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All Journal Jurnal Teknologi Dan Industri Pangan Jurnal Veteriner Microbiology Indonesia Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Medical Journal of Indonesia The Indonesian Biomedical Journal Jurnal Locus Penelitian dan Pengabdian eJournal Kedokteran Indonesia Journal of Clinical Microbiology and Infectious Diseases
Pratiwi Pujilestari Sudarmono
Departemen Mikrobiologi, Fakultas Kedokteran, Universitas Indonesia, Jakarta
Aerospace Engineering Agriculture, Biological Sciences & Forestry Automotive Engineering Biochemistry, Genetics & Molecular Biology Decision Sciences, Operations Research & Management Electrical & Electronics Engineering Immunology & microbiology Industrial & Manufacturing Engineering Mathematics Medicine & Pharmacology Neuroscience Public Health Veterinary

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Journal : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

 1 
Bacterionomics and vironomics in carcinogenesis Pratiwi Sudarmono
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 48, No 4 (2016): SUPPLEMENT
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (117.428 KB) | DOI: 10.19106/JMedScieSup004804201626

Abstract

Virus and bacteria are microbes which are very common cause human infection. Most of the bacterial infection can be eradicated by antibiotics and infection symptoms disappear. But for virus infection, once infected, the virus will persistently stay in the host, even undergo not only a lytic cycle but also integrated into host genome. Nowadays, at least 6 virus type are consistently related to human cancer, such as EBV,HPV,HTLV,HBV,HCV,HKSV, and the new one Merkel Virus (MCV). Although not every infected people will get cancer, but around 20% of the whole cancer in human are caused by viral oncogene.Class one oncogenic bacterial is Helicobacter pylori. Infection with this bacteria can cause persistent gastro duodenal inflammation which cause some alteration in gastric cell growth into transformation. Expression of Cag gene and Vac gene and some expression of OMP protein usually link to gastric cancer.Molecular mechanisms of carcinogenesis for every virus which cause infection  is a very complex , which include several processes caused by cell transformation. Besides, other host and environmental factors are also play a significant role in cancer development. Some scientist put a Hallmark analysis as a model to quickly summarize what pathobiology process will happen and what gene or protein caused the process. The Hallmark analysis comprise of several process which may happen simultaneously because some of the Hallmark is caused by the same protein. The Hallmark consists of various virus strategies in oncogenesis such as promoting angiogenesis, avoiding immune destruction, genome instability and mutation, deregulating cellular energetic, resisting cell death, sustaining proliferative signaling, evading growth suppressors, enabling cellular immortality, promoting inflammation and activation metastasis. For example, infection by HPV, will cause low grade dysplasia which can continue to invasive cervical cancer. After host cell transformation, in the long control region genes, E6 and E7 protein will cause several strategies in oncogenesis including resisting cell death and evading growth suppressors.  HBV infection will end without any serious liver damage, but after cell transformation, almost all Hallmark strategies of viral oncogenesis are happening step by step in line with the severity of liver cell damage.As the onset of cancer development after infection can last years, there are an opportunity to design either vaccine or genetic therapy to minimalize further risk of cancer in human 
Development of a SYBR Green real-time PCR-based assay system for detection of Neisseria gonorrhoeae Andi Yasmon; Rela Febriani; Louisa Ivana Utami; Fithriyah Fithriyah; Yeva Rosana; Fera Ibrahim; Pratiwi Sudarmono
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 54, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19106/JMedSci005401202201

Abstract

Diagnosis of Neisseria gonorrhoeae infection is needed for patient therapy and for reducing this bacterial transmission in the population. The culture method is a gold standard method for N. gonorrhoeae detection, however it has low sensitivity. Among molecular methods with high sensitivity and specificity, SYBR Green real-time PCR is the potential method for N. gonorrhoeae detection. In this study, we developed an SYBR Green real-time PCR-based system assay for N. gonorrhoeae detection. Several PCR conditions were optimized and analyzed including primer annealing temperature, DNA template volume, the limit of detection (LoD), cross-reaction with others (bacteria, viruses, fungus, protozoa), and quality assurance. The results showed that the annealing temperature and DNA template volume were 60oC and 5 µL, respectively. The LoD was 29 DNA copies corresponding to 3 bacterial cells per reaction. No cross-reaction was detected for other bacteria, viruses, fungus and protozoa. The external quality assurances enrolled in 2019 and 2021 showed 100% concordance. The preliminary testing for clinical samples was also 100% concordance. In conclusion, the SYBR Green real-time PCR-based system assay developed in this study is promising for application in clinical laboratories.
A comparison study of GeneXpert and In-House N1N2 CDC Real-Time RT-PCR for detection of SARS-CoV-2 infection Andi Yasmon; Lola Febriana Dewi; Fithriyah Fithriyah; Ariyani Kiranasari; Andriansjah Rukmana; Yulia Rosa Saharman; Fera Ibrahim; Pratiwi Sudarmono
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 54, No 3 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19106/JMedSci005403202203

Abstract

COVID-19 is a disease caused by SARS-CoV-2, a new virus from genus β-coronaviruses. This disease has been declared a pandemic by WHO on 11 March 2020 until now. The nucleic acid tests are the most frequently used assays because of their high sensitivity and specificity. One of the tests is the GeneXpert, a real-time reverse transcription polymerase chain reaction (rRT-PCR)-based assay platform. The use of the GeneXpert shows great public health interest because of the rapid (50 min), the minimum number of trained staff, and less infrastructure and equipment. However, there are limited data on the application of the GeneXpert for the detection of SARS-CoV-2. Therefore, we conducted a comparative study between the GeneXpert and in-house N1N2 CDC rRT-PCR assay. Of 86 samples, 17 were rRT-PCR positive while 13 were GeneXpert positive. Of rRT-PCR positive 17 samples, 7 were GeneXpert negative [58.82% (10/17] sensitivity]. We also found that 3 GeneXpert positive samples showed rRT-PCR negative (95.65% [66/69] specificity). It is concluded that negative results by the GeneXpert can not rule out the possibility of SARS-CoV-2 infection, particularly in close-contact individuals and the interpretation of the positive result should be analyzed carefully, particularly amplification with Ct>40.
Co-Authors . Andriansjah Ade Dharmawan Agus Sjahrurachman AHMAD WIBISANA Amin Soebandrio Andi Yasmon Anis Karuniawati Ariyani Kiranasari Asmarani Kusumawati Augustine Natasha Augustine Natasha Azmier Adib Betty Ernawati Chairunissa T. Rizal Cleopas Martin Rumende Delly Chipta Lestari Dewi, Intan Keumala Diniwati Mukhtar Fera Ibrahim Fera lbrahim Fithriyah Fithriyah Fithriyah Fithriyah HAK HOTTA Helwiah Umniyati Hidetaka Tsuji Holy Arief Ingrid S. Surono Leonardus B.S. Kardono Lola Febriana Dewi Louisa Ivana Utami Mardiastuti H Wahid Mardiastuti Mardiastuti Mirawati Sudiro Myrna Adianti Nie Nie Prawoto Prawoto Rela Febriani Robert Utji Shirly Kumala Susan Maphilindawati Noor Sweety Pribadi Tjahjani M. Sudiro TJAHJANI MIRAWATI SUDIRO Tomohiro Oshibe Triyani Sukarso Tunru, Insan Sosiawan VERONICA WIWING Vivi Lisdawati Wahono Sumaryono Yeva Rosana Yulia R. Saharman Yulia Rosa Saharman