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https://www.readbyqxmd.com/read/28938749/the-testicular-transcriptome-associated-with-spermatogonia-differentiation-initiated-by-gonadotrophin-stimulation-in-the-juvenile-rhesus-monkey-macaca-mulatta
#1
Suresh Ramaswamy, William H Walker, Paula Aliberti, Rahil Sethi, Gary R Marshall, Alyxzandria Smith, Seyedmehdi Nourashrafeddin, Alicia Belgorosky, Uma R Chandran, Mark P Hedger, Tony M Plant
STUDY QUESTION: What is the genetic landscape within the testis of the juvenile rhesus monkey (Macaca mulatta) that underlies the decision of undifferentiated spermatogonia to commit to a pathway of differentiation when puberty is induced prematurely by exogenous LH and FSH stimulation? SUMMARY ANSWER: Forty-eight hours of gonadotrophin stimulation of the juvenile monkey testis resulted in the appearance of differentiating B spermatogonia and the emergence of 1362 up-regulated and 225 down-regulated testicular mRNAs encoding a complex network of proteins ranging from enzymes regulating Leydig cell steroidogenesis to membrane receptors, and from juxtacrine and paracrine factors to transcriptional factors governing spermatogonial stem cell fate...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28936220/de-novo-assembly-of-the-camellia-nitidissima-transcriptome-reveals-key-genes-of-flower-pigment-biosynthesis
#2
Xingwen Zhou, Jiyuan Li, Yulin Zhu, Sui Ni, Jinling Chen, Xiaojuan Feng, Yunfeng Zhang, Shuangquan Li, Hongguang Zhu, Yuanguang Wen
The golden camellia, Camellia nitidissima Chi., is a well-known ornamental plant that is known as "the queen of camellias" because of its golden yellow flowers. The principal pigments in the flowers are carotenoids and flavonol glycosides. Understanding the biosynthesis of the golden color and its regulation is important in camellia breeding. To obtain a comprehensive understanding of flower development in C. nitidissima, a number of cDNA libraries were independently constructed during flower development. Using the Illumina Hiseq2500 platform, approximately 71...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28935979/intergrative-metabolomic-and-transcriptomic-analyses-unveil-nutrient-remobilization-events-in-leaf-senescence-of-tobacco
#3
Wei Li, Hailiang Zhang, Xiaoxu Li, Fengxia Zhang, Cheng Liu, Yongmei Du, Xiaoming Gao, Zenglin Zhang, Xiaobing Zhang, Zhihui Hou, Hui Zhou, Xiaofei Sheng, Guodong Wang, Yongfeng Guo
Leaf senescence in plants is a coordinated process that involves remobilization of nutrients from senescing leaves to sink tissues. The molecular events associated with nutrient remobilization are however not well understood. In this study the tobacco system with a source-sink relationship between different leaf positions was used in analyzing the spatiotemporal changes of 76 metabolites from leaves at 3 different stalk positions and 8 developmental stages. The metabolomic data was then compared with RNA-seq data from the same samples to analyze the activities of the metabolic pathways that are important for nutrient remobilization...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935950/transcriptome-analyses-suggest-a-novel-hypothesis-for-whitefly-adaptation-to-tobacco
#4
Wen-Qiang Xia, Xin-Ru Wang, Yan Liang, Shu-Sheng Liu, Xiao-Wei Wang
The adaptation of herbivorous insects to various host plants facilitates the spread and outbreak of many important invasive pests, however, the molecular mechanisms that underneath this process are poorly understood. In the past three decades, two species of the whitefly Bemisia tabaci complex, Middle East-Asia Minor 1 and Mediterranean, have invaded many countries. Their rapid and widespread invasions are partially due to their ability to infest a wide range of host plants. In this study, we determined the transcriptome and phenotypic changes of one Mediterranean whitefly population during its adaptation to tobacco, an unsuitable host plant...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935260/insights-of-lr28-mediated-wheat-leaf-rust-resistance-transcriptomic-approach
#5
Dharmendra Singh, Dhananjay Kumar, Lopamudra Satapathy, Jyoti Pathak, Saket Chandra, Adnan Riaz, Govindraj Bhaganagre, Raman Dhariwal, Manish Kumar, Kumble Vinod Prabhu, Harindra Singh Balyan, Pushpendra Kumar Gupta, Kunal Mukhopadhyay
Leaf rust is a fungal disease that causes severe yield losses in wheat. Resistant varieties with major and quantitative resistance genes are the most effective method to control the disease. However, the main problem is inadequate information for understanding resistance mechanism and its usefulness. This paper presents Lr28 mediated genome-wide response of known and unknown genes during wheat-Puccinia triticina interaction. In this study, we prepared Serial Analysis of Gene Expression (SAGE) libraries using seedling wheat mRNA for infected and mock conditions...
September 18, 2017: Gene
https://www.readbyqxmd.com/read/28934298/transcriptome-analysis-of-callery-pear-pyrus-calleryana-reveals-a-comprehensive-signalling-network-in-response-to-alternaria-alternata
#6
Jialiang Kan, Tingli Liu, Na Ma, Hui Li, Xiaogang Li, Jinyan Wang, Baolong Zhang, Youhong Chang, Jing Lin
The pear is an important temperate fruit worldwide that is produced by a group of species in the genus Pyrus. Callery pear (Pyrus calleryana Decne) is characterized by high resistance to multiple diseases, good adaptability, and high ornamental value, and is therefore widely planted in pear orchards for edible fruit production or as stock. Plant pathogens are a major threat to pear yield. Black spot disease, caused by the filamentous fungus Alternaria alternata, is one of the most serious diseases in pear. Elucidation of resistant genes to black spot disease is extremely important for understanding the underlying mechanisms as well as for the development of resistant cultivars...
2017: PloS One
https://www.readbyqxmd.com/read/28933084/-cloning-and-bioinformatics-analysis-of-1-hydroxy-2-methyl-2-e-butenyl-4-diphosphate-reductase%C3%AF-pchdr1%C3%AF-gene-in-phlegmarirus-carinatus
#7
Zhi-Li Zhang, Hai-Zhou Lv, Xu Guo, Liu He, Jing-Yuan Song, Chao Sun, Hong-Mei Luo
The open reading frame of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (HDR) was cloned from Phlegmarirus carinatus by RT-PCR method and the sequence was analyzed by bioinformatics tools. After searching the transcriptome dataset of P. carinatus, one unique sequence encoding 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase was discovered. The primers were designed according to the cDNA sequence of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase from the dataset. And then, the open reading frame (ORF) of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase, named as PcHDR1 (GenBank Accession number:JQ957845), was cloned by RT-PCR strategy with the template of mixed RNA extracted from roots, stem and leaf of P...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28933079/-advance-in-transcriptomic-studies-of-ginseng-species
#8
Li-Qiu Zou, Xue-Jun Kuang, Ying Li, Chao Sun
There are many valuable medicinal plants in Ginseng genus belonging to Araliaceae. Among them, Panax ginseng, P. quinquefolium and P. notoginseng are the most famous species. With the development of next-generation sequencing (NGS) technologies, sequencing and analysis of transcriptomes have become powerful tools for discovery of novel genes, screening molecular markers and elucidation of specific biosynthetic pathway of secondary metabolites. Their transcriptomes provided abundant genes for further study on functional genomics...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28933072/-metabolomics-research-of-medicinal-plants
#9
Li-Xin Duan, Yun-Tao Dai, Chao Sun, Shi-Lin Chen
Metabolomics is the comprehensively study of chemical processes involving small molecule metabolites. It is an important part of systems biology, and is widely applied in complex traditional Chinese medicine(TCM)system. Metabolites biosynthesized by medicinal plants are the effective basis for TCM. Metabolomics studies of medicinal plants will usher in a new period of vigorous development with the implementation of Herb Genome Program and the development of TCM synthetic biology. This manuscript introduces the recent research progresses of metabolomics technology and the main research contents of metabolomics studies for medicinal plants, including identification and quality evaluation for medicinal plants, cultivars breeding, stress resistance, metabolic pathways, metabolic network, metabolic engineering and synthetic biology researches...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28933036/resistance-genes-in-piper-colubrinum-in-silico-survey-from-leaf-transcriptome-and-expression-studies-upon-challenge-inoculation-with-phytophthora-capsici
#10
Neema Malik, Johnson K George
The oomycetes, Phytophthora capsici, cause foot rot disease in black pepper. Piper colubrinum Link, a distant relative of cultivated black pepper, is highly resistant to this destructive pathogen. Identification of resistance (R) genes in P. colubrinum and the study of its expression profile during interaction with the pathogen can help in understanding the resistance mechanism involved. In the present study, 1289 R gene-related transcripts were mined from P. colubrinum transcriptome, clustered, and classified according to the conserved motifs and domains...
September 20, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28932265/removal-of-glucuronic-acid-from-xylan-is-a-strategy-to-improve-the-conversion-of-plant-biomass-to-sugars-for-bioenergy
#11
Jan J Lyczakowski, Krzysztof B Wicher, Oliver M Terrett, Nuno Faria-Blanc, Xiaolan Yu, David Brown, Kristian B R M Krogh, Paul Dupree, Marta Busse-Wicher
BACKGROUND: Plant lignocellulosic biomass can be a source of fermentable sugars for the production of second generation biofuels and biochemicals. The recalcitrance of this plant material is one of the major obstacles in its conversion into sugars. Biomass is primarily composed of secondary cell walls, which is made of cellulose, hemicelluloses and lignin. Xylan, a hemicellulose, binds to the cellulose microfibril and is hypothesised to form an interface between lignin and cellulose. Both softwood and hardwood xylan carry glucuronic acid side branches...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28931938/dynamic-transcriptome-and-phytohormone-profiling-along-the-time-of-light-exposure-in-the-mesocotyl-of-rice-seedling
#12
Fangjun Feng, Hanwei Mei, Peiqing Fan, Yanan Li, Xiaoyan Xu, Haibin Wei, Ming Yan, Lijun Luo
Mesocotyl elongation is an important trait influencing seedling emergence and establishment in rice direct-seeding cultivation and is immediately inhibited after light exposure. Detailed researches on the molecular basis and biological processes underlying light repression of mesocotyl growth could probably provide useful information for key factors controlling this trait. Here we monitored the transcriptome and endogenous phytohormone changes specifically in the elongating mesocotyl in response to light exposure with a time-course...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931057/challenges-and-advances-for-transcriptome-assembly-in-non-model-species
#13
Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R J Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence)...
2017: PloS One
https://www.readbyqxmd.com/read/28929670/-herbgenomics
#14
Shi-Lin Chen, Jing-Yuan Song
Traditional Chinese medicine (TCM) has contributad greatly to improving human health. However, the biological characteristics and molecular mechanisms of TCM in the treatment of human diseases remain largely unknown. Genomics plays an important role in modern medicine and biology. Here, we introduce genomics and other related omics to the study of herbs to propose a new discipline, Herbgenomics, that aims to uncover the genetic information and regulatory networks of herbs and to clarify their molecular mechanisms in the prevention and treatment of human diseases...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28929648/-cloning-and-expression-analysis-of-tocopherol-cyclase-gene-in-carthamus-tinctorius
#15
Li-Li Guan, Qi Cui, Yu-Tong Han, Yun-Yun Wu, Ren-Ge Hu, Tian-Yao Gu, Hai-Yan Li, Xiao-Kun Li
The tocopherol cyclase was one of the key enzymes in plant vitamin E biosynthesis pathway. According to the study of Carthamus tinctorius transcriptome data,the Tocopherol cyclase gene was obtained using RT-PCR techniques and named CtTC . Bioinformatics analysis showed theopen reading frame (ORF)of CtTC was 1 524 bp. The putative protein contained 507 amino acids with a predicted molecular mass of 62.9 kDa and theoretically isoelectric point was 5.01.Signal peptide analysis showed that it was a non secretory protein, and there was no signal peptide...
October 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28927374/b-box-genes-genome-wide-identification-evolution-and-their-contribution-to-pollen-growth-in-pear-pyrus-bretschneideri-rehd
#16
Yunpeng Cao, Yahui Han, Dandan Meng, Dahui Li, Chunyan Jiao, Qing Jin, Yi Lin, Yongping Cai
BACKGROUND: The B-BOX (BBX) proteins have important functions in regulating plant growth and development. In plants, the BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, there still lack a genome-wide survey of BBX genes in pear. RESULTS: In the present study, a total of 25 BBX genes were identified in pear (Pyrus bretschneideri Rehd.). Subsequently, phylogenetic relationship, gene structure, gene duplication, transcriptome data and qRT-PCR were conducted on these BBX gene members...
September 19, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28927022/salt-stress-response-mechanisms-using-de-novo-transcriptome-sequencing-of-salt-tolerant-and-sensitive-corchorus-spp-genotypes
#17
Zemao Yang, Ruike Lu, Zhigang Dai, An Yan, Qing Tang, Chaohua Cheng, Ying Xu, Wenting Yang, Jianguang Su
High salinity is a major environmental stressor for crops. To understand the regulatory mechanisms underlying salt tolerance, we conducted a comparative transcriptome analysis between salt-tolerant and salt-sensitive jute (Corchorus spp.) genotypes in leaf and root tissues under salt stress and control conditions. In total, 68,961 unigenes were identified. Additionally, 11,100 unigenes (including 385 transcription factors (TFs)) exhibited significant differential expression in salt-tolerant or salt-sensitive genotypes...
September 18, 2017: Genes
https://www.readbyqxmd.com/read/28926584/transcriptome-analysis-reveals-molecular-anthelmintic-effects-of-procyanidins-in-c-elegans
#18
Verena Spiegler, Andreas Hensel, Jochen Seggewiß, Milena Lubisch, Eva Liebau
Worldwide, more than 1 billion people are affected by infestations with soil-transmitted helminths and also in veterinary medicine helminthiases are a severe threat to livestock due to emerging resistances against the common anthelmintics. Proanthocyanidins have been increasingly investigated for their anthelmintic properties, however, except for an interaction with certain proteins of the nematodes, not much is known about their mode of action. To investigate the anthelmintic activity on a molecular level, a transcriptome analysis was performed in Caenorhabditis elegans after treatment with purified and fully characterized oligomeric procyanidins (OPC)...
2017: PloS One
https://www.readbyqxmd.com/read/28925901/plant-cell-wall-proteomics-as-a-strategy-to-reveal-candidate-proteins-involved-in-extracellular-lipid-metabolism
#19
Adélaïde Jacq, Vincent Burlat, Elisabeth Jamet
Plant cell walls are composite structures surrounding cells and involved in both mechanical support and perception of their environment. They are mainly composed of polysaccharides (90-95% of their mass) and proteins (5-10%). The cell wall proteins (CWPs) contribute to the arrangements and modifications of polymer networks and to cell-to-cell communication. The structure and composition of cell walls are not uniform in the whole plants, but rather specialized in different cell types to fulfil different functions...
September 18, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28925160/-metabolic-pathway-of-flavonoids-in-blumea-balsamifera
#20
Qi-Feng Xia, Zhi Zhao, Hong-Chang Liu, Ling-Liang Guan, Yu-Xin Pang
To better understand the biosynthetic pathway of flavonoids in Blumea balsamifera, and to increase the biosynthesis of flavone and flavonol amount, we carried out this research. Basing on transcriptome information, B. balsamifera flavonoids metabolic pathway was analyzed in KEGG data base. The result demonstrated that two metabolic pathways of flavonoids were found in KEGG data base. They were flavonoid biosynthesis pathway (No.ko00941) that contained 32 genes and flavone and flavonol biosynthesis pathway (No...
October 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
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