scholarly journals The involvement of the novel proteins, perilipin, ATGL, and CGI-58, in lipolysis of early and mid lactation Holstein cows

2008 ◽  
Author(s):  
Dawn Elkins
Keyword(s):  
Holstein Cows ◽  
The Novel ◽  
Novel Proteins

scholarly journals C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking

2011 ◽  
Vol 22 (12) ◽  
pp. 2083-2093 ◽  
Author(s):  
P. James Scrivens ◽  
Baraa Noueihed ◽  
Nassim Shahrzad ◽  
Sokunthear Hul ◽  
Stephanie Brunet ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Multidisciplinary Approach ◽  
Early Stage ◽  
Binary Interaction ◽  
The Novel ◽  
Novel Proteins ◽  
Bona Fide ◽  
Interaction Map ◽  
Equivalent Complex

TRAPP is a multisubunit tethering complex implicated in multiple vesicle trafficking steps in Saccharomyces cerevisiae and conserved throughout eukarya, including humans. Here we confirm the role of TRAPPC2L as a stable component of mammalian TRAPP and report the identification of four novel components of the complex: C4orf41, TTC-15, KIAA1012, and Bet3L. Two of the components, KIAA1012 and Bet3L, are mammalian homologues of Trs85p and Bet3p, respectively. The remaining two novel TRAPP components, C4orf41 and TTC-15, have no homologues in S. cerevisiae. With this work, human homologues of all the S. cerevisiae TRAPP proteins, with the exception of the Saccharomycotina-specific subunit Trs65p, have now been reported. Through a multidisciplinary approach, we demonstrate that the novel proteins are bona fide components of human TRAPP and implicate C4orf41 and TTC-15 (which we call TRAPPC11 and TRAPPC12, respectively) in ER-to-Golgi trafficking at a very early stage. We further present a binary interaction map for all known mammalian TRAPP components and evidence that TRAPP oligomerizes. Our data are consistent with the absence of a TRAPP I–equivalent complex in mammalian cells, suggesting that the fundamental unit of mammalian TRAPP is distinct from that characterized in S. cerevisiae.

scholarly journals Metals, non-metals and minerals: The complexity of bacterial selenate respiration

2012 ◽  
Vol 34 (5) ◽  
pp. 23-27
Author(s):  
Clive S. Butler
Keyword(s):  
Electron Transfer ◽  
Electron Acceptors ◽  
Elemental Selenium ◽  
The Novel ◽  
Novel Proteins ◽  
New Family ◽  
Recent Advances ◽  
Wide Range ◽  
Sequential Reduction ◽  
Shed Light

Metalloproteins and enzymes are an essential part of all respiratory electron-transfer chains and provide a pathway for electron transfer to terminal electron acceptors. Since bacteria can utilize a wide range of respiratory substrates, this variety of potential electron acceptors has facilitated the need for many different respiratory metalloproteins. Bacterial selenate respiration requires the sequential reduction of the selenium oxyanions selenate and selenite resulting in the precipitation of elemental selenium. The initial bioenergetic processes of selenate respiration are driven by metalloproteins utilizing cofactors containing iron and molybdenum. However, the assembly of the elemental selenium into selenium nanosphere crystals has shed light on a new family of proteins involved in selenium biomineralization. This article highlights some of the recent advances in our understanding of selenate respiration in the bacterium Thauera selenatis, with particular focus on the metalloproteins involved in selenate reduction and the novel proteins that function to deal with these insoluble selenium deposits. “As mineralogy constitutes a part of chemistry, it is clear that this arrangement of minerals must derive its principles from chemistry” Jöns Jacob Berzelius 1814

Profiling novel alternative splicing within multiple tissues puts insight into the porcine genome annotation

2019 ◽  
Author(s):  
Jian-Feng Liu ◽  
Wen Feng ◽  
Pengju Zhao ◽  
Xianrui Zheng
Keyword(s):  
Alternative Splicing ◽  
Rna Sequencing ◽  
Genome Annotation ◽  
Donor Site ◽  
The Novel ◽  
Rna Seq ◽  
Novel Proteins ◽  
Genome Wide ◽  
Alternative Donor ◽  
Mrna Precursor

Abstract Background Alternative splicing (AS) is a process that mRNA precursor splices intron to form the mature mRNA. AS plays important roles in contributing to transcriptome and proteome divert. However, to date there is no research about pig AS in genome-wide level by RNA sequencing. Results To characterize the AS in pigs, herein we detected genome-wide transcripts and events by RNA sequencing technology (RNA-seq) 34 different tissues in Duroc pigs. In total, we identified 138, 403 AS events and 29, 270 expressed genes. We found alternative donor site was the most common AS form, which is accounted for 44% of the total AS events. The percentage of the other 3 AS forms are all around 19%. The results showed that the most common AS events (alternative donor site) can produce different transcripts or different proteins which affect the biological process. Among these AS events, 109, 483 were novel AS events, and the number of alternative donor splice site has increased the most (Accounting for 44% of the novel AS events).Conclusions The expression of gene with tissue specific AS events showed that the functions of these genes were consistent with the tissue function. AS increased proteome diversity and resulted in novel proteins that gained and lost important functional domains. In summary, these findings extend genome annotation and highlight roles that AS acts in tissue identity in pig.Key words: Alternative splicing; transcript; protein; SNP

AoP-LSE: Antioxidant Proteins Classification Using Deep Latent Space Encoding of Sequence Features

2021 ◽  
Vol 43 (3) ◽  
pp. 1489-1501
Author(s):  
Muhammad Usman ◽  
Shujaat Khan ◽  
Seongyong Park ◽  
Jeong-A Lee
Keyword(s):  
Feature Space ◽  
Vital Role ◽  
Computational Method ◽  
The Novel ◽  
Novel Proteins ◽  
Discriminating Power ◽  
Latent Space ◽  
Antioxidant Proteins ◽  
Class Labels ◽  
Space Encoding

It is of utmost importance to develop a computational method for accurate prediction of antioxidants, as they play a vital role in the prevention of several diseases caused by oxidative stress. In this correspondence, we present an effective computational methodology based on the notion of deep latent space encoding. A deep neural network classifier fused with an auto-encoder learns class labels in a pruned latent space. This strategy has eliminated the need to separately develop classifier and the feature selection model, allowing the standalone model to effectively harness discriminating feature space and perform improved predictions. A thorough analytical study has been presented alongwith the PCA/tSNE visualization and PCA-GCNR scores to show the discriminating power of the proposed method. The proposed method showed a high MCC value of 0.43 and a balanced accuracy of 76.2%, which is superior to the existing models. The model has been evaluated on an independent dataset during which it outperformed the contemporary methods by correctly identifying the novel proteins with an accuracy of 95%.

scholarly journals Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions

2015 ◽  
Vol 112 (12) ◽  
pp. 3841-3846 ◽  
Author(s):  
Xiong Ji ◽  
Daniel B. Dadon ◽  
Brian J. Abraham ◽  
Tong Ihn Lee ◽  
Rudolf Jaenisch ◽  
...  
Keyword(s):  
Es Cells ◽  
Cell Types ◽  
The Novel ◽  
Proteomic Profiling ◽  
Novel Proteins ◽  
Disease Mechanisms ◽  
Lysine Residues ◽  
Associated Proteins ◽  
And Function ◽  
Genomic Regions

More than a thousand proteins are thought to contribute to mammalian chromatin and its regulation, but our understanding of the genomic occupancy and function of most of these proteins is limited. Here we describe an approach, which we call “chromatin proteomic profiling,” to identify proteins associated with genomic regions marked by specifically modified histones. We used ChIP-MS to identify proteins associated with genomic regions marked by histones modified at specific lysine residues, including H3K27ac, H3K4me3, H3K79me2, H3K36me3, H3K9me3, and H4K20me3, in ES cells. We identified 332 known and 114 novel proteins associated with these histone-marked genomic segments. Many of the novel candidates have been implicated in various diseases, and their chromatin association may provide clues to disease mechanisms. More than 100 histone modifications have been described, so similar chromatin proteomic profiling studies should prove to be valuable for identifying many additional chromatin-associated proteins in a broad spectrum of cell types.

scholarly journals Potential role of chimeric genes in pathway-related gene co-expression modules

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Piaopiao Li ◽  
Yingxia Li ◽  
Lei Ma
Keyword(s):  
T Cells ◽  
Gene Fusion ◽  
Epigenetic Modification ◽  
Protein Localization ◽  
Binding Activity ◽  
The Novel ◽  
Chimeric Genes ◽  
Novel Proteins ◽  
Cell Growth And Differentiation ◽  
Underlying Mechanisms

Abstract Background Gene fusion has epigenetic modification functions. The novel proteins encoded by gene fusion products play a role in cancer development. Therefore, a better understanding of the novel protein products may provide insights into the pathogenesis of tumors. However, the characteristics of chimeric genes are rarely studied. Here, we used weighted co-expression network analysis to investigate the biological roles and underlying mechanisms of chimeric genes. Methods Download the pig transcriptome data, we screened chimeric genes and parental genes from 688 sequences and 153 samples, predict their domains, and analyze their associations. We constructed a co-expression network of chimeric genes in pigs and conducted Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis on the generated modules using DAVID to identify key networks and modules related to chimeric genes. Results Our findings showed that most of the protein domains of chimeric genes were derived from fused pre-genes. Chimeric genes were enriched in modules involved in the negative regulation of cell proliferation and protein localization to centrosomes. In addition, the chimeric genes were related to the growth factor-β superfamily, which regulates cell growth and differentiation. Furthermore, in helper T cells, chimeric genes regulate the specific recognition of T cell receptors, implying that chimeric genes play a key role in the regulation pathway of T cells. Chimeric genes can produce new domains, and some chimeric genes are a key role involved in pathway-related function. Conclusions Most chimeric genes show binding activity. Domains of chimeric genes are derived from several combinations of parent genes. Chimeric genes play a key role in the regulation of several cellular pathways. Our findings may provide new directions to explore the roles of chimeric genes in tumors.

scholarly journals Colocalization Analysis of PPP1 Isoforms and Two Novel Targeting Subunits in Breast Carcinoma

2008 ◽  
Vol 14 (S3) ◽  
pp. 134-136
Author(s):  
C. Sousa ◽  
A.P. Vintém ◽  
M. Fardilha ◽  
O. da Cruz e Silva ◽  
E. da Cruz e Silva
Keyword(s):  
Protein Phosphatase ◽  
Cellular Localization ◽  
Carcinoma Cells ◽  
Protein Phosphatase 1 ◽  
The Novel ◽  
Regulatory Subunits ◽  
Novel Proteins ◽  
Fluorescent Microscope ◽  
Gfp Fusion Protein ◽  
Overlap Coefficient

Protein phosphatase 1 (PPP1) is the PPP most ubiquitous and each isoform interact with regulatory subunits that may be responsible for their subcellular localization. We identified PPP1R15B, C1ORF71 as novel regulators and the aim of this study was their further characterization in carcinoma cells. We analysed localization of each regulator in MDA-MB-468 cells and we transfected with constructs that we made with each as a GFP-fusion protein. For PPP1 cellular localization we used specific antibodies for each isoform. We observed the cells under a fluorescent microscope and LSM and we quantified co-localization. We found a high overlap coefficient of both the novel proteins with PPP1alpha and PPP1gamma1. We propose a model in which PPP1 regulator interacts with one or two regulatory subunits that may be used as target for therapeutic strategies.

scholarly journals Identification of the novel proteins Yip4p and Yip5p as Rab GTPase interacting factors

FEBS Letters ◽  
2002 ◽  
Vol 515 (1-3) ◽  
pp. 89-98 ◽  
Author(s):  
Monica Calero ◽  
Nena J. Winand ◽  
Ruth N. Collins
Keyword(s):  
Rab Gtpase ◽  
The Novel ◽  
Novel Proteins

Protein Engineering for Improved Health: Technological Perspectives

2019 ◽  
Vol 20 (9) ◽  
pp. 856-860 ◽  
Author(s):  
Mandeep ◽  
Rajeshwari Sinha ◽  
Pratyoosh Shukla
Keyword(s):  
Artificial Intelligence ◽  
Protein Engineering ◽  
Disease Diagnosis ◽  
Future Research ◽  
The Novel ◽  
Post Translational Modifications ◽  
Novel Proteins ◽  
The World ◽  
Health Related ◽  
Research Endeavor

Protein engineering has enabled development of novel proteins aimed at disease diagnosis, alleviation and improved health attributes. The present article provides an overview of recent approaches and techniques used to modify proteins at diverse levels, which find therapeutically relevant applications. There is immense interest among researchers to discover new and increasingly valuable solutions for various health related issues and protein engineering could be a possible venue to sort out such problems. In this mini review we have tried to decipher some of the novel aspects of protein engineering in terms of protein-based therapeutics and diagnostics, in-silico tools and related approaches. A special emphasis has been given for some innovative aspects of protein-nanoparticle conjugates; use of artificial intelligence (AI)- based tools and post-translational modifications. Utilization of such approaches in protein engineering might be ground breaking in future research endeavor of researchers across the world.

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