DNA Polymorphism of 13 Autosomal Short Tandem Repeats (STR) Loci in Mentawai Populations.

<b>Background and Objective:</b> Indonesia consists of various ethnic groups with diverse cultures. However, research on allele frequencies and genetic variations of each ethnic group in Indonesia has not been well established. Therefore, a study was conducted on 13 STR loci panels to analyze the mentawai population as an enhancement of the Indonesian population's genetic data library and genetic variation. Mentawai is one of the Indonesian tribes who live on Mentawai Island, West Sumatera. <b>Materials and Methods:</b> The PrepFiler kit to extract DNA from blood and the GlobalFiler kit for amplifying the 13 loci were used. The genetic analyzer ABI PRISM 3500 was used to detect PCR products. Data were processed and analyzed by EasyDNA and FORSTAT software. <b>Results:</b> The allele frequency data for 13 autosomal loci in Mentawai populations were obtained. Expected heterozygosity was found with a minimum of 0.607 for TPOX and a maximum of 0.866 for FGA. Power of discrimination (PD) values ranges from TPOX (0.792) to FGA (0.968). Polymorphic information content (PIC) values for all loci were high, ranging from 0.642 for TPOX to 0.921 for vWA. Three off-ladder alleles in these findings were detected. Allele 6.3 at the TH01 loci and allele 14.2 at the D18S51 loci are exquisite. The mean expected heterozygosity and mean power of discrimination value across the 13 loci were 75.9 and 90.1%, indicating striking gene diversity. <b>Conclusion:</b> These 13 STR loci can be used for population genetic studies and forensic identification.

Utilization of Local Microorganisms as Bioactivators to Produce Organic Fertilizers and Analysis of Molecular Bacterial Diversity.

<b>Background and Objective:</b> Local micro organism (LMO) is the result of the fermentation of various mixtures of organic matter. One of the organic materials used, based on the local wisdom of West Sumatra, is tapai (fermented Cassava), which is used as a bio activator in the manufacture of organic fertilizer. The research aims to produce organic fertilizers that meet national quality standards in terms of the physical and chemical quality of fertilizers as well as to determine the diversity of bacteria in bio activators through next-generation sequencing analysis. <b>Materials and Methods:</b> The organic ingredients for bio activators, cow feces as basic fertilizer ingredients, materials for analyzing bacterial diversity, LMO gDNA was extracted using ZymoBIOMICS DNA Miniprep Kit DNA and sequenced using Oxford Nanopore Technology. <b>Results:</b> On a scale of 1-3, the physical quality of organic fertilizers had an average value of 2.58 for smell, 2.83 for texture and 2.58 for color. The chemical quality of organic fertilizers is C-organic (23.56%), nitrogen (1.60%), carbon and nitrogen ratio (14.75%), phosphate (0.47%) and potassium (0.64%). The results of the analysis of bacteria on the bioactivator consisted of 7 phyla, 9 families, 45 genres and 297 species. The most common species is <i>Lentilactobacillus hilgardii</i> (62%). <b>Conclusion:</b> The organic fertilizer produced using the mole tapai bio activator complies with Indonesian national standard 19-7030-2004 based on physical and chemical parameters. The type of bacteria that dominates the bioactivator is the lactic acid bacteria group, which reaches 90%.

The RYR3 gene is involved in Wharton's jelly derived mesenchymal stem cell treatment of Alzheimer's disease in rats.

Introduction: Our study aims to observe the effect of mesenchymal stem cells (MSCs) in lowering amyloid accumulation and ryanodine receptor 3 (RYR3) gene expression, further improving cognitive dysfunction in Alzheimer's disease (AD). Methods: Twenty male adult Wistar rats were randomly distributed into three groups of animals (n = 5). The AlCl3 group was given 300 mg/kg body weight (BW) of AlCl3 intraperitoneally for 5 days, further the MSC injection, and their effect after 30 days was observed. Results: MSCs improved amyloid accumulation and Y-maze scores, and expression of the RYR3 gene decreased compared to the control group. Conclusions: MSCs improved amyloid accumulation, Y-maze scores, and RYR3 expression in the AD animal model.

Common but ignored: a new species of Cyrtodactylus (Chordata, Reptilia, Squamata, Gekkonidae) from lowland Sumatra Barat, Indonesia.

The lowland region of Sumatra Barat has received little attention in previous biodiversity studies. Past studies have mainly focused on highland habitat and conservation areas. However, many populations of Cyrtodactylus in the lowland habitats of Sumatra Barat were not correctly identified. A phylogenetic tree based on the NADH dehydrogenase subunit 2 (ND2) gene showed that the lowland Sumatran population is the sister group of the Malaysian lowland species, C.semenanjungensis, together nesting within the agamensis group. The genetic divergence within the Sumatra Barat population is 0-4.2% and 18.3-20% to C.semenanjungensis. Further examination of morphological characters revealed that they differed from the sister clade and other Sumatran Cyrtodactylus members by a unique combination of characters such as absence of tubercle on brachium, presence of tubercle on ventrolateral fold, 32-41 paravertebral tubercles, 38-46 ventral scales, enlarged femoral scales, presence of precloacofemoral pores and 22-23 subdigital lamellae under fourth toe. Based on the morphological and molecular evidence, the lowland Sumatran population is herein described as a new species, increasing the number of species in Sumatra to seven. More comprehensive and intensive sampling efforts would most likely yield further discoveries in the group of Sumatran Cyrtodactylus in the near future.

Phylogenetic Relationships of Sun Bear (Helarctos malayanus) Based on Mitochondrial DNA from Sumatra and Other Southeast Asian Regions.

<b>Background and Objective:</b> The <i>Helarctos malayanus</i> is the sole bear species-living in Indonesia (Sumatra and Borneo). The available biological data for sun bears (<i>H. malayanus</i>) in Sumatra is limited, especially for morphological and genetic data. A morphological approach is difficult to do. Therefore, a molecular approach is the most likely choice. Phylogenetic analysis was carried out on <i>H. malayanus</i> in Central Sumatra (Dharmasraya, South Solok and Riau) using the Cytochrome B gene. <b>Materials and Methods:</b> Blood samples from three individuals of <i>H. malayanus</i> were obtained at the Sumatran Tiger Rehabilitation Center, Dharmasraya. Three <i>H. malayanus</i> Central Sumatra sequences and 62 GenBank sequences were used in the analysis. The DNA sequences were analyzed using the DNA Star, AliView, Bioedit, DNA SP, haplotype network, IQ Tree and MEGA software. <b>Results:</b> Forty-one haplotypes were identified in 65 sequences, with 17 haplotypes belonging to <i>H. malayanus</i>. Haplotype network analysis divides <i>H. malayanus</i> into Haplogroup I (Sundaland) and Haplogroup II (Mainland). All individuals of <i>H. malayanus</i> in Central Sumatra have the same haplotype as Peninsular Malaysia sequence. The sun bear (<i>H. malayanus</i>) has a monophyletic relationship with other bear species. The <i>H. malayanus</i> has a higher genetic distance between the two lineages (1.0-2.3%) than the genetic distance within the subpopulations of each lineage. <b>Conclusion:</b> The study results supported sun bear (<i>H. malayanus</i>) divided into two different lineages: Mainland (subcluster 1) and Sundaland (subcluster 2 and 3). The geographic isolation causes the absence of gene flow, which results in high genetic distance between sun bears (<i>H. malayanus</i>) in Sundaland and Mainland lineages.

GENETIC ANALYSIS 21 SHORT TANDEM REPEATS (STR) LOCUS IN MINANGKABAU POPULATION, WEST SUMATERA, INDONESIA.

Background: Minangkabau is the majority ethnic group in West Sumatra, Indonesia. West Sumatra is a disaster area, especially earthquakes and the potential for a tsunami. Allele frequency for 21 short tandem repeat locus and genetic variation are not well known. This data is essential for calculating the Paternity Index and Match Probability for forensic identification. Materials and methods: This was an observational study. We analyze the GlobalFiller STR loci in 25 unrelated individuals from Minangkabau ethnic group. The DNA was extracted using a Prefiller kit and amplified with a Global Filler kit by a GeneAmp PCR System, followed by capillary electrophoresis using ABI Prism 3500 Genetic Analyzer. Data analysis was performed by using Easy DNA and FORSTAT software. Results: We observed 162 alleles with allele frequencies between 0.02 - 0.36. The highest expected heterozygosity and the highest power of discrimination were at the SE33 loci, and the highest match probability was at the D2S441 locus. The Chi-square test showed that all STR loci followed Hardy-Weinberg equilibrium (p > 0.05). All loci were highly polymorphic (PIC > 0.5). The combined discrimination capacity of each locus in the population was 99,999%. Conclusion: The 21 STR loci are useful for forensic analysis and population genetic studies of the Minangkabau population.

Growth Phase Influence the Gene Expression and Metabolite Production Related to Indole-3-Acetic Acid (IAA) Biosynthesis by Serratia plymuthica UBCF_13.

<b>Background and Objective:</b> The optimization of the indole-3-acetic acid (IAA) producing capability of <i>Serratia plymuthica</i> UBCF_13 has been intensively studied. This work tried to reveal the effect of growth phases on IAA production, gene expression and metabolite synthesis related to the IAA biosynthesis pathway. <b>Materials and Methods:</b> The growth curve and IAA production were measured every 3 hrs. The putative IAA biosynthesis pathway was investigated based on the UBCF_13 genome. To identify the possible pathway of IAA biosynthesis in UBCF_13, we applied the Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) and High-Performance Liquid Chromatography (HPLC) analysis to measure the transcript levels of each gene and indole metabolite production based on tryptophan treatment at different times of incubation. <b>Results:</b> The optimal IAA production on colorimetric assay was at 9 hrs of incubation (initial stationary phase). The level expression of <i>puuC</i>, <i>DDC</i>, <i>oxdA</i>, <i>amiE</i>, <i>nthA</i> and <i>nthB</i> have been upregulated maximum in 3 hrs of culture time (lag phase), except <i>tyrB</i> and <i>ipdC</i>. The highest transcript level of the genes was found in nitrile hydratase genes (<i>nthA</i> and <i>nthB</i>) and indole-3- acetamide (IAM) has been detected as the only intermediate in the crude extract of UBCF_13 thus the IAM pathway may be used to produce IAA. The maximum IAA production on HPLC analysis was found at 21 hrs of incubation (late stationary phase). <b>Conclusion:</b> This study gives a new insight that the best time to measure gene expression and intermediates related to the IAA biosynthetic pathway in bacteria was found at a specific growth phase.

Polymorphisms of CYP2E1 rs2031920 is not Associated with Risk of Nasopharyngeal Carcinoma in Minangkabau Ethnic Group.

BACKGROUND: Various environmental factors have been suspected to be associated with the risk of developing Nasopharyngeal Carcinoma (NPC). Volatile nitrosamines found in salted fish are thought to be carcinogenic substances for NPC. Nitrosamines are activated by the CYP2E1 enzyme. Several studies investigated the relationship between polymorphism in the CYP2E1 gene and susceptibility to NPC, but the results obtained were inconsistent. AIM: This study was conducted to analyze the association of the CYP2E1 rs2031920 polymorphisms with the incidence of NPC in the Minangkabau ethnic group. METHODS: The subjects of this study were newly diagnosed NPC Minangkabau ethnic patients, while the controls were healthy people. A total of 23 cases of NPC and 23 aged (± 3 years) and sex-matched controls participated in the study. The method used to identify these polymorphisms is PCR sequencing. RESULTS: On recent study we found CYP2E1 rs2031920 gene polymorphism in both the NPC and control groups, in the NPC group there were 8.7% heterozygote mutants while in the control group there were 26.1% heterozygote mutants, and there were no homozygote mutants in the two groups, and statistically none a significant relationship between CYP2E1 gene polymorphism and the incidence of NPC, with p > 0.05. CONCLUSION: Our study reveals that there is no association of CYP2E1 gene polymorphism (rs2031920) with the incidence of nasopharyngeal carcinoma in the Minangkabau ethnic group.

Effect of Phaleria Macrocarpa Flesh Fruits Extract on MDA Level, SGOT and SGPT Activity in Serum of Experimental Rats Contaminated by Cd (II) Ion.

BACKGROUND: Cd (II) ion is a heavy metal that has a toxic ability in the human body. P. macrocarpa has been used as anticancer, Diabetes Mellitus and antimicrobe because it consists of flavonoid, steroid, and tannin. AIM: The purpose of this study was to investigate the effectiveness of P. macrocarpa fruits extract as an antidote for the toxicity of Cd (II) in the liver of experimental rats. METHODS: The experimental laboratory was done by using 9 female of Wistar rats (Rattus novergicus) that divided into 3 groups with the age between 2.5-3 months and weight between 133-160 grams. The first group was a control given distilled water and a normal diet. The second group was given antidote 5 mL of P. macrocarpa fruit extract x BW/200 g dosage for 7 days and induced by 1000 mg/L of Cd (II) ion with dosage of 1 mL x BW/200 g. The third group was given 1000 mg/L Cd (II) ion only of 1 mL x BW/200 g. After 5 hours, the blood sample was taken for analysis of MDA, SGOT, and SGPT. RESULTS: As the result of experimental rats exposed with Cd (II) ion, there are significant decreasing of all the observed parameters including MAD, SGOT and SGPT with percentage 71.5%, 72.1%, and 93.6% respectively. CONCLUSION: The rats given with the antidote of Phaleria macrocarpa flesh fruit were able to protect the liver from damage due to exposure to Cd (II) as seen from the decrease in liver function enzyme parameters namely SGOT and SGPT.

Genetic differentiation of the Fejervarya limnocharis complex from Bangladesh and other Asian countries elucidated by allozyme analyses.

The present study was conducted to elucidate the genetic divergence and the phylogenetic relationships in the F. limnocharis complex from Bangladesh and other Asian countries such as Sri Lanka, Thailand, Malaysia, Taiwan and Japan by allozyme analyses. We used a total of 95 frogs of the F. limnocharis complex from these countries and F. cancrivora from the Philippines as an outgroup. Based on body size, the F. limnocharis complex from Bangladesh was divided into three distinct groups: large, medium and small types. Allozyme analyses were carried out with 28 loci encoding 20 enzymes and two blood proteins by horizontal starch-gel electrophoresis. When genetic distance was calculated, distinct divergence was found among the three types: mean genetic distance was 0.782 between the small and medium types, 1.458 between the large and medium types, and 1.520 between the large and small types. Phylogenetic trees based on genetic distance showed that all populations of Bangladesh small type strongly formed a cluster and were found to be most closely related to the Sri Lanka population; that all populations of Bangladesh large type formed a very strong cluster and were grouped with several populations from Thailand, Malaysia, Japan, and Taiwan; and that the medium type was segregated from all other groups. This may imply that each of the three types is a different species, and that the medium type is possibly an undescribed taxon.