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translational proteomics

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https://www.readbyqxmd.com/read/27911187/fxr1a-associated-micrornp-a-driver-of-specialized-non-canonical-translation-in-quiescent-conditions
#1
Syed I A Bukhari, Shobha Vasudevan
Eukaryotic protein synthesis is a multifaceted process that requires coordination of a set of translation factors in a particular cellular state. During normal growth and proliferation, cells generally make their proteome via conventional translation that utilizes canonical translation factors. When faced with environmental stress such as growth factor deprivation, or in response to biological cues such as developmental signals, cells can have stalled canonical translation. In this situation, cells adapt alternative modes of translation to make specific proteins necessary for required biological functions under these distinct conditions...
December 2, 2016: RNA Biology
https://www.readbyqxmd.com/read/27902743/itraq-based-quantitative-proteomic-analysis-of-spirulina-platensis-in-response-to-low-temperature-stress
#2
Qingye Li, Rong Chang, Yijun Sun, Bosheng Li
Low temperature (LT) is one of the most important abiotic stresses that can significantly reduce crop yield. To gain insight into how Spirulina responds to LT stress, comprehensive physiological and proteomic analyses were conducted in this study. Significant decreases in growth and pigment levels as well as excessive accumulation of compatible osmolytes were observed in response to LT stress. An isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach was used to identify changes in protein abundance in Spirulina under LT...
2016: PloS One
https://www.readbyqxmd.com/read/27899286/natural-mitochondrial-proteolysis-confirms-transcription-systematically-exchanging-deleting-nucleotides-peptides-coded-by-expanded-codons
#3
Hervé Seligmann
Protein sequences have higher linguistic complexities than human languages. This indicates undeciphered multilayered, overprinted information/genetic codes. Some superimposed genetic information is revealed by detections of transcripts systematically (a) exchanging nucleotides (nine symmetric, e.g. A<->C, fourteen asymmetric, e.g. A->C->G->A, swinger RNAs) translated according to tri-, tetra- and pentacodons, and (b) deleting mono-, dinucleotides after each trinucleotide (delRNAs). Here analyses of two independent proteomic datasets considering natural proteolysis confirm independently translation of these non-canonical RNAs, also along tetra- and pentacodons, increasing coverage of putative, cryptically encoded proteins...
November 26, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27898073/proteomic-analysis-of-the-postsynaptic-density-implicates-synaptic-function-and-energy-pathways-in-bipolar-disorder
#4
M Föcking, P Dicker, L M Lopez, M Hryniewiecka, K Wynne, J A English, G Cagney, D R Cotter
The postsynaptic density (PSD) contains a complex set of proteins of known relevance to neuropsychiatric disorders such as schizophrenia and bipolar disorder. We enriched for this anatomical structure in the anterior cingulate cortex of 16 bipolar disorder samples and 20 controls from the Stanley Medical Research Institute. Unbiased shotgun proteomics incorporating label-free quantitation was used to identify differentially expressed proteins. Quantitative investigation of the PSD identified 2033 proteins, among which 288 were found to be differentially expressed...
November 29, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27897006/session-introduction
#5
Nikolay Samusik, Nima Aghaeepour, Sean Bendall
Recent technological developments allow gathering single-cell measurements across different domains (genomic, transcriptomics, proteomics, imaging etc). Sophisticated computational algorithms are required in order to harness the power of single-cell data. This session is dedicated to computational methods for single-cell analysis in various biological domains, modelling of population heterogeneity, as well as translational applications of single cell data.
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896924/detailed-tail-proteomic-analysis-of-axolotl-ambystoma-mexicanum-using-an-mrna-seq-reference-database
#6
Turan Demircan, Ilknur Keskin, Seda Nilgun Dumlu, Nilufer Ayturk, Mahmut Erhan Avsaroglu, Emel Akgun, Gurkan Ozturk, Ahmet Tarik Baykal
Salamander Axolotl has been emerging as an important model for stem cell research due to its powerful regenerative capacity. Several advantages, such as the high capability of advanced tissue, organ and appendages regeneration, promote Axolotl as an ideal model system to extend our current understanding on the mechanisms of regeneration. Acknowledging the common molecular pathways between amphibians and mammals, there is a great potential to translate the messages from Axolotl research to mammalian studies...
November 29, 2016: Proteomics
https://www.readbyqxmd.com/read/27896764/pulsed-silac-as-a-approach-for-mirna-targets-identification-in-cell-culture
#7
Daniella E Duque-Guimarães, Juliana de Almeida-Faria, Thomas Prates Ong, Susan E Ozanne
Pulsed stable isotope labeling by amino acids in cell culture (pSILAC) comprises a variation of the classical SILAC proteomic methodology that enables the identification of short-term proteomic responses such as those elicited by micro RNAs (miRNAs). Here, we describe a detailed pSILAC protocol for global identification and quantification of protein translation alterations induced by a miRNA using 3T3-L1 pre-adipocytes as a model system.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895655/protein-tyrosine-nitration-during-development-and-abiotic-stress-response-in-plants
#8
REVIEW
Capilla Mata-Pérez, Juan C Begara-Morales, Mounira Chaki, Beatriz Sánchez-Calvo, Raquel Valderrama, María N Padilla, Francisco J Corpas, Juan B Barroso
In recent years, the study of nitric oxide (NO) in plant systems has attracted the attention of many researchers. A growing number of investigations have shown the significance of NO as a signal molecule or as a molecule involved in the response against (a)biotic processes. NO can be responsible of the post-translational modifications (NO-PTM) of target proteins by mechanisms such as the nitration of tyrosine residues. The study of protein tyrosine nitration during development and under biotic and adverse environmental conditions has increased in the last decade; nevertheless, there is also an endogenous nitration which seems to have regulatory functions...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27895219/primer-in-genetics-and-genomics-article-1-dna-genes-and-chromosomes
#9
Janice S Dorman, Mandy J Schmella, Susan W Wesmiller
Precision medicine refers to the practice of determining a patient's unique genetic, biomarker, and other characteristics for the purpose of improving his or her clinical outcomes. Not all patients with the same clinical diagnosis respond equally to identical treatment regimens. By examining patients at the molecular level, health-care providers will be better able to apply the most effective therapies that each individual requires. To understand precision medicine, nurses must have a solid understanding of genomics and proteomics...
November 28, 2016: Biological Research for Nursing
https://www.readbyqxmd.com/read/27895139/human-spermatozoa-quantitative-proteomic-signature-classifies-normo-and-asthenozoospermia
#10
Mayank Saraswat, Sakari Joenväärä, Tushar Jain, Anil Kumar Tomar, Ashima Sinha, Sarman Singh, Savita Yadav, Risto Renkonen
Scarcely understood defects lead to asthenozoospermia which results in poor fertility outcomes. Incomplete knowledge of these defects hinders the development of new therapies and reliance on interventional therapies, such as in vitro fertilization, increases. Sperm cells, being transcriptionally and translationally silent, necessitate the proteomic approach to study the sperm function. We have performed a differential proteomics analysis of human sperm and seminal plasma and identified and quantified 667 proteins in sperm and 429 proteins in seminal plasma dataset which were used for further analysis...
November 28, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27888141/a-glimpse-into-the-modulation-of-post-translational-modifications-of-human-colonizing-bacteria
#11
REVIEW
Paulo André Dias Bastos, João Pinto da Costa, Rui Vitorino
Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health...
November 22, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27888076/proteome-wide-identification-of-lysine-succinylation-in-thermophilic-and-mesophilic-bacteria
#12
Hiroki Okanishi, Kwang Kim, Kenji Fukui, Takato Yano, Seiki Kuramitsu, Ryoji Masui
Lysine succinylation, one of post-translational acylations conserved from eukaryotes to bacteria, plays regulatory roles in various cellular processes. However, much remains unknown about the general and specific characteristics of lysine succinylation among bacteria, and about its functions different from those of other acylations. In this study, we characterized lysine succinylation, a newly discovered widespread type of lysine acylation in five bacterial species with different characteristics such as optimal growth temperature and cell wall structure...
November 22, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27886187/plasma-proteomic-study-in-pulmonary-arterial-hypertension-associated-with-congenital-heart-diseases
#13
Xi Zhang, Hai-Tao Hou, Jun Wang, Xiao-Cheng Liu, Qin Yang, Guo-Wei He
Pulmonary arterial hypertension associated with congenital heart disease (CHD-PAH) has serious consequence and plasma protein profiles in CHD-PAH are unknown. We aimed to reveal the differential plasma proteins in 272 CHD patients with or without PAH. Various types of CHD-PAH were studied. Differential plasma proteins were first detected by iTRAQ proteomic technology and those with significant clinical relevance were selected for further ELISA validation in new cohort of patients. Among the 190 differential plasma proteins detected by iTRAQ, carbamoyl-phosphate synthetase I (CPSI, related to urea cycle and endogenous nitric oxide production) and complement factor H-related protein 2 (CFHR2, related to complement system and coagulant mechanism) were selected for further ELISA validation in new cohort of 152 patients...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27883048/proteomic-profile-of-the-bradysia-odoriphaga-in-response-to-the-microbial-secondary-metabolite-benzothiazole
#14
Yunhe Zhao, Kaidi Cui, Chunmei Xu, Qiuhong Wang, Yao Wang, Zhengqun Zhang, Feng Liu, Wei Mu
Benzothiazole, a microbial secondary metabolite, has been demonstrated to possess fumigant activity against Sclerotinia sclerotiorum, Ditylenchus destructor and Bradysia odoriphaga. However, to facilitate the development of novel microbial pesticides, the mode of action of benzothiazole needs to be elucidated. Here, we employed iTRAQ-based quantitative proteomics analysis to investigate the effects of benzothiazole on the proteomic expression of B. odoriphaga. In response to benzothiazole, 92 of 863 identified proteins in B...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27882306/personalized-proteomics-the-future-of-precision-medicine
#15
Trevor T Duarte, Charles T Spencer
Medical diagnostics and treatment has advanced from a one size fits all science to treatment of the patient as a unique individual. Currently, this is limited solely to genetic analysis. However, epigenetic, transcriptional, proteomic, posttranslational modifications, metabolic, and environmental factors influence a patient's response to disease and treatment. As more analytical and diagnostic techniques are incorporated into medical practice, the personalized medicine initiative transitions to precision medicine giving a holistic view of the patient's condition...
2016: Proteomes
https://www.readbyqxmd.com/read/27879264/differential-regulation-of-the-melanoma-proteome-by-eif4a1-and-eif4e
#16
Cailin E Joyce, Adrienne G Yanez, Akihiro Mori, Akinori Yoda, Johanna S Carroll, Carl D Novina
Small molecules and antisense oligonucleotides that inhibit the translation initiation factors eIF4A1 and eIF4E have been explored as broad-based therapeutic agents for cancer treatment, based on the frequent upregulation of these two subunits of the eIF4F cap-binding complex in many cancer cells. Here we provide support for these therapeutic approaches with mechanistic studies of eIF4F-driven tumor progression in a preclinical model of melanoma. Silencing eIF4A1 or eIF4E decreases melanoma proliferation and invasion...
November 22, 2016: Cancer Research
https://www.readbyqxmd.com/read/27877135/metabolomics-of-head-and-neck-cancer-a-mini-review
#17
REVIEW
Jae M Shin, Pachiyappan Kamarajan, J Christopher Fenno, Alexander H Rickard, Yvonne L Kapila
Metabolomics is used in systems biology to enhance the understanding of complex disease processes, such as cancer. Head and neck cancer (HNC) is an epithelial malignancy that arises in the upper aerodigestive tract and affects more than half a million people worldwide each year. Recently, significant effort has focused on integrating multiple "omics" technologies for oncological research. In particular, research has been focused on identifying tumor-specific metabolite profiles using different sample types (biological fluids, cells and tissues) and a variety of metabolomic platforms and technologies...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27876621/translational-resistivity-conductivity-of-coding-sequences-during-exponential-growth-of-escherichia-coli
#18
Kazuyuki Takai
Codon adaptation index (CAI) has been widely used for prediction of expression of recombinant genes in Escherichia coli and other organisms. However, CAI has no mechanistic basis that rationalizes its application to estimation of translational efficiency. Here, I propose a model based on which we could consider how codon usage is related to the level of expression during exponential growth of bacteria. In this model, translation of a gene is considered as an analog of electric current, and an analog of electric resistance corresponding to each gene is considered...
November 19, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27874045/morphological-and-proteomic-analysis-of-biofilms-from-the-antarctic-archaeon-halorubrum-lacusprofundi
#19
Y Liao, T J Williams, J Ye, J Charlesworth, B P Burns, A Poljak, M J Raftery, R Cavicchioli
Biofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27871150/integrated-proteomics-and-metabolomics-suggests-symbiotic-metabolism-and-multimodal-regulation-in-a-fungal-endobacterial-system
#20
Zhou Li, Qiuming Yao, Stephen P Dearth, Matthew R Entler, Hector F Castro Gonzalez, Jessie K Uehling, Rytas J Vilgalys, Gregory B Hurst, Shawn R Campagna, Jessy L Labbé, Chongle Pan
Many plant-associated fungi host endosymbiotic endobacteria with reduced genomes. While endobacteria play important roles in these tri-partite plant-fungal-endobacterial systems, the active physiology of fungal endobacteria has not been characterized extensively by systems biology approaches. Here, we use integrated proteomics and metabolomics to characterize the relationship between the endobacterium Mycoavidus sp. and the root-associated fungus Mortierella elongata. In nitrogen-poor media, M. elongata had decreased growth but hosted a large and growing endobacterial population...
November 21, 2016: Environmental Microbiology
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