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https://www.readbyqxmd.com/read/29318538/dissecting-degradomes-analysis-of-protease-coding-genes
#1
Ángel Álvarez-Eguiluz, Ander Díaz-Navarro, Xose S Puente
Proteases constitute up to 3% of all protein-coding genes in a vertebrate genome and participate in numerous physiological and pathological processes. The characterization of the degradome of one organism, the set of all genes encoding proteolytic enzymes, and the comparison to the degradome of other species have proved useful to identify genetic differences that are helpful to elucidate the molecular basis of diverse biological processes, the different susceptibility to disease, and the evolution of the structure and function of proteases...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29280990/dpmind-degradome-based-plant-mirna-target-interaction-and-network-database
#2
Yuhan Fei, Rui Wang, Haoyuan Li, Shu Liu, Hongsheng Zhang, Ji Huang
Motivation: MicroRNAs (miRNAs) play essential roles in plant growth, development and stress responses through post-transcriptionally regulating the expression levels of their target mRNAs. Although some tools and databases were developed for predicting the relationships between miRNAs and their targets (miR-Tar), most of them were dependent on computational methods without experimental validations. With development of degradome sequencing techniques, researchers can identify potential interactions based on degradome sequencing data...
December 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29236948/tarhunter-a-tool-for-predicting-conserved-microrna-targets-and-target-mimics-in-plants
#3
Xuan Ma, Chunyan Liu, Lianfeng Gu, Beixin Mo, Xiaofeng Cao, Xuemei Chen
Summary: In plants, the targets of deeply conserved microRNAs (miRNAs) were comprehensively studied. Evidence is emerging that targets of less conserved miRNAs, endogenous target mimics (eTM) and non-canonical targets play functional roles. Existing plant miRNA prediction tools lack a cross-species conservation filter and eTM prediction function. We developed a tool named TarHunter that features a strict cross-species conservation filter and capability of predicting eTMs. TarHunter has higher recall or precision rate as compared with other tools, and the conservation filter effectively increases prediction precision...
December 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29236054/genome-wide-profiling-of-small-rnas-and-degradome-revealed-conserved-regulations-of-mirnas-on-auxin-responsive-genes-during-fruit-enlargement-in-peaches
#4
Mengya Shi, Xiao Hu, Yu Wei, Xu Hou, Xue Yuan, Jun Liu, Yueping Liu
Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we performed small RNA sequencing and degradome sequencing analyses to systematically explore post-transcriptional regulation in the mesocarp at the hard core stage following treatment of the peach (Prunus persica L.) fruit with the synthetic auxin α-naphthylacetic acid (NAA)...
December 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29215744/identification-of-virus-derived-sirnas-and-their-targets-in-rbsdv-infected-rice-by-deep-sequencing
#5
Ying Lan, Yanwu Li, Zhiguo E, Feng Sun, Linlin Du, Qiufang Xu, Tong Zhou, Yijun Zhou, Yongjian Fan
RNA interference (RNAi) is a conserved mechanism against viruses in plants and animals. It is thought to inactivate the viral genome by producing virus-derived small interfering RNAs (vsiRNAs). Rice black-streaked dwarf virus (RBSDV) is transmitted to plants by the small brown planthopper (Laodelphax striatellus), and seriously threatens production of rice in East Asia, particularly Oryza sativa japonica subspecies. Through deep sequencing, genome-wide comparisons of RBSDV-derived vsiRNAs were made between the japonica variety Nipponbare, and the indica variety 9311...
December 7, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/29185497/high-throughput-deep-sequencing-reveals-the-important-roles-of-micrornas-during-sweetpotato-storage-at-chilling-temperature
#6
Zeyi Xie, Aiming Wang, Hongmin Li, Jingjing Yu, Jiaojiao Jiang, Zhonghou Tang, Daifu Ma, Baohong Zhang, Yonghua Han, Zongyun Li
Sweetpotato (Impomoea batatas L.) is a globally important economic food crop with a potential of becoming a bioenergy and pharmaceutical crop. Thus, studying the molecular mechanism of tuberous root development and storage is very important. However, not too much progress has been made in this field. In this study, we employed the next generation high-throughput deep sequencing technology to sequence all small RNAs and degradome of sweetpotato for systematically investigating sweetpotato response to chilling stress during storage...
November 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29175018/understanding-serine-proteases-implications-on-leishmania-spp-lifecycle
#7
REVIEW
Carlos Roberto Alves, Raquel Santos de Souza, Karen Dos Santos Charret, Luzia Monteiro de Castro Cortes, Matheus Pereira de Sá Silva, Laura Barral Veloso, Luiz Filipe Gonçalves Oliveira, Franklin Souza-Silva
Serine proteases have significant functions over a broad range of biological processes relevant to the Leishmania spp lifecycle. Data gathered here present an update on the Leishmania spp serine proteases and the status of these enzymes as part of the parasite degradome. The serine protease genes (n = 26 to 28) in Leishmania spp, which encode proteins with a wide range of molecular masses (35 kDa-115 kDa), are described along with their degrees of chromosomal and allelic synteny. Amid 17 putative Leishmania spp serine proteases, only ∼18% were experimentally demonstrated as signal peptidases that remove the signal peptide from secretory pre-proteins, maturases of other proteins and with metacaspase-like activity...
November 21, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/29174487/mirnaome-mrnaome-and-degradome-analysis-of-tibetan-minipigs-anterior-pituitary
#8
Rui-Song Ye, Meng Li, Ting Chen, Qi-En Qi, Xiao Cheng, Chao-Yun Li, Qing-Yan Jiang, Qian-Yun Xi, Yong-Liang Zhang
Tibetan minipig is an important animal model for human diseases. The anterior pituitary is the master gland responsible for growth, reproduction, and metabolism and is regulated by thousands of miRNAs/mRNAs molecules. However, little is known about miRNAs and their relationships with mRNAs in Tibetan minipig anterior pituitary. Using microarray and mRNA-Sequencing, we identified 203 miRNAs and 12,040 mRNA transcripts from the anterior pituitary of Tibetan minipigs. These miRNAs were corresponding to 194 hairpin precursors, 25 miRNA clusters and 24 miRNA families...
November 23, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/29149599/autophagosomal-content-profiling-reveals-an-lc3c-dependent-piecemeal-mitophagy-pathway
#9
François Le Guerroué, Franziska Eck, Jennifer Jung, Tatjana Starzetz, Michel Mittelbronn, Manuel Kaulich, Christian Behrends
Autophagy allows the degradation of cytosolic endogenous and exogenous material in the lysosome. Substrates are engulfed by double-membrane vesicles, coined autophagosomes, which subsequently fuse with lysosomes. Depending on the involvement of specific receptor proteins, autophagy occurs in a selective or nonselective manner. While this process is well understood at the level of bulky cargo such as mitochondria and bacteria, we know very little about individual proteins and protein complexes that are engulfed and degraded by autophagy...
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29133823/identification-of-mirna-mediated-drought-responsive-multi-tiered-regulatory-network-in-drought-tolerant-rice-nagina-22
#10
Sonia Balyan, Mukesh Kumar, Roseeta Devi Mutum, Utkarsh Raghuvanshi, Priyanka Agarwal, Saloni Mathur, Saurabh Raghuvanshi
Comparative characterization of microRNA-mediated stress regulatory networks in contrasting rice cultivars is critical to decipher plant stress response. Consequently, a multi-level comparative analysis, using sRNA sequencing, degradome analysis, enzymatic and metabolite assays and metal ion analysis, in drought tolerant and sensitive rice cultivars was conducted. The study identified a group of miRNAs "Cultivar-specific drought responsive" (CSDR)-miRNAs (osa-miR159f, osa-miR1871, osa-miR398b, osa-miR408-3p, osa-miR2878-5p, osa-miR528-5p and osa-miR397a) that were up-regulated in the flag-leaves of tolerant cultivar, Nagina 22 (N22) and Vandana, but down-regulated in the sensitive cultivar, Pusa Basmati 1 (PB1) and IR64, during drought...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29121117/correction-genome-wide-investigation-using-srna-seq-degradome-seq-and-transcriptome-seq-reveals-regulatory-networks-of-micrornas-and-their-target-genes-in-soybean-during-soybean-mosaic-virus-infection
#11
https://www.readbyqxmd.com/read/29054270/the-peptidome-comes-of-age-mass-spectrometry-based-characterization-of-the-circulating-cancer-peptidome
#12
David W Greening, Eugene A Kapp, Richard J Simpson
Peptides play a seminal role in most physiological processes acting as neurotransmitters, hormones, antibiotics, and immune regulation. In the context of tumor biology, it is hypothesized that endogenous peptides, hormones, cytokines, growth factors, and aberrant degradation of select protein networks (e.g., enzymatic activities, protein shedding, and extracellular matrix remodeling) are fundamental in mediating cancer progression. Analysis of peptides in biological fluids by mass spectrometry holds promise of providing sensitive and specific diagnostic and prognostic information for cancer and other diseases...
2017: Enzymes
https://www.readbyqxmd.com/read/29054266/circulating-peptidome-and-tumor-resident-proteolysis
#13
Jia Fan, Bo Ning, Christopher J Lyon, Tony Y Hu
Mammalian proteases segregate into several distinct protein families that employ different functional domains to hydrolyze peptides bonds with different specificities and affinities. These enzymes play central roles in critical cellular and systemic processes, including regulation of cell growth, differentiation, homeostasis, and apoptosis; and cancer initiation, progression, and metastasis. Human proteases segregate into five distinct catalytic classes; the metalloprotease, serine protease, and cysteine protease families have the most members, while the aspartic and threonine peptidase families have relatively few examples...
2017: Enzymes
https://www.readbyqxmd.com/read/29036205/characterization-of-micrornas-of-beta-macrocarpa-and-their-responses-to-beet-necrotic-yellow-vein-virus-infection
#14
Jun-Ying Liu, Hui-Yan Fan, Ying Wang, Yong-Liang Zhang, Da-Wei Li, Jia-Lin Yu, Cheng-Gui Han
Plant microRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development, defense, and symptom development. Here, 547 known miRNAs representing 129 miRNA families, and 282 potential novel miRNAs were identified in Beta macrocarpa using small RNA deep sequencing. A phylogenetic analysis was performed, and 8 Beta lineage-specific miRNAs were identified. Through a differential expression analysis, miRNAs associated with Beet necrotic yellow vein virus (BNYVV) infection were identified and confirmed using a microarray analysis and stem-loop RT-qPCR...
2017: PloS One
https://www.readbyqxmd.com/read/28993932/genome-wide-identification-of-cd-responsive-nramp-transporter-genes-and-analyzing-expression-of-nramp-1-mediated-by-mir167-in-brassica-napus
#15
Jin Guo Meng, Xian Duo Zhang, Shang Kun Tan, Kai Xuan Zhao, Zhi Min Yang
In plants, metal transporters are responsible for metal uptake, translocation and homeostasis. These metals include essential nutrients such as zinc (Zn) and manganese (Mn) or non-essential metals like cadmium (Cd) and lead (Pb). Although a few metal transporters have been well characterized in model plants, little is known about their functionality in rapeseed (Brassica napus). In the study, 22 NRAMP transporter genes from B. napus genome were identified and annotated using bioinformatics and high-throughput RNA-sequencing (RNA-seq)...
December 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28899681/comparative-degradomics-of-porcine-and-human-wound-exudates-unravels-biomarker-candidates-for-assessment-of-wound-healing-progression-in-trauma-patients
#16
Fabio Sabino, Fabian E Egli, Simonas Savickas, Jörg Holstein, Daniela Kaspar, Mika Rollmann, Jayachandran N Kizhakkedathu, Tim Pohlemann, Hans Smola, Ulrich Auf dem Keller
Impaired cutaneous wound healing is a major complication in elderly people and patients suffering from diabetes with raising rates in industrialized countries. Heterogeneity of clinical manifestations hampers effective molecular diagnostics and decisions for appropriate therapeutic regimens. Using a customized positional quantitative proteomics workflow, we have established a time-resolved proteome and N-terminome resource from wound exudates in a clinically relevant pig wound model that we exploited as robust template to interpret a heterogeneous dataset from patients undergoing the same wound treatment...
September 9, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28885180/next-generation-sequencing-sheds-new-light-on-small-rnas-in-plant-reproductive-development
#17
Xiaobai Li
Reproductive development is a key step of the plant life cycles and indicates the start of a new life cycle. The reproductive organs including flower, fruit and seed, have diverse and complex structures, which is a syndrome in the evolution of angiosperms. The development of plant reproductive organs depends on the correct spatial and temporal expression of numerous genes acting in concert to form regulatory networks. Small non-coding RNAs (sRNAs) play a key role in the reproductive development through different modes of sequence-specific interaction with their targets...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28884358/effective-enhancement-of-resistance-to-phytophthora-infestans-by-overexpression-of-mir172a-and-b-in-solanum-lycopersicum
#18
Yushi Luan, Jun Cui, Jie Li, Ning Jiang, Ping Liu, Jun Meng
Overexpression of miR172a and b in tomato ( Solanum lycopersicum ) Zaofen No. 2 increased resistance to Phytophthora infestans infection by suppressing of an AP2/ERF transcription factor. The miR172 family has been shown to participate in the growth phase transition, flowering time control, abiotic and biotic stresses by regulating the expression of a small group of AP2/ERF transcription factors. In this study, the precursors of miR172a and b were cloned from tomato, Solanum pimpinellifolium L3708. We used the degradome sequencing to determine the cleavage site of miR172 to a member of the AP2/ERF transcription factor family (Solyc11g072600...
September 7, 2017: Planta
https://www.readbyqxmd.com/read/28877679/micrornas-participate-in-gene-expression-regulation-and-phytohormone-cross-talk-in-barley-embryo-during-seed-development-and-germination
#19
Bin Bai, Bo Shi, Ning Hou, Yanli Cao, Yijun Meng, Hongwu Bian, Muyuan Zhu, Ning Han
BACKGROUND: Small RNA and degradome sequencing have identified a large number of miRNA-target pairs in plant seeds. However, detailed spatial and temporal studies of miRNA-mediated regulation, which can reflect links between seed development and germination are still lacking. RESULTS: In this study, we extended our investigation on miRNAs-involved gene regulation by a combined analysis of seed maturation and germination in barley. Through bioinformatics analysis of small RNA sequencing data, a total of 1324 known miRNA families and 448 novel miRNA candidates were identified...
September 6, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28842680/small-rna-profiles-from-panax-notoginseng-roots-differing-in-sizes-reveal-correlation-between-mir156-abundances-and-root-biomass-levels
#20
Yun Zheng, Kun Chen, Zhenning Xu, Peiran Liao, Xiaotuo Zhang, Li Liu, Kangning Wei, Diqiu Liu, Yong-Fang Li, Ramanjulu Sunkar, Xiuming Cui
Plant genomes encode several classes of small regulatory RNAs (sRNAs) that play critical roles in both development and stress responses. Panax notoginseng (Burk.) F.H. Chen (P. notoginseng) is an important traditional Chinese herbal medicinal plant species for its haemostatic effects. Therefore, the root yield of P. notoginseng is a major economically important trait since the roots of P. notoginseng are the parts used to produce medicine. To identify sRNAs that are critical for the root biomass of P. notoginseng, we performed a comprehensive study of miRNA transcriptomes from P...
August 25, 2017: Scientific Reports
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