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https://www.readbyqxmd.com/read/29149599/autophagosomal-content-profiling-reveals-an-lc3c-dependent-piecemeal-mitophagy-pathway
#1
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
#2
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
#3
https://www.readbyqxmd.com/read/29054270/the-peptidome-comes-of-age-mass-spectrometry-based-characterization-of-the-circulating-cancer-peptidome
#4
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
#5
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
#6
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
#7
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)...
October 9, 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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28808767/identification-and-expression-analysis-of-micrornas-during-ovule-development-in-rice-oryza-sativa-by-deep-sequencing
#13
Ya Wu, Liyu Yang, Meiling Yu, Jianbo Wang
MicroRNA (miRNA) expression profiles during rice ovule development revealed the possible miRNA-mediated regulation between ovule sporophytic tissue and female gametophyte and the involvement of miRNAs in programmed cell death. MiRNAs are 20-24-nucleotide small RNAs that play key roles in the regulation of many growth and developmental processes in plants. Rice ovule development comprises a series of biological events, which are regulated by complex molecular mechanisms. To gain insight into miRNA-mediated regulation of rice ovule development, Illumina sequencing was used to examine the expression of miRNAs from the megaspore mother cell meiosis stage to the fertilized ovule stage...
November 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28803266/a-degradome-based-polymerase-chain-reaction-to-resolve-the-potential-of-environmental-samples-for-2-4-dichlorophenol-biodegradation
#14
Eslam S Ibrahim, Mona T Kashef, Tamer M Essam, Mohammed A Ramadan
A clean way to overcome environmental pollution is biodegradation. In this perspective, at the intersection of biodegradation and metagenomics, the degradome is defined as the totality of genes related to the biodegradation of a certain compound. It includes the genetic elements from both culturable and uncultured microorganisms. The possibility of assessing the biodegradation potential of an environmental samples, using a degradome-based polymerase chain reaction, was explored. 2,4-Dichlorophenol (2,4-DCP) was chosen as a model and the use of tfdB gene as a biodegradation marker was confirmed by bioinformatics study of TfdB protein...
December 2017: Current Microbiology
https://www.readbyqxmd.com/read/28797648/overview-of-transcriptomic-analysis-of-all-human-proteases-non-proteolytic-homologs-and-inhibitors-organ-tissue-and-ovarian-cancer-cell-line-expression-profiling-of-the-human-protease-degradome-by-the-clip-chip%C3%A2-dna-microarray
#15
REVIEW
Reinhild Kappelhoff, Xose S Puente, Claire H Wilson, Arun Seth, Carlos López-Otín, Christopher M Overall
The protease degradome is defined as the complete repertoire of proteases and inhibitors, and their nonfunctional homologs present in a cell, tissue or organism at any given time. We review the tissue distribution of virtually the entire degradome in 23 different human tissues and 6 ovarian cancer cell lines. To do so, we developed the CLIP-CHIP™, a custom microarray based on a 70-mer oligonucleotide platform, to specifically profile the transcripts of the entire repertoire of 473 active human proteases, 156 protease inhibitors and 92 non-proteolytically active homologs known at the design date using one specific 70-mer oligonucleotide per transcript...
November 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28733325/protease-cleavage-site-fingerprinting-by-label-free-in-gel-degradomics-reveals-ph-dependent-specificity-switch-of-legumain
#16
Robert Vidmar, Matej Vizovišek, Dušan Turk, Boris Turk, Marko Fonović
Determination of protease specificity is of crucial importance for understanding protease function. We have developed the first gel-based label-free proteomic approach (DIPPS-direct in-gel profiling of protease specificity) that enables quick and reliable determination of protease cleavage specificities under large variety of experimental conditions. The methodology is based on in-gel digestion of the gel-separated proteome with the studied protease, enrichment of cleaved peptides by gel extraction, and subsequent mass spectrometry analysis combined with a length-limited unspecific database search...
August 15, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28724775/n-degradomic-analysis-reveals-a-proteolytic-network-processing-the-podocyte-cytoskeleton
#17
Markus M Rinschen, Ann-Kathrin Hoppe, Florian Grahammer, Martin Kann, Linus A Völker, Eva-Maria Schurek, Julie Binz, Martin Höhne, Fatih Demir, Milena Malisic, Tobias B Huber, Christine Kurschat, Jayachandran N Kizhakkedathu, Bernhard Schermer, Pitter F Huesgen, Thomas Benzing
Regulated intracellular proteostasis, controlled in part by proteolysis, is essential in maintaining the integrity of podocytes and the glomerular filtration barrier of the kidney. We applied a novel proteomics technology that enables proteome-wide identification, mapping, and quantification of protein N-termini to comprehensively characterize cleaved podocyte proteins in the glomerulus in vivo We found evidence that defined proteolytic cleavage results in various proteoforms of important podocyte proteins, including those of podocin, nephrin, neph1, α-actinin-4, and vimentin...
October 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28705956/rapid-recovery-gene-downregulation-during-excess-light-stress-and-recovery-in-arabidopsis
#18
Peter A Crisp, Diep R Ganguly, Aaron B Smith, Kevin D Murray, Gonzalo M Estavillo, Iain Searle, Ethan Ford, Ozren Bogdanović, Ryan Lister, Justin O Borevitz, Steven R Eichten, Barry J Pogson
Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery. For instance, HSP101 abundance declined 2-fold every 5.1 min. We term this phenomenon rapid recovery gene downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting...
August 2017: Plant Cell
https://www.readbyqxmd.com/read/28698160/investigating-the-regulatory-roles-of-the-micrornas-and-the-argonaute-1-enriched-small-rnas-in-plant-metabolism
#19
Jingping Qin, Zhonghai Tang, Xiaoxia Ma, Yijun Meng
The biological roles of small RNAs (sRNAs) in metabolic processes are emerging. However, a systemic study is needed to investigate the wide-spread involvement of the sRNAs in plant metabolism. By using the metabolism-related transcripts retrieved from the public database Plant Metabolic Network, and the publicly available sRNA high-throughput sequencing data, large-scale target identification was performed for microRNAs (miRNAs) and Argonaute 1 (AGO1)-enriched sRNAs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa)...
September 10, 2017: Gene
https://www.readbyqxmd.com/read/28674878/characterization-of-the-low-molecular-weight-human-plasma-peptidome
#20
David W Greening, Richard J Simpson
The human plasma proteome represents an important secreted sub-proteome. Proteomic analysis of blood plasma with mass spectrometry is a challenging task. The high complexity and wide dynamic range of proteins as well as the presence of several proteins at very high concentrations complicate the profiling of the human plasma proteome. The peptidome (or low-molecular-weight fraction, LMF) of the human plasma proteome is an invaluable source of biological information, especially in the context of identifying plasma-based markers of disease...
2017: Methods in Molecular Biology
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