Kajian Bioinformatika Uncoupling Protein 2 (UCP2) dan Mutasi Ala55Val UCP2 Pada Obesitas dan Diabetes Melitus Tipe 2 (DMT2)

Pendahuluan. Kemajuan pengetahuan suatu penyakit sangat didukung oleh kajian tingkat molekuler sampai klinis. Bioinformatika menjembati perkembangan pengetahuan analisis seluler dan molekular dengan klinis. Selain dipengaruhi faktor lingkungan, faktor genetik diketahui berperan dalam   patomekanisme penyakit obesitas dan DMT2. UCP2 berpengaruh terhadap BMI (basal mass index) pada penderita obesitas dan berpengaruh terhadap sekresi insulin pada penderita diabetes melitus tipe 2. Kajian ini bertujuan mengetahui informasi genetik gen dan protein UCP2 serta peran mutasi Ala55Val pada obesitas dan diabetes melitus tipe 2. Metode.  Kajian  bioinformatika  gen  dan  mutasi  UCP2  menggunakan  data  base  situs  http://www.ncbi.nlm.gov,http://www.uniprot.org  dan  http://www.ensembl.org.  Profil, struktur  dan  fungsi  protein UCP2  dikaji  dengan  situs http://www.expasy.org, http://www.cbs.dtu/dk, http://www.wolfpsort.org,       http://bioinf.cs.ucl.ac.uk/psipred/ dan http://www.pdb.org. Disain primer dan titik mutasi Ala55Val UCP2 dikaji dengan situs Primer3 dan REBASE. Hasil dan kesimpulan. Gen UCP2 Homo sapiens (NC_000011.9) terdiri atas 8 ekson dan 7 intron dengan panjang basa nukleotida 8174 bp. Protein UCP2 (NP_003346)  mempunyai  309 asam  amino, merupakan protein integral yang berlokasi di membran  mitokondria bagian dalam. Struktur protein terdiri atas heliks dan koil.  Fungsi UCP2 sebagai protein transporter, uncoupling proton pada fosforilasi oksidatif, termogenesis dan keseimbangan energi dengan cara mengubah gradien proton. Mutasi Ala55Val dapat dianalisis dengan mengamplifikasi target sekuen yang diinginkan dengan cara mendesain primer dan titik mutasi dideteksi dengan enzim retriksi yang mengenali titik tersebut. Ala55Val merupakan mutasi missense yang terjadi di posisi mRNA ke 164, mengubah GCC menjadi GTC, mengubah translasi protein nomer 55 alanin menjadi valin. Titik mutasi ini berdekatan dengan situs fosforilasi Protein C Kinase (PCK) protein, situs yang berperan mengatur jumlah ATP dalam proses termogenesis dan sekresi insulin. Informasi genetik gen, protein UCP2 serta peranannya dalam obesitas dan diabetes melitus tipe 2  dapat diperoleh dengan menggunakan database bioinformatika

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite's biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality

Whole genome sequencing of Indonesian dengue virus isolates using next-generation sequencing

Indonesia is a tropical country and hyperendemic for dengue. The disease prevalently affected Indonesian and it caused high morbidity and substantial economic burden. This vector-borne viral disease is caused by infection of dengue viruses (DENVs), which are the member of Flaviviridae family. While most of dengue studies in Indonesia focused on the epidemiology, the clinical aspects, the vectors, and to certain extent the virology, there were still gaps in the DENVs genomic aspects. Considering their high mutation rate, the DENVs were known for their high genetic diversity and it might affect the characteristics of the viruses. Comprehensive DENV genomic data were thus important for many aspects of disease management, including virus surveillance, pathogenesis, diagnostics, antiviral drug design, and vaccine development. We established in this study a method for DENV whole genome sequencing using the advanced Next-Generation Sequencing (NGS) and Nextera XT DNA library preparation kit, coupled with simplified bioinformatic analysis methods. The Indonesian DENVs from four serotypes were isolated from patients’ sera, while library was prepared from enriched templates and sequenced using Illumina NGS. Our study highlighted the potential of a robust NGS method in producing whole genome sequence of DENVs, which would be important for future dengue studies

Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics.

The incidence of Plasmodium vivax infection has declined markedly in Malaysia over the past decade despite evidence of high-grade chloroquine resistance. Here we investigate the genetic changes in a P. vivax population approaching elimination in 51 isolates from Sabah, Malaysia and compare these with data from 104 isolates from Thailand and 104 isolates from Indonesia. Sabah displays extensive population structure, mirroring that previously seen with the emergence of artemisinin-resistant P. falciparum founder populations in Cambodia. Fifty-four percent of the Sabah isolates have identical genomes, consistent with a rapid clonal expansion. Across Sabah, there is a high prevalence of loci known to be associated with antimalarial drug resistance. Measures of differentiation between the three countries reveal several gene regions under putative selection in Sabah. Our findings highlight important factors pertinent to parasite resurgence and molecular cues that can be used to monitor low-endemic populations at the end stages of P. vivax elimination

Association of beta3-adrenergic receptor (ADRB3) Trp64Arg gene polymorphism with obesity and metabolic syndrome in the Balinese: a pilot study

Abstract Background Prevalence of obesity is increasing all over the world. ADRB3 Trp64Arg gene polymorphism was proposed to be associated with obesity, although inconsistent findings and differences of the Arg64 allele frequency among various ethnics were reported. Westernization was reported to increase the prevalence of obesity in developing world. In this study we determined the prevalence of obesity and metabolic syndrome among urban and rural Balinese, and studied the association of ADRB3 Trp64Arg polymorphism with obesity and MetS. Findings A total of 528 Balinese (urban 282, rural 246) were recruited. Body mass index (BMI) and waist circumference (WC) were determined; high-density lipoprotein cholesterol (HDL-C), triglyceride (TG), systolic and diastolic blood pressure (SBP and DBP), and fasting plasma glucose (FPG) were measured using standard procedures. BMI and WC classifications were based on WHO classifications for Asian. Metabolic syndrome (MetS) was defined as described in the Joint Interim Statement. Chi-square test was employed to test the association between the ADRB3 Trp64Arg genotype and disease traits. Urban have higher BMI (p = 2.8 × 10-13), WC ( p -16), TG (p = 0.0028), DBP (p = 1.8 × 10-5), and lower HDL-C (p = 0.0376) when compared to rural. Abdominal obesity and MetS prevalence were significantly higher in urban as compared to rural (both p p = 0.041 for BMI and p = 0.012 for WC), and consequently higher abdominal obesity prevalence (p = 0.007). Comparison between male and female, as well as urban and rural, showed different prevalence of MetS co-morbidities. Abdominal obesity and hypertriglyceridaemia were consistently appeared in all groups, suggesting to play a role as determinant of MetS in both urban and rural. Conclusions Prevalence of obesity and MetS in urban were two times higher when compared to rural. Abdominal obesity and hypertriglyceridaemia appears to be the key determinant of MetS in both urban and rural Balinese. Our results indicated an association of the ADRB3 Trp64Arg gene polymorphism with obesity in the rural female.</p

Genetic diversity and population structure of Plasmodium vivax in Central China.

BACKGROUND: In Central China the declining incidence of Plasmodium vivax has been interrupted by epidemic expansions and imported cases. The impact of these changes on the local parasite population, and concurrent risks of future resurgence, was assessed. METHODS: Plasmodium vivax isolates collected from Anhui and Jiangsu provinces, Central China between 2007 and 2010 were genotyped using capillary electrophoresis at seven polymorphic short tandem repeat markers. Spatial and temporal analyses of within-host and population diversity, population structure, and relatedness were conducted on these isolates. RESULTS: Polyclonal infections were infrequent in the 94 isolates from Anhui (4%) and 25 from Jiangsu (12%), with a trend for increasing frequency from 2008 to 2010 (2 to 19%) when combined. Population diversity was high in both provinces and across the years tested (H(E) = 0.8 - 0.85). Differentiation between Anhui and Jiangsu was modest (F'(ST) = 0.1). Several clusters of isolates with identical multi-locus haplotypes were observed across both Anhui and Jiangsu. Linkage disequilibrium was strong in both populations and in each year tested (I(A)(S) = 0.2 - 0.4), but declined two- to four-fold when identical haplotypes were accounted for, indicative of occasional epidemic transmission dynamics. None of five imported isolates shared identical haplotypes to any of the central Chinese isolates. CONCLUSIONS: The population genetic structure of P. vivax in Central China highlights unstable transmission, with limited barriers to gene flow between the central provinces. Despite low endemicity, population diversity remained high, but the reservoirs sustaining this diversity remain unclear. The challenge of imported cases and risks of resurgence emphasize the need for continued surveillance to detect early warning signals. Although parasite genotyping has potential to inform the management of outbreaks, further studies are required to identify suitable marker panels for resolving local from imported P. vivax isolates