Sequence Analysis, RNA

Publication Title: 
BMC genomics

BACKGROUND: MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression and play a critical role in development, homeostasis, and disease. Despite their demonstrated roles in age-associated pathologies, little is known about the role of miRNAs in human aging and longevity. RESULTS: We employed massively parallel sequencing technology to identify miRNAs expressed in B-cells from Ashkenazi Jewish centenarians, i.e., those living to a hundred and a human model of exceptional longevity, and younger controls without a family history of longevity.

Author(s): 
Gombar, Saurabh
Jung, Hwa Jin
Dong, Feng
Calder, Brent
Atzmon, Gil
Barzilai, Nir
Tian, Xiao-Li
Pothof, Joris
Hoeijmakers, Jan H. J.
Campisi, Judith
Vijg, Jan
Suh, Yousin
Publication Title: 
BMC genomics

BACKGROUND: MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression and play a critical role in development, homeostasis, and disease. Despite their demonstrated roles in age-associated pathologies, little is known about the role of miRNAs in human aging and longevity. RESULTS: We employed massively parallel sequencing technology to identify miRNAs expressed in B-cells from Ashkenazi Jewish centenarians, i.e., those living to a hundred and a human model of exceptional longevity, and younger controls without a family history of longevity.

Author(s): 
Gombar, Saurabh
Jung, Hwa Jin
Dong, Feng
Calder, Brent
Atzmon, Gil
Barzilai, Nir
Tian, Xiao-Li
Pothof, Joris
Hoeijmakers, Jan H. J.
Campisi, Judith
Vijg, Jan
Suh, Yousin
Publication Title: 
Genes & Development

Telomerase contains an essential RNA, which includes the template sequence copied by the reverse transcription action of telomerase into telomeric DNA. Using phylogenetic comparison, we identified seven conserved sequences in telomerase RNAs from Kluyveromyces budding yeasts. We show that two of these sequences, CS3 and CS4, are essential for normal telomerase function and can base-pair to form a putative long-range pseudoknot. Disrupting this base-pairing was deleterious to cell growth, telomere maintenance, and telomerase activity.

Author(s): 
Tzfati, Yehuda
Knight, Zachary
Roy, Jagoree
Blackburn, Elizabeth H.
Publication Title: 
PloS One

Extensive changes in DNA methylation have been observed in schizophrenia (SC) and bipolar disorder (BP), and may contribute to the pathogenesis of these disorders. Here, we performed genome-scale DNA methylation profiling using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) on two brain regions (including frontal cortex and anterior cingulate) in 5 SC, 7 BP and 6 normal subjects. Comparing with normal controls, we identified substantial differentially methylated regions (DMRs) in these two brain regions of SC and BP.

Author(s): 
Xiao, Yun
Camarillo, Cynthia
Ping, Yanyan
Arana, Tania Bedard
Zhao, Hongying
Thompson, Peter M.
Xu, Chaohan
Su, Bin Brenda
Fan, Huihui
Ordonez, Javier
Wang, Li
Mao, Chunxiang
Zhang, Yunpeng
Cruz, Dianne
Escamilla, Michael A.
Li, Xia
Xu, Chun
Publication Title: 
International Journal of Molecular Sciences

Thapsia laciniata Rouy (Apiaceae) produces irregular and regular sesquiterpenoids with thapsane and guaiene carbon skeletons, as found in other Apiaceae species. A transcriptomic analysis utilizing Illumina next-generation sequencing enabled the identification of novel genes involved in the biosynthesis of terpenoids in Thapsia. From 66.78 million HQ paired-end reads obtained from T. laciniata roots, 64.58 million were assembled into 76,565 contigs (N50: 1261 bp). Seventeen contigs were annotated as terpene synthases and five of these were predicted to be sesquiterpene synthases.

Author(s): 
Drew, Damian Paul
Dueholm, Bjørn
Weitzel, Corinna
Zhang, Ye
Sensen, Christoph W.
Simonsen, Henrik Toft
Publication Title: 
The Journal of Nutrition

Hepcidin, the pivotal regulator of iron metabolism, plays a critical role in multiple diseases including anemia of chronic disease and hemochromatosis. Recent studies have focused on identifying antagonists of hepcidin. We hypothesized that bioactive extracts from Chinese medicinal plants may be efficacious in the inhibition of expression of the hepcidin-encoding gene (HAMP) product, hepcidin.

Author(s): 
Guan, Yu
An, Peng
Zhang, Zhuzhen
Zhang, Fan
Yu, Yu
Wu, Qian
Shi, Yanbo
Guo, Xin
Tao, Yunlong
Wang, Fudi
Publication Title: 
BMC genomics

BACKGROUND: Siraitia grosvenorii (Luohanguo) is an herbaceous perennial plant native to southern China and most prevalent in Guilin city. Its fruit contains a sweet, fleshy, edible pulp that is widely used in traditional Chinese medicine. The major bioactive constituents in the fruit extract are the cucurbitane-type triterpene saponins known as mogrosides. Among them, mogroside V is nearly 300 times sweeter than sucrose. However, little is known about mogrosides biosynthesis in S. grosvenorii, especially the late steps of the pathway.

Author(s): 
Tang, Qi
Ma, Xiaojun
Mo, Changming
Wilson, Iain W.
Song, Cai
Zhao, Huan
Yang, Yanfang
Fu, Wei
Qiu, Deyou
Publication Title: 
BMC genomics

BACKGROUND: Traditional Chinese medicine uses various herbs for the treatment of various diseases for thousands of years and it is now time to assess the characteristics and effectiveness of these medicinal plants based on modern genetic and molecular tools. The herb Flos Lonicerae Japonicae (FLJ or Lonicera japonica Thunb.) is used as an anti-inflammatory agent but the chemical quality of FLJ and its medicinal efficacy has not been consistent.

Author(s): 
Yuan, Yuan
Song, Lipu
Li, Minhui
Liu, Guiming
Chu, Yanan
Ma, Luyu
Zhou, Yuanyuan
Wang, Xiao
Gao, Wei
Qin, Shuangshuang
Yu, Jun
Wang, Xumin
Huang, Luqi
Publication Title: 
PloS One

BACKGROUND: Cordyceps militaris, an ascomycete caterpillar fungus, has been used as a traditional Chinese medicine for many years owing to its anticancer and immunomodulatory activities. Currently, artificial culturing of this beneficial fungus has been widely used and can meet the market, but systematic molecular studies on the developmental stages of cultured C. militaris at transcriptional and translational levels have not been determined. METHODOLOGY/PRINCIPAL FINDINGS: We utilized high-throughput Illumina sequencing to obtain the transcriptomes of C.

Author(s): 
Yin, Yalin
Yu, Guojun
Chen, Yijie
Jiang, Shuai
Wang, Man
Jin, Yanxia
Lan, Xianqing
Liang, Yi
Sun, Hui
Publication Title: 
PloS One

BACKGROUND: MicroRNAs are now recognized as key post-transcriptional regulators in animal ontogenesis and phenotypic diversity. Eupolyphaga sinensis Walker (Blattaria) is a sexually dimorphic insect, which is also an important source of material used in traditional Chinese medicine. The male E. sinensis have shorter lifecycles and go through fewer instars than the female. Furthermore, the males have forewings, while the females are totally wingless.

Author(s): 
Wu, Wei
Ren, Qiuping
Li, Chengjun
Wang, Yanyun
Sang, Ming
Zhang, Yi
Li, Bin

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