2015

• PPARγ expression by rambutan peel extract in obesity rat model-induced high-calorie diet.

Sri Rahayu Lestari, Muhammad Sasmito Djati, Achmad Rudijanto, Fatchiyah Fatchiyah. Asian Pac J Trop Biomed 2015; 5(10): 812-817

Abstract

Objective: To monitor the physiological characteristics and genes expression of obesity rat model after rambutan peel extract (RPE) treatment.

Methods: Twenty-four 12-week-old male rats were divided into 4 groups: normal, obesity, obesity treated with ellagic acid (O-EA) and obesity treated with RPE30 (O-RPE30). Physiological characteristics were monitored by measuring body weight, calorie intake, size of adipocyte and level of triglyceride. Peroxisome proliferator activated receptor gamma (PPARγ), CCAAT/enhancer-binding proteins α and fatty acid binding protein 4 (FABP4) expression were observed using immunohistochemistry, western blotting and quantitative RT-PCR methods.

Results: Body weight gain of O-EA and O-RPE30 rats were lower than obesity group and size of adipocyte cells were smaller than obesity group (P < 0.05), but when we compared to normal group, those groups had higher body weight gain and larger adipocyte cells. The level of triglycerides, protein expression of PPARγ and mRNA level of FABP4 genes were significantly downregulated on O-EA and O-RPE30 compared to obesity group (P < 0.05). Our results indicated that RPE had potential substance as inhibitor of body weight gain, declining of size of adipocyte, level of triglycerides, PPARγ expression and mRNA level of FABP4 gene on obesity rat model.

Conclusions: RPE have anti-obesity activity by inhibiting body weight gain, declining size of adipocyte, decreasing triglyceride, PPARγ expression and mRNA level of FABP4 gene on obesity rat model.

Keywords: High calorie diet Obesity; Peroxisome proliferator activated receptor γ; Rambutan peel extract

• Proteomic Analysis Of Immunogenicproteins From Salivary Glands Of Aedesaegypti

 Rike Oktarianti, Kartika Senjarini, Toshiya Hayano, Fatchiyah Fatchiyah, Aulanni’am. Journal of Infection and Public Health (2015) xxx, xxx—xxx

 Summary

Humans develop anti-salivary proteins after arthropod bites or exposureto insect salivary proteins. This reaction indicates that vector bites have a positiveeffect on the host immune response, which can be used as epidemiological markersof exposure to the vector. Our previous study identified two immunogenic proteinswith molecular weights of 31 kDa and 56 kDa from salivary gland extract (SGE) ofAedes aegypti that cross-reacted with serum samples from Dengue HemorrhagicFever (DHF) patients and healthy people in an endemic area (Indonesia). Serum sam-ples from individuals living in non-endemic area (sub-tropical country) and infantsdid not show the immunogenic reactions. The objective of this research was to iden-tify two immunogenic proteins, i.e., 31 and 56 kDa by using proteomic analysis. Inthis study, proteomic analysis resulted in identification of 13 proteins and 7 proteinsfrom the 31 kDa- and 56 kDa-immunogenic protein bands, respectively. Among thoseproteins, the D7 protein (Arthropode Odorant-Binding Protein, AOBP) was the mostabundant in 31-kDa band, and apyrase was the major protein of the 56-kDa band.© 2015 King Saud Bin Abdulaziz University for Health Sciences. Published by ElsevierLimited. All rights reserved.

Keywords: Proteomic analysis;Immunogenic proteins;Salivary gland;Aedes aegypti

• Protective effect of CSN1S2 protein of goat milk on ileum microstructure and inflammation in rat-CFA-induced rheumatoid arthritis.

Rista Nikmatu Rohmah, Edi Widjajanto, Fatchiyah Fatchiyah. Asian Pac J Trop Dis 2015; 5(7): 564-568. http://dx.doi.org/10.1016/S2222-1808(15)60837-4

Objective: To observe the protective effect of goat milk alpha (S2)-casein (CSN1S2) protein on ileum microstructure and inflammation in rat-complete Freund’s adjuvant-induced rheumatoid arthritis model.

Methods: Twenty four male Wistar rats were divided into six groups of two models. The body weight, food intake and albumin level of all subjects were calculated. The ileum microstructures were analyzed by scanning electron microscopy. Histopathological analysis was observed by hematoxylin-eosin staining and the level expressions of immunoglobulin

E, secretory immunoglobulin A, interleukin-17, interleukin-10, Ki-67 and caspase-9 were measured by using western blotting.

Results: CSN1S2 protein of milk or yogurt could repair the ileum villi of rat arthritis group similar to the normal. The level expressions showed the immunoglobulin E, secretory immunoglobulin A, interleukin-17 and caspase-9 decreased in milk CSN1S2 protein and yogurt CSN1S2 protein rat groups. The level expression of interleukin-10 was increased, and also Ki- 67 was significantly increased in milk CSN1S2 protein and yogurt CSN1S2 protein rat groups. CSN1S2 protein of milk and yogurt could increase the body weight and albumin significantly, meanwhile food intake increased but not significantly.

Conclusions: CSN1S2 protein of goat milk and yogurt could repair the ileum microstructure, suppress inflammatory process and also increase the body weight, food intake and albumin level. This result indicates that goat CSN1S2 protein may protect the ileum disorder in rheumatoid arthritis disease.

Keywords: Arthritis rheumatoid, Casein, Goats, Ileum, Inflammation, Milk protein

• Goat milk CSN1S2 is able to decrease the severity scoring, tumor necrosis factor-alpha, and advanced glycation end products receptor expression in complete Freund’s adjuvant-induced rheumatoid arthritis model of rats.

Rivqi Rifa Bia, Regina Putri Virgirinia, Bambang Setiawan, Aris Soewondo , Fatchiyah atchiyah. Biomarkers and Genomic Medicine (2015) xx, 1-8

Abstract

This study aimed to elucidate whether CSN1S2 protein of goat’s milk was able to inhibit pro-inflammatory cytokine [interleukin (IL)-17 and tumor necrosis factor (TNF)-a], RAGE, and caspase-3 expression in rheumatoid arthritis (RA) rats. A total of 24 Wistar female rats, were randomly assigned into four groups: control group (C), CSN1S2 protein of goat’s milk group (CM), CFA-induced RA-rats group (RA), and the RA group treated by CSN1S2 protein of goat’s milk (RAM). The severity of erythema and swelling in lower extremities were counted by scoring. IL-17, TNF-a, RAGE, and caspase-3 expression in synovial membranes were analyzed by confocal laser scanning microscopy (CLSM) and western blotting. Erythema and swelling in the RA group was significantly attenuated by goat’s milk CSN1S2 (p < 0.05), but did not reach the level in the control group (p < 0.05). The use of CLSM, CSN1S2 protein of goat’s milk could decrease the TNF-a, caspase-3, and the number of hyperplasia cells in comparison with the RA group (p < 0.05), to reach the level in the control group (p > 0.05). Western blotting analysis showed that the expression of IL-17, RAGE, TNF-a, and caspase-3 were higher in the RA group compared with the control group. CSN1S2 protein.

Keywords: casein; inflammation; milk; nutritional therapy

• Selective Inhibition on RAGE-binding AGEs required by Bioactive Peptide Alpha-S2 Casein protein from Goat Ethawah Breed milk: Study of Biological modeling

 Fatchiyah Fatchiyah, Ferlany Hardiyanti, Nashi Widodo. Acta Inform Med. 2015 APR 23(2): 90-96 doi: 10.5455/aim.2015.23.90-96

Abstract

Background: Advanced Glycation End Products (AGE) play a pivotal role in the development various degenerative diseases such as diabetes, cardiovascular disease, stroke, neuropathy, and nephropathy. Different studies have been done to employ AGEs as drug targets for the diseases therapy. In previous study, we have found bioactive peptide from Ethawah goat milk for anti-diabetic that may work through inhibition of AGE receptor function. However, the mechanism of bioactive peptides inhibits AGE- AGE receptor (RAGE) bonding still not clear yet. Therefore we investigated the inhibition mechanism by calculate the potential energy binding among the peptides, AGEs and RAGE using molecular docking system.

Methods: Modeling 3D-structure was predicted by SWISS-MODEL web server. The virtual interaction was analyzed by docking system using HEX 8.0, Pymol and Discovery Studio 4.0 software.

Results: this study showed that AGEs (Argypirimidine, Imidazole, Pentosidine and Pyrraline) bind to C-domain of RAGE. The total energy binding of RAGE with Argypirimidine, Imidazole, Pentosidine and Pyrraline were 378.35kJ/mol, -74.57kJ/mol, -301.25kJ/mol and -400.72kJ/mol, respectively. We have found three peptides among eight peptides from Ethawah goat milk, which are able bind to C-domain of RAGE, there are CSN1S2 f41-47, CSN1S2 f182-189, and CSN1S2 f214-221. The CSN1S22 f41-47 at arginine residue 47 interacts with proline162, leusine163 and leusine158 of RAGE. The total binding energy between CSN1S2 f41-47, CSN1S2 f182-189, and CSN1S2 f214-221 with RAGE were -378.35 kJ/mol, -359.97kJ/mol, -356.78 kJ/mol, respectively. Total binding energy and binding pattern indicated that RAGE more prefer bind with peptide and block AGE bind to functional site of RAGE. Further analysis showed that complex peptide-RAGE shifted binding site of AGE on function domain RAGE.

Conclusion: This study suggested that the peptides from Ethawah goat milk may act as an inhibitor of AGEs-RAGE interaction that impaired signal transduction cascade at the cellular level.

Keywords:

Argypirimidine; bioactive peptide; glycation; goat milk; imidazole; receptor for glycation end products

• Relation of Elevated Serum Lipase to Indonesian Type 2 Diabetes Mellitus Progression.

 Arie Srihardyastutie, Djoko W Soeatmadji.  Fatchiyah, Aulanni’am4. Biomedical Research 2015; 26 (2): 293-298 ISSN 0970-938X www.biomedres.info

Abstract

The increasing level of serum pancreatic enzyme indicates an inflammation of exocrine pancreas, known as pancreatitis. One of the pancreatic enzymes that evaluated in pancreatitis is lipase. The aim of the study was to evaluate the correlation of increasing level of serum lipase with duration of disease and progression of diabetes in Indonesian T2D subject. Subjects were categorized according to ADA 2013 into three groups: healthy controls (n=21), prediabetes (n=12), and diabetes (n=34). The data were analyzed statistically and expressed as mean ± SD. Multivariate analysis of variance was used for showing the differences of the variables. Multiple

regressions were applied for correlation studies of the variables and it was continued with Structure Equation Modelling-Generalized Structure Component Analysis (SEM-GCSA) for evaluating the coefficient contribution of each variable in Hypothetic Model. The results showed there were elevated levels of blood glucose, insulin resistance, creatinine, and serum lipase activity in T2D. The increased serum lipase activities were positively correlated with duration of diseases, plasma glucose, HbA1c level, Insulin Resistance Index, and creatinine level, but did not correlate with lipid profile (Cholesterol, Triglyceride, HDL and LDL), and insulin level in Indonesian T2D Patients. Hypothetic structural model showed that decreasing level of insulin contributed to increase insulin resistance, likewise, insulin resistance contributed positively to glucose level, and glucose level contributed to increase HbA1c level and also lipase activity, but the increasing activity of lipase was not contributed significantly to increase glucose level. So, the high serum lipase has correlation with progression of T2D.

 Keywords: Disease progression; Serum lipase; Type 2 Diabetes mellitus

• Virtual Selectivity Peptides of CSN1S2 Protein of Local Goat Ethawah Breeds Milk Modulate Biological Mechanism of Calmodulin

Fatchiyah Fatchiyah, Sentot J Raharjo, Firli RP Dewi. Int J Pharm Bio Sci 2015 April;; 6(2): (B) 707 – 718

Abstract

The purpose of our study is to observe virtual selectivity peptides of caprine alpha-S2 casein (CSN1S2) protein of goat Ethawah breeds milk modulates biological mechanism of Calmodulin virtual prediction of biological function of peptides of goat fresh milk of local Ethawah breed. The caprine alpha-S2 casein protein was isolated and purified from fresh goat milk local Malang, and then caprine alpha-S2 casein protein was sequenced by MALDI-TOFF analysis. The function of specific peptides were docking with Calmodulin by in silico.The result of this study is the caprine alpha-S2 casein protein of Ethawah breed goat milk has eight peptide fragments: CSN1S2 f41-47, f87-96, f97-107, f131-141, f182-189, f205-213, 214-221 and f214-223. The most of alpha-S2 casein peptide fragment can interacted properly with Calmodulin, except CSN1S2 fragment 97-107 peptide. The caprine alpha-S2 casein protein peptides have ability to bind Calmodulin on specific site and may enhance sites for interactions with other cellular molecules.

Key Word: Bioactive peptides, CSN1S2, Calmodulin, Goat milk

• CSN1S2 protein of goat milk inhibits the decrease of viability and increases the proliferation of MC3T3E1 pre-osteoblast cell in methyl  glyoxal exposure

Choirunil Chotimah, Gatot Ciptadi, Bambang Setiawan, Fatchiyah Fatchiyah (Elsevier – Asian Pac J Trop Dis 2015; 5(3): 219-223)

Abstract

Objective: This study aimed to investigate whether the CNS1S2 protein of goat milk able to inhibit the toxicity of methyl glyoxal towards MC3T3E1 pre-osteoblast cells. Methods: At confluency, pre-osteoblast cells were divided into five groups, which included control (untreated), pre-osteoblast cells exposed to 5 µM methyl glyoxal (MG), pre-osteoblast cells exposed to MG in the presence of CSN1S2 protein at doses of 0.025, 0.050, and 0.100 mg/L. Analysis of reactive oxygen species was done with 2,7-dichlorodihydrofluorescein diacetate (H₂DCFDA) fluorochrome. The proliferation and viability of MC3T3E1 cells were measured by trypan blue staining. Malondialdehyde analysis was done colorimetrically. Results: Cell’s viabilities were  significantly lower in MG + M₅₀ compared to MG group (P < 0.05). MG + M₁₀₀ significantly increased the cells viability compared to MG group (P < 0.05). The levels of proliferation were significantly higher in MG + M₁₀₀ compared to control untreated group and all treatment groups,respectively (P < 0.05). Conclusion: High dose of CSN1S2 protein of goat milk (0.100 mg/L) in high MG environment inhibits the decrease of viability due to increases the proliferation of MC3T3E1 pre-osteoblast cell.

Keywords: bone formation cells; carbonyl compounds; oxidative stress; mitogenic

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2014

• Optimization of Neuron cells Maturation and Differentiation.

Choirunil Chotimah*, Masruroh Rahayu*, Gatot Ciptadi, Fatchiyah Fatchiyah. 2014.  Jurnal Biotropika Vol. 2 No. 4 : 191-197 (* equal authors)

ABSTRACT

Neurodegenerative disease is the brain and spinal cord attacks to turn off his cell. One of the diseases that prevalence of HAD neurodegenerative is now increased by approximately 37%. The purpose of this study was to determine the optimal time of growth of cultured brain neurons in rats (Rattus norvegicus) and know the stages of morphological differentiation of rat brain neurons. Isolate of neuron cells was provided from fetal rat neurons, aged 18-19 days, and then cells grown in vitro on MEM+10%FBS+3%Penstrep culture medium. Cells growth observed once each day during 14 days. The results obtained are optimal neuronal cell growth are on the eighth day. Morphological differentiation of neuronal cells began on day 1 of the form neuroblast cell morphology apolar (rounded), the 2nd day of neuronal cell morphology in the form of bipolar neuroblast (already formed axon and dendrites), on day 3 to day 14 cells already mature, with cell morphology namely bipolar neurons, pyramidal and multipolar. Mature neuron cells that have optimizations on the 10th day.

Key words : diferentiation, neuron culture, neuron morphology, proliferation.

• Binding energy calculation patchouli alcohol isomer-cyclooxygenase complexes  as suggestion COX-1/ COX-2 inhibitor selective. 

Sentot Joko Raharjo, Chanif Mahdi, Nurdiana, Takheshi Kikuchi, Fatchiyah Fatchiyah. (Hindawi –Advance in Bioinformatics, 2014 : 1-12,  http://dx.doi.org/10.1155/2014/850628

ABSTRACT

To understand the structural features that dictate the selectivity of the two isoforms of the prostaglandin H2   synthase   (PGHS/   COX),   the   three-dimensional   (3D)   structure   of  COX-1/   COX-2   was   assessed   by means   of   binding   energy  calculation   of   virtual   molecular   dynamic  with   using   ligand   alpha-patchouli alcohol isomers.     Molecular interaction studies with COX-1 and COX-2 were done using the molecular docking   tools  by  Hex  8.0.  Interactions   were   further   visualized   by   using  Discovery   Studio   Client  3.5 software  tool.  The  binding   energy     of   molecular   interaction   was  calculated   by   Amber12  and   Virtual Molecular     Dynamic     1.9.1  software.  The     analysis  of  the alpha-patchouli     alcohol  isomer    compounds showed   that  all  alpha-Patchouli   alcohol  isomers   have   suggested  as   inhibitor  of  COX-1   and   COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent) alpha-patchouli alcohol isomer compounds (CID442384, CID6432585, CID3080622, CID10955174, and CID56928117) suggests as candidate for a selective COX-1 inhibitor and CID521903 as non-selective COX-1/ COX-2.

Keywords:  virtual  molecular    dynamic,  binding    energy,  patchouli    alcohol,   COX-1/ COX-2,   inhibitor selective

• Immunogenic Protein from Salivary Gland of Aedes aegypti Against to Human Sera

Rike Oktarianti, Kartika Senjarini, Fatchiyah Fatchiyah, Aulanni’am (Advances in Natural and Applied Sciences, 8(8) July 2014, Pages: 101-107)

‘‘‘Dengue   Haemorraghic   Fever   (DHF)   is   an   acute   Flavivirus   infection   transmitted   by several   species   of   Aedes   mosquitoes   with  Aedes   aegypti   as   the   main   vector.   During blood    feeding,  arthropod   vectors  inject  saliva  into  vertebrate  hosts.  The  saliva  is biochemically     complex,   pharmacologically     active  and  plays   an  important   role  in pathogen    transmission.   The   objective  of  this  research  is  to  identify  immunogenic salivary   gland   proteins   of   Ae.   aegypti   against   human   blood   sera   of   people   living   in endemic area. Protein profile from Salivary Glands (SG) of         Ae. aegypti was observed by    12%    SDS-PAGE       from   lab.  scale  cultures   and   from   landing   populations.  Identification   of   immunogenic   proteins   from   both   sample   was   carried   out   by   using Western   Blot   Analysis   after   cross   reaction   of   Salivary   Gland   Extract   (SGE)   with   3 different   human   sera:   from   DHF   patients,   healthy   persons   who   were   exposed   to   Ae. aegypti and healthy person who were likely not exposed. Sera from healthy people from non   endemic   areas   and   from   infants   were   used   as   negative   controls.   Over   all,   the protein   profiles  from  lab.  scale  cultures  SGE   and  landing   populations   were  quite  similar.   We   found   13   protein   bands   were   identified   ranging   from   26   kDa   up   to   255 kDa. We predicted that     255, 56, 31, 27 and 26 kDa are target protein, which is      two of immunogenic proteins were able to cross-react with human sera from people living in endemic area on 31 and 56 kDa. These bands appeared only in samples from humans who were previously exposed to mosquitoes bites, and not in humans who had not been  exposed. These immunogenic salivary proteins may serve as human immune response against Ae. aegypti bites.   This result indicated that may the 31 and 56kDa protein has function as transmitted pathogens.

• The Relationship between HbA1c, Insulin Resistance and Changes of Insulin Secretion in Indonesian Type 2 Diabetic Subjects

Srihardyastutie, A, D.W.Soeatmadji, Fatchiyah, and Aulanni’am (Advances in Natural and Applied Sciences, 8(8) July 2014, Pages: 25-30)

Abstract

Type    2  Diabetes   Mellitus  (Type   2  DM)   is  considered   as  heterogenous   metabolic  disorder with the common characteristic of elevated blood glucose. The main cause of hyperglycemia in Type 2 DM are impaired of insulin secretion and increased insulin resistance. The HbA1c assay has become the most commonly used measure of chronic glycemia   in   epidemiological   studies,   clinical   trials   and   the   management   of   diabetes. However,     the  molecular    patophysiology    of  HbA1c,   insulin  resistance  and  insulin secretion profile in development of type 2 diabetes still unclear. The study was carried out to evaluate the relationship of HbA1c and insulin resistance, and insulin secretion changes   of   type   2   DM patients.   The   study  population   consists   of   67 peoples,   which include: healthy control (n=21), prediabetes (n=10), and diabetes (n=36). The level of blood    glucose,  lipid  profile  (total  cholesterol,  triglyceride,  HDL,  and  LDL)   were determined      fully  automated     analyzer   using   enzymatic     methods.    HbA1c     was  determined      by  ion-exchange     high-performance     liquid  chromatography     using   an  automated     analyzer,  insulin  and   pro-insulin  were  measured    by  Sandwich    enzyme immunoassay       methods.   The   insulin  resistance  was   calculated  using  mathematical  formula, such as HOMA-IR for β-cell function and QUICKI of insulin sensitivity. The results   showed   the   fasting   insulin   level   was   significantly   decreased   in   Type   2   DM,   prediabetes   and   healthy   control.   Total   insulin   +   pro-insulin   in   diabetes   subject   was significantly lower in diabetes than healthy control and prediabetes. Proinsulin level of healthy control was lower than prediabetes and diabetes, but proinsulin concentration  in prediabetes and diabetes were not different. HbA1c and Insulin resistance (HOMA-IR)   were   significantly   higher   in   Type   2DM   than   prediabetes   and   healthy   control. Conclusion of this study were increasing blood glucose level in type 2 DM contributed to HbA1c, correlated with change of insulin secretion profile, by increasing proinsulin  level and decreasing total insulin, and related with worsen insulin resistance.

• LMP-1 and Nasopharyngeal Carcinoma (NPC)

Anggun Indah Budiningrum, Achmad Rofi’i, Suharjono Suharjono, Fatchiyah Fatchiyah. Cukurova Med J. 2014; 39(3): 480-487

Abstract
Purpose: This study aims to determine the interaction of LMP-1 with H2O2 , nitrosamine, and nicotine to predict the external factor that affected LMP-1, which activates lytic phase on nasopharyngeal carcinoma (NPC).
Materials and Methods: The amino acid sequence of human LMP1 (GI: 343177335) and compound structure of H2O2 (ID:784), nicotine (ID: 89594), and nitrosamine (ID: 37183) was obtained from database The National center of Biotechnology Information. The 3-dimension modeling structure of LMP-1 predicted using SWISS-MODEL web server. Hex 6.12 was used for the purpose of docking of the lead with the target molecule. Ligand details interaction then detected by LigPlus+ v.1.4.4 software. Molecular graphics and analysis were performed with PyMOL.
Results: LMP-1 has interaction with H2O2 , nitrosamine, and nicotine. Total energy that use of LMP-1 to interaction with H2O2 (-67,79 kJ/mol) is lowest than interaction with nicotine (-149,43 kJ/mol) and nitrosamine (-82,93 kJ/mol). The kind of interaction between LMP-1 and H2O2 is hydrogen bond whereas interaction of LMP-1 between nicotine and nitrosamine are hydrophobic bond.
Conclusions:LMP-1 has strongest interaction with H2O2 than nicotine and nitrosamine. This is predicted that H2O2 is external factor that affect LMP-1 switching to lytic infection in NPC patients.

Key words: H2O2, LMP-1; nasopharyngeal carcinoma, nicotine, nitrosamine

• Partial Analysis 16S rRNA Gene in Lactobacillus spp. from Natural Fermented Milk [English]

Nur Kusmiyati, Nur Hidayat, Fatchiyah Fatchiyah (Cukurova Med J. 2014; 39(1): 99-104)

Abstract
The aim of this research is to analysis 16S rRNA gene sequence of Lactobacillus spp. from natural fermented milk. The methods that used in this study are total DNA isolation using alkaline lysis, PCR amplification carried out using of specific primers, and identification of amplified DNA using sequencing. The result of PCR process is a nuclotide with approximately 585 bp length which contained V1-V3 variable regions. 16S rRNA gene sequence then compared and aligned with existing 16S rRNA data sequence from GenBank. The conserved region of 16S rRNA gene from nuclotide number 189-358 and 384-445 were 95,9% and 94,9% respectively, and the total conserved region of 16S rRNA gene is 78.8%. From total 7 isolates that isolated from natural fermented milk , 2 isolates were identified as L. plantarum with similarity value 98.28% and 97.78%, the other 5 isolates were identified as L. rhamnosus (2 isolates) with similarity value 98.38% and 97.51%, L. zeae (2 isolates) with similarity value 97.36% and 98.38%, and L. casei (1 isolate) with similarity value 98.20%.

Key words: 16S rRNA gene, Lactobacillus, natural fermentation milk, partial analysis

• Revealing the Genetic Variation and Allele Heterozygote Javanese and Arab Families in Malang East Java Indonesia [English]

Nila Kartika Sari, Eriko Prawestiningtyas, Fatchiyah Fatchiyah .Cukurova Med J. 2014; 39(1): 39-47

Abstract

The purpose of this study is to identify genetic variability the family of Javanese married with Arab and their allele patterns for paternity testing. We used human white blood cell from three generations of three families, consists of: (1) grandmother-mother, father-daughter, (2) grandfather-mother, father-daughter, (3) grandfather, grandmother – mother, father-son. DNA blood samples were isolated by salting out standard procedure, and amplified by PCR with applying 13 CODIS which consists of TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 and amelogenin primer. The Fingerprint profile was visualized by 8% polyacrylamide gel and took the picture by ChemiDoc gel Imaging and measure the intensity band pattern by Quantity One software. Our result showed that the genetic variability and heterozygote allele increasing by using the 13 CODIS markers from the first generation to the next generation with paternity testing from each family were matched. We can conclude that in a Javanese-Arab family ethnic seems stimulate the increasing genetic variation and allele heterozygote.

Key words: Javanese – Arab Ethnics, DNA fingerprint, 13 CODIS

•  Forensic Profiling of Javanese and Madurese Families in Malang and Madura, East Java Indonesia.

Nikmatul Iza, Eriko Prawestiningtyas, Fatchiyah Fatchiyah. Cukurova Med J. 2014; 39(1): 26-38

Abstract
Purpose: The aims of this study are to identify the heritability of fingerprint patterns among three generations of Javanese and Madurese families and to determine the similarities, genetic variability and allele patterns for paternity testing.
Material and Methods: The methods used in this study were the identification of the fingerprint patterns, DNA extraction from blood samples by salting out, PCR amplification use 13 CODIS which consists of TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11, and visualized by 8% polyacrylamide gel. The allele of individual band profile was analyzed by using QuantityOne software.
Results: The results of fingerprint patterns showed that the families of Javanese ethnic has specific in ulnar patterns on both the middle and little fingers, meanwhile the families of Madurese ethnic has a plain whorl patterns on the right thumb and left index fingers which were inherited from the first generation to the next generation. The similarities of profile DNA forensic in Javanese ethnic generally have the same band patterns were produced by using D7S820 and CSF1PO markers, whereas in Madurese ethnic by using VWA and D18S51 markers. The genetic variability in Javanese ethnic by using D3S1358 and D21S11 markers, meanwhile the Madurese ethnic by using TH01 and D21S11 markers. Conclusion: We can conclude that there are the different characteristic of the fingerprint pattern of Javanese and Madurese families and the similarities and genetic variability in families of Javanese were different with the families of Madurese on the some markers.

Key words: DNA Forensic, Fingerprint, 13 CODIS, Javanese and Madurese ethnic

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2013

• Production and Potency of Local Rambutan at East Java as A Candidate Phytopharmaca.
  

Sri Rahayu Lestari, Muhammad Sasmito Djati, Ahmad Rudijanto, Fatchiyah Fatchiyah.  J. of Agricultural Science Agrivita, 2013, 35 (3): 270-276

ABSTRACT

Rambutan is a tropical fruit that grow well in Indonesia and the peel is considered as waste. Many researchers’ showed that rambutan peel contains polyphenol that could be expected to avoid obesity.  The objective of this study was to explore the increasing production of local rambutan and to identify the promising phytochemical compounds on its peel as phytopharmaca candidate against obesity. Survey was conducted on the production of rambutan, potential plantation area, and marketing. Sample of rambutan peel collected from the sub-district Kanigoro, Blitar. Phytochemical compounds were analyzed using TLC, HPLC and FT-IR. Bioassay analysis used obesity rat models. The survey result showed a mean of rambutan production increased 2,6% in 2007-2012. Average production of rambutan 70-120 kg/tree. Vegetative multiplication usually done to maintenance of rambutan quality. The main compound of  Rambutan peel  extract (RPE) is flavonoids, tannins, ellagic acid and the major functional group of CH₃, aliphatic CH₃, and C=O. These compounds have a potential activity against obesity.  RPE 30 mg/kgBW dose was significantly inhibit the weight gain of obese rats and reducing the adipocyte size (p<0.05).

• Genetic Diversity of Lactobacillus spp. of Natural Ethawah Goat Milk-fermented was determined by using  16SRDNA with DDGE Analysis

Nur Kusmiyati, Nur Hidayat, Fatchiyah Fatchiyah. Journal of Biological Researches: 18 (91-94), 2013

Abstract

The aim of this research is to characterize of Lactobacillus spp. from natural Ethawah goat milk-fermented were using 16SrDNA by denaturation gradient gel electrophoresis (DGGE) analysis. Goat and bovine (as negative control) milk naturally fermented among 24hour until 6 days. Morphological and biochemistry of bacteria were characterized by standard methods. The total DNA of bacteria were isolated using alkali lysis, PCR amplification was carried out using 3 pairs of specific primers, DNA-amplified using DGGE and then to determine the relationship among Lactobacteria using NTsys package software V2.0. Phenotypical and biochemical study showed that the 11 strains are belonging to genus Lactobacillus. The dendogram results show all of isolates had similarity characters with genus Lactobacillus around 56-76%. According to morphological and DDGE profiles, we were identified that bacteria isolate of goat milk-fermented are K1A, and K3A are L. casei, and bacteria isolate K3B is L. plantarum.

Key words: Ethawah goat, Lactobacillus, natural milk-fermented

Nutrigenomic study: Igf-1 inhibition in  adipogenesis of visceral adipose tissue of rat  using rambutan peel extract

Rizky Nurdiansyah , Sri Rahayu Lestari  and Fatchiyah Fatchiyah (Biotropika, 2013, vol 1 no 6: )

Abstract

This  study  observes  the  inhibition  of  rambutan  peel  extract  to  rat  visceral  adipose  tissue  adipogenesis  by  observing  the  expression  of  igf-1.  Experiment  stages  consist  of  rambutan  peel extraction, rat treatment, visceral adipose tissue protein isolation and separation,  and  western  blot.  Male  wistar  rats  were  divided  into normal and obese rats. The treatments consist of control, ellagic acid, placebo,  and  extract   at  5,  10,  15,  and  20  mg/kg  body  weight. Decreasing body weight gain observed in obese rats with similar food  intake  (P>0,05).  Effective  dose  observed  at  10mg/kg,  whilst  at  20  mg/kg    showed     increasing   body     weight.   Protein   profile   shows  different band numbers and intensity between groups and treatments.  Igf-1 expression is bound to Igfbp-1 at 36,7 kDa. Anti-obesity observed  at   10  mg/kg  extract  in  obese  rats.  Interestingly,  igf-1         expression is lower at 20mg/kg group. This result suggest that inhibition does not go through IR family tyrosin kinase.

• Patchouli Alkohol Isomers Pogostemon Herba Predicted Virtually as Selective Novel of Cox-1/ Cox-2 Inhibitor

Sentot J Raharjo, Chanif Mahdi, Nurdiana, Wolfgang Nellen, Fatchiyah F. Journal of Biological Researches: 18 (98-101), 2013

Abstract

The aim of our research is predicting the alpha-patchouli alcohol isomer Pogostemon Herba as inhibitors cyclooxygenase (COX-1 and COX-2) isoenzymes. The data for the alpha-patchouli alcohol isomer (CD521903, CD442384, and/or CD6432585) Pogostemon Herba were explored from the pubchem database. Molecular interaction studies with COX-1 and COX-2 from mouse were done using the molecular docking tools Hex 6.12 and LeadIT2 Bisolve. The analysis of the alpha-patchouli alcohol compounds of patchouli oil showed that alpha-Patchouli alcohol (CD521903) binds to COX-1 at active sites including: LEU223B, ASP228B, LEU237B, ARG 332B, TRP 138A, GLU 139A, SER 142A, ASN 143A, and the interaction to COX-2 at active site including: GLN 289B, GLU 290B, ARG 222B, LYS 211B, THR 212B, HIS 214B, ASN 382B, HEM682B, GLN 454B, HIS 386B, TRP 387B, HIS 388B, VAL 274B, GLN 203B, VAL 291B, VAL 295B. The interaction hydrogen bond energy between alpha-patchouli alcohol: (CD521903-COX-1 complexes (-4 kJ/mol) and CD521903-COX-2 complexes (-8 kJ/ mol) by LeadIT2 Biosolve. This suggests alpha-patchouli alcohol CD521903 as candidate for a selective COX-2 inhibitor. These in silico data need further analyses of biological function activity.

Keywords: alpha-patchouli alcohol, COX-1/ COX-2, inhibitor selective, predicted virtually

• Reducing IRS-1 Activation Cause Mutation of Tyrosine Kinase Domain hINSR Gene on Type-2 Diabetes Mellitus Patients.

Fatchiyah Fatchiyah, Nur Christian_, DjokoWahono Soeatmadji.Bioinformation 9(17): 853-857 (2013) 

Abstract

The purpose of this study is to examine the effect of mutation on tyrosine kinase hINSR gene of DM Type 2 patients reduce the IRS-1 activation by in silico analysis. Blood DNA of DM Type 2 patients from Saeful Anwar Hospital Malang were amplified and sequenced by specific primers of tyrosine kinase domain of hINSR gene. These gene sequences were converted to protein sequence by BLAST and the IRS-1 protein sequence is retrieved from NCBI database. Both of the protein sequence was aligned by using Bio-edit version 5.0.6. The model of three dimension protein was predicted by SWISS MODEL webserver, and visualized the structure alteration by using Pymol 0.99rc6 and Hex 5.0, and then superimpose of the hINSR and IRS-1 interaction were examined by docking using Hex 5.0. The results showed that one substitution and one deletion of 8-3F patient exon-22 hINSR gene tyrosine kinase domain cause loss of four helixes and three coils structures on tyrosine kinase hINSR protein. Six-deletions and six-substitutions on same gene domain of DMK9 patient changed the two helixes became coil structure. The binding energy of hINSR tyrosine kinase with IRS-1 of normal is E= -494.67 kJ/mol, DMK9 patient is E= -458.4 kJ/mol, and 8-3F patient is E=-544.20 kJ/mol. The DMK9 patient prognosis has better physiological condition than 8-3F patient. Interaction between 8-3F of hINSR tyrosine kinase domain mutation and PTB domain IRS-1 is more spontaneous than DMK9, but both of them were reduced on IRS-1 activation respectively.

Key words: Diabetes Mellitus Type-2, hINSR, In Silico, IRS-1

• PARP-1 expression against Epstein-Barr virus LMP-1 and BZLF-1 in undifferentiated nasopharyngeal carcinoma.

Anggun I. Budiningrum, Achmad Rofi’i, Suharjono Suharjono, Fatchiyah Fatchiyah. J Exp. Integr. Med. J  2013; 3(4):299-304

Abstract
Objective: This study aims to determine the poly(ADP-ribose) polymerase (PARP)-1 expression levels against the Epstein-Barr virus (EBV) latent membrane protein (LMP-1) and BamHI-Z leftward reading frame (BZLF)-1 of nasopharynx tissues and serum of nasopharyngeal carcinoma (NPC) patients and characterize the histopathology of necrosis cells of NPC tissues.
Methods: 32 tissues sections consisting 24 NPC and 12 polyp tissues, and also blood serum of patients were taken from Ulin General Hospital, Banjarmasin. Tissue samples were analyzed by using immunofluorescence staining in order to examine LMP-1 and PARP-1 expression. Analyses were done by using immunoblotting with anti-LMP-1, anti-BZLF-1, anti-PARP-1, and anti-caspase-3 antibodies. Histopathological profiles of necrosis cells were analyzed by using hematoxylin-eosin staining and necrotic cells were counted by using the standard software of the microscope.
Results: LMP-1, BZLF-1 and PARP-1 proteins have high levels of expression in patients with NPC. LMP-1 expression of NPC patients and control sera are equal. Interestingly we found that 35 kDa of BZLF-1 and 55 kDa PARP-1 only expressed in NPC patients, meanwhile caspase-3 expression was negative. Histopathologically, NPC tissues were more dominated by karyorrhexis than pyknosis and karyolysis.
Conclusions: This study showed that the expression level of PARP-1 in NPC tissues was increased against LMP-1 and BZLF-1 EBV to protect DNA damage of the recipient cells. This mechanism probably stimulated cell metamorphosis and consequently provoked necrosis.

Key words: BZLF-1; Epstein-Barr virus, LMP-1; Nasopharyngeal carcinoma; PARP-1

• Methylation impact analysis of erythropoietin (EPO) Gene to hypoxia inducible factor-1α (HIF-1α) activity

Firli Rahmah Primula Dewi & Fatchiyah Fatchiyah. Bioinformation 9(15): 782-787 (2013); PMC3766311

Abstract

Erythropoietin (EPO) is a glycoprotein hormone that play a role as key regulator in the production of red blood cells. The promoter region of EPO is methylated in normoxic (non-hypoxia) condition, but not in hypoxic condition. Methylation of the EPO enhancer region decline the transcription activity of EPO gene. The aim of this study is to investigate how different methylation percentage affected on the regulation and transcriptional activity of EPO gene. The DNA sequence of erythropoietin gene and protein sequence was retrieved from the sequence database of NCBI. DNA structure was constructed using 3D-DART web server and modeling structure of HIF1 predicted using SWISS-MODEL web server. Methylated DNA sequence of EPO gene using performed with YASARA View software and docking of EPO gene and transcription factor HIF1 analyzed by using HADDOCK webserver. Our result showed that binding energy in 46% methylated DNA was higher ( 161,45 kcal/mol) than in unmethylated DNA ( 194,16 kcal/mol) and 8% methylated DNA ( 175,94 kcal/mol). So, we presume that a silencing mechanism of the Epo gene by methylation is correlated with the binding energy, which is required for interaction. A higher methylation percentage correlates with a higher binding energy which can cause an unstable interaction between DNA and transcription factor. In conclution, methylation of promoter and enhancer region of Epo gene leads to silencing.

Key words: EPO, HIF-1, methylation, promoter, transcription.

• Impact of anemia on erythropoietin and erythropoietin receptor expression: correlation with the proliferation of breast cancer cells

Firli Rahmah Primula Dewi, Muhammad Darwin Prenggono, Fatchiyah Fatchiyah
J Exp. Integr. Med. 2013; 3(3): 199-204 

Abstract
Objective: The aim of this research is to investigate the relationship between anemia and erythropoietin (Epo) and erythropoietin receptor (EpoR) expression. This study also investigated the relationship between Epo and EpoR expression level and the proliferation rate of cancer cells.
Methods: 20 samples of breast cancer tissues were divided into two groups; anemic group (from patiens with Hb level < 12) and non-anemic group (from patients with Hb level > 12). All samples were analyzed by using immunofluorescence staining in order to examine Epo and EpoR expression. Proliferation of cancer cells were analyzed by using Hematoxylin-Eosin staining.
Results: Anemic breast cancer group represented higher Epo and EpoR expression than the non-anemic group. The results also indicated that in anemic samples expression levels of Epo and EpoR were negatively correlated with the number of cancer cells. In contrast, Epo and EpoR expression levels from non-anemic samples were positively correlated with the number of cancer cells.
Conclusion: These results conducted that anemia is a crucial factor of hypoxic condition. Hypoxia led by anemia cause a different control mechanism of Epo and EpoR expression and cancer cell proliferation.

Key words: Anemia; Breast cancer; Erythropoietin; Erythropoietin receptor; Non-anemia; Proliferation

• Reactive oxygen species, NF-kB, and p53 levels in tissue of undifferentiated nasopharyngeal carcinoma

Achmad Rofi’i, Fatchiyah Fatchiyah, Pudji Rahayu, Ruslan Muhyi, Sutiman Bambang Sumitro
Oxid. Antioxid. Med. Sci. 2013; 2(2): 143-147

Abstract
This study aimed to evaluate the level of reactive oxygen species, oxidative stress, and NF-κB and p53 in undifferentiated nasopharyngeal carcinoma. Twenty-four nasopharyngeal carcinoma patients and ten normal subjects were involved in order to compare the level of malondialdehyde (MDA), hydrogen peroxide (H2O2), and peroxidative index (PI). The level of reactive oxygen species (ROS), expression of NF-κB and p53 from a biopsy specimen of nasopharyngeal carcinoma tissue (histologically confirmed to be undifferentiated WHO III) were also compared with normal nasopharyngeal tissue. The Student t-test was used to analyze the different level of MDA, H2O2 and PI. Analysis of MDA level and H2O2 was done by colorimetric method. Levels of ROS, NF-κB, and p53 were analyzed using laser scanning confocal microscopy. MDA and H2O2 levels as well as PI of nasopharyngeal carcinoma patients were significantly higher compared to control. The levels of ROS and expression of NF-κB and p53 were higher in nasopharyngeal carcinoma tissue than those in normal nasopharyngeal tissue. We conclude that the tissue of nasopharyngeal carcinoma is one source of ROS and oxidative stress in nasopharyngeal carcinoma. NF-κB and p53 levels in nasopharyngeal carcinoma tissue may contribute to oxidative stress in undifferentiated nasopharyngeal carcinoma.

Key words: Lipid peroxidation; NF-kB; p53; Reactive oxygen species

• Nutritional Composition and Protein Profile of Goat Yogurt PE with Double Culture between Streptococcus thermophilus and Lactobacilus species [English]

Ismi Kurnia Budiarti, Masdiana C. Padaga, Fatchiyah Fatchiyah
Cukurova Med J. 2013; 38(4): 681-686 

Abstract
Aim: The aims of this study are to characterize the nutrient compositions and protein profiles of Etawah breed (PE) goat yogurt fermented by double cultures .
Material and Methods: To accomplish this, we used goat and bovine milk in five treatment groups: (1) fresh milk bovine, (2) goat,(3) milk fermented by L. acidophilus and S. thermophilus (LA + ST), (4) L. bulgaricus and S. thermophilus (LB+ ST),and (5) a comersial mixture. PE goat milk was fermented using 2.5% starting bacterial concentrations at 45oC with a pH ranging from 4.5 to 6.6. Nutrient compositions were measured by proximate analysis.SDS PAGE was conducted using 15% separating and 3% stacking gels. To measure the density of protein bands, we used QuantityOne software.
Results: Our results indicated that LA+ST and LB+ST treatments had higher levels of lipids than the control treatment. Conversely, both strain combinations had lower levels of proteins than the control. Organoleptic testing suggests that many attributes (e.g., colour, taste, smell, texture and viscosity) differ significantly from the control. Protein profiles revealed that while the LB + ST and commercial cultures contained proteins with a molecular weight of 36 kDa, the LA + ST cultures did not appear to possess this protein.Based on the molecular weight, we suggest that this protein is in the alpha casein group.
Conclusion: The protein composition of fermented goat and bovine milk is similiar, but the absence of band with molecular weight 36 kDa from goat milk, LB+ST and mix comercial.

Key words: Casein Protein, Goat Milk, L. bulgaricus L. acidophillus S. thermophillus

• Karakter Biokimia dan Profil Protein Yogurt Kambing PE Difermentasi Bakteri Asam Laktat (BAL)

Lulus K Khoiriyah, Fatchiyah Fatchiyah

JELS 2013 3 (1): 1-6