Optimizing Real-Time PCR methods for detection of ssaN gene Salmonella enterica subsp.enterica in the blood specimen

Background Typhoid fever caused by Salmonella typhi is a common acute infection of the reticuloendothelial system, intestinal lymphoid tissue, and gall bladder. Detection of Salmonella spp. is still based on cultures and serological methods.Widal test is one of the serological tests that is still widely used, especially in developing countries including Indonesia.Widal tests have low sensitivity and specificity. They often produce false positive or false negative results.ObjectiveThe aim of this study were i) real time PCR optimization to develop a Salmonella enterica detection system. ii) molecular detection of new target gene (ssaN gene) from blood specimens in typhoid fever patients.Methods An experimental laboratory study was performed from March to October 2016. Extraction of Salmonella typhi DNA is used as templates for the optimization of real time PCR reaction.The blood sample was from patients suspected with typhoid fever obtained from the Menteng Sub-district Health Center according to the inclusion criteria.ResultsSpecificity test of real time PCR showed that the primers and probes used are not cross-react against other microorganisms. Sensitivity test obtained minimal detection is at least 10 cfu/ml of blood specimen. In blood clinical specimens, real time PCR could detect 19 (38%) positive samples of 50 blood specimen from suspected typhoid fever patients. Eleven samples with negative Widal serology gives positive results in real time PCR.ConclusionReal time PCR used in this study can increase the level of rate of positive testing by 22% of the total specimens.Keywords : Salmonella enterica subsp.enterica, typhoid fever, ssaN gene, real time PC

RESPON IMUN SELULER DAN HUMORAL MENCIT YANG DIIMUNISASI KANDIDAT VAKSIN DNA DENGUE BERBASIS GEN preM-E SEROTIPE 4 STRAIN INDONESIA

AbstrakInfeksi virus dengue (DENV) terkadang tanpa gejala atau dapat menunjukkan gejala klinis yang luas, berkisar dari sindrom flu ringan (dengue fever/DF), dengue haemorrhagic fever (DHF), hingga syok hipovolemik (dengue shock syndrome/DSS). Hipotesis yang berkaitan dengan tingkat keparahan infeksi DENV meliputi mekanisme antibody-dependent enhancement (ADE) dan keterlibatan sitokin. Hingga kini, belum ada obat antiviral yang efektif untuk mengeradikasi dan mencegah infeksi DENV, sehingga pencegahan berupa vaksin perlu dikembangkan. Kandidat vaksin DNA berbasis gen preM-E serotipe 4 strain Indonesia yang dikembangkan pada penelitian terdahulu disuntikkan ke mencit ddY, kemudian diuji tantang dengan DENV. Pada hari ke-4 dan ke-21 pascauji tantang, keberadaan sitokin IL-2 dalam serum dideteksi dengan metode ELISA. Serum hari ke-21 digunakan dalam uji ADE menggunakan sel K562. Sel limpa diambil pada hari ke-21 pascauji tantang, kemudian keberadaan IL-2 dan antibodi in vitro dideteksi dengan metode ELISA. Tingkat IL-2 tertinggi terdapat pada serum hari ke-4 pada kelompok mencit yang tidak diimunisasi namun diuji tantang, yaitu sebesar 69,83 pg/ml. Konsentrasi IL-2 terendah ditunjukkan oleh kelompok mencit yang diimunisasi namun tidak diuji tantang, yaitu 0 pg/ml. Pengukuran IL-2 pada serum dan supernatan sel limpa hari ke-21 tidak mendapatkan konsentrasi IL-2. Titer antibodi tertinggi terdapat pada kelompok sel limpa mencit yang diimunisasi, diuji tantang, dan diinduksi in vitro dengan DENV. Hasil uji ADE menunjukkan tingkat pengenceran serum berpengaruh terhadap jumlah sel yang terinfeksi oleh DENV, namun tidak ditemukan kondisi netralisasi dan enhancing. Berdasarkan metode yang digunakan, kandidat vaksin DNA tersebut dapat memicu respon imun seluler dan humoral.AbstractDengue virus (DENV) infection can be asymptomatic or cause wide range of clinical symptoms, from mild febrille ilness (dengue fever/DF), dengue haemorrhagic fever (DHF), to hipovolemic shock (dengue shock syndrome/DSS). Hypotheses related to the severity of DENV infection mechanisms including antibody-dependent enhancement (ADE) and cytokines involvement. Until now, there are no effective antiviral drugs can eradicate and prevent DENV infection, therefore the development of vaccines is the alternative. DNA vaccine candidate preM-E serotype 4 strain of Indonesia which was developed in previous studies injected into ddY mice, then challenge with DENV. At day 4 and 21 post-challenge, serum was taken to detect the presence of cytokines IL-2 using ELISA method. Day 21 serum used in the antibody-dependent enhancement (ADE) assay using K562 cell line. Splenocytes were taken at day 21 post-challenge to measure the presence of IL-2 and in vitro antibody using ELISA method. Measurement of IL-2 on day 4 serum produced the highest levels of IL-2 (69.83 pg/ml) in the group of non-immunized, challenged mice, whereas the lowest concentration (0 pg/ml) shown by the group of immunized, non-challenged mice. Measurement of IL-2 in serum and splenocytes day 21 did not get the concentration of IL-2. The highest result of in vitro antibody measurements shown by the group of splenocytes from immunized, challenged mice then in vitro induced with DENV. ADE assay results showed that level of serum dilution has effect on the number of dengue-infected cells, but netralization and enhancing condition were not found in this assay. Based on this methods, the DNA vaccine candidate can trigger cellular and humoral immune responses

Aktivitas Sitotoksisitas Ekstrak Metanol Daun Sirsak (Annona muricata L.) terhadap Karsinoma Hepatoseluler Strain HUH7IT-1 Cell Line

ABSTRAKLatar Belakang: Karsinoma hepatoseluler (HCC) merupakan tumor ganas hati primer dengan prognosis pada umumnya dapat menyebabkan kematian. Studi awal penelitian antiviral hepatitis C pada tumbuhan Sirsak (Annona muricata L.) pada konsentrasi 20 μg/mL memperlihatkan toksisitas yang sangat tinggi terhadap Huh7it-1 cell line, yang diindikasi memiliki potensi anti kanker terhadap sel hati, sehingga penelitian ini bertujuan menguji beberapa konsentrasi lebih rendah pada ekstrak metanol daun Annona muricata L. (EMDAM) terhadap Karsinoma Hepatoseluler strain Huh7it-1 cell line.Metode: Sel diuji dengan konsentrasi 20, 10, 5, 2.5, 1.25, 0.6, 0.3 μg/mL selama 48 jam. Sitotoksisitas EMDAM terhadap Huh7it-1 dilihat dengan mikrokop inverted dan selanjutnya diukur dengan metode MTT [3-(4,5-dimethylthiazol-2-yl)-5(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium].Hasil: Hasil uji menunjukkan sel memperlihatkan bentuk tidak monolayer pada mikroskop inverted dengan sitotoksisitas hingga konsentrasi terendah pada 0.3 μg/mL mencapai 84,7%, sehingga konsentrasi 50% Sitotoksisitas (CC50) < 0.3 μg/mL.Simpulan: Hasil uji mengindikasi bahwa EMDAM memiliki potential terhadap aktivitas anti kanker hati. Studi lebih lanjut diperlukan untuk purifikasi untuk senyawa aktif sebagai antikanker atau target mekanisme terhadap aktivitas anti kanker hati.Kata kunci: Karsinoma Hepatoseluler, Huh7it-1, Sitotoksisitas, Annona muricataABSTRACTBackground: Hepatocellular carcinoma (HCC) is a malignant tumor of liver cells with prognosis can cause death within 2-3 months. Previous studies of Annona muricata L. on anti-HCV studies at concentrations of 20 μg / mL showed very high toxicity to Huh7it-1 cell line, it was indicated to have anti-cancer potential of liver cells, so this study tested the potency of anticancer activity extract methanol leaf Annona muricata L. (EMDAM) against Hepatocellular Carcinoma Huh7it-1 strain cell line with low dose.Methods: Cells were tested with concentrations of 20, 10, 5, 2.5, 1.25, 0.6, 0.3 μg / mL for 48 hours. The EMDAM cytotoxicity of Huh7it-1 was seen with an inverted microcomputer and then measured with MTT assay [3-(4,5-dimethylthiazol-2-yl)-5(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium].Results: The results showed that the cells presented non-monolayer form in an inverted microscope with cytotoxicity until the lowest concentration of 0.3 μg / mL reached 84.7%, thus concentrating 50% cytotoxicity (CC50) <0.3 μg / mL.Conclusion: The results indicate that EMDAM has the potential for anti-liver cancer activity. Further studies are needed for purification for active compounds as anticancer or target mechanisms against anti-liver cancer activity.Keywords: Hepatocellular carcinoma, Huh7it-1, Cytotoxicity, Annona muricat

COVID-19 Screening Score for Patients without Acute Respiratory Symptoms Undergoing Emergency Medical Procedures in Indonesia

To rule out coronavirus disease–2019 (COVID-19) in patients scheduled to undergo emergency medical procedures, SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) must be performed. In developing countries, the use of SARS-CoV-2 RT-PCR has been limited by its unavailability and long processing time. Hence, a quick screening score to predict COVID-19 may help healthcare practitioners determine which patients without acute respiratory symptoms can safely undergo an emergency medical procedure. We conducted a cross-sectional study of adult patients without acute respiratory symptoms who were admitted to the emergency department and underwent an emergency medical procedure within 24 hours after admittance. We collected baseline demographic data, COVID-19 screening variables, and SARS-CoV-2 RT-PCR as the gold standard for COVID-19 diagnosis. Bivariate and multivariate analyses were performed, and a scoring system was developed using statistically significant variables from the multivariate analysis. With data from 357 patients, multivariate backward stepwise logistic regression analysis resulted in two significant COVID-19 predictors: the presence of SARS-CoV-2–IgM antibody (adjusted odds ratio [aOR]: 7.02 [95% CI: 1.49–32.96]) and typical chest x-ray (aOR: 23.21 [95% CI: 10.01–53.78]). A scoring system was developed using these predictors with an area under the receiver operating characteristic curve of 0.71 (95% CI: 0.64–0.78). For a cutoff point of $ 2, the scoring system showed 42.5% sensitivity and 97.1% specificity but had poor calibration (Hosmer-Lemeshow test P value, 0.001). We believe that the development of this COVID-19 quick screening score may be helpful in a resource-limited clinical setting, but its moderate discrimination and poor calibration hinder its use as a replacement for the SARS-CoV-2 RT-PCR test for COVID-19 screening.</p

Primer Design for Sequencing DENV-4 to be used in Molecular Epidemiology of Dengue Viruses in Jakarta

AbstractThis study is aimed to recognize the characteristic of dengue patients in Jakarta, to identify the genotype of dengue virus serotype 4 (DENV-4) in Jakarta and to design primer for DENV-4. This cross-sectional study involved 100 patients with positive result of NS-1 examination. This research was conducted at the Department of Microbiology, Faculty of Medicine, Universitas Indonesia. The specimen were collected from March until December 2010, while the virus sequencing was perfomed between January and October 2011. The patients were categorized based on RT-PCR confirmation results, gender, age and domicile. The identification of serotipe of dengue viruses is determined by RT-PCR examination. The genotipe of DENV-4 is determined by sequencing of whole genome of DENV-4 by using Genetyx software. The primer design for DENV-4 was carried out by using Primer Designer program. The highest prevalence of DF was found among patients of 14-20 years old (41,4%) and those who lived in East Jakarta. The ratio of DF between male and female is not significantly different. &nbsp;The predominant serotype circulating in Jakarta was DENV 2. The genotype of serotype 4 circulating in Jakarta in 2010-2011 was type II. Primer design for dengue serotype 4 had a size of 406-692 base pairs, no hairpin developed, dimer formation was within two and Tm difference ranged from 0 to 8C.Keywords: DHF, serotype 4, genotype, primerAbstrakPenelitian ini bertujuan untuk mengidentifikasi karakteristik pasien demam berdarah dengue di Jakarta dan mengidentifikasi genotipe virus dengue serotype 4 (DENV 4) di Jakarta serta membuat desain primer DENV-4. Penelitian dilakukan secara potong lintang pada 100 pasien dengan hasil pemeriksaan NS-1 positif. Penelitian dilakukan di Departemen Mikrobiologi, Faculty of Medicine, Universitas Indonesia. Pengambilan data dilakukan pada bulan Maret-December 2010, virus sequencing dilakukan pada bulan Januari-Oktober 2011. Sampel dibagi berdasarkan hasil konfirmasi RT-PCR, jenis kelamin, usia dan tempat tinggal. Identifikasi virus dengue dan penentuan serotipe menggunakan RT-PCR. Penentuan genotipe DENV-4 dilakukan dengan melakukan sekuensing whole genome DENV-4 menggunakan software Genetyx. Pembuatan primer DENV-4dilakukan dengan program Primer Designer. Prevalensi demam berdarah dengue tertinggi terdapat pada usia 14-20 tahun (41,4%) dan pada pasien yang bertempat tinggal di Jakarta Timur. Ratio penderita perempuan dan laki-laki tidak menunjukkan perbedaan bermakna. Genotipe DENV-4 yang bersirkulasi di Jakarta adalah tipe II. Desain primer DENV-4 memiliki ukuran 406-692 pasang basa, tidak ada hairpin, formasi dimer dengan dua dan Tm yang berbeda yang berkisar antara 0-8 C.Kata Kunci: DBD, serotipe 4, genotipe, prime

Determination of Genotype of Dengue Virus Serotype 1 by Using Primer Design

Dengue fever has become a worldwide health problem. This disease occurs more and more frequently and often cause death, especially in some Asian countries including Indonesia. The purpose of this study was to determine the genotype of dengue virus serotype 1 in Indonesia by using primer design as a base to take part in the development of diagnostics and vaccines of the dengue virus. This research consisted of 100 respondents; male and female aged 14-60 years. All samples were selected by consecutive sampling and dengue viruses used in this study were randomly selected in March-December 2010. The next step was sequencing process in January-October 2011 in the Department of Microbiology FKUI by using cross sectional design. The result of this study was dengue virus serotype 1 strains from Indonesia belonged to genotype 4. Keywords: genotype of dengue virus serotype 1, Indonesia, diagnostic, vaccin

HUBUNGAN EKSPRESI miRNA-21 DENGAN TARGET PDCD4 DAN miRNA-143 DENGAN TARGET BLC-2 PADA KASUS KANKER SERVIKS

A study has been carried out to compare the expression of miRNA-21 and miRNA-143 with target mRNA PDCD4 and BCL-2 in cases of early-stage cervical cancer compared to advanced stages. These data can be used as information for the development of non-invasive cervical cancer prognostic methods. The study was conducted by taking serum samples and exfoliativecell samples from normal subjects and subjects with cervical cancer detection and then analyzed using qRT-PCR. Samples of cervical cancer patients consisting of 15 subjects and 4 normal subjects were used to obtain relative quantity values for the expression of miRNA-21, miRNA-143, mRNA PDCD4 and BCL-2. In the study of miRNA-21, there was no significant difference in determining cervical cancer with p&gt;0.05 using the t-test (0.594) and a significant relationship was found between miRNA 21 and PDCD4 with a strong correlation (p&lt;0.05, r = -0.563; Pearson). The relationship between miRNA-143 and the Bcl-2 target gene in this study showed a weak and insignificant correlation (r = -0.101; p &gt; 0.05; Pearson). There was a significant relationship between miRNA-21 and PDCD4 in early-stage and advanced-stage samples, while the relationship between miRNA-143 and the Bcl-2 mRNA target gene showed no significant correlation

Changes in Gut Microbiota and Systemic Inflammation after Synbiotic Supplementation in Patients with Systemic Lupus Erythematosus: A Randomized, Double-Blind, Placebo-Controlled Trial

Gut dysbiosis has a role in the pathogenesis of lupus. Synbiotic supplementation may restore the balance of gut microbiota. This study investigated whether synbiotics could improve gut microbiota and systemic inflammation in lupus patients. This randomized, double-blind, placebo-controlled trial was conducted in adult systemic lupus erythematosus (SLE) patients. Subjects were randomized to receive either synbiotics or a placebo. Fecal microbiota, hs-CRP, IL-6, and IL-17 were measured at baseline and after 60 days. Patients who fulfilled the inclusion criteria were randomized into synbiotic (n = 23) and placebo groups (n = 23). In the synbiotic group, hs-CRP was not significantly increased (1.8 [0.9; 4.85] vs. 2.1 [0.9; 4.25] mg/L; pre vs. post; p = 0.23), whereas in the placebo group hs-CRP was increased significantly (1.75 [0.4; 4.45] vs. 3.75 [0.58; 7.05] mg/L; pre vs. post; p = 0.005). In the synbiotic group, IL-6 decreased significantly (8.76 [6.62; 11.39] vs. 6.59 [4.96; 8.01]; pre vs. post; p = 0.02), while there was no significant change in IL-17 level. In the placebo group, there was no significant change in IL-6 and IL-17. Synbiotic supplementation increased the Firmicutes:Bacteroidetes ratio (0.05 &plusmn; 0.60 vs. &minus;0.08 &plusmn; 0.63, synbiotic vs. placebo p = 0.48) and butyrate metabolism (p = 0.037) and decreased amino sugar and nucleotide sugar metabolism (p = 0.040). There was improvement in the SLE disease activity index 2K (SLEDAI-2K) score in the synbiotic group (14 [9; 16] vs. 8 [2; 12]; pre vs. post; p &lt; 0.001), while no change in the placebo group (9 [8; 18.25] vs. 9 [5.5; 15]; pre vs. post; p = 0.31). Synbiotic supplementation could reduce systemic inflammation and SLE disease activity and alter the composition and functions of gut microbiota