scholarly journals Konstruksi Plasmid Rekombinan untuk Inisiasi Translasi Enhance Green Fluorescent Protein oleh Internal Ribosomal Entry Site HIV-1

2018 ◽  
Vol 28 (2) ◽  
pp. 67-72
Author(s):  
Cintera Rahmagiarti ◽  
Silvia Tri Widyaningtyas ◽  
Budiman Bela
Keyword(s):  
Human Immunodeficiency Virus ◽  
Untranslated Region ◽  
Fluorescent Protein ◽  
Internal Ribosomal Entry Site ◽  
Start Codon ◽  
Entry Site ◽  
Immunodeficiency Virus ◽  
Acquired Immunodeficiency ◽  
Ribosomal Entry ◽  
Hiv 1

Human immunodeficiency virus (HIV) is a virus that causes acquired immunodeficiency virus syndrome (AIDS). The HIV genome has a cap structure at 5’ and polyadenylation at 3’ on mRNA resulting in a translation initiation through scanning at 5'untranslated region (UTR). The Vpr protein produced during viral replication causes the 5'cap scanning to be inhibited so HIV-1 can directly recruit the ribosome at the start codon via internal ribosomal entry site (IRES). IRES activity is high at G2/M phase and highest expression in monocyte cell line (THP-1) and lymphocyte (HPB-ALL). The role of HIV IRES however, is not yet known in infection of nondividing cells by HIV-1. HIV-1 IRES and egfp from pcDNA5FRT/TO were amplified with PCR. The insert DNA (HIV-1 IRES_egfp) and pcDNA3.1(+) were digested with EcoRI and ApaI and then ligated. The verification was performed with PCR colonies, restriction verification, and sequencing. The size of insert DNA is 1067 bp while the vector is 5379 bp. E. coli transformed with DNA ligation produces 70 colonies, control of ligation produces 5 colonies, and negative control didn’t grow. 19 colonies contain recombinant DNA, restriction verification was of the appropriate size, and the sequence verification didn’t find any mutation. Therefore, the subcloning process pcDNA3.1_IRES HIV-1_egfp was successfully performed. Abstrak Human immunodeficiency virus (HIV) merupakan virus penyebab acquired immunodeficiency virus syndrome (AIDS). Genom HIV memiliki struktur cap di 5’ dan poliadenilasi di 3’ mRNA sehingga proses inisiasi translasi melalui pemindaian 5’cap pada struktur untranslated region (UTR) di 5’ mRNA HIV. Protein Vpr yang dihasilkan selama replikasi virus menyebabkan pemindaian melalui 5’cap terhambat sehingga HIV-1 dapat langsung merekrut ribosom pada kodon awal translasi melalui struktur internal ribosomal entry site (IRES). Aktivitas IRES tinggi pada fase G2/M dan ekspresi gen tinggi pada sel line monosit (THP-1) dan limfosit (HPB-ALL). Namun, peran IRES HIV-1 belum diketahui pada sel tidak membelah yang merupakan sel target pada infeksi HIV-1. DNA sekuen IRES HIV-1 dan egfp dari pcDNA5FRT/TO diamplifikasi dengan PCR. DNA sisipan (IRES HIV-1_egfp) dan pcDNA3.1(+) dipotong dengan EcoRI dan ApaI lalu DNA sisipan diligasi dengan pcDNA3.1(+). Verifikasi hasil klona dilakukan dengan PCR koloni, verifikasi restriksi, dan sekuensing. Restriksi DNA sisipan menghasilkan pita berukuran 1067 pb. Restriksi vektor plasmid menghasilkan pita berukuran 5379 pb. E.coli yang ditransformasi DNA ligasi menghasilkan 70 koloni, kontrol ligasi 5 koloni, dan kontrol negatif tidak tumbuh. 19 koloni terverifikasi mengandung DNA rekombinan, verifikasi restriksi memiliki ukuran sesuai, dan verifikasi sekuensing tidak terdapat perubahan basa. Oleh karena itu, proses subkloning pcDNA3.1_IRES HIV-1_egfp berhasil dilakukan.

scholarly journals PARAMETER OPTIMIZATION AND VIRTUAL SCREENING INDONESIAN HERBAL DATABASE AS HUMAN IMMUNODEFICIENCY VIRUS -1 INTEGRASE INHIBITOR USING AUTODOCK AND VINA

2017 ◽  
Vol 9 ◽  
pp. 90
Author(s):  
Arry Yanuar ◽  
Rezi Riadhi Syahdi ◽  
Widya Dwi Aryati
Keyword(s):  
Human Immunodeficiency Virus ◽  
Virtual Screening ◽  
Integrase Inhibitor ◽  
Water Molecules ◽  
Autodock Vina ◽  
Unit Space ◽  
Immunodeficiency Virus ◽  
Acquired Immunodeficiency ◽  
Immunodeficiency Syndrome ◽  
Hiv 1

Objective: Human immunodeficiency virus (HIV-1) is a virus that causes acquired immunodeficiency syndrome, a disease considered to be one of themost dangerous because of its high mortality, morbidity, and infectivity. The emergence of mutant HIV strains has led treatment to target proteaseas reverse transcriptase and integrase enzyme become less effective. This study aims to provide knowledge about the potential of HIV-1 integraseinhibitors for use as guiding compounds in the development of new anti-HIV drugs.Methods: This study used AutoDock and AutoDock Vina for virtual screening of the Indonesian herbal database for inhibitors of HIV-1 integrase andis validated using a database of the directory of useful decoys. Optimization was accomplished by selecting the grid size, the number of calculations,and the addition of two water molecules and a magnesium atom as cofactor.Results: This study determined that the best grid box size is 21.1725×21.1725×21.1725 in unit space size (1 unit space equals to macromolecules 1Ǻ),using AutoDock Vina with EF and AUC values, 3.93 and 0.693, respectively. Three important water molecules have meaning in molecular dockingaround the binding pocket.Conclusions: This study obtained the top ten ranked compounds using AutoDock Vina. The compounds include: Casuarinin; Myricetin-3-O-(2’’,6’’-di-O-α-rhamnosyl)-β-glucoside; 5,7,2’,4’-tetrahydroxy-6,3’-diprenylisoflavone 5-O-(4’’-rhamnosylrhamnoside); myricetin 3-robinobioside; cyanidin3-[6-(6-ferulylglucosyl)-2-xylosylgalactoside]; mesuein, cyanidin 7-(3-glucosyl-6-malonylglucoside)-4’-glucoside; kaempferol 3-[glucosyl-(1→3)-rhamnosyl-(1→6)-galactoside]; 3-O-galloylepicatechin-(4-β→8)-epicatechin-3-O-gallate; and quercetin 4’-glucuronide.

scholarly journals The non-primate hepacivirus 5′ untranslated region possesses internal ribosomal entry site activity

2013 ◽  
Vol 94 (12) ◽  
pp. 2657-2663 ◽  
Author(s):  
Hazel Stewart ◽  
Cheryl Walter ◽  
Dale Jones ◽  
Sinead Lyons ◽  
Peter Simmonds ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Internal Ribosomal Entry Site ◽  
Rna Replication ◽  
Entry Site ◽  
Subgenomic Replicon ◽  
Stem Loop ◽  
Long Range Interactions ◽  
Ribosomal Entry ◽  
Internal Translation ◽  
And Function

The 5′ untranslated region (5′UTR) of the recently described non-primate hepacivirus (NPHV) contains a region with sequence homology to the internal ribosomal entry site (IRES) of hepatitis C virus (HCV) and GB virus B (GBV-B). Here, we demonstrated internal translation initiation by the NPHV 5′UTR in a bicistronic vector. An RNA stem–loop upstream of the NPHV IRES was structurally distinct from corresponding regions in HCV and GBV-B, and was not required for IRES function. Insertion of the NPHV stem–loop into the corresponding region of the HCV 5′UTR within the HCV subgenomic replicon significantly impaired RNA replication, indicating that long-range interactions between the 5′UTR and cis-acting downstream elements within the NPHV genome are not interchangeable with those of HCV. Despite similarities in IRES structure and function between hepaciviruses, replication elements in the NPHV 5′UTR appear functionally distinct from those of HCV.

scholarly journals Human Immunodeficiency Virus Env-Independent Infection of Human CD4− Cells

2000 ◽  
Vol 74 (23) ◽  
pp. 10994-11000 ◽  
Author(s):  
Shen Pang ◽  
Duan Yu ◽  
Dong Sung An ◽  
Gayle C. Baldwin ◽  
Yiming Xie ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Cell Lines ◽  
Fluorescent Protein ◽  
Vaccine Development ◽  
Alternative Pathway ◽  
Neutralizing Antibody ◽  
Green Fluorescent Protein Gene ◽  
Immunodeficiency Virus ◽  
Green Fluorescent ◽  
Hiv 1

ABSTRACT CD4− epithelial cells covering mucosal surfaces serve as the primary barrier to prevent human immunodeficiency virus type 1 (HIV-1) infection. We used HIV-1 vectors carrying the enhanced green fluorescent protein gene as a reporter gene to demonstrate that HIV-1 can infect some CD4− human epithelial cell lines with low but significant efficiencies. Importantly, HIV-1 infection of these cell lines is independent of HIV-1 envelope proteins. The Env-independent infection of CD4− cells by HIV-1 suggests an alternative pathway for HIV-1 transmission. Even on virions bearing Env, a neutralizing antibody directed against gp120 is incapable of neutralizing the infection of these cells, thus raising potential implications for HIV-1 vaccine development.

scholarly journals Acquired immunodeficiency syndrome-associated T-cell lymphoma: evidence for human immunodeficiency virus type 1-associated T-cell transformation

Blood ◽  
1992 ◽  
Vol 79 (7) ◽  
pp. 1768-1774 ◽  
Author(s):  
BG Herndier ◽  
BT Shiramizu ◽  
NE Jewett ◽  
KD Aldape ◽  
GR Reyes ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
T Cell ◽  
B Cell ◽  
Virus Type ◽  
Cell Lymphoma ◽  
Immunodeficiency Virus ◽  
Acquired Immunodeficiency ◽  
Immunodeficiency Syndrome ◽  
Hiv 1

Abstract The majority of lymphomas in the setting of acquired, iatrogenic, or congenital immunodeficiencies are B-cell lymphoproliferations. We describe a rare T-cell lymphoma in a fulminantly ill patient infected with human immunodeficiency virus type 1 (HIV-1). The T-cell nature of the process was defined genotypically (monoclonal T-cell receptor beta- chain [CT beta] rearrangement) and phenotypically (CD45RO+, CD4+, CD5+, CD25+, CD8-, CD3- and negative for a variety of B-cell and monocyte markers). The CD4+, CD25+ (interleukin-2 receptor [IL-2R]) phenotype with production of IL-2 and IL-2R RNA is analogous to human T- lymphotropic virus type I (HTLV-I)-associated adult T-cell leukemia/lymphoma (ATLL); however, no HTLV-1 could be detected. Southern blot analysis did demonstrate monoclonally integrated HIV-1 within the tumor genome. Furthermore, the tumor cells were producing HIV p24 antigen as shown by immunohistochemistry. This is the first case of acquired immunodeficiency syndrome (AIDS)-associated non- Hodgkin's lymphoma in which HIV-1 infection may have played a central role in the lymphocyte transformation process.

scholarly journals Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription

2005 ◽  
Vol 79 (11) ◽  
pp. 6610-6619 ◽  
Author(s):  
M. K. Lewinski ◽  
D. Bisgrove ◽  
P. Shinn ◽  
H. Chen ◽  
C. Hoffmann ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Fluorescent Protein ◽  
Centromeric Heterochromatin ◽  
Regulatory Sequences ◽  
Hiv Transcription ◽  
Genome Wide ◽  
A Genome ◽  
Immunodeficiency Virus ◽  
Hiv 1 ◽  
In Cells

ABSTRACT We have investigated regulatory sequences in noncoding human DNA that are associated with repression of an integrated human immunodeficiency virus type 1 (HIV-1) promoter. HIV-1 integration results in the formation of precise and homogeneous junctions between viral and host DNA, but integration takes place at many locations. Thus, the variation in HIV-1 gene expression at different integration sites reports the activity of regulatory sequences at nearby chromosomal positions. Negative regulation of HIV transcription is of particular interest because of its association with maintaining HIV in a latent state in cells from infected patients. To identify chromosomal regulators of HIV transcription, we infected Jurkat T cells with an HIV-based vector transducing green fluorescent protein (GFP) and separated cells into populations containing well-expressed (GFP-positive) or poorly expressed (GFP-negative) proviruses. We then determined the chromosomal locations of the two classes by sequencing 971 junctions between viral and cellular DNA. Possible effects of endogenous cellular transcription were characterized by transcriptional profiling. Low-level GFP expression correlated with integration in (i) gene deserts, (ii) centromeric heterochromatin, and (iii) very highly expressed cellular genes. These data provide a genome-wide picture of chromosomal features that repress transcription and suggest models for transcriptional latency in cells from HIV-infected patients.

Sign in / Sign up

Export Citation Format

Share Document