Distinctive Microbiome Type Distribution in a Young Adult Balinese Cohort May Reflect Environmental Changes Associated with Modernization.

An important public health question is understanding how changes in human environments can drive changes in the gut microbiota that influence risks associated with human health and wellbeing. It is well-documented that the modernization of societies is strongly correlated with intergenerational change in the frequency of nutrition-related chronic diseases in which microbial dysbiosis is implicated. The population of Bali, Indonesia, is well-positioned to study the interconnection between a changing food environment and microbiome patterns in its early stages, because of a recent history of modernization. Here, we characterize the fecal microbiota and diet history of the young adult women in Bali, Indonesia (n = 41) in order to compare microbial patterns in this generation with those of other populations with different histories of a modern food environment (industrialized supply chain). We found strong support for two distinct fecal microbiota community types in our study cohort at similar frequency: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community (p < 0.001, analysis of similarity, Wilcoxon test). Although Type-P individuals had lower alpha diversity (p < 0.001, Shannon) and higher incidence of obesity, multivariate analyses with diet data showed that community types significantly influenced associations with BMI. In a multi-country dataset (n = 257), we confirmed that microbial beta diversity across subsistent and industrial populations was significantly associated with Prevotella and Bacteroides abundance (p < 0.001, generalized additive model) and that the prevalence of community types differs between societies. The young adult Balinese microbiota was distinctive in having an equal prevalence of two community types. Collectively, our study showed that the incorporation of community types as an explanatory factor into study design or modeling improved the ability to identify microbiome associations with diet and health metrics.

Association between pre-pregnancy body mass index and gestational weight gain on pregnancy outcomes: a cohort study in Indonesian pregnant women.

BACKGROUND: Pre-pregnancy BMI (PP BMI) and gestational weight gain (GWG) are prominent anthropometric indicators for maternal nutritional status and are related to an increased risk of adverse pregnancy outcomes. This study aimed to determine the factors affecting total GWG, PP BMI and pregnancy outcomes among pregnant women in West Sumatra, Indonesia. METHODS: This observational analysis was conducted among healthy women in the Vitamin D Pregnant Mother (VDPM) cohort study. A total of 195 pregnant women and their newborn babies were enrolled, and information regarding their socio-demographic characteristics, obstetric history, dietary intake and anthropometric data were assessed through direct interviews. Furthermore, the Institute of Medicine (IOM) 2009 guidelines were used to obtain the total GWG. RESULTS: PP BMI was used to categorise the 195 pregnant women as overweight/obese (43.1%), normal (46.7%) and underweight (10.2%). There were 53.3%, 34.4% and 12.3% of women who had inadequate, adequate and excessive GWG, respectively. The multinomial logistic regression model indicated that overweight or obese women at the pre-pregnancy stage were 4.09 times more likely to have an excessive rate of GWG (AOR = 4.09, 95% CI: 1.38-12.12, p = 0.011) than those whose weight was normal. Furthermore, women with excessive GWG were 27.11 times more likely to have a baby with macrosomia (AOR = 27.11, 95% CI: 2.99-245.14) (p = 0.001) and those with inadequate GWG were 9.6 times more likely to give birth to a baby with low birth weight (LBW) (AOR = 9.60, 95% CI; 0.88-105.2) (p = 0.002). CONCLUSIONS: This study demonstrates that the malnutrition status prior to pregnancy and inadequate or excessive GWG status during pregnancy as significant risk factors for developing adverse pregnancy outcomes. These findings highlight the importance of providing information, preconception counselling and health education on weight management for healthy pregnancies.

Impact of maternal dietary carbohydrate intake and vitamin D-related genetic risk score on birth length: the Vitamin D Pregnant Mother (VDPM) cohort study.

BACKGROUND: Our objectives were to investigate the relationship between maternal vitamin D status and IGF-1 levels in healthy Minangkabau pregnant mothers and their impact on newborn anthropometry outcomes and to examine whether this relationship was modified by dietary intake using a nutrigenetic approach. METHODS: Healthy singleton pregnant mother and infant pairs (n = 183) were recruited. We created three genetic risk scores (GRSs): a six-SNP GRS based on six vitamin D-related single nucleotide polymorphisms (SNPs) involved in the synthesis of vitamin D (vitamin D-GRS), a two-SNP GRS using SNPs in VDR genes (VDR-GRS) and a four-SNP GRS using SNPs from DHCR7, GC, CYP24A1 and CYP2R1 genes (non-VDR GRS). The effect of the GRSs on IGF-1, vitamin D and newborn anthropometry and the interaction between the GRSs and dietary factors were tested using linear regression analysis. RESULTS: The vitamin D- and non-VDR GRSs were significantly associated with lower 25(OH)D concentration (p = 0.005 and p = 0.001, respectively); however, there was no significant association with IGF-1, and newborn anthropometry outcomes. However, there was a significant interaction of VDR-GRS with carbohydrate intake on birth length outcome (Pinteraction = 0.032). Pregnant mothers who had higher carbohydrate intake (405.88 ± 57.16 g/day) and who carried ≥ 2 risk alleles of VDR-GRS gave birth to babies with significantly lower birth lengths compared to babies born to mothers with < 2 risk alleles (p = 0.008). CONCLUSION: This study identified a novel interaction between VDR-GRS and carbohydrate intake on birth length outcome. These findings suggest that reducing the intake of carbohydrates during pregnancy, particularly for those who have a higher genetic susceptibility, might be an effective approach for preventing foetal growth abnormalities.

Cumulative exposure characteristics of vegetable farmers exposed to Chlorpyrifos in Central Java - Indonesia; a cross-sectional study.

BACKGROUND: Agriculture is a major economic sector in Indonesia. Chemical pesticides are widely being used in agriculture for controlling pest. There is a growing concern that pesticide exposure, particularly chlorpyrifos (CPF) exposure, combined with other occupational characteristics that determine the level of exposure, can lead to further health impacts for farmers. Our objective was to evaluate the cumulative exposure characteristics among farmers exposed to CPF by using a validated algorithm. METHODS: We conducted a cross-sectional study of 152 vegetable farmers aged 18-65 who actively used CPF for at least 1 year in Central Java, Indonesia. Subject characteristics were obtained using a structured interviewer-administered questionnaire, addressed for sociodemographic and work-related characteristics. The cumulative exposure level (CEL) was estimated as a function of the intensity level of pesticide exposure (IL), lifetime years of pesticide use and the number of days spraying per year. CEL was subsequently classified into two groups, high and low exposure groups. The difference in characteristics of the study population was measured using Chi-square, independent-t or Mann-Whitney test. Association between CEL and its characteristics variables were performed by multiple linear regression. RESULTS: Seventy-one subjects (46.7%) were classified as the high exposure group. The use of multiple pesticide mixtures was common among our study population, with 94% of them using 2 or more pesticides. 73% reported direct contact with concentrated pesticides product, and over 80% reported being splashed or spilt during preparation or spraying activity. However, we found that the proportion of proper personal protective equipment (PPE) use in our subjects was low. Higher volume of mixture applied (p <  0.001) and broader acres of land (p = 0.001) were associated with higher cumulative exposure level, while using long-sleeved clothes and long pants (p <  0.05) during pesticide spraying were associated with lower cumulative exposure after adjusted for age and gender. CONCLUSIONS: These findings indicate an inadequate knowledge of using pesticides properly. Thus, we recommend comprehensive training on pesticide usage and encourage proper PPE to reduce the exposure level.

Non-nutritional anemia: Malaria, thalassemia, G6PD deficiency and tuberculosis in Indonesia.

Anemia affects people worldwide and results in increased morbidity and mortality, particularly in children and reproductive-age women. Anemia is caused by an imbalance between red blood cell (RBC) loss and production (erythropoiesis), which can be caused by not only nutritional factors but also non-nutritional factors, such as inflammation and genetics. Understanding the complex and varied etiology of anemia is crucial for developing effective interventions and monitoring anemia control programs. This review focusses on two interrelated nonnutritional causes of anemia: malaria infection and RBC disorders (thalassemia and G6PD deficiency), as well as tuberculosis. According to the Haldane hypothesis, thalassemia occurs as a protective trait toward malaria infection, whereas G6PDd arises in malaria-endemic regions because of positive selection. Indonesia is a malariaendemic region; thus, the frequency of thalassemia and G6PD deficiency is high, which contributes to a greater risk for non-nutritional anemia. As Indonesia is the second global contributor to the newly diagnosed tuberculosis, and active pulmonary tuberculosis patients are more anemic, tuberculosis is also contributes to the increasing risk of anemia. Therefore, to reduce anemia rates in Indonesia, authorities must consider non-nutritional causes that might influence the local incidence of anemia, and apply co-management of endemic infectious disease such as malaria and tuberculosis, and of genetic disease i.e. thalassemia and G6PDd.

Maternal Multiple Micronutrient Supplementation Stabilizes Mitochondrial DNA Copy Number in Pregnant Women in Lombok, Indonesia.

BACKGROUND: The Supplementation with Multiple Micronutrients Intervention Trial (SUMMIT) in Lombok, Indonesia showed that maternal multiple micronutrients (MMN), as compared with iron and folic acid (IFA), reduced fetal loss, early infant mortality, and low birth weight. Mitochondria play a key role during pregnancy by providing maternal metabolic energy for fetal development, but the effects of maternal supplementation during pregnancy on mitochondria are not fully understood. OBJECTIVE: The aim of this study was to assess the impact of MMN supplementation on maternal mitochondrial DNA copy number (mtDNA-CN). METHODS: We used archived venous blood specimens from pregnant women enrolled in the SUMMIT study. SUMMIT was a cluster-randomized double-blind controlled trial in which midwives were randomly assigned to distribute MMN or IFA to pregnant women. In this study, we selected 108 sets of paired baseline and postsupplementation samples (MMN = 54 and IFA = 54). Maternal mtDNA-CN was determined by real-time quantitative polymerase chain reaction in baseline and postsupplementation specimens. The association between supplementation type and change in mtDNA-CN was performed using rank-based estimation for linear models. RESULTS: In both groups, maternal mtDNA-CN at postsupplementation was significantly elevated compared with baseline (P < 0.001). The regression revealed that the MMN group had lower postsupplementation mtDNA-CN than the IFA group (ß = -4.63, P = 0.003), especially for women with mtDNA-CN levels above the median at baseline (ß = -7.49, P = 0.007). This effect was rapid, and observed within 33 d of initiation of supplementation (ß = -7.39, P = 0.017). CONCLUSION: Maternal MMN supplementation rapidly stabilized mtDNA-CN in pregnant women who participated in SUMMIT, indicating improved mitochondrial efficiency. The data provide a mechanistic basis for the beneficial effects of MMN on fetal growth and survival, and support the transition from routine IFA to MMN supplementation.This trial was registered at www.isrctn.com as ISRCTN34151616.

Vitamin D deficiency status and its related risk factors during early pregnancy: a cross-sectional study of pregnant Minangkabau women, Indonesia.

BACKGROUND: Vitamin D deficiency (VDD) is a common problem in reproductive-aged women and has become a major public health problem worldwide. The effect of VDD in pregnancy has been associated with several adverse pregnancy outcomes. This study aims to assess the serum levels of 25-hydroxyvitamin D (25(OH)D) in the first trimester and its associated factors (socio-demographics, pregnancy profiles, dietary intake, and maternal anthropometry measurements) for the determination of vitamin D deficiency status in early pregnancy. METHODS: A cross-sectional study of 239 pregnant mothers in West Sumatra, Indonesia was conducted. We measured lifestyle, socio-demographics and pregnancy profile through a structured questionnaire and interview process. A semi quantitative-food frequency questionnaire (SQ-FFQ) was used to analyse the dietary intake of the pregnant women. Serum 25(OH)D concentrations were measured at < 13 weeks gestation using ELISA and logistic regression models were employed to identify the predictors of low vitamin D status. RESULTS: The prevalence of first-trimester maternal VDD and sufficiency were 82.8 and 17.2% respectively. The median 25(OH)D was 13.15 ng/mL (3.00-49.29 ng/mL). The significant independent predictors were no working status (OR: 0.029;0.001-0.708) (p = 0.030); nulliparous parity status (OR: 7.634;1.550-37.608) (p = 0.012); length of outdoor activity status of less than an hour (OR: 9.659;1.883-49.550) (p = 0.007); and no consumption of supplements before pregnancy (OR: 4.49;1.081-18.563) (p = 0.039). CONCLUSIONS: The prevalence of VDD is common in early pregnancy among Minangkabau women. Recommendations and policies to detect and prevent such insufficiency during pregnancy should be developed by considering the associated factors.

Obesity risk and preference for high dietary fat intake are determined by FTO rs9939609 gene polymorphism in selected Indonesian adults.

BACKGROUND AND OBJECTIVES: Data suggest that genetic factors are associated with BMI. The fat mass and obesity- associated (FTO) gene modulates adipogenesis through alternative splicing and m6A demethylation. Individuals with FTO rs9939609 gene polymorphism have a preference for energy-dense foods. This study investigates the relationship between FTO rs9939609 and obesity and preference for dietary fat intake among selected Indonesian adults. METHODS AND STUDY DESIGN: A total of 40 non-obese and 40 obese participants aged 19-59 living in Jakarta were recruited. Body composition measurements included body weight, height, BMI, waist circumference, and body fat mass. Dietary intake was assessed using a semiquantitative food frequency questionnaire and food recall over 2 × 24-h periods. Genetic variation was determined using amplification-refractory mutation system polymerase chain reaction. RESULTS: The genotype distribution of the FTO gene (rs9939609) was at Hardy- Weinberg equilibrium (p=1) with minor allele frequency=0.19. Individuals with AT/AA genotypes had 3.72 times higher risk of obesity (p=0.009) and 5.98 times higher dietary fat intake (p=0.02) than those with TT genotype. Obese participants with the AT/AA genotypes had 1.40 times higher dietary fat intake than those with the TT genotype (p=0.016). CONCLUSIONS: These findings suggest that Indonesian adults with AT/AA genotypes of the FTO rs9939609 have higher obesity risks and preferences for high dietary fat intake than those with TT genotype.

The Role of Serum Expression Levels of Microrna-21 on Bone Mineral Density in Hypostrogenic Postmenopausal Women with Osteoporosis: Study on Level of RANKL, OPG, TGFß-1, Sclerostin, RANKL/OPG Ratio, and Physical Activity.

BACKGROUND: MiR-21 is known to play a role in osteoclast proliferation and differentiation, but the role of serum miR-21 expression in osteoporosis remains unclear. Previous research found that serum miR-21 expression was positively correlated with bone mineral density in postmenopausal osteoporosis patients, but other factors involved in postmenopausal osteoporosis still unknown. This study aimed to determine the role of serum miR-21 expression, concentration of RANKL, OPG, TGF-ß1, sclerostin and serum calcium, RANKL/OPG ratio, and physical activity on bone mineral density of spine in hypoestrogenic postmenopausal women with osteoporosis (PMOP) compared with no osteoporosis (PMNOP), with point of interest on the expression of serum miR-21. METHODS: this study was conducted by comparative cross-sectional design. The subjects were divided into 2 groups of PMOP and PMNOP. We used an absolute quantification real-time PCR method to determine serum miR-21 expressions level. RESULTS: Median of serum miR-21 expression at the PMOP group was significantly higher compared to PMNOP group (p = 0.001). Serum miR-21 expression, RANKL, RANKL/OPG ratio, and physical activity were significantly correlated with BMD values in the PMOP group. Moderate physical activity was significantly negatively correlated with serum miR-21 expression. We also obtained a linear regression equation BMD = 1.373-0.085*Ln.miR-21-0.176*Log10.RANKL (R2 = 52.5%). CONCLUSION: serum miR-21 expression in PMOP was higher compared with PMNOP. Serum miR-21 expression proved to have a negative effect on spinal BMD values in hypoestrogenic postmenopausal women with osteoporosis of 8.5%. Obtained equation of BMD = 1.373-0.085*Ln.miR-21-0.176*Log10.RANKL can explain the value of spinal BMD by 52.5%.

Transcription factor 7-like 2 single nucleotide polymorphisms are associated with lipid profile in the Balinese.

Transcription factor 7-like 2 (TCF7L2) protein plays an important role in glucose and lipid metabolisms. Single nucleotide polymorphisms (SNPs) in the TCF7L2 gene contribute to increased fasting plasma glucose (FPG) and body mass index (BMI), and altered lipid concentrations in various population. We investigated whether the TCF7L2 SNPs were associated with obesity, high FPG and altered lipid profile in the Balinese. A total of 608 Balinese from rural and urban Bali, Indonesia, were recruited. Triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC) and FPG were measured, and BMI was calculated. Ratios of TG/HDL-C, LDL-C/HDL-C, and TC/HDL-C were determined. Genotyping of SNPs rs7903146, rs10885406, and rs12255372 were done in all samples. Genetic association analyses under a dominant model showed that the rs7903146 (OR 5.50, 95% CI 2.34-12.91, p = 8.5 × 10-5), rs12255372 (OR 4.15, 95% CI 1.66-10.33, p = 0.003) and rs10885406 (OR 2.43, 95% CI 1.39-4.25, p = 0.003) were significantly associated with high TC/HDL-C ratio. The rs10885406 also presented a significant association with high TG (OR 2.21, 95% CI 1.29-3.81, p = 0.004) and low HDL-C (OR 3.02, 95% CI 1.58-5.80, p = 0.001) concentrations, as well as high TG/HDL-C ratio (OR 1.95, 95% CI 1.16-3.27, p = 0.013). None of the SNPs exhibited significant association with obesity or high FPG. SNPs in the TCF7L2 gene are associated with altered lipid profile in the Balinese.

Higher peripheral blood mitochondrial DNA copy number and relative telomere length in under 48 years Indonesian breast cancer patients.

OBJECTIVE: Breast cancer is the leading cause of cancer incidence and mortality among Indonesian women. A comprehensive investigation is required to enhance the early detection of this disease. Mitochondrial DNA copy number (mtDNA-CN) and relative telomere length (RTL) have been proposed as potential biomarkers for several cancer risks, as they are linked through oxidative stress mechanisms. We conducted a case-control study to examine peripheral blood mtDNA-CN and RTL patterns in Indonesian breast cancer patients (n = 175) and healthy individuals (n = 181). The relative ratios of mtDNA-CN and RTL were determined using quantitative real-time PCR (qPCR). RESULTS: Median values of mtDNA-CN and RTL were 1.62 and 0.70 in healthy subjects and 1.79 and 0.73 in breast cancer patients, respectively. We found a positive association between peripheral blood mtDNA-CN and RTL (p < 0.001). In under 48 years old breast cancer patients, higher peripheral blood mtDNA-CN (mtDNA-CN ≥ 1.73 (median), p = 0.009) and RTL (continuous variable, p = 0.010) were observed, compared to the corresponding healthy subjects. We also found a significantly higher 'High-High' pattern of mtDNA-CN and RTL in breast cancer patients under 48 years old (p = 0.011). Our findings suggest that peripheral blood mtDNA-CN and RTL could serve as additional minimally invasive biomarkers for breast cancer risk evaluation.

Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia.

The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 SARS-CoV-2 isolates collected from selected regions of Indonesia between January and October 2021 was performed to identify the distribution of SARS-CoV-2 variants and common mutations in Indonesia. During January-April 2021, Indonesian lineages B.1.466.2 and B.1.470 dominated, but from May 2021, Delta's AY.23 lineage outcompeted them. An analysis of 7515 published sequences from January 2021 to June 2022 revealed a decline in Delta in November 2021, followed by the emergence of Omicron variants in December 2021. We identified C241T (5'UTR), P314L (NSP12b), F106F (NSP3), and D614G (Spike) mutations in all sequences. The other common substitutions included P681R (76.4%) and T478K (60%) in Spike, D377Y in Nucleocapsid (61%), and I82T in Membrane (60%) proteins. Breakthrough infection and prolonged viral shedding cases were associated with Delta variants carrying the Spike T19R, G142D, L452R, T478K, D614G, P681R, D950N, and V1264L mutations. The dynamic of SARS-CoV-2 variants in Indonesia highlights the importance of continuous genomic surveillance in monitoring and identifying potential strains leading to disease outbreaks.

The determinants of thyroid function among vegetable farmers with primary exposure to chlorpyrifos: A cross-sectional study in Central Java, Indonesia.

Objectives: Occupational pesticide exposure, chlorpyrifos (CPF) in particular, may adversely affect the thyroid. The purpose of this study was to evaluate the determinants of thyroid function as indicated by the serum concentration of thyroid-stimulating hormone (TSH) among Indonesian vegetable farmers with primary exposure to CPF. Methods: A total of 151 vegetable farmers participated in this study. The sociodemographic and occupational characteristics of the participants were obtained using a structured interviewer-administered questionnaire. A validated quantitative method was used to estimate the cumulative exposure level (CEL). Serum TSH, thyroglobulin (Tg), free thyroxine (FT4), and urinary iodine excretion (UIE) were measured in the laboratory. The difference in TSH concentrations according to CEL and other characteristics were analysed using the Mann-Whitney U test. A multiple linear regression model was used to evaluate the potential determinants of TSH. Results: The mean age was 50 (SD 9.4) years. The median concentrations of TSH, FT4, and Tg/FT4 ratio were 1.46 mIU/L, 1.17 ng/dL, and 6.23 × 102, respectively. We observed that higher TSH concentrations were found among those with a higher Tg/FT4 ratio, were classified as high CEL, and had lower UIE or FT4. Conclusions: Our findings show that Tg/FT4 ratio, CEL, FT4, UIE concentrations, and post-spraying days were determinants of TSH concentrations among farmers with primary exposure to CPF. These results indicate that farmers are exposed to agents with thyroid-disrupting properties, thus supporting previous evidence showing the potential for thyroid disorders in agricultural populations exposed to pesticides.

Significant increase in anti-SARS-CoV-2 antibodies after administration of heterologous mRNA-based vaccine booster in individuals receiving two doses of inactivated COVID-19 vaccine: A single-center study in healthcare workers in Jakarta, Indonesia.

BACKGROUND: Vaccine plays an important role in breaking SARS-CoV-2 transmission and accelerating the path to pandemic recovery. Currently, there is still limited data on heterologous COVID-19 booster vaccination efficacy and effectiveness in Indonesia. METHODS: Antibody response was retrospectively analyzed from 156 serum collected from healthcare workers that have received mRNA-1273 vaccine as the booster against SARS-CoV-2. These individuals had previously received the full two doses of inactivated anti-SARS-CoV-2 vaccine. Serological analysis was performed to measure total antibody, as well as IgA and IgG antibodies specific to spike (S) protein using ECLIA and ELISA methods. RESULTS: A significant increase in total, IgA, and IgG antibody titers was reported in vaccine receiving a third heterologous booster dose of mRNA-based COVID-19 vaccine following two doses of inactivated type. CONCLUSION: The third heterologous booster dose of vaccine may be beneficial to individuals with or without previous history of SARS-CoV-2 infection.

Uncoupling protein 2 gene polymorphisms are associated with obesity.

BACKGROUND: Uncoupling protein 2 (UCP2) gene polymorphisms have been reported as genetic risk factors for obesity and type 2 diabetes mellitus (T2DM). We examined the association of commonly observed UCP2 G(-866)A (rs659366) and Ala55Val (C > T) (rs660339) single nucleotide polymorphisms (SNPs) with obesity, high fasting plasma glucose, and serum lipids in a Balinese population. METHODS: A total of 603 participants (278 urban and 325 rural subjects) were recruited from Bali Island, Indonesia. Fasting plasma glucose (FPG), triglyceride (TG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C) and total cholesterol (TC) were measured. Obesity was determined based on WHO classifications for adult Asians. Participants were genotyped for G(-866)A and Ala55Val polymorphisms of the UCP2 gene. RESULTS: Obesity prevalence was higher in urban subjects (51%) as compared to rural subjects (23%). The genotype, minor allele (MAF), and heterozygosity frequencies were similar between urban and rural subjects for both SNPs. All genotype frequencies were in Hardy-Weinberg equilibrium. A combined analysis of genotypes and environment revealed that the urban subjects carrying the A/A genotype of the G(-866)A SNP have higher BMI than the rural subjects with the same genotype. Since the two SNPs showed strong linkage disequilibrium (D' = 0.946, r2 = 0.657), a haplotype analysis was performed. We found that the AT haplotype was associated with high BMI only when the urban environment was taken into account. CONCLUSIONS: We have demonstrated the importance of environmental settings in studying the influence of the common UCP2 gene polymorphisms in the development of obesity in a Balinese population.

The Role of CYP2B6*6 Gene Polymorphisms in 3,5,6-Trichloro-2-pyridinol Levels as a Biomarker of Chlorpyrifos Toxicity Among Indonesian Farmers.

OBJECTIVES: One of the most widely used pesticides today is chlorpyrifos (CPF). Cytochrome P450 (CYP)2B6, the most prominent catalyst in CPF bioactivation, is highly polymorphic. The objective of our study was to evaluate the role of CYP2B6*6, which contains both 516G>T and 785A>G polymorphisms, in CPF toxicity, as represented by the concentration of 3,5,6-trichloro-2-pyridinol (TCPy), among vegetable farmers in Central Java, Indonesia, where CPF has been commonly used. METHODS: A cross-sectional study was conducted among 132 vegetable farmers. Individual socio-demographic and occupational characteristics, as determinants of TCPy levels, were obtained using a structured interviewer-administered questionnaire and subsequently used to estimate the cumulative exposure level (CEL). TCPy levels were detected with liquid chromatography-mass spectrometry. CYP2B6*6 gene polymorphisms were analyzed using a TaqMan® SNP Genotyping Assay and Sanger sequencing. Linear regression analysis was performed to analyze the association between TCPy, as a biomarker of CPF exposure, and its determinants. RESULTS: The prevalence of CYP2B6*6 polymorphisms was 31% for *1/*1, 51% for *1/*6, and 18% for *6/*6. TCPy concentrations were higher among participants with CYP2B6*1/*1 than among those with *1/*6 or *6/*6 genotypes. CYP2B6*6 gene polymorphisms, smoking, CEL, body mass index, and spraying time were retained in the final linear regression model as determinants of TCPy. CONCLUSIONS: The results suggest that CYP2B6*6 gene polymorphisms may play an important role in influencing susceptibility to CPF exposure. CYP2B6*6 gene polymorphisms together with CEL, smoking habits, body mass index, and spraying time were the determinants of urinary TCPy concentrations, as a biomarker of CPF toxicity.

Transcription factor 7-like 2 single nucleotide polymorphisms rs290487 and rs290481 are associated with dyslipidemia in the Balinese population.

Background: Dyslipidemia is one of the major risks for the development of cardiovascular diseases which has been the leading cause of death in developing countries. Previously, common polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene have been associated with altered lipid profiles. In this study, we investigated the associations of TCF7L2 SNPs, rs290487 and rs290481, with dyslipidemia and altered lipid profile in the Balinese. Methods: A total of 565 subjects from four locations in the Bali Province, Indonesia, were recruited. Serum lipid concentrations (triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC)) were measured using standard protocol. SNP genotyping was done using the amplification refractory system mutation polymerase chain reaction (ARMS-PCR) method. Results: We found the shifted major/minor allele frequencies of both SNPs (0.56 for rs290487 T allele, 0.53 for rs290481 T allele) in the Balinese, as compared to dbSNP. The rs290487 and rs290481 C alleles were significantly associated with dyslipidemia, particularly high TC and high LDL-C. These associations were independent of age, sex, population, obesity, diabetes mellitus, and high TyG index as a proxy for insulin resistance. The haplotype CC also showed similar association with these traits. Our findings indicate that TCF7L2 polymorphisms are associated with dyslipidemia and altered lipid profile in the Balinese.

Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center study.

We determined the prevalence and epidemiological characteristics of COVID-19 in Jakarta and neighboring areas, Indonesia from March 2020 to February 2021, based on nasopharyngeal/oropharyngeal (NP/OP) swab specimens that were tested at the Eijkman Institute for Molecular Biology, Jakarta. NP/OP swab specimens were collected from COVID-19 suspects or individuals in contact tracing programs from primary healthcare centers (PHC) and hospitals. The specimens were screened for the SARS-CoV-2 by qRT-PCR. Demography data and clinical symptoms were collected using national standardized laboratory form. Of 64,364 specimens, 10,130 (15.7%) were confirmed positive for SARS-CoV-2, with the peak prevalence of infection in March 2020 (26.3%) follow by in January 2021 (23.9%) and February 2021 (21.8%). We found that the positivity rate of the specimens from Jakarta, West Java, and Banten was 16.3%, 13.3%, and 16.8%, respectively. Positivity rate was higher in specimens from hospitals (16.9%) than PHC (9.4%). Of the positive specimens, 29.6% were from individuals aged >60 years old, followed by individuals aged 41-60 years old (24.2%). Among symptomatic cases of SARS-CoV-2, the most common symptoms were cough, fever, and a combination of both cough & fever. In conclusion, this study illustrates the prevalence and epidemiological characteristics from one COVID-19 diagnostic center in Jakarta and neighbouring areas in Indonesia.

Genomic profiles of Indonesian colorectal cancer patients.

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.

Deep ancestry of collapsing networks of nomadic hunter-gatherers in Borneo.

Theories of early cooperation in human society often draw from a small sample of ethnographic studies of surviving populations of hunter-gatherers, most of which are now sedentary. Borneo hunter-gatherers (Punan, Penan) have seldom figured in comparative research because of a decades-old controversy about whether they are the descendants of farmers who adopted a hunting and gathering way of life. In 2018 we began an ethnographic study of a group of still-nomadic hunter-gatherers who call themselves Punan Batu (Cave Punan). Our genetic analysis clearly indicates that they are very unlikely to be the descendants of neighbouring agriculturalists. They also preserve a song language that is unrelated to other languages of Borneo. Dispersed travelling groups of Punan Batu with fluid membership use message sticks to stay in contact, co-operate and share resources as they journey between rock shelters and forest camps. Message sticks were once widespread among nomadic Punan in Borneo, but have largely disappeared in sedentary Punan villages. Thus the small community of Punan Batu offers a rare glimpse of a hunting and gathering way of life that was once widespread in the forests of Borneo, where prosocial behaviour extended beyond the face-to-face community, facilitating successful collective adaptation to the diverse resources of Borneo's forests.