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https://www.readbyqxmd.com/read/28733325/protease-cleavage-site-fingerprinting-by-label-free-in-gel-degradomics-reveals-ph-dependent-specificity-switch-of-legumain
#1
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...
July 21, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28724775/n-degradomic-analysis-reveals-a-proteolytic-network-processing-the-podocyte-cytoskeleton
#2
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...
July 19, 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
#3
Peter Alexander Crisp, Diep Ganguly, Aaron B Smith, Kevin D Murray, Gonzalo M Estavillo, Iain R 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, PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as three minutes. We demonstrate that 87% of the stress-upregulated mRNAs analysed exhibit very rapid recovery. For instance, HSP101 abundance declined two-fold every 5.1 minutes. We term this phenomenon Rapid Recovery Gene Downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting...
July 13, 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
#4
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)...
July 8, 2017: Gene
https://www.readbyqxmd.com/read/28674878/characterization-of-the-low-molecular-weight-human-plasma-peptidome
#5
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
https://www.readbyqxmd.com/read/28639897/gene-signature-based-on-degradome-related-genes-can-predict-distal-metastasis-in-cervical-cancer-patients
#6
Jorge Fernandez-Retana, Horacio Zamudio-Meza, Miguel Rodriguez-Morales, Abraham Pedroza-Torres, David Isla-Ortiz, Luis Herrera, Nadia Jacobo-Herrera, Oscar Peralta-Zaragoza, César López-Camarillo, Fermin Morales-Gonzalez, David Cantu de Leon, Carlos Pérez-Plasencia
Cervical cancer is one of the leading causes of death in women worldwide, which mainly affects developing countries. The patients who suffer a recurrence and/or progression disease have a higher risk of developing distal metastases. Proteases comprising the degradome given its ability to promote cell growth, migration, and invasion of tissues play an important role during tumor development and progression. In this study, we used high-density microarrays and quantitative reverse transcriptase polymerase chain reaction to evaluate the degradome profile and their inhibitors in 112 samples of patients diagnosed with locally advanced cervical cancer...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28637931/comparative-miromics-of-salt-tolerant-and-salt-sensitive-rice
#7
Kavita Goswami, Anita Tripathi, Neeti Sanan-Mishra
Increase in soil salt causes osmotic and ionic stress to plants, which inhibits their growth and productivity. Rice production is also hampered by salinity and the effect of salt is most severe at the seedling and reproductive stages. Salainity tolerance is a quantitative property controlled by multiple genes coding for signaling molecules, ion transporters, metabolic enzymes and transcription regulators. MicroRNAs are key modulators of gene-expression that act at the post-transcriptional level by translation repression or transcript cleavage...
June 22, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28635129/micrornas-involved-in-auxin-signalling-modulate-male-sterility-under-high-temperature-stress-in-cotton-gossypium-hirsutum
#8
Yuanhao Ding, Yizan Ma, Nian Liu, Jiao Xu, Qin Hu, Yaoyao Li, Yuanlong Wu, Sai Xie, Longfu Zhu, Ling Min, Xianlong Zhang
Male sterility caused by long-term high temperature (HT) stress occurs widely in crops. MicroRNAs (miRNAs), a class of endogenous non-coding small RNAs, play an important role in the plant response to various abiotic stresses. To dissect the working principle of miRNAs in male sterility under HT stress in cotton, a total of 112 known miRNAs, 270 novel miRNAs and 347 target genes were identified from anthers of HT-insensitive (84021) and HT-sensitive (H05) cotton cultivars under normal temperature (NT) and HT conditions through small RNA and degradome sequencing...
June 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28633390/investigating-microrna-mediated-regulation-of-the-nascent-nuclear-transcripts-in-plants-a-bioinformatics-workflow
#9
Dongliang Yu, Zhonghai Tang, Chaogang Shao, Xiaoxia Ma, Taihe Xiang, Zhihong Fan, Huizhong Wang, Yijun Meng
Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO) loading and subsequent target binding. Recently, this notion was challenged by increasing pieces of evidence in the animal cells that uncovered the nuclear importation and action of the AGO-associated miRNAs...
June 14, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28627779/new-horizon-for-breast-cancer-biomarker-discoveries-what-might-the-liquid-biopsy-of-nipple-aspirate-fluid-hold
#10
Ferdinando Mannello
The existence of cellular, molecular and biochemical heterogeneity of human breast cancers reveals the intricacy of biomarkers complexity, stimulating studies on new approaches (like "liquid biopsies") for the improvements in precision medicine. Breast cancer is recognized as a leading cause of morbidity and mortality worldwide with tumors significantly diverse and containing many types of cells showing different genetic and epigenetic profiles. In this field, the technology of liquid biopsy (applied to a fluid produced by breast gland, named nipple aspirate fluids, NAF) highlights the power of combining basic and clinical research...
June 19, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28608337/identification-of-argonaute-small-rna-cleavage-sites-by-degradome-sequencing
#11
Ivett Baksa, György Szittya
The method described here enables the high-throughput identification of cleaved mRNA targets of ARGONAUTE/small RNA complexes. The protocol is based on a modified 5'-rapid amplification of cDNA ends combined with deep sequencing of 3' cleavage products of mRNAs. Poly(A) RNA is purified from the tissue of interest which is followed by a 5'-RNA adapter ligation. The ligated products are then reverse transcribed, amplified, and digested with MmeI. After gel separation, a 3' double-stranded DNA adapter is ligated to the fragments, which are then amplified and index labeled for the high-throughput sequencing of pooled degradome libraries...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28603532/identification-of-salt-tolerance-related-micrornas-and-their-targets-in-maize-zea-mays-l-using-high-throughput-sequencing-and-degradome-analysis
#12
Rong Fu, Mi Zhang, Yinchuan Zhao, Xuechuan He, Chenyun Ding, Shuangkuai Wang, Yan Feng, Xianliang Song, Ping Li, Baohua Wang
To identify the known and novel microRNAs (miRNAs) and their targets that are involved in the response and adaptation of maize (Zea mays) to salt stress, miRNAs and their targets were identified by a combined analysis of the deep sequencing of small RNAs (sRNA) and degradome libraries. The identities were confirmed by a quantitative expression analysis with over 100 million raw reads of sRNA and degradome sequences. A total of 1040 previously known miRNAs were identified from four maize libraries, with 762 and 726 miRNAs derived from leaves and roots, respectively, and 448 miRNAs that were common between the leaves and roots...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28600507/global-gene-expression-defines-faded-whorl-specification-of-double-flower-domestication-in-camellia
#13
Xinlei Li, Jiyuan Li, Zhengqi Fan, Zhongchi Liu, Takayuki Tanaka, Hengfu Yin
Double flowers in cultivated camellias are divergent in floral patterns which present a rich resource for demonstrating molecular modifications influenced by the human demands. Despite the key principle of ABCE model in whorl specification, the underlying mechanism of fine-tuning double flower formation remains largely unclear. Here a comprehensive comparative transcriptomics interrogation of gene expression among floral organs of wild type and "formal double" and "anemone double" is presented. Through a combination of transcriptome, small RNA and "degradome" sequencing, we studied the regulatory gene expression network underlying the double flower formation...
June 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28596514/genome-wide-identification-and-characterization-of-phased-small-interfering-rna-genes-in-response-to-botrytis-cinerea-infection-in-solanum-lycopersicum
#14
Fangli Wu, Yue Chen, Xing Tian, Xiaole Zhu, Weibo Jin
Phased small interfering RNAs (phasiRNAs) are encoded by a novel class of genes known as phasiRNA producing (PHAS) genes. These genes play important regulatory roles by targeting protein coding transcripts in plant species. In this study, 91 regions were identified as potential PHAS loci in tomato, with additional evidence that seven of them can be triggered by five miRNAs. Among the identified loci, 51 were located in genic regions, and the remaining 40 were located in intergenic regions. The transient overexpression of PHAS15 and PHAS26 demonstrated that phasiRNAs predicted by PhaseTank were indeed generated from their respective PHAS loci...
June 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28594355/comparing-proteolytic-fingerprints-of-antigen-presenting-cells-during-allergen-processing
#15
Heidi Hofer, Tamara Weidinger, Peter Briza, Claudia Asam, Martin Wolf, Teresa E Twaroch, Frank Stolz, Angela Neubauer, Elfriede Dall, Peter Hammerl, Alain Jacquet, Michael Wallner
Endolysosomal processing has a critical influence on immunogenicity as well as immune polarization of protein antigens. In industrialized countries, allergies affect around 25% of the population. For the rational design of protein-based allergy therapeutics for immunotherapy, a good knowledge of T cell-reactive regions on allergens is required. Thus, we sought to analyze endolysosomal degradation patterns of inhalant allergens. Four major allergens from ragweed, birch, as well as house dust mites were produced as recombinant proteins...
June 8, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28587273/proteases-of-dermatophagoides-pteronyssinus
#16
Thomas A Randall, Robert E London, Michael C Fitzgerald, Geoffrey A Mueller
Since the discovery that Der p 1 is a cysteine protease, the role of proteolytic activity in allergic sensitization has been explored. There are many allergens with proteolytic activity; however, exposure from dust mites is not limited to allergens. In this paper, genomic, transcriptomic and proteomic data on Dermatophagoides pteronyssinus (DP) was mined for information regarding the complete degradome of this house dust mite. D. pteronyssinus has more proteases than the closely related Acari, Dermatophagoides farinae (DF) and Sarcoptes scabiei (SS)...
June 6, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28572808/transcriptome-wide-analysis-of-botrytis-elliptica-responsive-micrornas-and-their-targets-in-lilium-regale-wilson-by-high-throughput-sequencing-and-degradome-analysis
#17
Xue Gao, Qi Cui, Qin-Zheng Cao, Qiang Liu, Heng-Bin He, Dong-Mei Zhang, Gui-Xia Jia
MicroRNAs, as master regulators of gene expression, have been widely identified and play crucial roles in plant-pathogen interactions. A fatal pathogen, Botrytis elliptica, causes the serious folia disease of lily, which reduces production because of the high susceptibility of most cultivated species. However, the miRNAs related to Botrytis infection of lily, and the miRNA-mediated gene regulatory networks providing resistance to B. elliptica in lily remain largely unexplored. To systematically dissect B. elliptica-responsive miRNAs and their target genes, three small RNA libraries were constructed from the leaves of Lilium regale, a promising Chinese wild Lilium species, which had been subjected to mock B...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28559305/biochemical-and-functional-characterization-of-the-human-tissue-kallikrein-9
#18
Panagiota S Filippou, Sofia Farkona, Davor Brinc, Yijing Yu, Ioannis Prassas, Eleftherios P Diamandis
Human tissue kallikrein 9 (KLK9) is a member of the kallikrein-related family of proteases. Despite its known expression profile, much less is known about the functional roles of this protease and its implications in normal physiology and disease. We present here the first data on the biochemical characterization of KLK9, investigate parameters that affect its enzymatic activity (such as inhibitors) and provide preliminary insights into its putative substrates. We show that mature KLK9 (mat-KLK9) is a glycosylated chymotrypsin-like enzyme with strong preference for tyrosine over phenylalanine at the P1 cleavage position...
May 30, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28508371/efficient-and-accurate-algorithm-for-cleaved-fragments-prediction-cfpa-in-protein-sequences-dataset-based-on-consensus-and-its-variants-a-novel-degradomics-prediction-application
#19
Atlal El-Assaad, Zaher Dawy, Georges Nemer, Hazem Hajj, Firas H Kobeissy
Degradomics is a novel discipline that involves determination of the proteases/substrate fragmentation profile, called the substrate degradome, and has been recently applied in different disciplines. A major application of degradomics is its utility in the field of biomarkers where the breakdown products (BDPs) of different protease have been investigated. Among the major proteases assessed, calpain and caspase proteases have been associated with the execution phases of the pro-apoptotic and pro-necrotic cell death, generating caspase/calpain-specific cleaved fragments...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28508358/degradomics-in-neurotrauma-profiling-traumatic-brain-injury
#20
Hadi Abou-El-Hassan, Fares Sukhon, Edwyn Jeremy Assaf, Hisham Bahmad, Hussein Abou-Abbass, Hussam Jourdi, Firas H Kobeissy
Degradomics has recently emerged as a subdiscipline in the omics era with a focus on characterizing signature breakdown products implicated in various disease processes. Driven by promising experimental findings in cancer, neuroscience, and metabolomic disorders, degradomics has significantly promoted the notion of disease-specific "degradome." A degradome arises from the activation of several proteases that target specific substrates and generate signature protein fragments. Several proteases such as calpains, caspases, cathepsins, and matrix metalloproteinases (MMPs) are involved in the pathogenesis of numerous diseases that disturb the physiologic balance between protein synthesis and protein degradation...
2017: Methods in Molecular Biology
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