scholarly journals A hidden human proteome encoded by ‘non-coding’ genes

2019 ◽  
Vol 47 (15) ◽  
pp. 8111-8125 ◽  
Author(s):  
Shaohua Lu ◽  
Jing Zhang ◽  
Xinlei Lian ◽  
Li Sun ◽  
Kun Meng ◽  
...  
Keyword(s):  
Multiple Reaction Monitoring ◽  
Chemical Properties ◽  
Shotgun Proteomics ◽  
Ribosome Profiling ◽  
Translation Efficiency ◽  
Reaction Monitoring ◽  
Translation Elongation ◽  
Protein Functions ◽  
Human Proteins ◽  
Physical And Chemical

Abstract It has been a long debate whether the 98% ‘non-coding’ fraction of human genome can encode functional proteins besides short peptides. With full-length translating mRNA sequencing and ribosome profiling, we found that up to 3330 long non-coding RNAs (lncRNAs) were bound to ribosomes with active translation elongation. With shotgun proteomics, 308 lncRNA-encoded new proteins were detected. A total of 207 unique peptides of these new proteins were verified by multiple reaction monitoring (MRM) and/or parallel reaction monitoring (PRM); and 10 new proteins were verified by immunoblotting. We found that these new proteins deviated from the canonical proteins with various physical and chemical properties, and emerged mostly in primates during evolution. We further deduced the protein functions by the assays of translation efficiency, RNA folding and intracellular localizations. As the new protein UBAP1-AST6 is localized in the nucleoli and is preferentially expressed by lung cancer cell lines, we biologically verified that it has a function associated with cell proliferation. In sum, we experimentally evidenced a hidden human functional proteome encoded by purported lncRNAs, suggesting a resource for annotating new human proteins.

scholarly journals Efficient Data Mining Algorithms for Screening Potential Proteins of Drug Target

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Qi Wang ◽  
JinCai Huang ◽  
YangHe Feng ◽  
JiaWei Fei
Keyword(s):  
Decision Trees ◽  
Drug Target ◽  
Drug Targets ◽  
Chemical Properties ◽  
Superior Performance ◽  
Target Proteins ◽  
Data Mining Algorithms ◽  
Open Access Database ◽  
Human Proteins ◽  
Physical And Chemical

The past few decades have witnessed the boom in pharmacology as well as the dilemma of drug development. Playing a crucial role in drug design, the screening of potential human proteins of drug targets from open access database with well-measured physical and chemical properties is a task of challenge but significance. In this paper, the screening of potential drug target proteins (DTPs) from a fine collected dataset containing 5376 unlabeled proteins and 517 known DTPs was researched. Our objective is to screen potential DTPs from the 5376 proteins. Here we proposed two strategies assisting the construction of dataset of reliable nondrug target proteins (NDTPs) and then bagging of decision trees method was employed in the final prediction. Such two-stage algorithms have shown their effectiveness and superior performance on the testing set. Both of the algorithms maintained higher recall ratios of DTPs, respectively, 93.5% and 97.4%. In one turn of experiments, strategy1-based bagging of decision trees algorithm screened about 558 possible DTPs while 1782 potential DTPs were predicted in the second algorithm. Besides, two strategy-based algorithms showed the consensus of the predictions in the results, with approximately 442 potential DTPs in common. These selected DTPs provide reliable choices for further verification based on biomedical experiments.

scholarly journals Multiple-Reaction Monitoring–Mass Spectrometric Assays Can Accurately Measure the Relative Protein Abundance in Complex Mixtures

2012 ◽  
Vol 58 (4) ◽  
pp. 777-781 ◽  
Author(s):  
Andrew N Hoofnagle ◽  
Jessica O Becker ◽  
Michael N Oda ◽  
Giorgio Cavigiolio ◽  
Philip Mayer ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Isotope Dilution ◽  
Matrix Effects ◽  
Multiple Reaction Monitoring ◽  
Internal Standard ◽  
Shotgun Proteomics ◽  
Mass Spectrometric ◽  
Reaction Monitoring ◽  
Label Free ◽  
Operating Characteristics

Abstract BACKGROUND Mass spectrometric assays could potentially replace protein immunoassays in many applications. Previous studies have demonstrated the utility of liquid chromatography–multiple-reaction monitoring–mass spectrometry (LC-MRM/MS) for the quantification of proteins in biological samples, and many examples of the accuracy of these approaches to quantify supplemented analytes have been reported. However, a direct comparison of multiplexed assays that use LC-MRM/MS with established immunoassays to measure endogenous proteins has not been reported. METHODS We purified HDL from the plasma of 30 human donors and used label-free shotgun proteomics approaches to analyze each sample. We then developed 2 different isotope-dilution LC-MRM/MS 6-plex assays (for apoliporoteins A-I, C-II, C-III, E, B, and J): 1 assay used stable isotope-labeled peptides and the other used stable isotope-labeled apolipoprotein A-I (an abundant HDL protein) as an internal standard to control for matrix effects and mass spectrometer performance. The shotgun and LC-MRM/MS assays were then compared with commercially available immunoassays for each of the 6 analytes. RESULTS Relative quantification by shotgun proteomics approaches correlated poorly with the 6 protein immunoassays. In contrast, the isotope dilution LC-MRM/MS approaches showed correlations with immunoassays of r = 0.61–0.96. The LC-MRM/MS approaches had acceptable reproducibility (<13% CV) and linearity (r ≥0.99). Strikingly, a single protein internal standard applied to all proteins performed as well as multiple protein-specific peptide internal standards. CONCLUSIONS Because peak area ratios measured in multiplexed LC-MRM/MS assays correlate well with immunochemical measurements and have acceptable operating characteristics, we propose that LC-MRM/MS could be used to replace immunoassays in a variety of settings.

Tandem Mass Spectrometry in Physiology

Physiology ◽  
2007 ◽  
Vol 22 (6) ◽  
pp. 390-400 ◽  
Author(s):  
Trairak Pisitkun ◽  
Jason D. Hoffert ◽  
Ming-Jiun Yu ◽  
Mark A. Knepper
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Tandem Mass Spectrometry ◽  
Recent Progress ◽  
Multiple Reaction Monitoring ◽  
Complex Mixture ◽  
Shotgun Proteomics ◽  
Cell Physiology ◽  
Tandem Mass ◽  
Reaction Monitoring

Tandem mass spectrometry coupled to liquid chromatography (LC-MS/MS) allows identification of proteins in a complex mixture without need for protein purification (“shotgun” proteomics). Recent progress in LC-MS/MS-based quantification, phosphoproteomic analysis, and targeted LC-MS/MS using multiple reaction monitoring (MRM) has made LC-MS/MS a powerful tool for the study of cell physiology.

scholarly journals Full-length ribosome density prediction by a multi-input and multi-output model

2021 ◽  
Vol 17 (3) ◽  
pp. e1008842
Author(s):  
Tingzhong Tian ◽  
Shuya Li ◽  
Peng Lang ◽  
Dan Zhao ◽  
Jianyang Zeng
Keyword(s):  
Ribosome Profiling ◽  
Full Length ◽  
Translation Efficiency ◽  
Long Distance ◽  
Translation Elongation ◽  
Coding Sequence ◽  
Density Distributions ◽  
Density Prediction ◽  
Ribosome Density ◽  
Elongation Process

Translation elongation is regulated by a series of complicated mechanisms in both prokaryotes and eukaryotes. Although recent advance in ribosome profiling techniques has enabled one to capture the genome-wide ribosome footprints along transcripts at codon resolution, the regulatory codes of elongation dynamics are still not fully understood. Most of the existing computational approaches for modeling translation elongation from ribosome profiling data mainly focus on local contextual patterns, while ignoring the continuity of the elongation process and relations between ribosome densities of remote codons. Modeling the translation elongation process in full-length coding sequence (CDS) level has not been studied to the best of our knowledge. In this paper, we developed a deep learning based approach with a multi-input and multi-output framework, named RiboMIMO, for modeling the ribosome density distributions of full-length mRNA CDS regions. Through considering the underlying correlations in translation efficiency among neighboring and remote codons and extracting hidden features from the input full-length coding sequence, RiboMIMO can greatly outperform the state-of-the-art baseline approaches and accurately predict the ribosome density distributions along the whole mRNA CDS regions. In addition, RiboMIMO explores the contributions of individual input codons to the predictions of output ribosome densities, which thus can help reveal important biological factors influencing the translation elongation process. The analyses, based on our interpretable metric named codon impact score, not only identified several patterns consistent with the previously-published literatures, but also for the first time (to the best of our knowledge) revealed that the codons located at a long distance from the ribosomal A site may also have an association on the translation elongation rate. This finding of long-range impact on translation elongation velocity may shed new light on the regulatory mechanisms of protein synthesis. Overall, these results indicated that RiboMIMO can provide a useful tool for studying the regulation of translation elongation in the range of full-length CDS.

Statistical criteria of stellar population types

1966 ◽  
Vol 24 ◽  
pp. 101-110
Author(s):  
W. Iwanowska
Keyword(s):  
Stellar Population ◽  
Chemical Properties ◽  
Spectrophotometric Study ◽  
Physical And Chemical Properties ◽  
Population Type ◽  
The Galaxy ◽  
Distribution Parameters ◽  
Physical And Chemical ◽  
Statistical Criteria ◽  
And Chemical Properties

In connection with the spectrophotometric study of population-type characteristics of various kinds of stars, a statistical analysis of kinematical and distribution parameters of the same stars is performed at the Toruń Observatory. This has a twofold purpose: first, to provide a practical guide in selecting stars for observing programmes, second, to contribute to the understanding of relations existing between the physical and chemical properties of stars and their kinematics and distribution in the Galaxy.

Biophysical Measurement of Molecular Weight of Foot-and-Mouth Disease RNA Fragments

1974 ◽  
Vol 32 ◽  
pp. 262-263
Author(s):  
Sydney S. Breese ◽  
Howard L. Bachrach
Keyword(s):  
Chemical Properties ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Distilled Water ◽  
Bovine Plasma ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Carbon Coated ◽  
Rna Fragments ◽  
Physical And Chemical

Continuing studies on the physical and chemical properties of foot-and-mouth disease virus (FMDV) have included electron microscopy of RNA strands released when highly purified virus (1) was dialyzed against demlneralized distilled water. The RNA strands were dried on formvar-carbon coated electron microscope screens pretreated with 0.1% bovine plasma albumin in distilled water. At this low salt concentration the RNA strands were extended and were stained with 1% phosphotungstic acid. Random dispersions of strands were recorded on electron micrographs, enlarged to 30,000 or 40,000 X and the lengths measured with a map-measuring wheel. Figure 1 is a typical micrograph and Fig. 2 shows the distributions of strand lengths for the three major types of FMDV (A119 of 6/9/72; C3-Rezende of 1/5/73; and O1-Brugge of 8/24/73.

Tailoring microstructures of materials through biomimetics

1993 ◽  
Vol 51 ◽  
pp. 500-501
Author(s):  
Mehmet Sarikaya ◽  
Ilhan A. Aksay
Keyword(s):  
Chemical Properties ◽  
Design And Synthesis ◽  
Structure Sensitive ◽  
Macro Scale ◽  
Methods Of Synthesis ◽  
Successive Level ◽  
Engineering Materials ◽  
Physical And Chemical ◽  
And Chemical Properties ◽  
Synthesis Of Materials

Biomimetics involves investigation of structure, function, and methods of synthesis of biological composite materials. The goal is to apply this information to the design and synthesis of materials for engineering applications.Properties of engineering materials are structure sensitive through the whole spectrum of dimensions from nanometer to macro scale. The goal in designing and processing of technological materials, therefore, is to control microstructural evolution at each of these dimensions so as to achieve predictable physical and chemical properties. Control at each successive level of dimension, however, is a major challenge as is the retention of integrity between successive levels. Engineering materials are rarely fabricated to achieve more than a few of the desired properties and the synthesis techniques usually involve high temperature or low pressure conditions that are energy inefficient and environmentally damaging.In contrast to human-made materials, organisms synthesize composites whose intricate structures are more controlled at each scale and hierarchical order.

Response of corn (Zea mays L.) to various organic-based fertilizers in marginal upland of Sta. Rita, Samar

2017 ◽  
pp. 31-43
Author(s):  
Berta Ratilla ◽  
Loreme Cagande ◽  
Othello Capuno
Keyword(s):  
Block Design ◽  
Management Strategies ◽  
Chemical Properties ◽  
Organic Fertilizers ◽  
Growth And Yield ◽  
Physical And Chemical Properties ◽  
Total N ◽  
Randomized Complete Block Design ◽  
Physical And Chemical ◽  
And Chemical Properties

Organic farming is one of the management strategies that improve productivity of marginal uplands. The study aimed to: (1) evaluate effects of various organic-based fertilizers on the growth and yield of corn; (2) determine the appropriate combination for optimum yield; and (3) assess changes on the soil physical and chemical properties. Experiment was laid out in Randomized Complete Block Design, with 3 replications and 7 treatments, namely; T0=(0-0-0); T1=1t ha-1 Evans + 45-30-30kg N, P2O5, K2O ha-1; T2=t ha-1 Wellgrow + 45-30-30kg N, P2O5, K2O ha-1; T3=15t ha-1 chicken dung; T4=10t ha-1 chicken dung + 45-30-30kg N, P2O5, K2O ha-1; T5=15t ha-1 Vermicast; and T6=10t ha-1 Vermicast + 45-30-30kg N, P2O5, K2O ha-1. Application of organic-based fertilizers with or without inorganic fertilizers promoted growth of corn than the control. But due to high infestation of corn silk beetle(Monolepta bifasciata Horns), its grain yield was greatly affected. In the second cropping, except for Evans, any of these fertilizers applied alone or combined with 45-30-30kg N, P2O5, K2O ha-1 appeared appropriate in increasing corn earyield. Soil physical and chemical properties changed with addition of organic fertilizers. While bulk density decreased irrespective of treatments, pH, total N, available P and exchangeable K generally increased more with chicken dung application.

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