Actinomycetes of secondary metabolite producers from mangrove sediments, Central Java, Indonesia.
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ABSTRACT:
SUBMITTER: Setyati WA
PROVIDER: S-EPMC8654771 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background: This study aimed to investigate the abundance of microplastics in the eastern water of Java Sea. The study areas are well known for the high population and high industrial activities that can contribute to the plastic pollution. Methods: Microplastics were sampled from the surface sediments at five different stations representing different local activities: fish landing area (St 1), mangrove forest (St 2), abandoned shrimp pond (St 3), river mouth (St 4) and open sea (St 5). Results: Three types of microplastics were found; the most common was plastic fragments (54.34±6.39%) followed by fibers (41.45±4.59%) and films (4.21±3.90%). The highest abundance of microplastics was observed in the mangrove area (896.96±160.28 particles/kg), dominated with fragments and fibers. Films were found in greatest quantities in the fish landing area, but compared to the other types of microplastics, the abundance was much lower (80.73±37.62 particles/kg). Domestic wastes and fisheries activities were the main causes of the high microplastics in the study areas. Conclusions: The results of this study showed that microplastic pollution is a serious problem that needs to be paid attention not only from the government but also from the local people. Plastics management waste is needed.
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Project description:Soil-transmitted helminth (STH) infections are endemic in Indonesia. However, prevalence data for many parts of the country are incomplete. The aim of this study was to determine human STH prevalence and knowledge and practices relating to STH risk behaviour, to provide a current view of the status of STH infection in rural communities in Central Java. A cross-sectional survey of 16 villages was conducted in Semarang, Central Java in 2015. Demographic and household data together with information about knowledge and practices relating to STH and hygiene were elicited through face-to-face interviews. Stool samples were collected and examined using the flotation method. Children (aged 2-12 years) also had their haemoglobin (Hb) levels, height and weight data collected, and BMI estimated. Data were analysed using univariate logistic regression analysis. A total of 6,466 individuals with a mean age of 33.5 years (range: 2-93) from 2,195 households were interviewed. The overall prevalence of STH was 33.8% with Ascaris lumbricoides (roundworm) the predominant nematode identified (prevalence = 26.0%). Hookworm and Trichuris trichiura (whipworm) were found in 7.9% and 1.8% of participants, respectively. Females were at increased odds of infection with A. lumbricoides (adjusted OR 1.14, 95% CI [1.02-1.29], p = 0.02). Adults in age groups 51-60 and over 60 years had the highest odds of being infected with hookworm (adjusted OR 3.01, 95% CI [1.84-4.91], p<0.001 and adjusted OR 3.79, 95% CI [2.30-6.26], p<0.001, respectively) compared to 6-12 year olds. Farmers also had higher odds of being infected with hookworm (adjusted OR 2.36, 95% CI [1.17-4.76], p = 0.02) compared to other occupation categories. Poverty (OR 2.14, 95% CI [1.77-2.58], p<0.001), overcrowding (OR 1.35, 95% CI [1.27-1.44], p<0.001), goat ownership (OR 1.61, 95% CI [1.10-2.41], p = 0.02) and the presence of dry floor space in the home (OR 0.73, 95% CI [0.58-0.91], p = 0.01) were all household factors significantly associated with an increased odds of infection. Infection with STH was not significantly associated with the gastrointestinal illness (p>0.05), BMI or Hb levels; however, one third of all 2-12 year olds surveyed were found to be anaemic (i.e. Hb concentrations below 110g/l or 115g/l for children under 5 and 5 years or older, respectively), with a greater proportion of school-age children at risk. Knowledge and behaviour related to hygiene and gastrointestinal diseases varied widely and were generally not associated with STH infection. The study revealed that STH infection remains endemic in Central Java despite ongoing deworming programs. Current control efforts would benefit from being re-evaluated to determine a more effective way forward.
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Project description:Microbial secondary metabolites represent a rich source of valuable compounds with a variety of applications in medicine or agriculture. Effective exploitation of this wealth of chemicals requires the functional expression of the respective biosynthetic genes in amenable heterologous hosts. We have previously established the TREX system which facilitates the transfer, integration and expression of biosynthetic gene clusters in various bacterial hosts. Here, we describe the yTREX system, a new tool adapted for one-step yeast recombinational cloning of gene clusters. We show that with yTREX, Pseudomonas putida secondary metabolite production strains can rapidly be constructed by random targeting of chromosomal promoters by Tn5 transposition. Feasibility of this approach was corroborated by prodigiosin production after yTREX cloning, transfer and expression of the respective biosynthesis genes from Serratia marcescens. Furthermore, the applicability of the system for effective pathway rerouting by gene cluster adaptation was demonstrated using the violacein biosynthesis gene cluster from Chromobacterium violaceum, producing pathway metabolites violacein, deoxyviolacein, prodeoxyviolacein, and deoxychromoviridans. Clones producing both prodigiosin and violaceins could be readily identified among clones obtained after random chromosomal integration by their strong color-phenotype. Finally, the addition of a promoter-less reporter gene enabled facile detection also of phenazine-producing clones after transfer of the respective phenazine-1-carboxylic acid biosynthesis genes from Pseudomonas aeruginosa. All compounds accumulated to substantial titers in the mg range. We thus corroborate here the suitability of P. putida for the biosynthesis of diverse natural products, and demonstrate that the yTREX system effectively enables the rapid generation of secondary metabolite producing bacteria by activation of heterologous gene clusters, applicable for natural compound discovery and combinatorial biosynthesis.
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Project description:Here we report associations between secondary metabolite production and phylogenetically distinct but closely related marine actinomycete species belonging to the genus Salinispora. The pattern emerged in a study that included global collection sites, and it indicates that secondary metabolite production can be a species-specific, phenotypic trait associated with broadly distributed bacterial populations. Associations between actinomycete phylotype and chemotype revealed an effective, diversity-based approach to natural product discovery that contradicts the conventional wisdom that secondary metabolite production is strain specific. The structural diversity of the metabolites observed, coupled with gene probing and phylogenetic analyses, implicates lateral gene transfer as a source of the biosynthetic genes responsible for compound production. These results conform to a model of selection-driven pathway fixation occurring subsequent to gene acquisition and provide a rare example in which demonstrable physiological traits have been correlated to the fine-scale phylogenetic architecture of an environmental bacterial community.
| S-EPMC1828645 | biostudies-literature
Project description:Microbial secondary metabolites are a potent source of antibiotics and other pharmaceuticals. Genome mining of their biosynthetic gene clusters has become a key method to accelerate their identification and characterization. In 2011, we developed antiSMASH, a web-based analysis platform that automates this process. Here, we present the highly improved antiSMASH 2.0 release, available at http://antismash.secondarymetabolites.org/. For the new version, antiSMASH was entirely re-designed using a plug-and-play concept that allows easy integration of novel predictor or output modules. antiSMASH 2.0 now supports input of multiple related sequences simultaneously (multi-FASTA/GenBank/EMBL), which allows the analysis of draft genomes comprising multiple contigs. Moreover, direct analysis of protein sequences is now possible. antiSMASH 2.0 has also been equipped with the capacity to detect additional classes of secondary metabolites, including oligosaccharide antibiotics, phenazines, thiopeptides, homo-serine lactones, phosphonates and furans. The algorithm for predicting the core structure of the cluster end product is now also covering lantipeptides, in addition to polyketides and non-ribosomal peptides. The antiSMASH ClusterBlast functionality has been extended to identify sub-clusters involved in the biosynthesis of specific chemical building blocks. The new features currently make antiSMASH 2.0 the most comprehensive resource for identifying and analyzing novel secondary metabolite biosynthetic pathways in microorganisms.
| S-EPMC3692088 | biostudies-literature
Project description:Maternal health remains a persisting public health challenge in Indonesia. Postnatal complications, in particular, are considered as maternal health problems priority that should be addressed. Conducting adequate care for postnatal complications will improve the quality of life of mothers and babies. With the universal health coverage implementation, the Indonesian government provides free maternal and child health services close to clients at the village level, which include postnatal care. Our study aimed to explore barriers to utilization of postnatal care at the village level in Klaten district, Central Java Province, Indonesia.A qualitative study was conducted in March 2015 - June 2016 in Klaten district, Central Java, Indonesia. We selected a total of 19 study participants, including eight mothers with postnatal complications, six family members, and five village midwives for in-depth interviews. We conducted a content analysis technique on verbatim transcripts of the interviews using open code software.This study found three categories of barriers to postnatal care utilization in villages: mother and family members' health literacy on postnatal care, sociocultural beliefs and practices, and health service responses. Most mothers did not have adequate knowledge and skills regarding postnatal care that reflected how they lacked awareness and practice of postnatal care. Inter-generational norms and myths hindered mothers from utilizing postnatal care and from having adequate nutritional intake during the postnatal period. Mothers and family members conducted unsafe self-treatment to address perceived minor postnatal complication. Furthermore, social power from extended family influenced the postnatal care health literacy for mother and family members. Postnatal care in the village lacked patient-centered care practices. Additionally, midwives' workloads and capacities to conduct postnatal information, education and counseling were also issues.Despite the government's efforts to provide free postnatal care closer to mothers' homes, other barriers to postnatal care utilization remained. Specifically, among mothers, community, and health services. An innovative approach to increase the health literacy on postnatal care is required. In particular, improving the capacity of midwives to conduct patient-centered care. In addition, village midwives' tasks should be evaluated and reoriented.
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Project description:This study aims to develop a software framework for predicting aridity using vegetation indices (VI) from LANDSAT 8 OLI images. VI data are predicted using machine learning (ml): Random Forest (RF) and Correlation and Regression Trees (CART). Comparison of prediction using Artificial Neural Network (ANN), Support Vector Machine (SVM), k-nearest neighbors (k-nn) and Multivariate Adaptive Regression Spline (MARS). Prediction results are interpolated using Inverse Distance Weight (IDW). This study was conducted in stages: (1) Image preprocessing; (2) calculating numerical data extracted from the LANDSAT band imagery using vegetation indices; (3) analyzing correlation coefficients between VI; (4) prediction using RF and CART; (5) comparing performances between RF and CART using ANN, SVM, k-nn, and MARS; (6) testing the accuracy of prediction using Mean Square Error (MSE) and Mean Absolute Percentage Error (MAPE); (7) interpolating with IDW. Correlation coefficient of VI data shows a positive correlation, the lowest r (0.07) and the highest r (0.98). The experiments show that the RF and CART algorithms have efficiency and effectivity in determining the aridity areas better than the ANN, SVM, k-nn, and MARS algorithm. RF has a difference between the predicted results and 1.04% survey data MAPE and the smallest value close to zero is 0.05 MSE. CART has a difference between the predicted results and 1.05% survey data MAPE and the smallest value approaching to zero which is 0.05 MSE. The prediction results of VI show that in 2020 most of the study areas were low vegetation areas with the Normalized Difference Vegetation Index (NDVI) < 0.21, had an indication of drought with the Vegetation Health Index (VHI) < 31.10, had a Vegetation Condition Index (VCI) in some areas between 35%-50% (moderate drought) and < 35% (high drought). The Burn Area Index (dBAI) values are between -3, 971 and -2,376 that show the areas have a low fire risk, and index values are between -0, 208 and -0,412 that show the areas are starting vegetation growth. The result of this study shows that the machine learning algorithms is an accurate and stable algorithm in predicting the risks of drought and land fire based on the VI data extracted from the LANDSAT 8 OLL imagery. The VI data contain the record of vegetation condition and its environment, including humidity, temperatures, and the environmental vegetation health.
| S-EPMC8157165 | biostudies-literature
Project description:Since 2005, over 30 epidemiological studies have evaluated the association between nitrate in drinking water and adverse health outcomes. Conditions that lead to nitrate pollution in water, such as open defecation, the proximity of septic tanks to water sources, and the use of inorganic fertilizer, are rampant in Indonesia, which has experienced little research evaluating nitrate in drinking water. We conducted a health risk assessment for exposure to nitrate in drinking water and evaluated the nitrate concentration in key water sources in two villages of rural Central Java, Indonesia. The nitrate concentrations in the drinking water ranged from 3.55 mg/L to 26.75 mg/L as NO3-. Daily nitrate intake estimates, calculated at 50% and 95% exposure to the maximum nitrate concentration of the drinking water in both villages, were above the levels associated with birth defects, colorectal cancer, and thyroid conditions observed in other studies. There was a large variation in nitrate concentrations between and within the villages at different water sources. Further research into whether these health outcomes exist in rural Central Java, Indonesia will be required to better understand this risk.
| S-EPMC7957596 | biostudies-literature
Project description:Mangroves are intertidal extreme environments with rich microbial communities. Actinobacteria are well known for producing antibiotics. The search for biosynthetic potential of Actinobacteria from mangrove environments could provide more possibilities for useful secondary metabolites. In this study, whole genome sequencing and MS/MS analysis were used to explore the secondary metabolite production potential of one actinobacterial strain of Streptomyces olivaceus sp., isolated from a mangrove in Macau, China. The results showed that a total of 105 gene clusters were found in the genome of S. olivaceus sp., and 53 known secondary metabolites, including bioactive compounds, peptides, and other products, were predicted by genome mining. There were 28 secondary metabolites classified as antibiotics, which were not previously known from S. olivaceus. ISP medium 2 was then used to ferment the S. olivaceus sp. to determine which predicted secondary metabolite could be truly produced. The chemical analysis revealed that ectoine, melanin, and the antibiotic of validamycin A could be observed in the fermentation broth. This was the first observation that these three compounds can be produced by a strain of S. olivaceus. Therefore, it can be concluded that Actinobacteria isolated from the mangrove environment have unknown potential to produce bioactive secondary metabolites.
| S-EPMC8228178 | biostudies-literature
Project description:BackgroundIn Indonesia, the burden of severe hyperbilirubinemia is higher compared to other countries. Whether this is related to ineffective phototherapy (PT) is unknown. The aim of this study is to investigate the performance of phototherapy devices in hospitals on Java, Indonesia.MethodsIn 17 hospitals we measured 77 combinations of 20 different phototherapy devices, with and without curtains drawn around the incubator/crib. With a model to mimic the silhouette of an infant, we measured the irradiance levels with an Ohmeda BiliBlanket Meter II, recorded the distance between device and model, and compared these to manufacturers' specifications.ResultsIn nine hospitals the irradiance levels were less than required for standard PT: < 10 μW/cm2/nm and in eight hospitals irradiance failed to reach the levels for intensive phototherapy: 30 μW/cm2/nm. Three hospitals provided very high irradiance levels: > 50 μW/cm2/nm. Half of the distances between device and model were greater than recommended. Distance was inversely correlated with irradiance levels (R2 = 0.1838; P < 0.05). The effect of curtains on irradiance levels was highly variable, ranging from - 6.15 to + 15.4 μW/cm2/nm, with a mean difference (SD) of 1.82 (3.81) μW/cm2/nm (P = 0.486).ConclusionsIn half of the hospitals that we studied on Java the levels of irradiance are too low and, in some cases, too high. Given the risks of insufficient phototherapy or adverse effects, we recommend that manufacturers provide radiometers so hospitals can optimize the performance of their phototherapy devices.
| S-EPMC6555918 | biostudies-literature