Volume 3 Issue 1

Research Article: The classification of HIV and non-HIV related DLBCL subtypes using MALDI Imaging Mass Spectrometry

Pumza Magangane#, Raveendra Sookhayi# and Richard Naidoo*

Background: Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry (MALDI IMS) is a powerful technology which determines the localization of proteins directly on tissue sections. This technology can also be used to classify distinct disease entities. Diffuse Large B Cell Lymphoma (DLBCL) is a heterogeneous disease that is subdivided into Germinal Centre (GC) and non-GC subtypes using immunohistochemical staining. The diagnosis, management and treatment of the disease may benefit from molecular classification of the tissue as new target proteins can be identified.
Methods: The tissue samples included Germinal Centre (GC) subtypes (n = 3), (n = 4) and non-GC subtypes (n = 4), (n = 4) from HIV negative and positive cases, respectively. Classification models were created and validated with an independent set of tissue from GC (n = 2) and non-GC (n = 2) subtypes for both HIV negative and HIV positive cohorts, respectively.
Results: In the HIV negative cohort, we found that 27 proteins were differentially expressed in GC compared to non-GC. The generated classification model based on the most significant 8 differentially expressed proteins allowed for reliable prediction of subtype in the validation set with a prediction score of 100%. The HIV positive cohort had a lower number of differentially expressed peptide ions which were all included in the classification model. This model was not as reliable as the HIV negative model which had a prediction score of 79%.
Conclusions: The classification models identified herein may be used in routine diagnostics so to confirm the subtype status of DLBCL patients.
Keywords: MALDI IMS; DLBCL; Classification; proteomics; Subtypes

Cite this Article: Magangane P, Sookhayi R, Naidoo R. The classification of HIV and non-HIV related DLBCL subtypes using MALDI Imaging Mass Spectrometry. Int J Proteom Bioinform. 2018;3(1): 010-015

Published: 19 December 2018

Review Article: A Brief Overview of NgAgo-gDNA system for Genome Editing: from Reality to Sophistication

Ali Shojaeian1, Fereshteh Shojaei2, Shima Rahmati3 and Mehdi Banitalebi Dehkordi4*

Background and aims: It has been reported that Natronobacterium Gregoryi Argonaute (NgAgo) protein is a type of endonucleases which is guided by an ssDNA to target ssDNA and RNA. In fact, it requires only a single, 24 base paired, and 5' phosphorylated ssDNAs guide DNA (gDNA) for DNA targeting. In this review, we aim to introduce the NgAgo / gDNA system and report different studies on investigating its reproducibility based on Dr. Han's protocol.
Methods: This review was prepared using the databases of Science Direct, Pub-Med, Scopus, Web of Science, reference lists check and hand searching using keywords such as "gene editing", "CRISPR-Cas","NgAgo", "challenge", "tool editing". The selected papers were fully reviewed and required information for the review was extracted and summarized.
Results: The NgAgo-gDNA system was introduced by Chinese scientists from the Hebei University for the first time. These scientists claimed that these proteins have several advantages over the CRISPR-Cas9 system especially in the flexibility and efficiency of gene editing. While the declaration of NgAgo has enraptured numerous specialists, resulting worries over the reproducibility of the tests which alert us against drawing such big claims by a researcher from an article. After publishing his article in Nature Biotechnology, many scientists criticized the fact that they were not able to confirm and repeat the results of Dr. Han's experiment. However there are reports in gene knockdown activity and gene down regulation achieved by this system due to the DNA-dependent RNA cleavage activity of NgAgo not DNA editing.
Conclusion: NgAgo/gDNA system does not provide genome editing activity like ZNF, TALEN and CRISPR-Cas system. Despite all of these reports, the genome editing ability of NgAgo-gDNA is probable in the future under a specific condition that is yet to be known. Thus, more trial and error is required to design and develop a new gene editing tool over the recent well-known genome engineering toolkits such as ZNFs, TALEN and CRISPR-Cas system.

Cite this Article: Shojaeian A, Shojaei F, Rahmati S, Dehkordi MB. A Brief Overview of NgAgo-gDNA system for Genome Editing: from Reality to Sophistication. Int J Proteom Bioinform. 2018;3(1): 007-009.

Published: 12 December 2018

Research Article: In silico Modeling and Drug Interaction Analysis of Molecular Structure of Ecto-Domain of E1 Glycoprotein of HCV

Rohan J Meshram1, Anand M Dangre2 and Rajesh N Gacche2*

Over 2% world population has been estimated to be infected with Hepatitis C Virus (HCV) and it has been identified as a global threat for human health. In the current state of the art, there are some anti-HCV drugs which functions as inhibitors for viral RNA synthesis, however these drugs are associated with side effects which adversely affect the metabolic and physiological functions of the body. The envelope glycoprotein complex E1-E2 has been proposed to be essential for HCV entry into host cell. The efforts of developing vaccines against HCV are evolving; however there is no effective vaccine available for the management of HCV infection. As a part of developing candidate epitope vaccines against HCV, computational structural model of E2 glycoprotein ecto-domain has been proposed previously, but no advances were reported till date in case of E1 glycoprotein. In the present study we have attempted the modeling of E1 glycoprotein using Ab initio approach and deduced the structure using the de novo Rosetta fragment insertion method on ROBETTA Server. The models generated were evaluated using Procheck, WhatCheck/WhatIf. The promising model was used for docking studies using AutoDock, Docking server and SwissDock tools. Among the two selected anti-HCV drugs, Ribavirin (RBV) and Sofosbuvir (SFB), the docking studies revealed that RBV binding potential were lower than SFB, which infers that the RBV-glycoprotein E1 binding is comparatively stable than SFB. Moreover, the overall intermolecular energy with RBV binding was greater than SFB bound intermolecular energy. The results of the present studies may find applications in development of epitope vaccine targeting E1 ecto-domain glycoprotein of HCV.
Keywords: Hepatitis C virus; HCV infection; HCV glycoprotein; Molecular modeling; Molecular docking

Cite this Article: Meshram RJ, Dangre AM, Gacche RN. In silico Modeling and Drug Interaction Analysis of Molecular Structure of Ecto-Domain of E1 Glycoprotein of HCV. Int J Proteom Bioinform. 2018;3(1): 001-006.

Published: 04 June 2018

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