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

Experimentelle Untersuchungen uber die anaeroben Darmbakterien. I. Mitteilung : Studien uber Bakteroides bei gemischter Kost, und seine Zustandsanderung durch die einseitige Reisnahrung

Der Verfasser hat experimentelle Untersuchungen uber die anaeroben Darmbakterien besonders die sogenannten Bakteroides gemacht, denen bis heute zu wenig Beachtung geschenkt worden ist. Als Versuchstiere hat er sieben gesunde erwachsene Hunde gewahlt. In diesen Studien wurden das 15-proz.-Serum-Leberagar-Schuttelkulturverfahren und das 2-proz.-Traubenzucker-Leberagar-Plattenkulturverfahren als Isolierungsmethode gebraucht. Bei der gemischten Kost (enthulster Reis, Misosuppe mit massiger Menge Fleisch und Fisch) betrugen die obligaten anaeroben Darmbakterien 70% unter allen Bakterien, und die anderen 30%. Der Verfasser hat die folgenden Resultate bekommen: unter den obligaten anaeroben Darmbakterien; Bakteroides oviformis (II. Gruppe Fujikawa, Coccobacillus oviformis Tissier?, Bacillus dimorphus var. longa Distaso?) 23%, Bakteroides bifidus (Bacillus bifidus Tissier) 12%, Bakteroides variabilis Distaso (1. Gruppe Fujikawa, Bacillus variabilis Distaso?, Bacillus thetaiotaomicron Distaso?) 9%, Bacillus Welchii 6% und die anderen verschiedenen anaeroben Darmbakterien 17%. Bei der einseitigen Reisnahrung (erhulster Reis allein) gediehen immer die Bakteroides bifidus uppig und er wurde haufig am Ende der Experimente in 100% gefunden. Der Bacillus acidophilus wuchs massig, besonders am Anfang der Experimente. Die anderen Bakteroides und Bacillus Welchii verminderten sich oder zuweilen verschwunden sie ganzlich. (Autoreferat.

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

Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas

Colombia aims to eliminate malaria by 2030 but remains one of the highest burden countries in the Americas. Plasmodium vivax contributes half of all malaria cases, with its control challenged by relapsing parasitaemia, drug resistance and cross-border spread. Using 64 Colombian P. vivax genomes collected between 2013 and 2017, we explored diversity and selection in two major foci of transmission: Chocó and Córdoba. Open-access data from other countries were used for comparative assessment of drug resistance candidates and to assess cross-border spread. Across Colombia, polyclonal infections were infrequent (12%), and infection connectivity was relatively high (median IBD = 5%), consistent with low endemicity. Chocó exhibited a higher frequency of polyclonal infections (23%) than Córdoba (7%), although the difference was not significant (P = 0.300). Most Colombian infections carried double pvdhfr (95%) and single pvdhps (71%) mutants, but other drug resistance mutations were less prevalent (< 10%). There was no evidence of selection at the pvaat1 gene, whose P. falciparum orthologue has recently been implicated in chloroquine resistance. Global population comparisons identified other putative adaptations. Within the Americas, low-level connectivity was observed between Colombia and Peru, highlighting potential for cross-border spread. Our findings demonstrate the potential of molecular data to inform on infection spread and adaptation

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

Genomic profiles of Indonesian colorectal cancer patients [version 2; peer review: 2 approved]

Background: Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide and genetic mutation plays a vital role in CRC development. A previous study has suggested that genetic alterations among Indonesian patients with CRC might differ from those known in developed countries. This study aimed to describe the genomic profiles of Indonesian patients with CRC. Methods: A total of 13 patients were recruited for this study from May to July 2019. Tissue samples were collected, and genomic DNA was extracted from the samples. AmpliSeq for Illumina Cancer HotSpot Panel v2 Next-generation sequencing was used for DNA sequencing and a genome analysis toolkit was used for local realignment around the discovered variants. Results: A total of 45 genes comprising 391 single nucleotide variants (SNVs) with a depth >10 were observed. The genes with the most variants were STK11, SMAD4, EGFR, and ERBB4 and the genes with the most non-synonymous variants were SMAD4, TP53, FGFR3, CDKN2A, and STK11. Genes and SNVs in at least 90% of all samples consisted of 43 genes comprising 286 variants. Genes with the most non-synonymous SNVs were EGFR, SMO, FGFR3, TP53, STK11, CDKN2A. Genes related to the chromosomal instability pathway, such as TP53, SMAD4, KRAS, and APC, are also found in the analysis. Conclusions: Our findings showed that all patients with CRC in this study had genetic mutations in the chromosomal instability pathway. Analysis of genetic mutation of Indonesian patients with CRC might be crucial for advanced targeted therapy and for better clinical outcomes

Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia

Ethiopia has the greatest burden of Plasmodium vivax in Africa, but little is known about the epidemiological landscape of parasites across the country. We analysed the genomic diversity of 137 P. vivax isolates collected nine Ethiopian districts from 2012 to 2016. Signatures of selection were detected by cross-country comparisons with isolates from Thailand (n = 104) and Indonesia (n = 111), representing regions with low and high chloroquine resistance respectively. 26% (35/137) of Ethiopian infections were polyclonal, and 48.5% (17/35) of these comprised highly related clones (within-host identity-by-descent > 25%), indicating frequent co-transmission and superinfection. Parasite gene flow between districts could not be explained entirely by geographic distance, with economic and cultural factors hypothesised to have an impact on connectivity. Amplification of the duffy binding protein gene (pvdbp1) was prevalent across all districts (16-75%). Cross-population haplotype homozygosity revealed positive selection in a region proximal to the putative chloroquine resistance transporter gene (pvcrt-o). An S25P variant in amino acid transporter 1 (pvaat1), whose homologue has recently been implicated in P. falciparum chloroquine resistance evolution, was prevalent in Ethiopia (96%) but not Thailand or Indonesia (35-53%). The genomic architecture in Ethiopia highlights circulating variants of potential public health concern in an endemic setting with evidence of stable transmission

Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas

Colombia aims to eliminate malaria by 2030 but remains one of the highest burden countries in the Americas. Plasmodium vivax contributes half of all malaria cases, with its control challenged by relapsing parasitaemia, drug resistance and cross-border spread. Using 64 Colombian P. vivax genomes collected between 2013 and 2017, we explored diversity and selection in two major foci of transmission: Chocó and Córdoba. Open-access data from other countries were used for comparative assessment of drug resistance candidates and to assess cross-border spread. Across Colombia, polyclonal infections were infrequent (12%), and infection connectivity was relatively high (median IBD = 5%), consistent with low endemicity. Chocó exhibited a higher frequency of polyclonal infections (23%) than Córdoba (7%), although the difference was not significant (P = 0.300). Most Colombian infections carried double pvdhfr (95%) and single pvdhps (71%) mutants, but other drug resistance mutations were less prevalent (< 10%). There was no evidence of selection at the pvaat1 gene, whose P. falciparum orthologue has recently been implicated in chloroquine resistance. Global population comparisons identified other putative adaptations. Within the Americas, low-level connectivity was observed between Colombia and Peru, highlighting potential for cross-border spread. Our findings demonstrate the potential of molecular data to inform on infection spread and adaptation