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ANNALES BOGORIENSES

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Published by Lembaga Ilmu Pengetahuan Indonesia

ISSN : 05178452 EISSN : 24077518 DOI : -

Core Subject : Health, Science, Agriculture, Engineering,

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Immunology & microbiology Medicine & Pharmacology

The Annales Bogorienses (ISSN: 0517-8452, E-ISSN: 2407-7518) is a peer-reviewed Journal that is published biannually. First published in 1955, it is now one of the oldest scientific journal in the nation. The Annales Bogorienses publishes original articles in basic and applied research as well as critical reviews and short communication in the fields of life sciences with the emphasis in biotechnology, molecular biology, and biochemistry.

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Articles 540 Documents

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Front Cover AB Vol 9 No 1 (2004) Puspita Lisdiyanti
ANNALES BOGORIENSES Vol 9, No 1 (2004): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2004.v9.n1.%p

Comparison of Gene Expression Between Two Types of Anti-EGFRvIII ScFv Antibodies Having Different Variable Domain Orders in Escherichia coli Kartika Sari Dewi; Asrul Muhamad Fuad
ANNALES BOGORIENSES Vol 21, No 1 (2017): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Several studies reported that the expression of various kinds of Single-chain variable fragment (scFv) antibodies in Escherichia coli are significantly influenced by the order of their variable domains. To date, the effect of the order of variable domains in the expression of scFv antibodies against epidermal growth factor receptor variant III (EGFRvIII) has not been reported. This study aimed to compare the expression between VH-linker-VL and VL-linker-VH domain orders of the anti-EGFRvIII scFv antibodies in E. coli expression system. Recombinant plasmids inserted with DNA encoding scFv proteins were transformed into E. coli NiCo21(DE3) competent cells and characterized by colony PCR. The expression of scFv proteins was done by using optimum concentration of inducer. Total proteins, soluble periplasmic and cytoplasmic proteins, also extracellular proteins were isolated, subsequently characterized by SDS-PAGE, Slot Blot, and ImageJ software analyses. The antigen-binding activity of both scFvs proteins against EGFRvIII was observed. The results showed that the relative percentage of scFv expression with VH-linker-VL domain order is higher than that of VL-linker-VH in each compartment. Moreover, both of scFvs proteins have antigen-binding activity against EGFRvIII.

Improvement of Genetic Transformation Efficiency in Vanda tricolor Orchid Using Acetosyringone Rindang Dwiyani; Azis Purwantoro; Ari Indrianto; Endang Semiarti
ANNALES BOGORIENSES Vol 14, No 2 (2010): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Vanda tricolor Lindl. var. suavis is an Indonesian wild orchid which is now extremely rare in nature due to its habitat destruction. Development of an appropriate method for improving Vanda orchid through genetic modification could be valuable for horticulture and, indirectly, also for conservation. In this research, a method of Agrobacterium-mediated transformation of two Vanda tricolor obtained from Salak Mount, West Java and merapi Mount, Yogyakarta in Indonesia protocorms was improved using acetosyringone (AS). Concentrations of 0 and 25 ppm AS were used in transformation of pG35S binary vector containing kanamycin resistance gene into V. tricolor protocorms. The result showed that 25 ppm AS was required on innoculation with Agrobacterium solution, without AS on cocultivation. Five week s after treatment on the 300 ppm kanamicyncontaining medium, green protocorms were obtained, that was 11.01% for V. tricolor from Salak Mount with pre-culture treatment prior to innoculation, 9.39% for V. tricolor from Merapi Mount with pre-culture treatment prior to innoculation, and 1.37% for V. tricolor from Merapi Mount without pre-culture treatment prior to innoculation. The best condition to set high efficiency of transformation is pre -culture protocorms prior inoculation, soaking protocorm on 25 ppm AS for 30 minutes, then cocultivate its on AS-free callus induction medium Key words: Vanda tricolor, Agrobacterium, orchid protocorms, acetosyringone

Editor's Preface AB Vol 16 No 2 (2012) Puspita Lisdiyanti
ANNALES BOGORIENSES Vol 16, No 2 (2012): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Guide for Authors AB Vol 12 No 1 (2008) Puspita Lisdiyanti
ANNALES BOGORIENSES Vol 12, No 1 (2008): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

DNA Condensation Study of Fully Synthesized Lipopeptide-Based Transfection Agent for Gene Delivery Vehicle Tarwadi Tarwadi; Heni Rachmawati; Rahmana E. Kartasasmita; Sabar Pambudi; Alfan Danny Arbianto; Dewi Esti Restiani; Sukmadjaja Asyarie
ANNALES BOGORIENSES Vol 22, No 2 (2018): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

The main requirement of transfection agent has to condense DNA in nanoparticle size, protect the DNA from nucleases and other degrading enzymes during its transport in cell cytoplasm and nucleus and should not toxic to target cells. In this research, lipopeptide composed of palmitoyl (C-16) and short peptide sequence have been designed fully synthesized and tested to DNA condensation capability and toxicity. The DNA condensation study was performed using EtBr exclusion assay and cytotoxicity determination was carried out by colorimetric MTT assay. It was revealed that lipopeptide-based transfection agent of Pal-CKKHH and Pal-CKKHH-YGRKKRRQRRR-PKKKRKV condensed DNA molecules efficiently. The lipopeptide was less toxic compared to Lipofectamine and Poly-L-Lysine, that shown by 90% of CHO-K1 cells remained viable when they were treated with 4.36 µM Pal-CKKHHYGRKKRRQRRR-PKKKRKV. Meanwhile, there were only ~75% and 80% of CHO-K1 viable cells when it was treated with PLL and Lipofectamine®2000, respectively. Moreover, cell viability of HepG2 was ~ 75% after treated with 2.18 µM of Pal-CKKHH-YGRKKRRQRRR-PKKKRKV and decreased to ~65% when the lipopeptide concentration increased to 8.72 M. In summary, the synthesized lipopeptide condenses DNA molecules efficiently, less toxic than Lipofectamine®2000 and PLL and has possibility to be explored as a non-viral gene delivery vehicle.

Construction and Expression of Immunotoxin Anti EGFRvIII scFv-HPR Conjugate in Pichia pastoris as A Targeted Drug Candidate for Cancer Therapy Yuliawati Yuliawati; Retno Damayanti Soejoedono; Asrul Muhamad Fuad
ANNALES BOGORIENSES Vol 18, No 1 (2014): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Epidermal growth factor receptor variant III (EGFRvIII) is a mutant of EGFR lacking 267 amino acids (exon-2 through 7) within its extracellular domain, resulting in the formation of a new epitope as a tumorspecific target. EGFRvIII is commonly found in GBM, breast, ovarian, prostate, and lung carcinomas. Antibodies or part of antibodies (e.g. single chain variable fragment or scFv) with specific activity against this receptor have been developed. These antibodies are internalized into the cell after receptor binding. Ribonucleases can be cytotoxic due to their inherent ability to degrade RNA, therefore causing cell death via inhibition of protein synthesis. The aim of this research is to construct, clone and express an immunotoxin-based conjugate combining an anti-EGFRvIII scFv with a HPRmut (human pancreatic ribonuclease mutant variant) in Pichia pastoris. The anti-EGFRvIII scFv gene was cloned into yeast expression vector pPICZαA and fused with EGFP gene as a marker. The HPRmut gene was subsequently cloned at the C-terminal of the scFv::EGFP fusion, resulting in the scFv::EGFP::HPR fusion construct. The fusion construct was successfully obtained and nucleotide sequence of plasmid was verified. This construct was used to transform Pichia pastoris SMD 1168H. The gene fusion was successfully transformed and expressed in P. pastoris with a transformation efficiency of 102 cfu/μg DNA. The transformed yeasts were screened on agar media containing up to 1000 μg/ml zeocin. Yeast transformants showed green fluorescent due to the expression of EGFP gene. The recombinant proteins have been expressed and secreted from P. pastoris as showed by immunoblotting and SDS-PAGE analyses, then purified by affinity chromatography method. The selected yeast transformant produced at least 15.85 mg of purified protein per liter of yeast culture.

Sequential Adaptation in Mammalian CHO-K1 Cells Producing Human Erythropoietin Popi Hadi Wisnuwardhani; Endah Puji Septisetyani; Adi Santoso
ANNALES BOGORIENSES Vol 21, No 1 (2017): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

The production of recombinant proteins for clinical applications using mammalian cell technology has become a prevalent system because of its capacity in assembling functional proteins. One of the main problems with CHO-K1 cells is that this cell has to grow in the presence of serum. However, the presence of serum will complicate the downstream step for protein production. Thus, protein produced in media without serum, theoretically, would be easier to purify. Technically, this type of cell can be produced by growing the CHO-K1 cells in serum-free media by using adaptation method in suspension condition. This research showed that through sequential adaptation using conditioned media, the CHO-K1 cell line that produces the human erythropoietin gene (hEPO) was able to grow in suspension culture using serum-free media. Based on Western blot analysis, it showed that the protein (hEPO) was able to be expressed in suspension culture with molecular mass of about 47 kDa.

The Investigation of Polycyclic Aromatic Hydrocarbon and Oil Degrading Bacteria Isolated from The Marina Port Ancol, Jakarta Bay Puspita Lisdiyanti; Yopi Yopi; Tutik Murniasih
ANNALES BOGORIENSES Vol 15, No 2 (2011): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

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.Key words: polycyclic aromatic hydrocarbons, crude oil, degrading bacteria, bioremediation.

Constitutive Expression of Candida antarctica Lipase B (CALB) in Pichia pastoris Using pGAPZα Vector Febriana Dwi Wahyuni; Asrul Muhamad Fuad; Suharsono Suharsono
ANNALES BOGORIENSES Vol 20, No 1 (2016): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

The CalBsyn gene was previously constructed synthetically to encode Candida antarctica lipase B (CALB). Lipase from CalBsyn gene is slightly different from that of wild type CALB (CALB-wt) where it has three amino acids substitutions at different positions, i.e. V210I, A281E, and V221D, to improve enzyme’s thermostability and catalytic efficiency. The CalBsyn gene was isolated from pJ912-CalBsyn vector by digestion using XhoI restriction enzyme. The CalBsyn gene then was ligated to pGAPZα expression vector and transformed into E. coli TOP10F’ in order to obtain recombinant vector pGAPZα-CalBsyn. The result showed that pGAPZα-CalBsyn recombinant vector was successfully transformed into E. coli TOP10F’ with transformation efficiency of 4.11 x 103 cfu/µg plasmid DNA. The pGAPZα-CalBsyn recombinant plasmid was successfully introduced into Pichia pastoris SMD1168H using electroporation method with transformation efficiency of 1.01 x 102 cfu/µg DNA. Qualitative lipase activity assays showed that transformed P. pastoris secreted recombinant lipase (CALB) and has lipolytic activity; while quantitative lipase activity assays showed that the lipase activity was 63.5 Units/ml in 48 hours. Analysis using SDS-PAGE showed that CALB protein was expressed successfully and the recombinant protein’s molecular size was approximately 45 kDa.

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