Publications by authors named "Soegianto Ali"

10 Publications

  • Page 1 of 1

Broad Spectrum Peptide Vaccine Design Against Hepatitis C Virus.

Curr Comput Aided Drug Des 2019 ;15(2):120-135

Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia.

Background: Hepatitis C virus (HCV) infection is a global burden. There is no peptide vaccine found as modality to cure the disease is available due to the weak cellular immune response and the limitation to induce humoral immune response.

Methods: Five predominated HCV subtypes in Indonesia (1a, 1b, 1c, 3a, and 3k) were aligned and the conserved regions were selected. Twenty alleles of class I MHC including HLA-A, HLA-B, and HLAC types were used to predict the potential epitopes by using NetMHCPan and IEDB. Eight alleles of HLA-DRB1, together with a combination of 3 alleles of HLA-DQA1 and 5 alleles of HLA-DQB1 were utilized for Class II MHC epitopes prediction using NetMHCIIPan and IEDB. LBtope and Ig- Pred were used to predict B cells epitopes. Moreover, proteasome analysis was performed by NetCTL and the stability of the epitopes in HLA was calculated using NetMHCStabPan for Class I. All predicted epitopes were analyzed for its antigenicity, toxicity, and stability. Population coverage, molecular docking and molecular dynamics were performed for several best epitopes.

Results: The results showed that two best epitopes from envelop protein, GHRMAWDMMMNWSP (E1) and PALSTGLIHLHQN (E2) were selected as promising B cell and CD8+ T cell inducers. Other two peptides, LGIGTVLDQAETAG and VLVLNPSVAATLGF, taken from NS3 protein were selected as CD4+ T cell inducer.

Conclusion: This study suggested the utilization of all four peptides to make a combinational peptide vaccine for in vivo study to prove its ability in inducing secondary response toward HCV.
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http://dx.doi.org/10.2174/1573409914666181003151222DOI Listing
July 2019

Cosmeceutical Effects of Galactomannan Fraction from Fruits .

Pharmacognosy Res 2017 Jan-Mar;9(1):39-45

Master of Science in Biotechnology Program, Faculty of Biotechnology, Atma Jaya Catholic University, Jakarta 12930, Indonesia; Medicine Program, Faculty of Medicine, Atma Jaya Catholic University, Jakarta 14440, Indonesia.

Background: Cosmeceuticals refer to natural cosmetics with medical-like benefits due to their bioactive contents. Sugar palm fruit () extract has been claimed for its anti-aging effect . However, its active compounds for cosmeceuticals is still unclear.

Objective: This study was aimed to extract galactomannan from fruits and test its efficacy for tyrosinase inhibition, antioxidant, and anti-photoaging activities .

Materials And Methods: Galactomannan from fruits was extracted by freeze drying and identified for its chemical compounds by using pyrolysis gas chromatography-mass spectrometry (py-GC/MS). Galactomannan was tested for its tyrosinase inhibition in both cell-based (melanocytes) and enzymatic assays, antioxidant activity using ferrous ion chelating assay (FCA) assay, and anti-photoaging activity for inhibiting the gene expression of matrix metalloproteinase-1 (MMP-1) and MMP-13 in macrophages using quantitative real-time polymerase chain reaction (qRT-PCR) analysis.

Results: Identification of galactomannan fraction from fruits by py-GC/MS mainly consisted of oxonium ion and glucosides. For cellular assay, galactomannan at 5 μg/mL inhibited >50% of tyrosinase activity in melanocytes induced by phorbol myristate acetate. At the enzymatic level, galactomannan at similar concentration showed less tyrosinase activity inhibition (~20%). FCA results showed that galactomannan at 10 μg/mL exerted >50% of antioxidant activity. The qRT-PCR data indicated that galactomannan at 5 μg/mL inhibited >50% of MMP-1 and MMP-13 gene expressions in ultraviolet B-treated macrophages.

Conclusion: Galactomannan fraction from fruits has efficacy for enlightening effect, antioxidant, and anti-photoaging activity in the dose-independent pattern, indicating its cosmeceutical effects for skin healthcare.

Summary: fruit containing galactomannan has cosmeceutical potentials through enlightening effect, antioxidant, and anti-photoaging activity in vitro.Galactomannan fraction has inhibitory effect on tyrosinase activity in both cellular melanocytes and enzymatic systems.Galactomannan fraction has strong protection against UVB-irradiation effect by inhibiting collagenase genes (MMP-1 and MMP-13) in macrophages. : Py-GC/MS: Pyrolysis-Gas Chromatography-Mass Spectrometry; FCA: Ferrous chelating activity; MMP: Matrix metalloproteinase; qRT-PCR: Quantitative Real-Time Polymerase Chain Reaction; PMA: Phorbol myristate acetate; UV: Ultraviolet; RPMI: Roswell Park Memorial Institute; DMEM: Dulbecco's modified eagle media; FBS: Fetal bovine serum; PBS: Phosphate buffered saline; MTT: 3-(4,5-diethylthiazol-2-yl)-2,5-dipheniltetrazolium bromide; L-DOPA: L-3,4-dihydroxyphenylalanine; EDTA: Ethylenediaminetetraacetic acid; GAPDH: Glyceraldehyde 3-phosphate dehydrogenase; DPPH: 1,1-diphenyl-2-picryl-hydrazyl; SPF: Sun protection factor.
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http://dx.doi.org/10.4103/0974-8490.199773DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330101PMC
March 2017

Distribution of CFTR variations in an Indonesian enteric fever cohort.

Clin Infect Dis 2010 May;50(9):1231-7

Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands.

Background: Enteric fever is defined by circulating Salmonella serotype Typhi or Paratyphi in the blood. The first step in developing enteric fever is internalization of salmonellae in the gut epithelium. In in vitro experiments, attachment of S. Typhi to the cystic fibrosis transmembrane conductance regulator (CFTR) on the intestinal mucosa is crucial for bacterial uptake. We recently found a microsatellite polymorphism in the CFTR gene, IVS8CA, to be associated with susceptibility to enteric fever in a case-control study in Indonesia.

Methods: To determine which functional variation in CFTR is associated with susceptibility to enteric fever, we sequenced all 27 exons of the CFTR gene in 25 individuals from Indonesia. Polymorphisms that occurred more than once were genotyped in the full enteric fever cohort of 116 case patients and 322 control subjects.

Results: We identified 12 variants in, or adjacent to, the exons: 1 novel variant (L435V), 3 known mutations (N287K, I556V, Q1352H), and 8 known polymorphisms. Variations that occurred more than once were genotyped in the full cohort. The IVS8 TG(11)TG(12) genotype appears to provide some protection from acquiring enteric fever: having this protective genotype or a variation that is known to affect CFTR protein expression provides modest protection from enteric fever (odds ratio, 0.57; 95% confidence interval, 0.37-0.87; P<.01).

Conclusions: The findings demonstrate that a correlation exists between variations in the CFTR gene and protection from enteric fever. The IVS8CA polymorphism that was identified previously may, however, be the principal functional variation causing the difference in susceptibility.
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http://dx.doi.org/10.1086/651598DOI Listing
May 2010

Polymorphisms in proinflammatory genes and susceptibility to typhoid fever and paratyphoid fever.

J Interferon Cytokine Res 2007 Apr;27(4):271-9

Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands.

Host genetic factors are thought to contribute to susceptibility and outcome in infectious diseases. A polymorphism in a proinflammatory gene, tumor necrosis factor-alpha (TNFA - 308), was recently found to be associated with susceptibility to typhoid fever. As the observation was made in hospitalized patients, a potential confounder could be that the TNFA polymorphism is associated with the severity of established illness resulting in hospital admission rather than susceptibility to disease. We tested whether the association with TNFA - 308 is present also in typhoid fever patients enrolled in a community-based case-control study in an endemic area in Indonesia. Common polymorphisms in other proinflammatory genes were assayed as well. Samples of patients with blood culture-confirmed typhoid fever (n = 90) and paratyphoid fever (n = 26) and fever controls (n = 337) were compared with those of community controls (n = 322). In these groups, we analyzed polymorphisms in TNFA by PCR and RFLP, polymorphisms of IFNG, IL1A, IL1B, IL1R1, TNFRSF1A, CASP1, and CRP by Sequenom MassArray (San Diego, CA), and polymorphisms in IL12B and IFNGR1 by fragment length analysis. The IL1R1 polymorphisms were nearly absent in the Indonesian population. The TNFA - 308 polymorphism was not associated with typhoid fever (OR 0.35, 95% CI 0.1-1.0) in this population. The polymorphisms at TNFA - 238 or in IFNG, IL1A, IL1B, IL12B, TNFRSF1A, IFNGR1, CASP1, and CRP were also not associated with typhoid or paratyphoid fever. We conclude that polymorphisms in proinflammatory genes do not contribute to susceptibility to typhoid fever and, in view of earlier findings, suggest that the TNFA - 308 polymorphism is likely related to severity of established disease rather than to susceptibility per se.
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http://dx.doi.org/10.1089/jir.2006.0129DOI Listing
April 2007

A survey of the supply and bacteriologic quality of drinking water and sanitation in Jakarta, Indonesia.

Southeast Asian J Trop Med Public Health 2005 Nov;36(6):1552-61

Department of Infectious Diseases, Leiden University Medical Center, The Netherlands.

We assessed the water supply, water quality and human waste disposal and their association with diarrheal illness in Jatinegara, East-Jakarta, where part of the area has been involved in the Kampung Improvement Program (KIP). Three hundred seventy-eight households, randomly selected in the study area, were visited and questioned about water source, sanitation and diarrheal illness during the previous 3 months. Microbiological quality of drinking water was assessed. The water sources were boreholes (243; 64%), the water mains (77; 20%), bottled water (45; 12%), and vendors or dug wells (243; 4%). Fecal coliforms were isolated in 56% of the samples [median 23 (IQR 6-240) /100 ml in the contaminated samples]. Only 2 (3%) of the water mains' samples contained >100 fecal coliforms/100 ml, compared to 57 (24%) groundwater samples. Most residents used private toilets with drainage into on-site septic tanks, yet in over one quarter of households human excreta was disposed of into rivers or gutters. KIP areas lagged behind in environmental hygiene. Diarrheal episodes, reported in one third of the households, were significantly associated with water contaminated with >100 fecal coliforms/100 ml [OR 2.4 (95% CI: 1.4-4.2)], but no association with water source or environmental contamination was found. Significantly, all individuals reported boiling water before consumption.
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November 2005

Susceptibility to typhoid fever is associated with a polymorphism in the cystic fibrosis transmembrane conductance regulator (CFTR).

Hum Genet 2005 Oct 28;118(1):138-40. Epub 2005 Oct 28.

Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.

The cystic fibrosis transmembrane conductance regulator (CFTR) is the affected protein in cystic fibrosis (CF). The high rate of CF carriers has led to speculation that there must be, similar to the sickle cell haemoglobin advantage in malaria, a selective advantage for heterozygotes. Such a selective advantage may be conferred through reduced attachment of Salmonella typhi to intestinal mucosa, thus providing resistance to typhoid fever. We tested this hypothesis by genotyping patients and controls in a typhoid endemic area in Indonesia for two highly polymorphic markers in CFTR and the most common CF mutation. We found an association between genotypes in CFTR and susceptibility to typhoid fever (OR=2.6). These analyses suggest that the role CFTR plays in vitro in S. typhi infection is also important for infection in the human population.
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http://dx.doi.org/10.1007/s00439-005-0005-0DOI Listing
October 2005

Identification of typhoid fever and paratyphoid fever cases at presentation in outpatient clinics in Jakarta, Indonesia.

Trans R Soc Trop Med Hyg 2005 Jun;99(6):440-50

Department of Infectious Diseases, C5-P, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.

In Jakarta, Indonesia, over 80% of patients with typhoid fever or paratyphoid fever are treated in outpatient settings. In a community-based prospective passive surveillance study, we identified 59 typhoid, 23 paratyphoid fever and 259 non-enteric fever outpatients, all blood culture-confirmed. We compared their symptoms with the aim of developing a clinical prediction rule that may help direct empirical antibiotic treatment to cases with suspected (para)typhoid fever, rather than all febrile patients, or refer patients for additional diagnostic tests. Paratyphoid fever (Salmonella paratyphi A) could not be distinguished clinically from typhoid fever. Decisions on empirical antibiotic treatment and advice on hygiene measures in patients with suspected (para)typhoid fever should take into account chills and absence of cough in the first week of fever and delirium in the second week of illness. This prediction rule increases the likelihood of (para)typhoid fever from 1:10 in the first week to, at most, 2:3 in the second week of a febrile illness. However, we were not able to propose a robust clinical prediction rule that could be used as absolute screening method for decisions on additional diagnostic tests, because of the low sensitivity of presenting symptoms in (para)typhoid fever.
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http://dx.doi.org/10.1016/j.trstmh.2004.09.012DOI Listing
June 2005

TT virus infection in acute and chronic liver diseases and in patients regularly receiving blood products in Belgium.

Acta Gastroenterol Belg 2004 Apr-Jun;67(2):161-5

Department of Hepatobiliary and Pancreas Diseases, University Hospital Gasthuisberg, B-3000, Leuven, Belgium.

Background: TT viruses are single-stranded DNA viruses, suggested to be involved in non A-E hepatitis. We studied the prevalence of TTV infection in acute or chronic hepatitis in Belgium in comparison with that in blood donors and in patients regularly receiving blood products.

Methods: TTV-DNA was detected by PCR using the primer set of Takahashi et al (1998) or a nested-PCR specific for genotype-2, because it had been reported that this subtype might be more pathogenic (Tagger et al. 1999).

Results: TTV-DNA was present in 49% of 128 patients with chronic hepatitis C, in 54% of 54 with chronic hepatitis B and in 54% of 24 with acute liver failure. This prevalence is similar to the 47% in 127 patients with clotting disorders, or the 64% in 103 undergoing chronic haemodialysis, but lower than the 29.7% found in 340 healthy blood donors. Significant differences in clinical or biochemical characteristics between TTV- positive or TTV-negative patients could not be substantiated. The genotype-2 subgroup comprised 3.9%, but they also did not differ from non genotype-2 patients.

Conclusions: The prevalence of TTV infection was higher in patients than in healthy blood donors. Its clinical significance remains questionable since clinical and biochemical characteristics were not different between TTV positive and TTV negative patients. The higher prevalence of TTV in patients might be related to parenteral transmission, but the relatively high prevalence in healthy blood donors points to an additional presumably faeco-oral infection. The presence of TTV in animals suggests that infection might also originate from food. Long term follow-up will have to define whether co-infection with TTV eventually alters the natural history of chronic hepatitis.
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September 2004

Risk factors for typhoid and paratyphoid fever in Jakarta, Indonesia.

JAMA 2004 Jun;291(21):2607-15

Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands.

Context: The proportion of paratyphoid fever cases to typhoid fever cases may change due to urbanization and increased dependency on food purchased from street vendors. For containment of paratyphoid a different strategy may be needed than for typhoid, because risk factors for disease may not coincide and current typhoid vaccines do not protect against paratyphoid fever.

Objective: To determine risk factors for typhoid and paratyphoid fever in an endemic area.

Design, Setting, And Participants: Community-based case-control study conducted from June 2001 to February 2003 in hospitals and outpatient health centers in Jatinegara district, Jakarta, Indonesia. Enrolled participants were 1019 consecutive patients with fever lasting 3 or more days, from which 69 blood culture-confirmed typhoid cases, 24 confirmed paratyphoid cases, and 289 control patients with fever but without Salmonella bacteremia were interviewed, plus 378 randomly selected community controls.

Main Outcome Measures: Blood culture-confirmed typhoid or paratyphoid fever; risk factors for both diseases.

Results: In 1019 fever patients we identified 88 (9%) Salmonella typhi and 26 (3%) Salmonella paratyphi A infections. Paratyphoid fever among cases was independently associated with consumption of food from street vendors (comparison with community controls: odds ratio [OR], 3.34; 95% confidence interval [CI], 1.41-7.91; with fever controls: OR, 5.17; 95% CI, 2.12-12.60) and flooding (comparison with community controls: OR, 4.52; 95% CI, 1.90-10.73; with fever controls: OR, 3.25; 95% CI, 1.31-8.02). By contrast, independent risk factors for typhoid fever using the community control group were mostly related to the household, ie, to recent typhoid fever in the household (OR, 2.38; 95% CI, 1.03-5.48); no use of soap for handwashing (OR, 1.91; 95% CI, 1.06-3.46); sharing food from the same plate (OR, 1.93; 95% CI, 1.10-3.37), and no toilet in the household (OR, 2.20; 95% CI, 1.06-4.55). Also, typhoid fever was associated with young age in years (OR, 0.96; 95% CI, 0.94-0.98). In comparison with fever controls, risk factors for typhoid fever were use of ice cubes (OR, 2.27; 95% CI, 1.31-3.93) and female sex (OR, 1.79; 95% CI, 1.04-3.06). Fecal contamination of drinking water was not associated with typhoid or paratyphoid fever. We did not detect fecal carriers among food handlers in the households.

Conclusions: In Jakarta, typhoid and paratyphoid fever are associated with distinct routes of transmission, with the risk factors for disease either mainly within the household (typhoid) or outside the household (paratyphoid).
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http://dx.doi.org/10.1001/jama.291.21.2607DOI Listing
June 2004

TTV infection and its relation to serum transaminases in apparently healthy blood donors and in patients with clotting disorders who have been investigated previously for hepatitis C virus and GBV-C/HGV infection in Belgium.

J Med Virol 2002 Apr;66(4):561-6

Division of Liver and Pancreatic Diseases, Department of Medicine, University Hospital Gasthuisberg, Leuven, Belgium.

A novel DNA virus, TT virus (TTV), has been proposed as a possible etiologic agent for non A-E hepatitis. The aim of the present study was to determine the prevalence of TTV infection using PCR in healthy blood donors and in patients with clotting disorders who have been investigated previously for GBV-C/HGV and HCV infection in Belgium. In this study, PCR using primers proposed by Takahashi et al. [(1998) Hepatology Research 12:233-239] proved far more sensitive than those used by Okamoto et al. [(1998) Journal of Medical Virology 56:128-132]. The sequence of the PCR products showed 87% identity to the published sequence. TTV was present in 29.7% of healthy blood donors, a figure intermediate between the low rate of infection observed in Scotland and the high rates in the Far East. TTV was detected in 46.5% of 127 patients studied with clotting disorders as compared to 79.5% for HCV and 11.8% for GBV-C/HGV infection. However, there was no impact on the level of serum transaminases. Treatment with interferon for HCV infection co-infected with TTV suppressed temporarily serum TTV DNA. Therefore, it was concluded that TTV DNA is detected frequently in serum of healthy blood donors in Belgium and more often in patients with clotting disorders. TTV does not cause liver disease or contribute to the severity of liver disease.
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April 2002
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