Analisis Bioinformatika Berbasis WEB untuk Eksplorasi Enzim Kitosanase Berdasarkan Kemiripan Sekuens

Eksplorasi enzim secara tradisional dengan kultivasi mikroba sekarang ini tidak lagi efisien, karena menghabiskan waktu dan biaya. Bioinformatik berbasis web hadir untuk melakukan serangkaian analisis sekuen, baik itu DNA maupun protein, yang dapat digunakan sebagai penelitian pendahuluan, sehingga ekplorasi enzim menjadi lebih tepat sasaran. Penelitian ini telah melakukan analisis potongan sekuen 16S ribosomal RNA yang didapat dari 6 bakteri yang berasosiasi dengan udang. Analisis yang dilakukan adalah untuk mencari tahu tersedianya sekuen tersebut telah ada di Gene Bank atau merupakan strain baru khas Indonesia yang belum terpublikasi. Dengan menggunakan database 16S Microbial dan Reference Genomic Sequence, serta fasilitas BLAST nucleotide dan CLUSTALW2 didapatkan 5 nama bakteri yaitu Micromonospora sp. L5, Aeromonas veronii B565, Staphylococcus epidermidis ATCC 12228, Burkholderia sp. JV3, dan Acinetobacter baumanniiAB307-0294. Kelima mikroba ini memiliki tidak mempunyai gen kitosanase tetapi penyandi kitinase. Ketidakhadiran gen kitosanase dalam genome mikroba menjadikan mikroba unik untuk diketahui sekuens gen kitosanasenya, yang juga berpeluang untuk dipublikasikan

Reverse-Transcriptase Characteristics of Hepatitis B Virus Polymerase Gene in Treatment-Naïve Asymptomatic Chronic Hepatitis B Individuals

Nucleos(t)ide analogues (NUCs) remain the main treatment for chronic hepatitis B (CHB). Long-term use of NUCs significantly reduces disease progression; however, it might lead to resistance-associated mutations. We studied characteristics of polymerase gene related to NUCs resistance in naïve hepatitis B surface antigen (HBsAg)-positive individuals. The research was done at Laboratory of Hepatitis, Eijkman Institute, Jakarta Thirty eight samples were obtained and submitted for HBV DNA detection. Identification of mutations was performed by PCR-sequencing, and analyzed to obtain NUCs resistance motifs. Genotype and subtype were determined based on HBsAg sequence. Mutation of rtQ238H/N was found in 37 (97.4%) samples. Of those, 23 (62.2%) showed rtQ238H mutation, 10 (27.0%) had rtQ238N mutation, and four (10.8%) with double mutations of rtA194T and rtQ238H. Genotype B was found in 26 (68.4%), C in 11 (28.9%), and D in one (2.6%) samples. Statistically, the mutation variant of rtQ238H was associated with genotype B (p<0.001), while rtQ238N with C (p<0.001). The ayw subtype was found in 25 (65.8%), adr in 11 (28.9%), and adw in two (5.3%) samples. No mutation associated with NUCs resistance was found in most samples. This emphasizes that NUCs are still a prospective treatment in naïve CHB patients.  Mutation of rtQ238H was a variant found to be significantly associated with HBV genotype B and rtQ238N with genotype C

Open Science – for whom?

Who can participate in Open Science and whose interests are served? Open Science in principle holds the potential to reduce inequality, but this is not going to happen unless it operates within a consistent framework and environment that supports this goal. Unequal power and opportunities from institutional to global level constitutes a major obstacle to human development, while we need to appreciate diversity as a key asset. How can we build an equitable global research ecosystem in accordance with the United Nations 2030 Agenda for Sustainable Development that recognises science as a global common good and an integral part of the shared cultural heritage of humankind?Publisher PDFPeer reviewe

Antibiotic Resistomes and Microbiomes in the Surface Water along the Code River in Indonesia Reflect Drainage Basin Anthropogenic Activities

Water and sanitation are important factors in the emergence of antimicrobial resistance in low-and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and enfluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and MGEs and 16S rRNA gene amplicon sequencing to analyze the bacterial communities. The community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs, which correlated with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs were no longer detectable in marine waters at the ocean entrance. Our work provides information on the impact of different influents on river health as well as sheds light on how land use contributes to the river resistome and microbiome.Peer reviewe

Molecular, Genetic, and Functional Analysis of Ptr3p, A Novel Protein Involved in Amino Acid and Dipeptide Regulation of Di/Tri-peptide Transport System in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae utilizes nutrient sensor activity at the plasma membrane to regulate growth. Amino acids are sensed by the membrane protein Ssy1p, and a signal is transduced to the novel intracellular regulatory protein Ptr3p. This leads to an upregulation of the expression of amino acid permease genes and PTR2, the gene encoding the di/tri-peptide transporter Ptr2p. Using a reporter gene assay, this study found that various amino acids induced PTR2 expression to different levels. Peptide and amino acid induction required Ptr3p, while Ssy1p was required for amino acid induction, but not peptide induction. Ptr3p-mediated, amino acid/dipeptide-induced expression of PTR2 did not involve transcriptional regulation of CUP9, a gene encoding a repressor of PTR2 expression. A functional chimeric protein formed by the fusion of GFP to the N-terminus of Ptr3p was found to be associated with the plasma membrane in a punctate pattern. A two-hybrid and co-immunoprecipitation analysis showed that Ptr3p interacted with the cytoplasmic, N-terminal 282 amino acid domain of Ssy1p further supporting the suggestion that Ssy1p/Ptr3p interaction was involved in generating a signal after amino acid sensing. We also showed that STP1 and STP2, genes previously hypothesized to encode pre-tRNA splicing proteins and bind to the BAP2 promoter as transcription factors, were required for regulation of the di/tri-peptide transport system. The data provide the first evidence about the involvement of STP1 and STP2 in the di/tri-peptide transport system suggesting their function as transcription factors of PTR2. In contrast to the PTR2 expression pattern, in medium containing a rich nitrogen source STP1 and STP2 are expressed at higher levels in comparison to their expression in medium with a poor nitrogen source. STP2 likely acts downstream of PTR3 as shown by epistasis studies, and PTR3 does not regulate the expression of STP1 or STP2. To provide insights into the function of Ptr3p, we performed a two-hybrid analysis to identify proteins that may interact with Ptr3p. We identified proteins involved in transport, transcription processes, and unknown functions suggesting that Ptr3p plays role in numerous pathways. We used two different computational algorithms to predict that Ptr3p contains two putative nuclear localization signals (NLS), and alanine substitution of one of these NLS decreased its function as a regulator of PTR2. PROSPECT, a 3-dimensional protein structure algorithm, also calculated that Ptr3p has a RING finger and a seven-bladded β-propeller motif. Alanine site-directed mutagenesis of some conserved residues in the ring finger motif reduced the function of Ptr3p. Mutations within the predicted β-propeller motif indicated that this motif may act as an autoinhibitory domain, because their substitution resulted in a more functional mutant than the wild type Ptr3p. Finally, we identified functionalm domains of Ptr3p. The expression of Ptr3p residues 1-250 or 1-500 partially complemented ptr3Δ phenotype, and residues 250-678 appeared to be as functional as full length Ptr3p. These results add further to an understanding of the role of Ptr3p in the amino acid induced signal transduction pathway

Potensi Risiko Penyebaran Kasus Demam Berdarah Dengue di Jakarta Pusat

Dengue Hemorrhagic Fever (DHF) caused by four virus serotypes is a disease with A. aegyti and A. albopictus mosquitoes as vectors. DHF is a recurrent and high burdened disease in Indonesia. The purpose of this study is to analyze the spreading of DHF risk in Central Jakarta based on environmental factors. The cases number data year 2000-2009 was obtained from Center of Infectious Disease Research, National Institute of Health in Research and Development. Survey was performed in 38 subdistricts using random and purposive methods. Risk indicators were used in environmental data collection. The results of this study showed similar cyclical pattern each year.  March until May had a high DHF incident, while November until January had a relatively low DHF incident. In general, Central Jakarta had a medium risk potential of DHF spreading. Spearman rank analysis on adjacent areas gave various values. Subdistricts of Senen and Kemayoran had a low correlation, while subdistricts of Johar Baru and Cempaka Putih had the highest correlation among other subdistricts showing that there were vector migrations between these two subdistricts. Finally, the data obtained should be useful for minimalizing the risk of DHF spreading especially by vector control management

Analisis Pohon Filogenik dari Protein Non-Struktural 1 (NS1) Virus Dengue di Kawasan Asia Tenggara

Protein non-struktural 1 adalah protein Virus Dengue yang terkonservasi, tetapi protein non-struktural 1 dari Virus Dengue yang berbeda strain memiliki epitop berbeda yang dapat dikenali oleh sel-B. Epitop-epitop ini mungkin disusun oleh asam amino yang sama dalam urutan yang berbeda. Kemungkinan ini perlu dipertimbangkan dalam rangka memprediksi epitop sekuensial Virus Dengue. Tujuan penelitian kami adalah menganalisis hubungan kekerabatan dan susunan asam amino pada epitop spesifik yang telah dikonfirmasi dari sampel representatif gen protein NS1 dari Virus Dengue di kawasan Asia Tenggara. Hubungan kekerabatan protein non-struktural 1 dianalisis dengan perangkat lunak Lasergene®. Sekuen gen ditranslasi terlebih dahulu ke urutan asam amino, dan analisis pohon filogenetik kemudian dilakukan. Hasilnya menunjukkan bahwa hubungan kekerabatan protein non-struktural 1 berkisar antara 72-98%. Selanjutnya, epitop serospesifik dibandingkan berdasarkan hasil pengolahan data dnegan Lasergene. Perbandingan epitop serospesifik menunjukkan bahwa asam amino yang dominan dalam epitop adalah histidin, tirosin, glutamine dan serin  AbstractNon-structural 1 protein is a conserved protein of dengue virus, but non-structural 1 proteins of dengue virus from different strains have different epitopes which can be recognized by B-cell. These epitopes may be constructed of similar amino acids in a different arrangement. This possibility  must be considered in order to predict the sequencial epitope of dengue virus. The objective of our study was to analyze the phylogenetic relation and the arrangment of confirmed specific epitopes of dengue strains  from representatives of South East Asia’s NS1 dengue gene samples. The phylogenetic relation of non-structural 1 protein sequences from South East Asia was analyzed with Lasergene® software. The gene sequences were translated to amino acid sequences, and phylogenetic tree analysis was performed. The results showed that the relatedness values among full sequences of non-structural 1 protein were 72-98%. Furthermore, the serospesific epitopes were compared according to the Lasergene results. The serospesific epitope comparation showed that the dominant   amino acids in these epitopes were histidine, tyrosine, glutamine and serine