyelitis in broilers. To identify the genetic mechanisms involved in epiphysiolysis, differentially expressed (DE) genes in the femur of normal and FHS-affected broilers were identified using RNA-Seq technology. Femoral growth plate (GP) samples from 35-day-old commercial male broilers were collected from 4 healthy and 4 FHS-affected broilers. Sequencing was performed using an Illumina paired-end protocol. Differentially expressed genes were obtained using the edgeR package based on the False Discovery Rate (FDR < 0.05).ResultsApproximately 16 million reads/sample were generated with 2 × 100 bp paired-end reads. After data quality control, approximately 12 million reads/sample were mapped to the reference chicken genome (Galgal5). A total of 12,645 genes were expressed in the femur GP. Out of those, 314 were DE between groups, being 154 upregulated and 160 downregulated in FHS-affected broilers. In the functional analyses, several biological processes (BP) were overrepresented. Among them, those related to cell adhesion, extracellular matrix (ECM), bone development, blood circulation and lipid metabolism, which are more related to chicken growth, are possibly involved with the onset of FHS. On the other hand, BP associated to apoptosis or cell death and immune response, which were also found in our study, could be related to the consequence of the FHS.ConclusionsGenes with potential role in the epiphysiolysis were identified through the femur head transcriptome analysis, providing a better understanding of the mechanisms that regulate bone development in fast-growing chickens. In this study, we highlighted the importance of cell adhesion and extracellular matrix related genes in triggering FHS. Furthermore, we have shown new insights on the involvement of lipidemia and immune response/inflammation with FHS in broilers. Understanding the changes in the GP transcriptome might support breeding strategies to address poultry robustness and to obtain more resilient broilers.
Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae – a pathogen of the Brassicaceae family
Authors: Rajarammohan Sivasubramanian , Paritosh Kumar , Pental Deepak , Kaur Jagreet 
Published: December 2019

AbstractBackgroundAlternaria brassicae, a necrotrophic pathogen, causesAlternariaLeaf Spot, one of the economically important diseases ofBrassicacrops. Many otherAlternaria spp.such asA. brassicicolaandA. alternataare known to cause secondary infections in theA. brassicae-infected Brassicas. The genome architecture, pathogenicity factors, and determinants of host-specificity ofA. brassicaeare unknown. In this study, we annotated and characterised the recently announced genome assembly ofA. brassicaeand compared it with otherAlternaria spp.to gain insights into its pathogenic lifestyle.ResultsWe also sequenced the genomes of twoA. alternataisolates that were co-infectingB. junceausing Nanopore MinION sequencing for additional comparative analyses within theAlternariagenus. Genome alignments within theAlternaria spp.revealed high levels of synteny between most chromosomes with some intrachromosomal rearrangements. We show for the first time that the genome ofA. brassicae, a large-sporedAlternariaspecies, contains a dispensable chromosome. We identified 460A. brassicae-specific genes, which included many secreted proteins and effectors. Furthermore, we have identified the gene clusters responsible for the production of Destruxin-B, a known pathogenicity factor ofA. brassicae.ConclusionThe study provides a perspective into the unique and shared repertoire of genes within theAlternariagenus and identifies genes that could be contributing to the pathogenic lifestyle ofA. brassicae.
Gut bacteria of weevils developing on plant roots under extreme desert conditions
Authors: Meng Fengqun , Bar-Shmuel Nitsan , Shavit Reut , Behar Adi , Segoli Michal 
Published: December 2019

Abstract
Background
Many phytophagous insects, whose diet is generally nitrogen-poor, rely on gut bacteria to compensate for nutritional deficits. Accordingly, we hypothesized that insects in desert environments may evolve associations with gut bacteria to adapt to the extremely low nutrient availability. For this, we conducted a systematic survey of bacterial communities in the guts of weevils developing inside mud chambers affixed to plant roots in the Negev Desert of Israel, based on 16S rRNA gene amplicon sequencing.

Results
Our analyses revealed that gut bacterial communities in weevil larvae were similar across a wide geographical range, but differed significantly from those of the mud chambers and of the surrounding soils. Nevertheless, a high proportion of bacteria (including all of the core bacteria) found in the weevils were also detected in the mud chambers and soils at low relative abundances. The genus Citrobacter (of the Enterobacteriaceae family) was the predominant group in the guts of all individual weevils. The relative abundance of Citrobacter significantly decreased at the pupal and adult stages, while bacterial diversity increased. A mini literature survey revealed that members of the genus Citrobacter are associated with nitrogen fixation, recycling of uric acid nitrogen, and cellulose degradation in different insects.

Conclusions
The results suggest that although weevils could potentially acquire their gut bacteria from the soil, weevil host internal factors, rather than external environmental factors, were more important in shaping their gut bacterial communities, and suggest a major role for Citrobacter in weevil nutrition in this challenging environment. This study highlights the potential involvement of gut bacteria in the adaptation of insects to nutritional deficiencies under extreme desert conditions.
Altered functional connectivity of the nucleus accumbens subdivisions in amphetamine-type stimulant abusers: a resting-state fMRI study
Authors: Wang Yun , Yan Kai-Juan , Fan Chen-Xiao , Luo Xiao-Nian , Zhou Yuan 
Published: December 2019

Abstract
Background
The growing abuse of amphetamine-type stimulants leads to new challenges to human health. A possible addiction mechanism has been proposed by altered functional architecture of the nucleus accumbens (NAc) during resting state. NAc contains different subdivisions and they may play different roles in addiction. The aim of the present study was to examine whether there are common or distinct patterns of functional connectivity of the NAc subdivisions in amphetamine-type stimulant abusers (ATSAs).

Methods
The present study recruited 17 male ATSAs and 22 healthy male controls. All the subjects underwent resting-state functional magnetic resonance imaging (fMRI) with their eyes closed. The NAc was divided into core-like and shell-like subdivisions. We used seed-based resting-state functional connectivity (RSFC) analyses to identify differences in brain functional architecture between ATSAs and healthy controls (HCs).

Results
ATSAs had lower positive RSFCs with all of the NAc subdivisions over the left orbital part of superior frontal gyrus and higher positive RSFCs with the NAc subdivisions over the left opercular part of inferior frontal gyrus than HCs, which indicates common abnormalities across the NAc subdivisions in ATSAs. In addition, the RSFCs between the NAc subdivisions and the left orbital part of superior frontal gyrus were negatively correlated with the addiction severity in ATSAs.

Conclusion
These results provide evidence that there are common RSFC patterns of the NAc subdivisions in ATSAs. The abnormality indicated by disrupted functional connectivity between the NAc subdivisions and prefrontal cortex suggests abnormal interaction between the rewarding process and cognitive control in ATSAs. Our results shed insight on the neurobiological mechanisms of ATSA and suggest potential novel therapeutic targets for treatment and intervention of ATSAs.
GmWRKY40, a member of the WRKY transcription factor genes identified from Glycine max L., enhanced the resistance to Phytophthora sojae
Authors: Cui Xiaoxia , Yan Qiang , Gan Shuping , Xue Dong , Wang Haitang , Xing Han , Zhao Jinming , Guo Na 
Published: December 2019

Abstract
Background
The WRKY proteins are a superfamily of transcription factors and members play essential roles in the modulation of diverse physiological processes, such as growth, development, senescence and response to biotic and abiotic stresses. However, the biological roles of the majority of the WRKY family members remains poorly understood in soybean relative to the research progress in model plants.

Results
In this study, we identified and characterized GmWRKY40, which is a group IIc WRKY gene. Transient expression analysis revealed that the GmWRKY40 protein is located in the nucleus of plant cells. Expression of GmWRKY40 was strongly induced in soybean following infection with Phytophthora sojae, or treatment with methyl jasmonate, ethylene, salicylic acid, and abscisic acid. Furthermore, soybean hairy roots silencing GmWRKY40 enhanced susceptibility to P. sojae infection compared with empty vector transgenic roots. Moreover, suppression of GmWRKY40 decreased the accumulation of reactive oxygen species (ROS) and modified the expression of several oxidation-related genes. Yeast two-hybrid experiment combined with RNA-seq analysis showed that GmWRKY40 interacted with 8 JAZ proteins with or without the WRKY domain or zinc-finger domain of GmWRKY40, suggesting there were different interaction patterns among these interacted proteins.

Conclusions
Collectively, these results suggests that GmWRKY40 functions as a positive regulator in soybean plants response to P. sojae through modulating hydrogen peroxide accumulation and JA signaling pathway.
ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea
Authors: Sudan Jebi , Singh Ravinder , Sharma Susheel , Salgotra Romesh K. , Sharma Varun , Singh Gurvinder , Sharma Indu , Sharma Swarkar , Gupta Surinder K. , Zargar Sajad Majeed 
Published: December 2019

AbstractBackgroundNarrow genetic base, complex allo-tetraploid genome and presence of repetitive elements have led the discovery of single nucleotide polymorphisms (SNPs) inBrassica juncea(AABB; 2n = 4x = 36) at a slower pace. Double digest RAD (ddRAD) - a genome complexity reduction technique followed by NGS was used to generate a total of 23 million paired-end reads from three genotypes each of Indian (Pusa Tarak,RSPR-01andUrvashi) and Exotic (Donskaja IV,Zem 1andEC287711) genepools.ResultsSequence data analysis led to the identification of 10,399 SNPs in six genotypes at a read depth of 10x coverage among the genotypes of two genepools. A total of 44 hyper-variable regions (nucleotide variation hotspots) were also found in the genome, of which 93% were found to be a part of coding genes/regions. The functionality of the identified SNPs was estimated by genotyping a subset of SNPs on MassARRAY® platform among a diverse set ofB. junceagenotypes. SNP genotyping-based genetic diversity and population studies placed the genotypes into two distinct clusters based mostly on the place of origin. The genotypes were also characterized for six morphological traits, analysis of which revealed a significant difference in the mean values between Indian and Exotic genepools for six traits. The association analysis for six traits identified a total of 45 significant marker-trait associations on 11 chromosomes of A- and B- group of progenitor genomes.ConclusionsDespite narrow diversity, the ddRAD sequencing was able to identify large number of nucleotide polymorphisms between the two genepools. Association analysis led to the identification of common SNPs/genomic regions associated between flowering and maturity traits, thereby underscoring the possible role of common chromosomal regions-harboring genes controlling flowering and maturity inBrassica juncea.
Identification and characterization analysis of sulfotransferases (SOTs) gene family in cotton (Gossypium) and its involvement in fiber development
Authors: Wang Liyuan , Liu Xiyan , Wang Xiaoyang , Pan Zhaoe , Geng Xiaoli , Chen Baojun , Liu Baoshen , Du Xiongming , Song Xianliang 
Published: December 2019

AbstractBackgroundSulfotransferases (SOTs) (EC 2.8.2.-) play a crucial role in the sulphate conjugation reaction involved in plant growth, vigor, stress resistance and pathogen infection.SOTsin Arabidopsis have been carried out and divided into 8 groups. However, the systematic analysis and functional information ofSOTfamily genes in cotton have rarely been reported.ResultsAccording to the results of BLASTP and HMMER, we isolated 46, 46, 76 and 77SOTgenes in the genomeG. arboreum,G. raimondii,G. barbadenseandG. hirsutum, respectively. A total of 170 in 245SOTswere further classified into four groups based on the orthologous relationships comparing withArabidopsis, and tandem replication primarily contributed to the expansion ofSOTgene family inG. hirsutum. Expression profiles of theGhSOTshowed that most genes exhibited a high level of expression in the stem, leaf, and the initial stage of fiber development. The localization analysis indicated thatGhSOT67expressed in cytoplasm and located in stem and leaf tissue. Additionally, the expression ofGhSOT67were induced and the length of stem and leaf hairs were shortened after gene silencing mediated byAgrobacterium, compared with the blank and negative control plants.ConclusionsOur findings indicated thatSOTgenes might be associated with fiber development in cotton and provided valuable information for further studies ofSOTgenes inGossypium.
Ectopic expression of citrus UDP-GLUCOSYL TRANSFERASE gene enhances anthocyanin and proanthocyanidins contents and confers high light tolerance in Arabidopsis
Authors: Rao Muhammad Junaid , Xu Yuantao , Huang Yue , Tang Xiaomei , Deng Xiuxin , Xu Qiang 
Published: December 2019

Abstract
Background
Citrus fruits are consumed freshly or as juice to directly provide various dietary flavonoids to humans. Diverse metabolites are present among Citrus genera, and many flavonoids biosynthetic genes were induced after abiotic stresses. To better understand the underlying mechanism, we designed experiments to overexpress a UDP-GLUCOSYL TRANSFERASE gene from sweet orange (Citrus sinensis) to evaluate its possible function in metabolism and response to stress.

Results
Our results demonstrated that overexpression of Cs-UGT78D3 resulted in high accumulation of proanthocyanidins in the seed coat and a dark brown color to transgenic Arabidopsis seeds. In addition, the total contents of flavonoid and anthocyanin were significantly enhanced in the leaves of overexpressed lines. Gene expression analyses indicated that many flavonoid (flavonol) and anthocyanin genes were up-regulated by 4–15 folds in transgenic Arabidopsis. Moreover, after 14 days of high light stress, the transgenic Arabidopsis lines showed strong antioxidant activity and higher total contents of anthocyanins and flavonoids in leaves compared with the wild type.

Conclusion
Our study concluded that the citrus Cs-UGT78D3 gene contributes to proanthocyanidins accumulation in seed coats and confers tolerance to high light stress by accumulating the total anthocyanin and flavonoid contents with better antioxidant potential (due to photoprotective activity of anthocyanin) in the transgenic Arabidopsis.
Comparison of videolaryngoscope-guided versus standard digital insertion techniques of the ProSeal™ laryngeal mask airway: a prospective randomized study
Authors: Ozgul Ulku , Erdil Feray Akgul , Erdogan Mehmet Ali , Begec Zekine , Colak Cemil , Yucel Aytac , Durmus Mahmut 
Published: December 2019

AbstractBackgroundThis study were designed to investigate the usefulness of the videolaryngoscope-guided insertion technique compared with the standard digital technique for the insertion success rate and insertion conditions of the Proseal™ laryngeal mask airway (PLMA).MethodsProspective, one hundred and nineteen patients (ASA I–II, aged 18–65 yr) were randomly divided for PLMA insertion using the videolaryngoscope-guided technique or the standard digital technique. The PLMA was inserted according to the manufacturer’s instructions in the standard digital technique group. The videolaryngoscope-guided technique was performed a C-MAC® videolaryngoscope with D-Blade, under gentle videolaryngoscope guidance, the epiglottis was lifted, and the PLMA was advanced until the tip of the distal cuff reached the oesophagus inlet. The number of insertion attempts, insertion time, oropharyngeal leak pressure, leak volume, fiberoptic bronchoscopic view, peak inspiratory pressure, ease of gastric tube placement, hemodynamic changes, visible blood on PLMA and postoperative airway morbidity were recorded.ResultsThe first-attempt success rate (the primary outcome) was higher in the videolaryngoscope-guided technique than in the standard digital technique (p = 0.029). The effect size values with 95% confidence interval were 0.19 (0.01–0.36) for the first and second attempts, 0.09 (− 0.08–0.27) for the first and third attempts, and not computed for the second and third attempts by the groups, respectively.ConclusionVideolaryngoscope-guided insertion technique can be a help in case of difficult positioning of a PLMA and can improve the PLMA performance in some conditions. We suggest that the videolaryngoscope-guided technique may be a useful technique if the digital technique fails.Trial registrationClinicalTrials.govNCT03852589 date of registration: February 22th 2019.