Annales Bogorienses

1-16

Authors: Anggia Prasetyoputri, Wien Kusharyoto

Control and eradication of a number of infectious diseases are primarily attributed to effective vaccination programs. A concerted effort is still imperative to develop novel vaccines and improve the immunogenicity of existing ones with regards to efficacy, immunogenicity and safety. Rational design of vaccines using subunit vaccines is a potentially safer alternative to conventional vaccines, yet they are poorly immunogenic without additional adjuvant. Using antigen carriers to enhance their immunogenicity in the forms of adsorption or encapsulation with a delivery system has been widely investigated as an alternative to currently available adjuvants. This review aims to elaborate on the existing nanotechnology being used to develop more immunogenic subunit vaccines, with focus on particulate delivery systems for development of prophylactic vaccine candidates.

27-33

Authors: Akhirta Atikana, Mohamad Azrul Naim, Detmer Sipkema

Sponges are sources of various useful natural products. The natural compounds derived from sponges are mostly complex polyketide. The polyketide synthase genes (PKS) is responsible for the biosynthesis of complex polyketides. During this research, we detected ketosynthase (KS) gene domain from 10 species of marine sponges, collected from Mediterranean Sea (Aplysina aerophoba, Petrocia ficiformis, Axinella damicornis, Axinella veronicas, Crambe crambe) and North Sea (Halichondria panicea, Haliclona xena, Haliclona oculata, Suberites massa, Ephydatia fluviatilis). We also detected KS gene domain from 12 bacterial sponge isolated from H. panacea. We used a PCR-based approach to detect the ketosynthase (KS) gene domain of Polyketosynthase (PKS) genes. Our result showed that the sponges and the bacterial sponges are mostly KS-positive (700 bp). The presence of the PKS gene indicates the ability of the sponges to produce bioactive compound and potential natural product. The presence of the KS domain in both of the sponges and the bacterial sponges might also indicate that the bacterial sponges involved in the biosintesis of secondary metabolite of the sponges

43-53

Authors: Dwi Susilaningsih, Fumiyoshi Okazaki, Yopi Yopi, Yantyati Widyastuti, Shigeaki Harayama

Page Header OPEN ACCESS POLICY Annales Bogorienses is Open Acces Journal for public. Feel free for viewing, downloading and contributing articles (free of charges). For more informations do not hesitate to contact us or click the page. Creative Commons License This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. Information For Readers For Authors For Librarians Current Issue Atom logo RSS2 logo RSS1 logo Notifications View Subscribe User Username Password Remember me Home About Login Register Search Current Archives Announcements Editorial Board Peer Reviewer Home > Vol 17, No 2 (2013) > Susilaningsih Isolation and Screening of Surfactant-producing Bacteria from Indonesian Marine Environments and Its Application on Bioremediation Dwi Susilaningsih, Fumiyoshi Okazaki, Yopi Yopi, Yantyati Widyastuti, Shigeaki Harayama Abstract Isolation and screening have been undertaken on oil-degrading microbes from Indonesian marine environments. During screening process it has been found many bacterial isolates capable of degrading crude oil. Hence, study has been focused on the biodiversity of biosurfactant-producing bacterial species in Indonesian marine environment and its function for remedial the pollutant in marine and soil areas. A total of 103 out of 463 isolates showed positive surfactant-degrading properties. By means of partial 16S rRNA gene analyses, it has been found that the majority of taxa are related to Alcanivorax, Pseudomonas, Bacillus, Bortetela, Brucella, Acenitobacter, Staphia, Lysobacter, and Talasosophira. Biosurfactant properties assay showed that they were capable of lowering the surface- and interfacial water tension from 74 mN/m to 40-65 mN/m and from 24 mN/m to 6-10 mN/m, respectively. In addition, most of the surfactants were capable of emulsifying hydrocarbon (crude oil) of 0.01 to 0.15 units, comparable to 0.08 units of synthetic surfactant (20% Tween). Further observation showed that the majority of the surfactants were able to degrade a long chain of alkane, but not branched alkane, with a recovering rate of 20-80%. The application of the surfactant towards oil polluted model beach was done in laboratory scale and showing the surfactant obtained from microbial broth cultures capable for recovering the oil pollutant significantly, compared to the control (without addition microbial broth).

1-6

Authors: Tjandra Chrismadha, Rizky Agus Waluya

A blue green alga Spirulina fusiformis was grown under various light regimes in a laboratory scale experiment. A 500 watt halogen lamp was employed as the light source, while the light variation of 2,000 lux, 4,000 lux, 6,000 lux, 8,000 lux, and 10,000 lux was obtained by placing a series of 2 L experimental bottles at various distance. The growth medium used was modified Zarrouk medium with initial pH of 8.72, and room temperature was 28-30oC. After inoculation the alga was let to grow for 30 days, and observation on the biomass, chlorophyll, crude protein, and phycocyanin content were carried out every 10 days. The algal biomass was determined gravimetrically, the chlorophyll, phycocyanin, and protein content were measured using spectrophotometer after extraction in 90% aceton, pH 7.0 buffered water, and folin-phenol dye binding, respectively. The result shows a remarkable effect of light intensity to the algal biomass as well as the biochemical content. The specific growth rate increased from 0.08 doubling/day at light intensity 2,000 lux to 0.14 doubling/dat at 10,000 lux, which was equivalent to an increase in the biomass productivity of more than 3 times. The highest algal chlorophyll content was observed at light intensity between 4,000-8,000 lux, indicating the optimum light condition at that irradiance range. The protein content was consistently lower with light intensity, from 42.96-52.91% DW at 2,000 lux to 33.71-41.08 % at 10,000 lux. A consistent drop in the protein content also observed with the culture growth phase, from 39.82-52.91% DW in the early growth stage down to 33.71-42.96% at day 30. Light intensity in concomitance with the growth phase remarkably increase the algal phycocyanin content. In the early growth stage the phycocyanin content was ranged from 0.16% DW at 2,000 lux up to 1.229% DW at 10,000 lux, whereas at the end of the experiment the algal phycocyanin content were 1.04% DW and 2.436% DW, at 2,000 lux and 10,000 lux, respectively. It gave a consequence of more than 7 times higher phycocyanin productivity, which was from 0.09 mg/L/day at 2,000 lux to 0.62 mg/L/day at 10,000 lux. This result shows the importance of light factor in producing phycocyanin from the blue green alga Spirulina fusiformis.

1-6

Authors: Dian Andriani, Ira Handayani, Wien Kusharyoto

Transferrin receptor (TfR) levels are elevated in various types of cancer cells and correlate with the aggressive or proliferative ability of tumor cells. Therefore, TfR levels are considered useful as a prognostic tumor marker, and TfR is a potential target for drug delivery in therapy of malignant cells. In such kind of targeted delivery system, antibody fragments are frequently used as targeting moiety. Here, we report the generation of an anti-TfR single-chain antibody variable (scFv). The cDNA encoding the variable of heavy and light chain domains of the scFv antibody fragment was derived from the anti-TfR monoclonal antibody of LUCA31. The gene encoding the anti-TfR scFv fragment was codon, optimized for expression in Escherichia coli, subsequently synthesized, and cloned into the pJExpress-804 Rhamex vector. The expression vector utilizes the E. colirhaB promoter and corresponds to the regulatory genes, and is tightly regulated by the presence of L-L-rhamnose. It is also tightly regulated in the absence of L-L-rhamnose by the addition of D-glucose The His6-tagged anti-TfR scFv fragment was expressed in E. coliNiCo21 and purified by means of immobilized metal chelate affinity chromatography on TALON™ matrix. In SDS-PAGE, a single band corresponding to a molecular mass of approximately 30 kDa was observed whether it corresponded to the predicted molecular mass based on the amino acid sequence.

9-18

Authors: Nina Artanti, Ian James Mcfarlane

Asparagine synthetase (AS) is one of the enzyme involves in ammonium metabolism in plant, it catalyzes the transfer of the amino group of glutamine to aspartate giving asparagine. Asparagine serves as a major nitrogen transport and storage molecule in many higher plants. This research used legume plant Coronilla rostrata callus culture for primary and secondary metabolism study. On primary metabolism, the culture were used to study the phenomenon of asparagine accumulation. Because of the responsiveness of the culture, we investigated the use of this culture for model system to conduct molecular biology study of the nitrogen metabolism. The aim of this study was to isolate...cDNAs enconding Asparagine synthetase from C. rostrata because of the asparagine accumulate in this culture. Several PCR based approaches were conducted such as RT-PCR, LM-PCR and RACE. Using these methods, two AS cDNAs was isolated from C. rostrata. AS1 (GenBank no AY081945) which a complete cDNA sequence and AS2 which a partial cDNA sequence. (GenBank no AF488726). These two cDNAs had high homology with the legume AS.

19-25

Authors: Amy Estiati, Yuli Sulistyowati, Fatimah Zahra, Ade Nena Nurhasanah, Syamsidah Rahmawati, Inez H S-Loedin

Transgenic rice plants harboring resistant gene to yellow stem borer, cry1B gene had been obtained. However, the cry1B gene in second generation of transgenic rice lines still segregating following Mendelian ratio 3:1. For further use in the breeding programs, it is important to ensure that the gene is dominant gene and the plants are homozygous for cry1B gene. Selection of homozygous transgenic rice lines containing cry1B gene at third, fourth and fifth generation had been conducted by PCR. The presence of cry1B gene was determined by showing the PCR product of 1.9 kb. Segregation analysis proved that six transgenic rice lines i.e. 3R7.8.15.1, 3R7.8.15.9, 3R7.8.15.10, 3R7.8.15.15, 3R7.8.15.21, 3R7.8.15.29 are homozygous lines for cry1B gene. Moreover, bioassay studies at vegetative stage on six homozygous transgenic rice lines showed that these transgenic rice lines are potential resistant to yellow stem borer comparing with non-transgenic plants, with the score of 0 (indicated no symptom) for six transgenic lines and score of9 (more than 60% damaged tillers ) for non-transgenic plants. However, to confirm the efficacy of cry 1B gene to yellow stem borer in natural condition, confined field trial in endemic area of yellow stem borer should be conducted.

23-28

Authors: Yuliasri Jamal, Aris Medta Pariwidjayanti, Andria Agusta

Steam distillation of essential oil from fresh leaves of Key Lime (Citrus aurantifolia Swingle) gave 0.4% yellow essential oil with distinctive fragrance. Five out of 40 components of the essential oil were identified as the major components with content above 5%, they were geranial (10.3%), limonene (10.2%), neral (8.94%), caryophyllene (5.72%), and citronellal (5.41%). The essential oil was active against four bacterial test, Bacillus subtilis NBRC 3134, Staphylococcus aureus NBRC 14276, Micrococcus luteus NBRC 14218, and Escherecia coli NBRC 14237. B. Subtilis was the most sensitive bacterium with the widest inhibition area at 50% concentration of essential oil. Minimum Inhibition Concentration (MIC) value of essential oil against B. Subtilis was 0.125%

1-8

Authors: Witjaksono Witjaksono, Aryani Leksonowati

We have developed an effective plant propagation method of “hausa potato‟ through shoot proliferation in vitro, acclimatization in the greenhouse and transplantation of the plantlet on the individual media container for planting material production. The shoot cultures were initiated from shoots that grew from tuber collected from the field, disinfested using standard method and transferred to MS medium with 1 mg/l of BA for shoot proliferation. The proliferating shoots were then subcultured to MS medium with no growth regulators to induce rooting and enlarge the shoot. The plantlets were acclimatized in a plastic box containing medium of a mixture of cocopeat, sands, rice husk charcoal and top soil covered with plastic film to maintain humidity. The plantlets survived at 85% and almost 100% grew into planting materials ready for transplanting in the soil. The planting materials survived in the field and produced tuber normally.

35-40

Authors: Puspita Lisdiyanti, Tomohiko Tamura, Shanti Ratnakomala, Roni Ridwan, Gina Kartina, Yulin Lestari, Ando Katsuhiko, Yantyati Widyastuti

total of 137 strains of Actinomycetes were isolated from 14 soil samples collected in 3 part of Lombok Island, Indonesia using SDS-YE (SY) and Rehydration and Centrifugation (RC) isolation methods and Humic Acic Vitamin (HV) agar as isolation media. All the isolates were identified by morphological characteristic and by analysis of 16S rRNA gene sequence. On the basis of their morphology and 16S rRNA gene sequence, 67% of isolates were belonged to the Streptomyces Group and 33% of isolates were belonged to the Rare-Actinomycetes (Non-Streptomyces) Group. Nine families and 15 genera were found from the samples. It is indicated the richness of actinomycetes in these area. The genus Streptomyces is the most abundant in all soil samples, occupying 67% of all isolates by using SY method; while the genusActinoplanes is mainly found by using RC as isolation method. Two strains belong to the genus Virgisporangium and Catenulispora that showed taxonomic interest need further study for describing as ne species.

1-8

Authors: Dyah Retno Wulandari, Tri Muji Ermayanti

Detection of Potyvirus using Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and Antigen Coated Plate-Enzyme Linked Immunoabsorbent Assay (ACP-ELISA) for Dioscorea alata, D. hispida and D. esculenta was conducted in order to establish in vitro culture of virus-free of these species. Plants were collected from Yogyakarta, Lampung, Pasuruan, Jakarta and Bogor. Total RNA of plants grown in a greenhouse was then isolated according to Simple Direct Tube (SDT) method. Total RNA from symptomatic leaf of Yard Long Bean (Vigna unguiculata) infected with Bean Common Mosaic Potyvirus (BCMV) was used as the positive control treatment. RT-PCR assay with degenerate primers MJ1(F) and MJ2(R) was used to identify the Potyviruses infecting Dioscorea. ACP-ELISA with antibodies specific to group Potyvirus was carried out to detect Potyvirus from leaves samples. The Dioscorea virus-free species was then cultured on modified MS medium. Shoot tips or internodes were used as explants. The results showed that using both RT-PCR and ACP-ELISA, all species tested were free from virus. The growth response of explants on MS medium was varied depending on the plant species and the concentration of BAP. Keywords: Dioscorea spp., Potyvirus, RT-PCR, ACP-ELISA, in vitro shoot multiplication

17-23

Authors: Puspita Lisdiyanti, Yopi Yopi, Tutik Murniasih

Polycyclic Aromatic Hydrocarbons (PAHs) as well as crude oil are widespread environmental pollutants. The contamination of air, soil, freshwater (surface water and groundwater), and marine environments by PAHs as well as crude oil has been reported. Of concern to public health is the fact that many PAHs or their metabolites are mutagenic, carcinogenic, or both. North Java coastal area such as Jakarta Bay is the polluted marine area in Indonesia as a result from anthropogenic wastes and the oil spill. Although evaporation and photo-oxidation play an important role in oil detoxification, ultimate and complete degradation is accomplished mainly by marine micro flora, and being dominant in this function. Certain bacteria are well-known could consume and degrade the PAHs as well as crude oil. Therefore investigating the potential PAH and oil degrading marine bacteria is important. In this study, we collected sample from oil polluted area in Marina Port Ancol, Jakarta Bay and isolated four PAH substrates and Arabian crude oil degrading marine bacteria using enrichment method and direct isolation method. As result, 223 strains could degrade PAHs, among these strains, 94 strains could degrade phenanthrene, 23 strains degrade fluoranthene, 92 strains could degrade dibenzotiophen, 14 strains could degrade phenotiazin and 106 isolates degrade crude oil.

31-36

Authors: Puspita Lisdiyanti, Shanti Ratnakomala, Roni Ridwan, Yantyati Widyastuti, Misa Otoguro, Ando Katsuhiko

A total of 268 strains of Actinomycetes were isolated from soil and leaf-litter samples collected in Jambi (Sumatera) and Cibinong (West Java) using three selective isolation methods. All the isolates were identified by morphological characteristic and by analysis of 16S rDNA sequence. On the basis of their morphology and 16S rDNA sequence, 164 isolates were belonged to the Streptomyces Group and 104 isolates were belonged to the Rare-Actinomycetes (Non-Streptomyces) Group. Furthermore, 40% of isolates in Streptomyces Group and 62% of isolates in Non-Streptomyces Group are supposed to be new taxa. It is indicated the richness of Actinomycetes in these two area. The genus Streptomyces is the most abundant in soil samples, occupying 60- 75% of all isolates; while the genus Actinoplanes is mainly found in leaf-litter samples (70%). The use of selective isolation media is important to elucidate the microbial diversity.