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.

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.

Effects of various culture conditions on lovastatin production were investigated in Aspergillus terreus (KM017963) grown under solid state fermentation with wheat bran. Lovastatin production was influenced by various physical factors such as pH, temperature, and nutritional factors such as carbon, nitrogen, metal ions/salts etc. Our study established that an initial pH of 6.0, growth temperature of 28 °C–30 °C, inoculum size of 108 spores/mL as the optimal physiological culture conditions for maximal production of lovastatin by A. terreus (KM017963). The carbon sources, glucose or dextrin when supplemented at 3% (w/w) enhanced lovastatin production by five fold when supplemented as individual component in wheat bran. Addition of metal salts such as CuSO4 (8%), FeSO4 (8%), CaCl2 (10%), NaCl (6%) and MgSO4 (6%) enhanced the production by five fold. Supplementation with nitrogen sources, amino acids, hydrocarbons, surfactants and amino acids did not have any profound effect on lovastatin production.

Studies about lichens and pollution in South-East Asia are restricted because the lichens are poorly known. A research project about air quality bioindicator using epiphytic macrolichens in Bogor City was conducted from March 2012 until July 2013. Purposive sampling method was applied in 3 plots: plot 1 was in the centre of Bogor Botanical Garden (BBG) that far from busy roads, plot 2 was in a part of BBG adjacent to main and busy roads, and plot 3 was along busy roads and near a factory. In each plot, macrolichens were observed in 8 canary trees using 2 mini quadrats (32 × 20 cm2). The population conditions of epiphytic macrolichens were analyzed and to be used as bioindicator of air quality. Seven genera of macrolichens were found: Coccocarpia, Leptogium, Canoparmelia, Parmotrema, Dirinaria, Physcia, and Pyxine. Plot 1 was having Coccocarpia and Leptogium that were not found in other plots and therefore they can be used as sensitive bioindicators, none of Canoparmelia and Pyxine, a few and infrequent Dirinaria but with larger average coverage (AC = 6.15 cm2), and Physcia was found abundantly (sensitive bioindicator). Conversely, plot 2 and 3 were having none of Coccocarpia and Leptogium, few or many Canoparmelia and Pyxine and therefore appeared to be tolerant, many and frequent Dirinaria but with smaller AC (plot 2 = 2.85 cm2, plot 3 = 1.16 cm2), and few or none of Physcia was found. Being found in all plots, Dirinaria showed a clear pattern of increasing thallus number and decreasing AC from plot 1 to plot 3, so it can be used as tolerant bioindicator. Conversely, Parmotrema had unclear pattern of population condition. Similar researches on different trees are necessary to explore more details regarding epiphytic macrolichens population condition.

Whiteleg shrimp (Litopenaeus vannamei) is one of the most important aquaculture commodity in Indonesia. However, the luminous disease primarily caused by Vibrio harveyi bacteria still becomes an obstacle in penaeid shrimp farming, especially in shrimp hatchery. This study was aimed to identify the presence of V. harveyi in L. vannamei through nested PCR using haemolysin gene primer. First, initial primers were designed using V. harveyi VIB 391 haemolysin gene sequence (accession number: DQ640264), flanking the position 133 to 756. This primer pairs were used to identify haemolysin gene in both V. harveyi MR5339 and V. harveyi 275 strain. Sequencing results from each sample showed 99% similarity with haemolysin gene sequence in Genebank. Furthermore, the sequence of V. harveyi MR5339 haemolysin gene was used to design the nested PCR primers. The first primer pairs of nested PCR have successfully amplified the haemolysin gene fragment of all V. harveyi strains samples from position 52 to 405. The second primer pairs of nested PCR have amplified position 204 to 405 where it can detect all of V. harveyi strains used as sample sources in this study. The application of nested PCR technique in this study was able to identify V. harveyi strains at serial dilution of cells density as low as 100 cfu/mL, which is equal to a single cell or at DNA concentration up to 101 fg/µL.

Mount Halimun Salak National Park is one of the tropical forest remnants in Java island. The national park has been recognized with high diversity of wild Zingiberaceae. Of that Zingiberaceae, two species namely Alpinia malaccensis (AM) and Horstendia conica (HC), were domesticated as garden plants in the surrounding area of the forest for medicinal use. The impact of domestication on the fungal endophytes associated with these two species of Zingiberaceae is reported here. Fungal endophyte diversity in the wild and domesticated AM and HC was analyzed based on the culturable fungi. Identification of species level used morphological and molecular approaches of ITS rDNA sequence. This study determined 19 species of fungal endophytes, namely Arthrinium malaysianum, Aspergillus flavipes, As. sydowii, Chaetomium globosum, Cladosporium oxysporum, Cladosporium sp., Colletotrichum boninense-complex, Co. cliviae-complex, Co. gloeosporioides-complex, Diaporthe sp., D. anacardii, D. gardenia, Exophiala sp., E. lecanii-corni, Guignardia mangiferae, Ochroconis gallopava, Penicillium citrinum, Pyricularia costina, and unsporulated Sydowiellaceae. Among them, A. malaysianum, C. globosum, Co. cliviae-complex, D. gardenia, and unsporulated Sydowiellaceae were only found in domesticated plants, while some others were absent. Colletotrichum boninense-complex was commonly found in both wild and domesticated plants. Domestication activity affected the diversity of endophytic fungi of AM and HC.

A community of thermophiles within Tanjung Sakti Hot Spring (South Sumatera) have been cultivated and identified based on 16S ribosomal RNA gene sequence. The hot spring has temperature 80 °C–91 °C and pH 7–8. We used a simple method for culturing the microbes, by enriching the spring water with nutrient broth media. Phylogenetic analysis showed that the method could recover microbes, which clustered within four distinct taxonomic groups: Anoxybacillus, Geobacillus, Brevibacillus, and Bacillus. These microbes closely related to Anoxybacillus rupiensis, Anoxybacillus flavithermus, Geobacillus pallidus, Brevibacillus thermoruber, Bacillus licheniformis, and Bacillus thermoamylovorans. The 16S ribosomal RNA gene sequence of one isolate only had 96% similarity with Brevibacillus sequence in GenBank.

Mitochondria of Paramecium caudatum stock GT704 has a set of four kinds of linear plasmids with sizes of 8.2, 4.1, 2.8 and 1.4 kb. The plasmids of 8.2 and 2.8 kb exist as dimers consisting of 4.1- and 1.4-kb monomers, respectively. The plasmid 2.8 kb, designated as pGT704-2.8, contains an open reading frame encodes for putative DNA-dependent RNA polymerase (RNAP). This study reveals that this RNAP belongs to superfamily of DNA/RNA polymerase and family of T7/T3 single chain RNA polymerase and those of mitochondrial plasmid of fungi belonging to Basidiomycota and Ascomycota. It is suggested that RNAP of pGT704-2.8 can perform transcription without transcription factor as promoter recognition. Given that only two motifs were found, it could not be ascertained whether this RNAP has a full function independently or integrated with mtDNA in carrying out its function.

Inhibition of α-glucosidase and hypoglycemic activity are two effects commonly used to identify bioactive compounds with potential to treat diabetes. The objectives of this study were to analyse and compare the bioactive compounds and α-glucosidase inhibitory effect of four different types of Swietenia mahagoni seed extract, and to analyse the hypoglycemic activity of the greatest inhibition of α-glucosidase-extract in rats. The extracts were obtained using two different solvents (aqueous and ethanol) and two different methods: maceration and reflux methods. This resulted in four types of extract varying by solvent and extraction method. Testing of these extracts for α-glucosidase inhibitory effect was carried out in vitro using spectrophotometer. Testing for hypoglycemic activity was carried out in vivo using rats. A total of 40 male Sprague-Dawley rats were divided into eight groups: (1) the negative control group, received an oral dose of aquadest only, (2) the positive control group, was given 90% sucrose orally without S. mahagoni seed extract, and five treated groups (3-7), were given 90% sucrose followed by the best extract-ethanolic S. mahagoni seed extract in doses of 100, 200, 300, 400, and 500 mg/kgBW, and (8) the acarbose group, was given 90% sucrose orally followed by acarbose. Glucose levels in each animal were measured at 0, 30, 60, 90, and 120 min after treatment. The results showed the greatest inhibition of α-glucosidase in ethanolic extract, using maceration methods. This ethanolic-maceration S. mahagoni seed extract also showed hypoglycemic effects in hyperglycemic rats at dose from 100 to 500 mg/kgBW. Ethanolic extract of S. mahagoni seed, using maceration method, can be proposed as potential antidiabetic agent.

Lignocellulose waste in nature is increasing due to the increasing activity of agroforestry. Up to 40% of lignocellulose biomass are consisted of xylan. Xylan complete breakdown requires the action of xylanase. Xylanase has been used to breakdown xylan into commercial product such as low calories sugar, prebiotic, and biofuel. Due to its wide application, several variation of xylanase characterization are needed. Our previous studies have collected Paenibacillus sp. XJ18 from TNBD forest, Jambi, Indonesia, to gain a unique enzyme characteristic. In this study the characteristic of crude xylanase from Paenibacillus sp. XJ18 was investigated. The highest activity of xylanase production was at 36 h. The xylanase showed activity in a broad range of pH (4.5-9.0). The highest activity showed at pH 5.0, 90 °C. Crude enzyme extract was unstable and had halftime at its pH and optimum temperature about 67 min. The xylanase activity was increased about 4.59 times after being concentrated by 70% acetone (2.4578 U/mL). Based on TLC result, xylanase from Paenibacillus sp. XJ18 was predicted to produce xylobiose exclusively from extracted corncob xylan.