Anja Meryandini

Import and assembly of the α and β-polypeptides of the light-harvesting complex I (B870) in the membrane system of Rhodobacter capsulatus investigated in an in vitro translation system.

Transcripts of the genes pufBA, pufB or pufA from Rhodobacter capsulatus were translated in a cell-free system of R. capsulatus. The incorporation of the nascent polypeptides LHIα and β in various types of membranes and the assembly of the light-harvesting (LH) complex I (B870) were investigated. The highest rate of stable incorporation of LHIα and β into the membrane was observed with membranes from the wild type strain grown under chemotrophic conditions. Addition of membranes from cells defective in biosynthesis of pigment-binding proteins resulted in a less efficient or less stable incorporation of LHIαβ. The single polypeptides LHIα or β were synthesized and inserted into the membrane but were extractable to a higher percentage by 6 M urea than the pairwise inserted LHI polypeptides.If the ribosomes and the S135 extract were depleted of DnaK the rate of synthesis of both polypeptides, LHIα and β, was strongly reduced. Removal of GroEL from the cell-free system did not impair the synthesis and membrane association of both proteins, but affected the stable insertion. A high percentage of the LHIαβ polypeptides became extractable by 6 M urea if the cell-free system was depleted of GroEL. Addition of GroEL to the cell-free system restored the capacity of stable insertion of both proteins into the membrane. GroEL interacted with LHIα and β before membrane targeting as shown by immunological means.A protein fraction, which can be removed from the membrane with a low-salt buffer, supported the effective and stable incorporation of LHIαβ into the membrane. It is concluded that the assembly of the LHI complex in the membrane system of R. capsulatus is a multistep process guided and supported by polypeptides located in the cytoplasm and in the membrane. In the cell-free in vitro system not only the correct insertion of the LHI polypeptides but also an assembly with bacteriochlorophyll was observed. BChl was synthesized from δ-amino levulinate in the cell free system.

Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia).

Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio, and extractable P content. Archaeal community composition and diversity were correlated to pH value, exchangeable Fe content, water content, and total N. The distribution of bacterial and archaeal taxa involved in biological N cycle indicated functional shifts of the cycle during conversion of rainforest to plantations.

Phosphorylation of the light-harvesting polypeptide LHIα of Rhodobacter capsulatus at serine after membrane insertion under chemotrophic and phototrophic growth conditions

Abstract The kinetics of protein phosphorylation was studied in cells of phototrophic cultures and in dark-grown cells induced to form the photosynthetic apparatus by lowering of the oxygen tension. Cells of Rhodobacter capsulatus grown in a malate medium with 0.2 mM potassium phosphate were shifted to semiaerobic conditions, and 32PO43− or [35S]Met was added 25 min after induction. The label of both radioactive precursors appeared in the membrane fraction about 20 min after addition. The maximum of 32P was found after 1 h of labeling in the α polypeptide of the light-harvesting (LH) complex 1 (13870). The LHIα protein was phosphorylated after insertion into the membrane. Chloramphenicol inhibited the phosphorylation of LHI a but not of phospholipids. The steady-state level of phosphorylation was higher in anaerobic cultures grown at the low light intensity of 2000 lux than in cultures grown at high light intensity of 35000 lux. The phosphate label did not change significantly during a chase with unlabelled phosphate for 2 h. The phosphoamino acids in LHIα were detected with monoclonal antibodies and radioautography of labeled and hydrolyzed LHIα. Serine was shown to be the amino acid with the highest phosphate content; threonine and tyrosine were weakly phosphorylated. From the positions of these three amino acids in LHIα it was concluded that serine-2, which is exposed on the cytoplasmic side of the membrane, is the main phosphorylated amino acid. P-threonine and P-tyrosine are exposed on the periplasmic surface of the membrane.

Characterization of Xylanase Streptomyces spp. SKK1-8

Streptomyces spp. SKK1-8 producing xylanase was isolated from soil sample from Sukabumi West Java. The xylanase have an optimum condition at pH 6 and 50 0 C. Addition of 5 mM Cu 2+ decreased the xylanase activity up to about 77%, whereas not by other cations. The xylanase was stable at 3 0 C for 48 hours, and the enzyme half lifetime was 1 hour 45 minute at 50 0 C. This xylanase showed the highest activity on oatspelt xylan, and their molecular masses were estimated approximately 16.80, 15.21, and 13.86 kDa. HPLC analysis showed that xylosa and arabinosa were the main hydrolytic product of birchwood xylan. Key words: xilanase, Streptomyces spp., characterization, zymogram and SDS-PAGE, stability

How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities

Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.

Karakterisasi Xilanase dari Bakteri Xilanolitik XJ20 asal Tanah Hutan Taman Nasional Bukit Duabelas Jambi Indonesia

Ostrinia furnacalis is a corn stem-borer that develops complete metamorphosis and all stages in life cycle in corn. This research was aimed to examine several biology aspects of O. furnacalis such as life cycle, egg incubaton period, egg fertility, female fecundity, longevity of imago, and copulation time on artificial diet, based on the previous study. The results of the observations showed that the life cycle of artificial-diet-given O. furnacalis was between 27-34 days range. Female fecundity was 16-452 eggs with fertility rate of 61,97% and 3-5 days renge of egg incubation period. Longevity of imago was between 6-11 days range, and the longevity was longer in female compared to the male. The imago of O. furnacalis copulate on 0-3 days after emerge from pupae and the highest number in on the day 1. Copulation time was occurred at 3-8 hour after scotophase commenced and the highest was at third hour. The artificial diet used in this research can be used for O. furnacalis mass rearing purpose and performed shorter length of egg stage until pupal stage compared to mass rearing with natural diet.

KINERJA FERMENTASI SAGU ASAM MENGGUNAKAN STARTER CAIR DAN PADAT DARI ISOLAT BAKTERI ASAM LAKTAT INDIGENOUS

The use of an antimicrobial edible coating is a technique that can be developed and applied to keep the quality and extend the shelf life of products, such as candied cherry tomato. This study purposed to get processing technology candied cherry tomatoes, to formulate edible coating with cinnamon oil as an antimicrobial, and to analyse the effect of edible coating to changes in the quality of candied cherry tomatoes during the storage process. The stages of this research were the production process of candied cherry tomatoes, which consisted of determining treatment cherry tomatoesas a whole and sliced cross, a combination of sugar concentration and immersion time in a sugar solution, and determination of drying time candied cherry tomatoes. The next steps were manufacturing and characterization of antimicrobial edible coating, and then application of antimicrobial edible coating during 12 weeks of storage. Based on the results, the best treatment processing of candied cherry tomatoes was a cherry tomato with an intact form and had 40-55-70% graded sugar concentration during 12 hours immersion time, and at 33 hours drying time. Moreover, resulted fromedible coating formula was tapioca starch, CMC, glycerol, stearic acid and cinnamon oil with percentages of 3.0%, 0.4%, 5.0%, 0.5%, and 0.6%, respectively. During storage, lowest secondary and tertiary bound water capacity on candied cherry tomatoes with an antimicrobial edible coating that was Ms of 25.32%, awsof 0.58 and Mt of 42.11%. Likewise, the lowest rate of microbial growth was from candied cherry tomatoes with an antimicrobial edible coating. Keywords: antimicrobial, bound water capacity, candied cherry tomato, cinnamon oil, edible coatingPartial oxidation pretreatment on sorghum straw using a consortium of microorganisms EM4 was done before used as raw material for production of biogas. Biogas production was performed by co-digestion method using sludge of waste water treatment plant. This research aimed to study the effect of sorghum straw and sludge ratio to the production of biogas by co-digestion method. Partial hydrolysis pretreatment using concentrations of EM4 0.0, 0.1, 0.5, and 1.0%. Pretreatment parameter measured was chemical oxygen demand dissolved (COD). The result of sorghum straw pretreatment was used as raw material for biogas production. Co-digestion method of sorghum straw and sludge was carried out by ratio variation of 80:20, 75:25, 70:30, and 65:35 (w/w). Parameters measured were cumulative biogas production (L/kg VS) and the composition of the biogas (CH4 and CO2). Results of partial oxidation pretreatment showed that the higher concentration of EM4 affected in higher levels of dissolved COD. Biogas production results by this pretreatment showed that the higher concentrations of EM4, the shorter adaptation phase of anaerobic microorganisms and higher production of biogas. The highest biogas production by co-digestion method was 371 L/kgVS, achieved by ratio of sorghum straw to sludge of 75:25 (w/w) in 65 days of fermentation. By using co-digestion method, biogas production increased 245-293%. From the results of this research note that biogas production on a pilot scale 25 L was lower than Erlenmeyer digester 0.5 L.Composition of biogas consisted of CH4 : CO2 76:26 and biogas was flammable. Keywords: sorghum straw, EM4, sludge, co-digestion, biogasCurrent technology for biodiesel production is a transesterification process of vegetable oil with metanol in batch system with the help of catalyst. The technology faces many disadvantageous for large scale, such as the requirement for rigorous stirring and purification of the product from the catalyst. Previous study showed that utilization of static mixing reactor can enhance the reaction rate and reduce the requirement of catalyst and can be operated continuously. The objective of this study was to examine the role of static mixer in reducing the catalyst requirement for the transesterification process of biodiesel production in continuous mode. Palm oleinwas used as feedstock for the transesterification process with 1:6 of mole ratio to metanol at 65oC reaction temperature. Catalyst used for the experiment was KOH with variations of 0.3% and 0.5% to the oil fed into the reactor and the numbers of static mixer modules were varied (1, 2, 3, 4, and 5 modules) to evaluate their effects to the required catalyst. As expected, the experimental results confirmed a higher conversion of the reactionby the increasing number of the static mixer modules at a specific catalyst percentage. Highest conversions obtained with 5 moduleswere 92.5% (w/w) and 88.9% (w/w), for 0.3% and 0.5% of catalyst, respectively. Analysis to the experimental results showed that 0.1% of catalyst could be replaced by the addition of 0.9 modules of static mixer, which was equivalent to 58.1 cm length ofthe used static mixer configuration. Keywords:continuous mode of transesterification, static mixing module, catalyst reduction

Biodegradation of Solid Wastes of Agar Seaweed Processing Industry by Indigenous Cellulolytic Bacillus Pumilus LA4P

Indonesia is known as second seaweed producer in the world after China. Gracilaria sp seaweed is important commodity in industry, as raw material to produce agar and it derivate products. Solid wastes of agar seaweed processing industry contain considerable amounts of cellulose. It can effectively be utilized either as a major source of energy feedstock or as a r aw material for production of high value product. Here, hundreds of cellulolytic bacteria were screened and isolated from solid wastes of agar seaweed processing industry. Among the isolates, LA4P strains showing higher potential for practical uses were purified on solid wastes of agar seaweed processing Industry; (SWA) agar plates and identified as Bacillus pumilus strains by morphological, physiological, and biochemical characterization and 16S rRNA gene analysis. The production patterns of cellulose degrading enzymes were investigated during cell culture. The isolated strains produced CMCase, Avicelase, â-glucosidase, and cellobiase enzymes, which suggested synergic cellulolytic systems in Bacillus pumilus LA4P.