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Annales Bogorienses
Published by Badan Riset dan Inovasi Nasional
ISSN : 05178452     EISSN : 24077518     DOI : https://doi.org/10.55981/ann.bogor
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Annales Bogorienses aims to disseminate high-quality scientific research in the field of life sciences, with a strong emphasis on advancing knowledge and applications in biotechnology, molecular biology, biochemistry, bioinformatics, and bioengineering. The journal serves as a platform for researchers, academicians, and practitioners to share original findings, innovative methodologies, and critical reviews that contribute to scientific progress and sustainable development. The journal covers research in biotechnology, molecular biology, biochemistry, bioinformatics, and bioengineering. It publishes original research articles, reviews, and short communications, and is committed to rigorous peer review and open access for the widest possible dissemination of scientific knowledge.
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Articles 189 Documents
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EDITOR'S PREFACE Lisdiyanti, Puspita
Annales Bogorienses Vol. 9 No. 1 (2004): Annales Bogorienses
Publisher : BRIN

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Abstract

The editors would like to announce that, in the years of 2002 and 2003, The Research Centre for Biotechnology The Indonesian Institute of Sciences (LIPI) did not publish Annales Bogorienses New Series due to some management problems. The last issue waspublished with Volume 8, Number 2, 2001. Under new editors, in this year of 2004, continuing the previous volume, this journal is published again starting with Volume 9, Number 1. In this ninth edition of Annales Bogorienses, we would also like to introduce anew look of this journal to our readers. We will I continue to publish this journal periodically twice a year (in June and December).Many thanks to all authors for their efforts, attentions, and time throughout the editing process that make this current edition become possible. Tolerance of our editorial judgments is much appreciated. We encourage our readers to submit original papers on topics of interest to life sciences researchers. June, 2004M. Ahkam SubrotoChief Editor
Sensitivity Improvement of A Direct Competitive Elisa for Atrazine by Exploiting Low Cross-Reactivity of An Atrazine-Specific Recombinant Antibody Fab-Fragment Kusharyoto, Wien; Schmid, Rolf D.
Annales Bogorienses Vol. 9 No. 1 (2004): Annales Bogorienses
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Abstract

The hapten-binding site of the antibody Fab-fragment K411B specific towards the herbicide atrazine (2-chloro-4-(ethylamino)-6-(isopropyJamino)-1,3,5-triazine) was modified by means of structural modeling and site-directed mutagenesis. A triple mutant (GlnL89Glu/ValH37Ile/GluL3Val) of the Fab-fragment showed an increased affinity towards the hapten H/Cl/C6 (4-amino-6-chloro-l,3,5-triazine-2-(6-aminohexanecarboxylic acid) compared to the affinity of the wild-type Fab-fragment towards the same hapten. However, the mutant exhibited substantially lower affinity towards the hapten H/Cl/C6 than towards atrazine and the hapten iPr/Cl/C6 (4-chloro-6-(isopropylamino)-1,3,5-triazine-2-(6-aminohexanecarboxylic acid), which is usually used in the synthesis of enzyme tracers in ELISA for atrazine. Advantage was taken of the low cross-reactivity and increased affinity of the mutant Fab fragment towards H/Cl/C6 to improve the sensitivity of a direct-competitive ELISA tor atrazine. H/Cl/C6 was covalently conjugated with horseradish peroxidase (HRP), and the conjugate H/CI/C6-HRP was used as enzyme tracer in the ELISA for atrazine. An eight-fold improvement in sensitivity of a direct-competitive ELISA for atrazine could be achieved using the tracer H/Cl/C6-HRP compared to the sensitivity of ELISA using the tracer iPr/Cl/C6-HRP. The detection limit for atrazine was as low as 0.01 i g/l.
An Application of Reverse Transcriptase Polymerase Chain Reaction in A Relative Quantification of Gene Expression Santoso, Adi
Annales Bogorienses Vol. 9 No. 1 (2004): Annales Bogorienses
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Abstract

The ability to quantify steady state levels of individual messenger-RNA (mRNA) transcripts has been the key issue for study on the control of gene expression. Although two available techniques, Northern blot and nuclease protection assays (NPA) have been widely used tor detecting mRNA, these techniques have critical limitations. The most obvious limitation of these two techniques is the required number of target mRNAs to be detected. Reverse transcription-polymerase chain reaction (RT-PCR), which has been accepted as a highly sensitive and specific method, provides a means for detecting and quantifying gene expression using, theoretically only a single molecule of mRNA. The sensitivity and reliability of RT-PCR is dependent upon both the RT and PCR steps. The PCR step has been problematic because of the exponential nature of this reaction where small variation can lead to dramatic changes in final result. Therefore, the use of RT-PCR for quantification of gene expression requires pre-experimental planning and design. In this experiment, the procedure for pre-experimental planning, linear range determination and subsequent relative quantification of gene expression are described in detail. A study of ornithine decarboxyJase gene, a gene involved in the polyamine biosynthesis and temporally expressed, during embryogenesis of Musca domestica (housefly) was used as the model. The results show that during early embryogenesis (t-1 to t-4) the expression level was very low. The increase in expression profile was observed started at t-5, peaked at t-9, and followed by substantial decrease from t-10 to t-12.
Maternal Contribution in Revealing The Effects of Methoxyacetic Acid (MAA) Administered Before Implantation on The Embryonic Development of Swiss Webster Mice (Mus musculus) Kaiin, Ekayanti M; Sumarsono, Sony H.; Surjono, Tien W.; Sudarwati, Sri
Annales Bogorienses Vol. 9 No. 1 (2004): Annales Bogorienses
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Abstract

Maternal contribution to and direct action of methoxyacetic acid (MAA) on the embryonic development bad been examined by conducting embryo transfer. To reveal the maternal contribution, compacted morulae and early blastocysts, which were collected from untreated Swiss Webster donor mice on day 3 of gestation, were transferred to day 2 pseudopregnant recipients, after having been treated with 2.0 mmo/lkg body weight (b.w.) MAA by gavage on day 1 of pseudopregnancy. Direct effect of MAA on the embryonic development were observed by transferring compacted morulae and early blastocysts, similarly recovered from day 3 pregnant donor mice, after MAA treatment on day 2 of gestation with the same method and dosing, to untreated day 2 pseudopregnant recipients. Control donor mice and recipient were given distilled water only as the MAA solvent. Observations on fetuses resulting from embryo transfer wert: carried out on day 16 of gestation . Administration of MAA to the donors tended to decrease the unplantatlon rate and the survival rate of the implanted embryos. When MAA was given to the recipients the implantation rate and survival rate of embryos transferred decreased significantly (p<0.05) but the survival rate of implanted embryos were significantly higher (p<0.05) Lf compared to those of MAA treated donors. The intrauterine death tended to inc rease either in the treated donors or recipients. There was no effect of MAA on the fetal body weight and in producing fetal malformations. It is concluded that at the beginning of implantation, maternal contribution in revealing the effects of MAA on the embryonic development of Swiss Webster mice is predominant, whereas after implantation took place, the quality of the embryos become more important for their survival.
The Use of 16S rRNA and nodC Gene Sequence in Resolving The Phylogenetic Relationship of Rhizobia Associated With Paraserianthes falcataria (L.) Nielsen Plant Prana, Titik K; Sone, Teruo; Kawasaki-Nakagawa, Hiroko; Yokota, Atsushi; Seki, Tatsuji; Tomita, Fusao
Annales Bogorienses Vol. 9 No. 1 (2004): Annales Bogorienses
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Abstract

Studies on genetic position of several isolates living symbiotically on Paraserianthes falcataria have been carried out using amplification and sequencing techniques of 16S rDNA and specific gene for nodulation. The phylogenetic tree constructed based on 16S rDNA showed that rhizobia growing symbiotically on Paraserianthes falcataria consisted of 3 groups. The first group, was fast growing rhIzobia which have close relationship to Rhizobium tropicii, the second and the third groups were slow-growing rhizobia which have close relationship to Bradyrhizobium elkanii and Bradyrhizobium japonicum. However, the phylogenetic tree constructed on the basis of partial nodC gene indicated the existence of an independent group, since they did not show any significant degree of relationship with the existing groups. This was also supported by differences in physiological characteristic i.e Indole Acetic Acid production and salt tolerance of the isolates. These differences shows us that direct sequencing method of certain specific genes could give a more specific result than would display more clearly the degree of relationship at species level.
EDITOR'S PREFACE Lisdiyanti, Puspita
Annales Bogorienses Vol. 9 No. 2 (2004): Annales Bogorienses
Publisher : BRIN

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Abstract

The editors would like to announce that, in the year of 2002 and 2003, The Research Centre for Biotechnology, The Indonesian Institute of Sciences (LIPI) did not publish Annales Bogorien es New Series due to some management problems. The last issue was published with Volume 8, Number 2, 2001. Under new editors, in this year of 2004, continuing the previous volume thi journal is published again starting with Volume 9, Number 1. In this ninth edition of Annales Bogorienses, we would also like to introduce a new I ok of this journal to our readers. We will continue to publish this journal periodically twice a year (in June and December).Many thank to all the author for their efforts, attention and time throughout the editing process that make this current edition become possible. Tolerance of our editorial judgment is mu h appreciated. We encourage our readers to submit original papers on topics of interest to life sciences researcher . December, 2004M. Ahkam Subroto Chief Editor
Modification of Plasmids and Cry Genes of Bacillus thuringiensis subsp. kurstaki HD-I After Treatment With Ethylmethanosulfonate (EMS) and UV Light Jusuf, Eddy
Annales Bogorienses Vol. 9 No. 2 (2004): Annales Bogorienses
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Abstract

Bacillus thuringiensis subsp. kurstaki HD-1 is a potential insecticidal bacterium producing five type of a-endotoxin crystal proteins. This bacterium is widely commercialized due to its wide spectrum toxicity against both Lepidopteran and Dipteran larvae. The objective of this work was to create autolysin deficient mutant causing cell fails to lyse. This mutant yield intact cells within spore and a-endotoxin crystal protein protected inside, from which an undamaged active bio-insecticide would be obtained. Two methods of mutagenesis, 2% of ethylmethanosulfonate and 10, 25, and 50 second of UV light exposure, resulted in mot (loss of motility) mutation. Observation showed that 14 of 20 survived mutants have lost some of its plasmids (varied from one to five). while the other six maintained their plasmids. By employing the polymerase chain reaction (PCR) the change on the cry genes was studied.
Cytological Analysis of Root Cultures of Artemisia cina Ermayanti, Tri Muji; Yanti, Oktavia; Hafiizh, Erwin Al
Annales Bogorienses Vol. 9 No. 2 (2004): Annales Bogorienses
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Abstract

Artemisia cina is a medicinal plant species producing bioactive compounds which are potential a antitumor, antifungal and antibacterial. The aim of this study was to analyze the stability of chromosome number in root cultures of A. cina. Transformed root culture was established by infection of leaves of A. cina with Agrobacterium rhizogenes strains 07-20001, ATCC 15834, A4; and Agrobacterium tumefaciens strain R1000. Roots isolated from glasshouse plants, plantlets grown in solid and liquid MS medium were utilized for investigation of chromosome examination of untransformed roots. Chromosome examination was conducted by squashing method and chromosome numbers were calculated under microscope. The results showed that both untransformed and transformed root had in lability in the chromosome number, but had the modal number of chromosome x=8 with the diploid number of 2n =4x = 32. Roots isolated from glasshouse plants of A. cina had 53.7~ of cell with the diploid numbers of 2n = 3 and 46.3% of cells had chromosome numbers ranged from 2n = 12 to 2n = 64. Untransformed roots isolated from plantlets cultured in solid medw had only 36.1% or cells with chromo orne number of 20 = 32, and untransformed roots grown in liquid medium had 49.4% of cells with 2n =32. The chromosome numbers of A. cina transformed roots was affected by trains of Agrobacterium. Root transformed with the bacterium Strain 07-20001 showed the highest in normal chromosome number of 2n = 32 (62.4%) followed by roots transformed with strains ATCC 15834 (61.9%). R1000 (43.6%) and A4 (43.0%). The range of the chromosome number of untransformed roots was from 2n=17 to  2n=64 whilst that of transformed roots was from 2n=11 to 2n=66.
Denitrification of Activated Sludge in The Presence of Different Organic Substrates Agustiyani, Dwi; Yamagishi, Takao
Annales Bogorienses Vol. 9 No. 2 (2004): Annales Bogorienses
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Abstract

The effect of organic carbon denitrifying activity was studied in batch reactor. Fom reactors were operated in parallel under anoxic condition in four different donor electrons. which were acetic acid (Reactor A), methanol (Reactor M), phenol (Reactor P), and glucose (Reactor G). The reactors were fed with the artificial waste, which contain 721.8 mg/l NaNO3. The concentration organic carbon added to the reactors were varied from TOD:N ratio of 0.5:1; 1: 1, 1.5:1, to 2:1. The denitrification activity was estimated by measuring the reduction rate of nitrogenous oxide and N2O gas production. The denitrification capacity of adapted-sludge was also investigated, and the rates were estimated from the cumulative N2O (without acetylene inhibition) and N2 gas production. Reduction rate of nitrogenous oxide in all reactors increased during the investigation; lhe increase reduction rate were correlated to the increase of organic carbon concentration. The maximum reduction rate of nitrogenous oxide in Reactor A was higher than those of the others. However, reduction rate in Reactor M was more constant, so that nitrogenous oxides existed in this reactor was removed faster. The highest potential denitrification rate (N20 production) was observed in sludge of Reactor A. However, N2 gas recovery trom nitrate and nitrite transformed by sludge of Reactor M was the highest. Linear correlation between nitrogenous oxide reduction with gas production was observed in Reactor A, M and P, but not in Reactor G.
Development of Somatic Embryo in Lithospermum erythrorhizon Siebb. et Zucc and The Study on The Effect of Methyl Jasmonate on its Maturation Mariani, Totik Sri; Ramayanti, Octavia; Yazaki, Kazufumi; Miyake, Hiroshi
Annales Bogorienses Vol. 9 No. 2 (2004): Annales Bogorienses
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A research on the somatic embryogenesis in Lithospermum erythrorhizon has been conducted. Embryogenic callus was inoculated in EIM9 liquid medium (modification of LS medium), i.e. L2PVP (initiation medium) and the development of somatic embryo was observed. Ten uM and 100 uM methyl jasmonate was added into L3PVP medium (differentiation medium) for somatic embryo maturation. The purposes of this research were to observe the development of somatic embryo and to observe the effect of methyl jasmonate on maturation of the somatic embryo in L. erythrorhizon. The results showed that somatic embryogenesis in L. erythrorhizon derived from single cells differentiated further forming proembryo, globular heart, torpedo and cotyledon stage. Treatment with 10 uM and 100 uM methyl jasmonate induced maturation of somatic embryos (cotyledon stage) after transferring them to embryo development medium (L4PVP).

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