MOJ proteomics & bioinformatics最新文献

{"title":"3D printing for foot","authors":"Ir. Sreenivas Reddy Bathula, Virupakshi, Harika Mali","doi":"10.15406/MOJPB.2017.05.00176","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00176","url":null,"abstract":"","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73547644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Toward the integration of mate pair and RNA sequencing to identify gene fusions in cancer research: a mini review","authors":"Carlos P. Sosa, Daniel N. Sosa, G. Vasmatzis","doi":"10.15406/MOJPB.2017.05.00175","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00175","url":null,"abstract":"Mate pair (MPseq) and RNA sequencing (RNAseq) are important next-generation sequencing (NGS) techniques that are utilized to provide insight into tumorigenesis. Currently, MPseq is being successfully utilized in the clinic to predict chromosomal rearrangements while RNAseq is extensively used in the identification of gene expression, transcript expression and fusion detection. One of the strengths of MPseq is the fact that the fragments are longer than conventional pair-end fragments. This provides better coverage of genomic events such as structural variations. Fusions are structural rearrangements where there is an exchange of DNA sequences between genes. These kind of chromosomal rearrangements have great clinical importance. They are considered important biomarkers in neoplasia as well as therapeutic targets. However, as previously reported, fusion prediction tends to be difficult. This has been attributed to the large number of false positives due to sequencing errors. There are other factors such as poor alignment, library preparation, and insufficient depth of coverage. In addition, fusion predictions based purely on DNA technologies do not include gene expression information. Although, multiple software packages have been developed for fusions prediction, in many cases a consensus approach is required to eliminate false positives. MPseq’s capabilities to detect genomic structural rearrangements can provide an unbiased orthogonal approach to predicting fusions when combined with RNAseq. In this mini-review we explore the benefits of MPseq and RNAseq as two complementary tools in the prediction of gene fusions.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81609889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How to cluster protein sequences: tools, tips and commands","authors":"Georgios A. Pavlopoulos","doi":"10.15406/MOJPB.2017.05.00174","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00174","url":null,"abstract":"The protein landscape changes continuously as new and hypothetical proteins appear every day. IMG1 today hosts 55,482 Bacterial genomes, 1,580 Archaeal, 258 Eukaryotic, 1,222 Plasmids, 7,521 Viruses, 1,196 genome fragments and 14,265 private and public met genomes and meta transcriptomes. With a very approximate estimation, this corresponds to ~70Million non-redundant proteins at 100% similarity for the isolate side and ~3billion non-redundant proteins for the met genome/metatranscriptome side (coming from scaffolds of length ~500). Release 15-Feb-2017 of UniProtKB/ TrEMBL2 contains 77,483,538 sequence entries. This number corresponds to 1,465,039 (2%) Archaeal proteins, 49,717,238 (64%) Bacterial proteins, 22,299,253 (29%) Eukaryotic proteins, 2,918,867 (4%) Viral proteins and 1,083,141 (<1%) others. Moreover, Uniparc3 contains 148,791,725 protein entries. The UniProt Archive (UniParc) is a comprehensive and non-redundant database that contains most of the publicly available protein sequences in the world. Protein families can be characterized by molecules which share significant sequence similarity.4 Notably, this biological problem is very difficult to solve and most available clustering techniques fail in the case of eukaryotic proteins, which contain large numbers of protein domains.5 Nevertheless, ongoing efforts in detecting the best and more accurate protein clustering are still a very active research field. PFAM6 version 31.0 for example, a database of a large collection of protein families, organizes proteins in families by similar domains and includes 16,712 entries. Several tools today, follow various methodologies and strategies to perform protein clustering.7 Outstanding tools such as the CD-HID,8 UCLUST,9 kClust10 and the newly developed MMSEQ/ LinClust11 follow a k-mer and dynamic programming-based sequence alignment approach whereas tools such as the MCL12 clustering algorithm and others a network topology based clustering.13–18 In the second case, prior to clustering, a pairwise similarity matrix is required. While such similarities can be calculated in various ways, BLAST+19 and LAST20 are the most widely used. In this article, in order to encourage users getting familiar with several tools and avoid troubleshooting, simple command lines to perform such analyses are provided.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"124 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74759853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics and protein microarray: boon to cancer research and diagnosis","authors":"Megha Jain, V. Jain, A. Gupta, S. Khan","doi":"10.15406/MOJPB.2017.05.00172","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00172","url":null,"abstract":"Cancer, being one of the most taxing conditions requires functional studies to understand its complex and hetrogenous behavior. Microarray is powerful tool that allows the simultaneous analysis of the expression of thousands of genes or their RNA products on single platform. Proteome chip technology is a remarkable highthroughput method used to probe an entire collection of proteins and proved to be valuable tool in Cancer research and diagnosis.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"7 1","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2017-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84281877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Drugging protein kinases in cancer: from small molecules to nanoparticles","authors":"Devan, G. Venkatasubbu","doi":"10.15406/MOJPB.2017.05.00173","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00173","url":null,"abstract":"MOJ Proteomics Bioinform 2017, 5(5): 00173 upstream protein kinase. Deregulated kinase activity is a frequent cause of disease, particularly cancer, where they regulate many aspects important in tumor progression and metastasis. In several instances protein kinases regulates cancer progression by phosphorylating ontogenesis and tumor suppressor proteins thereby regulating the activity, stability, and function [4-8]. Interestingly, many of the tumor suppressor genes and dominant oncogenes identified so far are also protein kinases. Kinases such as c-Src, c-Abl, mitogen activated protein (MAP) kinase, phosphotidylinositol-3-kinase (PI3K) AKT, and the epidermal growth factor (EGF) receptor are commonly activated in cancer cells, and are known to contribute to tumor genesis [9-13].Given their importance in human diseases such as cancer, protein kinases have emerged as attractive therapeutic targets.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83880289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scaffold hopping to percept the achiral compound and functionalizing on target protein plasmepsin II","authors":"Suganya, Murugesh Easwaran, Praveen Kumar, N. Ch, rasekar, R. Durairaj, R. Vadivelu, Shanmughavel Piramanayagam","doi":"10.15406/MOJPB.2017.05.00171","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00171","url":null,"abstract":"Malaria is a vector-borne disease caused by protozoan parasites of the genus Plasmodium i.e. Plasmodium vivax, Plasmodium ovale, Plasmodium falciparum and Plasmodium malariae. Only these four types of the plasmodium parasite can infect humans as partial prophylaxis infection; the most serious form of disease caused by Plasmodium falciparum. During infection, Plasmodium merozoites invade and then replicate within red blood cells. During the log phase within the host cell, the parasite obtains nutrients by taking up and then digesting hemoglobin within an acidic food vacuole. The digestion of hemoglobin releases monomeric α-hematin (ferriprotoporphyrin IX). Released compound predicting its hypertoxicity property, since it is a pro-oxidant and it catalyzes the production of reactive oxygen species. Oxidative stress is believed to be generated during the conversion of heme to hematin.1 Free hematin can also bind and then the disrupt cell membranes, damaging cell structures and causing the lysis of the host erythrocyte. Reporting a novel mechanism that the host utilizing Toll-like receptor (TLR) 9 to recognize Plasmodium DNA, which may be a prior induction of fever during the replicative, process (Lag Phase) disease. These findings reveal an important mechanism of disease patho-physiology that may also apply to other microbial diseases.2 It also corrects previous findings claiming that hemozoin is a direct TLR9 stimulus and refines them by showing that hemozoin itself important for presenting the DNA to TLR9 but does not stimulate the receptive process (Figure 1). Although it is too early to predict how these findings will influence the development of future malaria treatment options, it is likely that it will open new pathways of interference with the malaria fever reaction, and this may influence the course of disease.3,4 Figure 1 Illustrates the potential mechanism of malaria-induced fever, shows that hemozoin contains plasmodial DNA and that it “presents” or internalizes DNA. Plasmodial DNA then intracellularly interacts with TLR9, initiating signal transduction.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79594844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics of triple negative breast cancers in Asian population-the need for further studies","authors":"K. Vaidyanathan","doi":"10.15406/mojpb.2017.05.00170","DOIUrl":"https://doi.org/10.15406/mojpb.2017.05.00170","url":null,"abstract":"great need to develop new markers to identify breast cancer at an early stage. There is also a need for newer chemotherapeutic agents, which are more effective and less toxic. Cancers which are negative for ER, PR and HER2 are known as triple negative breast cancers (TNBC). They are very resistant to conventional treatment protocols and hence their management is one of the greatest challenges in contemporary clinical practice. Our own preliminary studies have identified 83 cases that did not express the 3 markers, ER, PR and HER2, i.e. triple negative breast cancer (TNBC) out of a total of 358 cases, 23.2%.2","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"55 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85839598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In-vitro and In-vivo Characterizations of Novel Modified Starch Transdermal Drug Delivery System","authors":"M. Saboktakin","doi":"10.15406/mojpb.2017.05.00168","DOIUrl":"https://doi.org/10.15406/mojpb.2017.05.00168","url":null,"abstract":"","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"47 1","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2017-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85475063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genes, proteins and metabolites","authors":"C. Mitra","doi":"10.15406/MOJPB.2017.05.00169","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00169","url":null,"abstract":"","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"262 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76771322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The controversial role of osteopontin in vascular calcification: from bench to bedside","authors":"Alex, er E. Berezin","doi":"10.15406/MOJPB.2017.05.00167","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00167","url":null,"abstract":"Osteopontin (OPN) is integrin-binding ligand belonged to the family of N-linked glycoprotein, which is produced by activated mononuclears and linking systemic inflammation, atherosclerosis, and vascular remodeling. There is a large body of evidence regarding the controversial role of OPN in vascular calcification, while OPN is considered a pretty accurate biomarker of vascular remodeling with promising predictive value for cardiovascular (CV) disease and CV events. The short communication is depicted the discussion about some controversies regarding exclusive role of OPN in several phases of vascular remodeling.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"89 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89021043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}