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ANALISIS BIOINFORMATIKA MUTASI S228I PROTEIN PCNA DAN PENGARUHNYA PADA STRUKTUR 3 DIMENSI PROTEIN Dewi, Syarifah
Indonesian Journal of Biotechnology and Biodiversity Vol 1, No 1 (2017): Indonesian Journal of Biotechnology and Biodiversity
Publisher : Universitas Esa Unggul

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AbstrakProliferating cell nuclear antigen (PCNA) adalah protein penjepit DNA yang meningkatkan efektivitas kerja DNA polimerase eukariot. Protein ini mempunyai struktur berbentuk cincin yang mengelilingi DNA dan meningkatkan processivity pada proses replikasi DNA. Mutasi titik pada gen PCNA manusia, Ser228Ile, akan menghasilkan kelainan autosomal resesif dengan gejala penyakit gangguan perbaikan kerusakan DNA seperti Xeroderma pigmentosum, Cockayne syndrome, dan Ataxia telangiectasia. Mutasi ini letaknya berdekatan dengan dengan situs pengikatan protein pengikat PCNA. Mutasi Ser228Ile pada protein PCNA akan menyebabkan perubahan pada struktur IDCL (interdomain connecting loop) dan PIP-binding pocket sehingga mengganggu pengikatan protein ligan ke PCNA dan fungsinya yang sebagian besar berhubungan dengan proses replikasi dan perbaikan DNAÂ Kata kunci: analisis, bioinformatika, dimensi protein

HDAC2 and PCNA expression is correlated to decreasing of endoxifen sensitivity in human breast cancer stem cells ALDH+ Syarifah Dewi; Mohamad Sadikin; Muchlis Ramli; Septelia Inawati Wanandi
Health Science Journal of Indonesia Vol 10 No 2 (2019)
Publisher : Sekretariat Badan Penelitian dan Pengembangan Kesehatan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22435/hsji.v12i2.2449

Latar belakang: Sel punca kanker payudara (breast cancer stem cells/BCSC) adalah subpopulasi sel kanker yang memiliki kemampuan menghasilkan tumor baru dan bersifat seperti sel punca. Penelitian kami sebelumnya menggunakan jaringan kanker payudara mengungkapkan bahwa ekspresi gen histone deacetylase 2 (HDAC2) dan proliferating cell nuclear antigen (PCNA) ditemukan perbedaan signifikan setelah terapi neoajuvan hormon dan kemoterapi. Penelitian ini bertujuan untuk menganalisis hubungan antara ekspresi HDAC2 dan PCNA dengan kelangsungan hidup sel punca kanker payudara dengan penanda aldehyde dehydrogenase + (ALDH+) yang diberi perlakuan endoksifen. Metode: Sampel adalah BCSC primer manusia ALDH+ yang diberi perlakuan endoksifen 4 uM masingmasing selama 2, 4, 6, 8, 10, 12, 14 hari. Viabilitas sel dilihat dengan menggunakan trypan blue dan ekspresi mRNA HDAC2 dan PCNA ditentukan menggunakan qRT-PCR. Hasil: Viabilitas BCSCs ALDH + menurun setelah 2 sampai 4 hari pemberian endoksifen. Pada periode ini juga didapatkan ekspresi mRNA HDAC2 dan PCNA mengalami penurunan. Tetapi setelah pemberian endoksifen selama 8 hari, viabilitas BCSCs ALDH + mengalami peningkatan dan ditemukan peningkatan yang signifikan pada hari ke-14 pemberian endoksifen. Ekspresi mRNA HDAC2 dan PCNA juga menunjukkan peningkatan mulai pada hari ke-8 dan terus meningkat hingga hari ke-14 pemberian endoksifen. Penelitian ini menunjukkan pola yang sama antara ekspresi mRNA HDAC2 dan PCNA dan viabilitas sel. Kesimpulan: Induksi endoksifen yang lama menurunkan sensitivitas efek endoksifen pada BCSC manusia dan ekspresi HDAC2 dan PCNA berkorelasi dengan viabilitas BCSC manusia setelah induksi endoksifen. (Health Science Journal of Indonesia 2019;10(2):77-81) Kata kunci: sel punca kanker payudara, viabilitas sel, HDAC2, PCNA, endoksifen Abstract Background: Breast cancer stem cells (BCSCs) are subpopulation of cancer cells that has the ability to generate new tumor and similar properties to stem cell. Our previous study using breast cancer patients revealed that gene expression of histone deacetylase 2 (HDAC2) and proliferating cell nuclear antigen (PCNA) were significantly altered after neoadjuvant hormone and chemotherapy. This study aimed to analyze the correlation between HDAC2 and PCNA expressions with the viability of breast cancer stem cells aldehyde dehydrogenase + (BCSC ALDH+) treated by endoxifen. Method: Samples are human primary BCSCs ALDH+ that treated with 4 uM of endoxifen for 2, 4, 6, 8, 10, 12, 14 days, respectively. Cell viability was measured using trypan blue exclusion assay and the mRNA expressions of HDAC2 and PCNA were determined using qRT-PCR. Results: The viability of BCSCs ALDH+ was decreased after 2 days until 4 days-endoxifen treatment. It also demonstrated that mRNA expression of HDAC2 and PCNA were decreased in this period. But after 8 days endoxifen treatment, the viability of BCSCs ALDH+ was increased. The increasing of viability was higher in 14 days-endoxifen treatment. The mRNA expression of HDAC2 and PCNA also showed increasing begin on 8 days and continued to increase until 14-days endoxifen treatment. We found a similar pattern between HDAC2 and PCNA expression and cell viability. Conclusion: Prolonge endoxifen treatment decrease sensitivity of endoxifen effect in human BCSC and the expression of HDAC2 and PCNA are correlated to human BCSCs viability after endoxifen treatment. (Health Science Journal of Indonesia 2019;10(2):77-81) Keywords: human breast cancer stem cells, viability, HDAC2, PCNA, endoxifen

The effect of intermittent hypobaric hypoxia on oxidative stress status and antioxidant enzymes activity in rat brain Syarifah Dewi; Wawan Mulyawan; Septelia Inawati Wanandi; Mohamad Sadikin
Acta Biochimica Indonesiana Vol. 1 No. 2 (2018): Acta Biochimica Indonesiana
Publisher : Indonesian Society for Biochemistry and Molecular Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32889/actabioina.v1i2.16

Background: High altitude can cause hypobaric hypoxia (HH), resulted from the lower barometric pressure and hence partial pressure of oxygen. Hypoxia can lead to a lot of deleterious molecular and cellular changes, such as generation of free radicals or reactive oxygen species (ROS). Increasing of ROS can cause oxidative stress if the antioxidant enzyme does not increase simultaneously. Oxidative damage in brain has toxic effect on cognitive functions. Objective: In this study, we investigate effect of acute intermittent HH on oxidative stress and antioxidant enzyme activity in rat brain. Method: Wistar rats divided into 5 groups, consisting control group and four experimental groups which treated to HH. Rats were exposed to simulated HH equivalent to 35.000 feet in hypobaric chamber for 1 minute, repeated once a week. Results: Level of malondialdehyde and carbonyl in rat brain under acute HH increased at HH exposure (group I) compare to control group. These levels decreased afterward at intermittent HH exposure (group II-IV). Specific activity of superoxide dismutase (SOD) shows increasing level at intermittent HH exposure, especially group IV was increasing of SOD level significantly. The increasing pattern of specific activity of catalase was inversely from SOD pattern, but it still has higher activity in intermittent HH compare to control group. Conclusion: Brain tissue seems to be able to perform an adequate adaptive response to hypobaric hypoxia after the training, shown by its significantly decreased MDA and carbonyl level and also increased specific activity of SOD and catalase.

Correlation between malondialdehyde level and FOXO3 and CASP3 mRNA expression changed in early-onset preeclampsia placenta Ni Made Wiasty Sukanty; Febriana Catur Iswanti; Syarifah Dewi; Muhammad Faruqi; Alyssa Shafa Andiana; Ani Retno Prijanti
Acta Biochimica Indonesiana Vol. 4 No. 2 (2021): Acta Biochimica Indonesiana
Publisher : Indonesian Society for Biochemistry and Molecular Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32889/actabioina.61

Background: Preeclampsia is one of the factors causing the high maternal mortality rate. The risk of morbidity and mortality is higher in Early Onset Preeclampsia (EOPE). Failure of spiral artery remodeling can cause oxidative stress that can inhibit placental development and increase trophoblast apoptosis. Objective: This study aims to analyze the oxidative stress and apoptosis of EOPE placentas. Methods: This study is an observational study with a cross-sectional design. A total of 31 EOPE placentas and 31 normal term placentas were used to measure the concentration of malondialdehyde (MDA) and the relative mRNA expression of FOXO3 and CASP3 using the spectrophotometric and RT-qPCR methods. Results: There was no difference in MDA concentration (p = 0.580) and FOXO3 (p = 0.467) and CASP3 (p = 0.243) mRNA expression in the normal and EOPE groups. There was a strong positive correlation between FOXO3 and CASP3 mRNA expression in the normal (p= 0.0001; r = 0.938) and EOPE groups (p = 0.0001; r = 0.855). There was no correlation between MDA concentration to FOXO3 (p = 0.124; r = 0.282) and CASP3 (p = 0.569; r = 0.106) mRNA expression in normal placenta. There was positive correlation between MDA concentration to FOXO3 (p = 0.016; r = 0.429) and CASP3 mRNA expression in EOPE placenta (p = 0.028; r = 0.395). Conclusion: These results indicate that cell integrity is still maintained through the autophagy process and the level of apoptosis in the EOPE placenta is regulated by ROS through FOXO3.

Malondialdehyde and carbonyl levels in skeletal muscle tissues after intermittent hypobaric hypoxia exposures Syarifah Dewi; Alexander Rafael Satyadharma; Albertus Raditya Danendra; Wardaya
Acta Biochimica Indonesiana Vol. 5 No. 2 (2022): Acta Biochimica Indonesiana
Publisher : Indonesian Society for Biochemistry and Molecular Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32889/actabioina.113

Background: Hypobaric hypoxia is a state of decreased oxygen pressure at high altitudes that can lead to hypoxia and oxidative stress as a result. Skeletal muscle is one of the important organs that can be affected by oxidative stress and cause contractile dysfunction. Objective: This study aimed to evaluate the impact of intermittent hypobaric hypoxia on oxidative stress markers in rat skeletal muscle, by measuring malondialdehyde (MDA) and carbonyl levels. Methods: Twenty-five Wistar rats were allocated into five groups, including one control group and four hypoxic groups (I-IV). The hypoxic groups were exposed to an altitude of 25,000 feet for 5 minutes using hypobaric chamber in once (I), twice (II), three (III), and four (IV) times, with a 7-day interval period between exposures. The control group remained in normobaric conditions throughout the study. MDA levels were measured by thiobarbituric acid (TBA) test, while carbonyl levels were measured using 2,4-dinitrophenylhydrazine (DNPH) reagent. Results: The MDA level was significantly increased in group I compared to the control group (p=0.008). There were decreasing MDA levels in groups II, III, and IV compared to group I. The carbonyl level was significantly higher in group I than the control group (p=0.000), with an even higher level observed in group II. Although the carbonyl levels tended to decrease in groups III and IV, they still remained higher than those of the control group. Conclusion: Exposure to hypobaric hypoxia leads to an increase in MDA and carbonyl levels in the skeletal muscles, indicating an elevation of oxidative stress levels. However, the subsequent intermittent hypobaric hypoxia exposure resulted in a reduction in these levels, implying that skeletal muscles may adapt to hypoxic conditions.

EKSPRESI RELATIF mRNA HIF-1α PADA JANTUNG, OTAK DAN DARAH TIKUS SELAMA INDUKSI HIPOKSIA SISTEMIK Wanandi, Septelia Inawati; Dewi, Syarifah; Paramita, Reni
Makara Journal of Science Vol. 13, No. 2
Publisher : UI Scholars Hub

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Relative Expression of HIF-1α mRNA in Rat Heart, Brain and Blood During Induced Systemic Hypoxia. Hypoxia is a pathological condition in which the body as a whole or region of the body (tissue or cell) deprived of adequate oxygen supply. The transcriptional regulator hypoxia inducible factor-1 (HIF-1) is an essential mediator of O2 homeostasis. Unlike the β sub unit (HIF-1β), the activity of HIF-1α is controlled in an oxygen-dependent manner. It has been reported that the stability and expression of HIF-1α during hypoxia is remarkably higher than those under normoxic conditions.The aim of this study was to analyze the adaptive tissue responses during induced systemic hypoxia by comparation of relative expression of mRNA HIF-1α in rat heart, brain and blood. Twenty-five male Sprague Dawley rats were subjected to systemic hypoxia by placing them in the hypoxic chamber supplied by 8-10% of O2 for 0, 1, 7, 14 and 21 days, respectively. The relative expression level of HIF-1α mRNA in brain, heart and leucocyte cells were analyzed using quantitative RT-PCR assay (Real Time PCR) based on Pfaff’s formula. This study demonstrates that the increased of relative expression of HIF-1α mRNA during induced systemic hypoxia reached its maximum level at day 7 (in heart) or at day 14 (in brain), whereas in leucocyte cells the stimulation of HIF-1α expression was intensively maintained up to 21 days although the expression has reached the remarkably high level. We could conclude that HIF-1α as an oxygen sensing during systemic hypoxia has different capacity and sensitivity in brain, heart and blood tissues, due to the importance of oxygen homeostasis in each tissue

EKSPRESI RELATIF mRNA HIF-1α PADA JANTUNG, OTAK DAN DARAH TIKUS SELAMA INDUKSI HIPOKSIA SISTEMIK Wanandi, Septelia Inawati; Dewi, Syarifah; Paramita, Reni
Makara Journal of Science Vol. 13, No. 2
Publisher : UI Scholars Hub

Show Abstract | Download Original | Original Source | Check in Google Scholar

Relative Expression of HIF-1α mRNA in Rat Heart, Brain and Blood During Induced Systemic Hypoxia. Hypoxia is a pathological condition in which the body as a whole or region of the body (tissue or cell) deprived of adequate oxygen supply. The transcriptional regulator hypoxia inducible factor-1 (HIF-1) is an essential mediator of O2 homeostasis. Unlike the β sub unit (HIF-1β), the activity of HIF-1α is controlled in an oxygen-dependent manner. It has been reported that the stability and expression of HIF-1α during hypoxia is remarkably higher than those under normoxic conditions.The aim of this study was to analyze the adaptive tissue responses during induced systemic hypoxia by comparation of relative expression of mRNA HIF-1α in rat heart, brain and blood. Twenty-five male Sprague Dawley rats were subjected to systemic hypoxia by placing them in the hypoxic chamber supplied by 8-10% of O2 for 0, 1, 7, 14 and 21 days, respectively. The relative expression level of HIF-1α mRNA in brain, heart and leucocyte cells were analyzed using quantitative RT-PCR assay (Real Time PCR) based on Pfaff’s formula. This study demonstrates that the increased of relative expression of HIF-1α mRNA during induced systemic hypoxia reached its maximum level at day 7 (in heart) or at day 14 (in brain), whereas in leucocyte cells the stimulation of HIF-1α expression was intensively maintained up to 21 days although the expression has reached the remarkably high level. We could conclude that HIF-1α as an oxygen sensing during systemic hypoxia has different capacity and sensitivity in brain, heart and blood tissues, due to the importance of oxygen homeostasis in each tissue

Development of RNA interference-based therapy for rare genetic diseases Milya Urfa Ahmad; Syarifah Dewi
Acta Biochimica Indonesiana Vol. 7 No. 1 (2024): Acta Biochimica Indonesiana
Publisher : Indonesian Society for Biochemistry and Molecular Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32889/actabioina.171

In December 2022, the Indonesian Ministry of Health projected that rare diseases might affect 8–10% of the population, equating to approximately 27 million people. These diseases, often congenital, are linked to genetic inheritance or mutations, leading to structural or functional defects. Despite advancements in diagnostic and treatment methods, many rare diseases remain challenging for healthcare practitioners. RNA interference (RNAi) presents a promising therapeutic approach by enabling the selective inhibition of genes responsible for genetic disorders. RNAi employs small RNA molecules, such as small interfering RNA (siRNA) and microRNA (miRNA), to bind specific mRNA molecules and prevent their translation into proteins. Current research showed that RNAi-based therapies have the potential to treat various genetic diseases, including acute hepatic porphyria (AHP) and primary hyperoxaluria type 1 (PH1). However, the mechanisms of RNAi in hereditary disorders like AHP and PH1 require further documentation. RNAi offers several advantages, including gene-specific targeting, versatility in treating diverse genetic disorders, and scalability for mass production. Nonetheless, challenges remain, such as side effects, difficulties in targeting specific cells, and high development cost. Despite these obstacles, RNAi-based therapy holds significant potential for revolutionize the treatment of genetic disorders.

Andrographis paniculata Ethanolic Extract Improved Doxorubicin-induced Cardiac Inflammation, Alterations in Liver Function Parameters and Anemia Eziefule, Oluebube Magnificient; Arozal, Wawaimuli; Wanandi, Septelia Inawati; Louisa, Melva; Wuyung, Puspita Eka; Dewi, Syarifah; Nafrialdi, Nafrialdi; Dewi, Yulia Ratna; Nabillah, Deya Adiby
Molecular and Cellular Biomedical Sciences Vol 8, No 2 (2024)
Publisher : Cell and BioPharmaceutical Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21705/mcbs.v8i2.444

Background: Doxorubicin (DOX), an efficacious chemotherapy drug is compromised by cardiotoxicity, myelosuppression, and hepatotoxicity. Due to the limited success of current treatments for DOX toxicity, there is a pressing need to explore alternative medical interventions, particularly from plant sources. This study was conducted to investigate the potential protective effect of ethanolic extract of Andrographis paniculata leaves (EEAP) against DOX-induced cardiac inflammation, liver toxicity, and anemia.Materials and methods: Sprague-Dawley rats were intraperitoneally injected with DOX at a total dose of 16 mg/kgBW. EEAP was administered orally for 4 weeks at doses of 125, 250, and 500 mg/kgBW/day according to the assigned treatment groups. The mRNA expression levels of interleukin-1β (IL-1β) and nucleotide-binding domain, leucine-rich-containing family, pyrin domain-containing-3 (NLRP3) in the heart tissue, along with the concentrations of nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) and calcium level were examined. Additionally, the hematological parameters (including hematocrit, hemoglobin and red blood cells (RBCs)), aspartate aminotransferase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), and malondialdehyde (MDA) levels in blood were also analyzed.Results: EEAP dose-dependently decreased the mRNA expressions of IL-1β (p<0.05), tended to decrease mRNA expression of NLRP3 and the concentrations of NFκB and calcium in heart tissue compared with the DOX-only group. Additionally, EEAP dose-dependently decreased ALP values (p<0.0001) and tended to improve hematological parameters, as well as AST and MDA levels in serum.Conclusion: This extract may prevent DOX-induced cardiac inflammation, anemia, and hepatotoxicity. However, further studies are needed to confirm these findings, including the efficacy profile of the extract in cancer rats treated with DOX.Keywords: doxorubicin, Andrographis paniculata, inflammation, anemia, hepatotoxicity, herbal medicine

6-Gingerol Slightly Reduces Hepatic Endoplasmic Reticulum Stress Markers in Rats with High-Fat, High-Fructose Diet-Induced Metabolic Syndrome Ahmad, Nouman; Syarifah Dewi; Soetikno, Vivian
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 26 No. 01 (2025): Eksakta : Berkala Ilmiah Bidang MIPA (E-ISSN : 2549-7464)
Publisher : Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Negeri Padang, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/eksakta/vol26-iss01/581

Metabolic syndrome (MetS) is linked to hepatic endoplasmic reticulum (ER) stress. This study evaluated 6-gingerolâ€™s potential to alleviate ER stress in a high-fat high-fructose (HFHF)-induced MetS rat model. Male Sprague-Dawley rats (8 weeks, 180â€“220 g) were assigned to five groups: Normal, HFHF, and HFHF with 6-gingerol (50, 100, or 200 mg/kg). The Normal group received a standard diet, while others had HFHF for 16 weeks. From Week 8, intervention groups received 6-gingerol daily. Except for Normal, other groups also received Streptozotocin (22mg/kg, i.p.) at Week 8. At Week 16, rats were euthanized, and liver tissues collected to assess ER stress markers (GRP78, IRE1, TRAF2, PERK, CHOP) via qPCR and apoptotic markers (Bax, Bcl-2) via ELISA. 6-Gingerol slightly reduced liver ER stress markers, including GRP78 (P=0.392), CHOP (P=0.798), IRE1 (P=0.419), TRAF2 (P=0.470), and PERK (P=0.357), but these changes were not significant. Similarly, apoptotic markers Bax and Bcl-2 showed no significant differences, though the Bax/Bcl-2 ratio decreased (P=0.186). These results indicate that 6-gingerol had only a slight effect on ER stress and apoptosis within the parameters of this experiment.

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