Microorganisms were isolated from soil taken from Tangkuban Perahu mountain. Five strains were investigated in this study, designated TP1, TP2, TP3, TP4, and TP5, respectively. Morphological, biochemical and molecular identifications were conducted for all five strains. These isolates were shown to be closely related to Nocardia sp. YIM 65630 (90%), Streptomyces galbus (99%), Aspergillus unguis (86%), Paecilomyces marquandii (100%) and Nocardia niigatensis (95%), respectively. Production of antibacterial, antifungal and anticancer metabolites was done by fermentation. Screening for bioactivity of five isolates was done by testing the fermentation broth against resistant and pathogenic bacteria, fungi and T47D breast cancer cell line. TP2 strain showed the best bioactivity; the metabolite was purified by extraction with ethyl acetate. Antibacterial, antifungal and anticancer activities from the ethyl acetate extract of TP2 strain were tested by agar diffusion, microdilution and MTT. The extract was shown to be active against methicillin resistant Staphylococcus, methicillin sensitive Staphylococcus aureus, methicillin resistant coagulase negative Staphylococcus, vancomycin resistant Enterococcus, Escherichia coli, Microsforum gypseum with the minimum inhibitory concentration (μg/mL) and diameter of inhibition (mm): 150, 35; 150, 30; 300, 35; 300, 35; 300, 29; 4.7, 36, respectively. The IC50 value of the T47D cell line was 457 μg/mL.

The hypervariable region I of mitochondrial DNA has frequently been used to distinguish among populations, in particular in species with strong female philopatry. In such cases, populations are expected to diverge rapidly for hypervariable region I markers because of the smaller effective population size and thus increased genetic drift. This rapid divergence leads to the accumulation of mutations exclusively found in one population, which may serve as diagnostic single nucleotide polymorphisms (SNPs). To date, diagnostic SNPs distinctive to Sumatran orangutan populations have not yet been described. However, given the continuously declining numbers of Sumatran orangutans, this information can be vital for effective conservation measures, especially regarding reintroductions of orangutans in rehabilitation centers. Phylogenetic analyses of 54 samples of Sumatran orangutans from nine sampling sites with good provenance, we found five major clades and a total of 20 haplotypes. We propose a total of 52 diagnostic SNPs that are specific to Sumatran orangutan populations. Data can be used to develop restriction fragment length polymorphism assays to carry out genetic assignments using basic laboratory equipment to assign Sumatran orangutan to their population of origin.

Exopolysaccharides (EPSs) produced by lactic acid bacteria have been well known for their important economic value in food, pharmaceutical and health industries. Large extracellular enzyme sucrases are used by lactic acid bacteria to polymerize EPS, i.e. fructansucrase and glucansucrase. This study aimed to characterize sucrase activity of three Weissella confusa strains MBF8-1, MBF8-2 and MBFCNC-2(1), which were isolated previously from local beverages and their EPS products as well. All strains showed ability to form mucoid and slimy colonies by visual inspection on agar plate using raffinose as substrate suggesting that they possessed fructansucrase activity besides glucansucrase. Obtained EPS products were characterized by HPLC analysis after hydrolysis using 3% TCA at 100°C for 1 hour, and by viscosity as well. All strains exhibited similar peak patterns, assuming that all of them possessed fructan EPS product. Supernatant and cell pellet were also analyzed by in situ activity assay performing periodic acid Schiff staining after polyacrylamide gel electrophoresis; only cell pellet showed sucrase activity. Viscosity observation showed that EPS products from all strains were able to increase the viscosity slightly.

The aim of this study was to evaluate the effect of encapsulated synbiotic (Bacillus sp. NP5 and oligosaccharide) dietary at different dosages on growth performance, survival rate, feed conversion ratio, and immune responses of Litopenaeus vannamei against Vibrio infection. The shrimps of the main treatments were fed by the diet that contained three different dosages of encapsulated synbiotic [0.5% (A), 1% (B), and 2% (C) (w/w)] with feeding rate of 5% of shrimp biomass (4 times a day). The shrimps of two control treatments (negative control and positive control) were fed only by commercial feed without supplementation of encapsulated synbiotic. The growth, feed conversion ratio, and survival rate were observed after 30 days of encapsulated synbiotic dietary. The shrimps were then challenged by injection of Vibrio harveyi (6 log colony forming units/mL) 0.1 mL/shrimp, excluded the negative control treatment. Afterward, the survival and immune responses were observed for 9 days after experimental infection. The shrimps treated with 2% encapsulated synbiotic (treatment C) in the diet showed the highest growth performance (2.98 ± 0.42%), feed conversion ratio (1.26 ± 0.19), and better immune responses i.e. total hemocyte counts, differential hemocyte count, phenoloxidase, and intestine bacteria observation compared to those of positive control treatment.

The hypervariable region I of mitochondrial DNA has frequently been used to distinguish among populations, in particular in species with strong female philopatry. In such cases, populations are expected to diverge rapidly for hypervariable region I markers because of the smaller effective population size and thus increased genetic drift. This rapid divergence leads to the accumulation of mutations exclusively found in one population, which may serve as diagnostic single nucleotide polymorphisms (SNPs). To date, diagnostic SNPs distinctive to Sumatran orangutan populations have not yet been described. However, given the continuously declining numbers of Sumatran orangutans, this information can be vital for effective conservation measures, especially regarding reintroductions of orangutans in rehabilitation centers. Phylogenetic analyses of 54 samples of Sumatran orangutans from nine sampling sites with good provenance, we found five major clades and a total of 20 haplotypes. We propose a total of 52 diagnostic SNPs that are specific to Sumatran orangutan populations. Data can be used to develop restriction fragment length polymorphism assays to carry out genetic assignments using basic laboratory equipment to assign Sumatran orangutan to their population of origin.

Tomato is a climacteric fruit, which is characterized by ripening-related increase of respiration and elevated ethylene synthesis. Ethylene is the key hormone in ripening process of climacteric fruits. The objective of this research is to study the expression of three ethylene synthesis genes: LeACO1, LeACS1A, LeACS2, and a housekeeping gene LeGAPDH in ripening tomato fruit. Specific primers have been designed to amplify complementary DNA fragment of LeGAPDH (143 bp), LeACO1 (240 bp), LeACS1A (169 bp), and LeACS2 (148 bp) using polymerase chain reaction. Nucleotide BLAST results of the complementary DNA fragments show high similarity with LeGAPDH (NM_001247874.1), LeACO1 (NM_001247095.1), LeACS1A (NM_001246993.1), LeACS2 (NM_001247249.1), respectively. Expression study showed that LeACO1, LeACS1A, LeACS2, and LeGAPDH genes were expressed in ripening tomato fruit. Isolation methods, reference sequences, and primers used in this study can be used in future experiments to study expression of genes responsible for ethylene synthesis using quantitative polymerase chain reaction and to design better strategy for controlling fruit ripening in agroindustry.

Copra meal contained high polysaccharide mannan. Mannanase Streptomyces sp. BF3.1 efficiently hydrolyzed copra meal to mannooligosaccharides. This research determined the optimum conditions of enzyme mannanase Streptomyces sp. BF3.1 to hydrolyze copra meal. The results of the hydrolysis products were analyzed concentrations of reducing sugars, total sugars and the degree of polymerization. In order to determine the type of product, mannooligosaccharides were analyzed by thin layer chromatography and high performance liquid chromatography. The mannanase had an optimum condition at 70 °C and pH 6. Optimum conditions of hydrolysis was 10% copra meal concentration with incubation time of 5 h at 30 °C which able to produce a variety of mannooligosaccharides products. Under such conditions, the yield of reducing sugar was 3.83 mg/mL with polymerization degree of 4. Analysis of mannooligosaccharides by thin layer chromatography and high performance liquid chromatography revealed mannobiose, mannotriose, mannotetrose, mannopentose, and mannoheksose.

Tempeh is a well-known Indonesian fermented food made from soybean. During the fermentation process, microorganisms play an important role in the flavor, texture, and nutritional quality of tempeh. Tempeh has been show to have immuno-modulatory and immune-stimulating properties that may also be caused by the microorganisms in tempeh as they interact between the microbial population in the intestinal tract. The objective of this study was to quantify IgA gene expression at both the transcription and translation levels in Sprague Dawley (SD) rats supplemented with tempeh. A total of 6 female SD rats were divided into 3 groups of 2 rats. The first group was the control and was fed a standard diet without tempeh. The second- and third group were fed with a standard diet supplemented with raw and cooked tempeh, respectively. Ileum tissue samples were collected after tempeh supplementation for 28 days. RNA was extracted from ileum samples, and measurement of IgA gene expression was further analyzed using semi quantitative real-time PCR. The concentration of IgA protein was quantified from ileum lysate using the half sandwich ELISA method. IgA gene expressions in rats supplemented with raw, and with cooked tempeh, were 1.18 and 1.17 fold higher, respectively, compared to the control group. Moreover, IgA protein secretion levels also increased 2.46 and 2.08 fold, respectively, compared to the control group. The result of this study indicates that both raw and cooked tempeh may stimulate IgA secretion, and also that both viable and non-viable microorganisms might stimulate IgA gene expression.

Plant breeding program consists of establishment of the population, selection, and evaluation. The study aimed to observe the variability of yield components, the heritability, and the distribution of the yield component characters in the F3 populations. The experiment was conducted at Muara Experimental Farm Bogor, from April to August 2012 on Latosol soil. The F3 populations derived from crosses of Bintang Ladang x US2, Gampai x IR77674, and Progol x Asahan and their parental were used as plant materials. Twenty one-day-old seedlings from each population were planted in plots of 2 × 12 m, with planting space of 20 × 20 cm and 3-5 seedlings per hole. Panicle length and weight were observed on 300 randomly selected plant samples from each population. The results showed that there was a variation of agronomic characters among genotypes. The heritability of characters, the panicle length and weight was low to high. Panicle length and weight were controlled by many genes with additive gene action in the Gampai x IR77674 derived population, while panicle weight was controlled by few genes with complementary epistatic additive gene action in both Bintang Ladang x US2 and Progol x Asahan derived populations. The more genes controlling a character, the more distribution classes formed and the greater variance among genotypes.

Daphnia magna is a potential feed for fish. The aim of this research was to find the best treatment and effect of D. magna culture addition from fermented organic fertilizer, to growth and survival rate of Oreochromis niloticus larvae. There were five treatments, each with three repetitions used in the study. All treatments used chicken dung, and different combinations of rice bran, coconut oilcake waste and tilapia larvae. Feeding on tilapia was given by ad libitum method for five times a day until 14 days. Water quality during the research was maintained at temperature 28–29°C, DO 0.3 ppm and pH 8.1–8.2. Observed variables include relative growth rate, survival rate, food consumption rate and water quality. Our results showed that D. magna cultured by fermented organic fertilizer for tilapia larvae (O. niloticus) had high significant effect (p < 0.01) on the relative growth rate and survival rate. Treatment of D. magna cultured by 1.2 g/L chicken manure, 0.9 g/L rice bran and 0.3 g/L coconut oilcake showed the highest value on the relative growth rate (10.86%); survival rate (98.46%) and food consumption at first week (106.43%) and second week (152.76%).