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KARAKTERISASI GENETIK FRAGMEN GEN PENYANDI RNA POLIMERASE INFECTIOUS MYONECROSIS VIRUS (IMNV) YANG MENGINFEKSI UDANG VANNAMEI (LITOPENAEUS VANNAMEI BOONE.) DARI LAMPUNG, GRESIK DAN PONTIANAK Sudjito, Yason Lukman; Handayani, Christina Retna; Kusumaningrum, Hermin Pancasakti; Budiharjo, Anto
Bioma : Berkala Ilmiah Biologi Vol. 16, No.1, Tahun 2014
Publisher : Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (178.652 KB) | DOI: 10.14710/bioma.16.1.18-25

Abstract

A massive death of vannamei shrimp (Litopenaeus vannamei Boone.) due to Infectious Myonecrosis Virus (IMNV) infection has occurred in Indonesia recently and still cannot be eradicated efficiently. The fast reproduction of IMNV depends on the RdRp gene that encodes for RNA polymerase. Genetic characterization of IMNV RdRp gene from Indonesia is important in order to compare with other IMNV to find out genetic variation as a base for combating this virus. IMNV-infected vannamei were taken from major aquaculture region in Indonesia (Lampung, Gresik and Pontianak). RNA polymerase coding genes (12 and 13 region) from infected vannamei were amplified using RT-PCR with appropriate primer. Amplification products were sequenced and the results were analyzed using BioEdit 7.1.3.0, ClustalW2, CLC free workbench 6.6.2. and ClustalX programs. Results showed that homology value of IMNV RdRp gene  from Lampung and Gresik were 98,04-9958% compared with IMNV from Brazil (Acc. No. AY570982). Amino acid analysis revealed homology value of IMNV RdRp gene  from Lampung  and Gresik were 100% and 99.04% compared with IMNV from Brasil. IMNV RdRp gene  from Pontianak cannot be analysed due to low quality of RNA.   Key words: vannamei, IMNV, RdRp, genetic characterization
KARAKTERISASI MOLEKULER TANAMAN SAMBUNG NYAWA (GYNURA PROCUMBENS [LOUR.] MERR) BERDASARKAN 18S RRNA Christiningrum, Octavia Dewi; Budiharjo, Anto; Kusdiyantini, Endang
Jurnal Akademika Biologi Vol. 5 No. 3 Juli 2016
Publisher : Departemen Biologi, Fakultas Sains dan Matematika Undip

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Abstract

Sambung Nyawa (Gynura procumbens) is a traditional medicinal plant used by people as an antihyperglycemic drug, antihyperlipidemic and chemoprevention agents. Comprehensive information on this plant needs to be done, including DNA analysis, so it can complement morphological character of an organisms. This study aimed to molecularly characterize and determine the relationship between G. procumbens with other organisms using ribosomal 18S rRNA gene. PCR (Polymerase Chain Reaction) was used to amplify the 18S rRNA gene fragments G. procumbens. DNA sequences were analyzed using the BLAST program at the NCBI portal and construction of phylogenetic trees were tested using Bootstrap method 1000x. The results showed the 18S rRNA sequence of Gynura procumbens fragments was 1600 bp, and G. procumbens belonged in the family of Asteraceae.Key words : Gynura procumbens, PCR (Polymerase Chain Raction), 18S rRNA, Bootstrap method
PELACAKAN FRAGMEN GEN PENYANDI ENZIM ß-KETOASIL-ACP SINTASE II (KAS II) DARI MESOKARP KELAPA SAWIT (ELAEIS GUINEENSIS JACQ. L.) Chandrawijaya, Yohanes; Tajuddin, Teuku; Kusumaningrum, Hermin Pancasakti; Budiharjo, Anto
Jurnal Akademika Biologi Vol. 2 No. 2 April 2013
Publisher : Departemen Biologi, Fakultas Sains dan Matematika Undip

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Abstract

        The standard of quality is one of the determining values of crude palm oil as an international trade commodity. Better standard of quality for crude palm oil is a constant demand of the market. Quality improvement can be made by increasing the contents of oleic acid in the mesocarp of  E. guinensis. Among the uses of oleic acid are as follows: anti-carcinogenic agent, anti-oxidant, source of pro-vitamin A, and source of Vitamin E. Oleic acid is a form of non-saturated fatty acid encoded by KAS II genes. The expression profiling of KAS II is achieved through isolation of total RNA by Trizol reagent, RNA purification, using DNAse RNAse free, synthesis of cDNA using Reverse Transcriptation PCR approach, and amplification of KAS II genes with Nested PCR approach. The amplification process of KAS II genes is carried out using both internal and external primers. The first step of the external primer PCR is F-KAS-1 and R-KAS-1. Internal primer of PCR in the second step is F-KAS-2 and R-KAS-2. The results of this research are fragments of KAS II genes between 1500?2000 bp. These amplicons are suitable with primers designed at the approximation of 1796 bp. Selection of three amplicons at the annealing temperatures of 54oC, 55.9oC, and 58oC shows good DNA band visualizations. Annealing at 58oC shows the best result with high intensity DNA band and no smear. Further research is needed to determine the accuracy of the amplicons through sequencing step.  Keywords: KAS II, Elaeis guineensis, annealing, Nested PCR, RT-PCR
OPTIMASI PERTUMBUHAN DAN POTENSI ANTAGONISTIK BACILLUS PUMILUS TERHADAP PATOGEN XANTHOMONAS CAMPESTRIS SERTA IDENTIFIKASI MOLEKULER GEN PENYANDI PKS DAN NRPS Faizah, Laila Nur; Budiharjo, Anto; Kusdiyantini, Endang
Jurnal Akademika Biologi Vol. 6 No. 1 Januari 2017
Publisher : Departemen Biologi, Fakultas Sains dan Matematika Undip

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Abstract

Xanthomonas campestris is one of the broccoli pathogen that difficult to be eradicated. B. pumilus is a prospective biocontrol agent due to its ability to produce antibiotical subtances that inhibit the growth of pathogenic bacteri and fungi. Beside that, B. pumilus have a great endurance to extreme environment by its ability to form spores. Some species of Bacillus genus have been reported to have PKS (Polyketide Synthetase) and NRPS (Non-Ribosomal Peptide Synthetase) coding gene which is a mega shyntetase that have a role in the production of antibiotic subtances. This reseach aims to test the inhibitory potency of B. pumilus toward X. campestris, identify the PKS and NRPS coding gene and to knwing the optimum growth of B. pumilus on the medium with different pH and carbon source. Reseach is conducted with Completely Randomized Design (CRD) with three replications on two growth parameters that is pH and carbon source. pH treatment is conducted with pH 5, 6, 7, and 8, while carbon source treatment is conducted with glucose, fructose, and sucrose as the carbon source. The obtained result is analized with ANOVA with significant level of 95%. The result shows B. pumilus ability to inhibits the growth of X. campestris producing inhibitory zone with 1,84 mm of diameter. The reseach showed negative result in NRPS coding gene detection and a positive result in PKS coding gene. PKS coding gene identification which is analized with BLAST shows 98% homology with PKS coding gene of Bacillus subtilis HNS005. Growth optimization shows the optimum groth of B. pumilus at pH 6 and glucose as the carbon source.Keywords: biocontrol, B. pumilus, PKS, NRPS, growth optimization
DETEKSI JENIS PADI INDICA DAN JAPONICA PADI GOGO RANCAH BERAS MERAH VARIETAS SLEGRENG DAN MANDEL BERBASIS FRAGMEN ORF100 DAN ORF29 Haryanti, Wahyu Dewi U.; Kusumaningrum, Hermin P.; Budiharjo, Anto
JURNAL SAINS DAN MATEMATIKA Volume 21 Issue 4 Year 2013
Publisher : JURNAL SAINS DAN MATEMATIKA

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Abstract

Deteksi fragmen Open Reading Frame (ORF)100 dan ORF29 telah dilakukan pada dua jenis padi gogo rancah beras merah yaitu varietas Slegreng dan Mandel. Metode penelitian dilakukan dengan cara isolasi DNA kloroplas padi diikuti dengan amplifikasi PCR menggunakan optimasi suhu annealing pada tiga suhu yang berbeda, yaitu 53°C, 55°C, dan 56°C. Selanjutnya hasil amplifikasi divisualisasikan menggunakan elektroforesis pada gel agarose 1%. Suhu annealing 53°C merupakan suhu yang optimal untuk memperlihatkan fragmen ORF100 dan ORF29. Hasil penelitian menunjukkan bahwa fragmen ORF100 dan ORF29 dapat teramplifikasi pada padi Slegreng dan mandel, sehingga kedua jenis padi tersebut menunjukkan kecenderungan subspesies japonica. Perbedaan ketebalan dan ukuran pita tidak mempengaruhi keberadaan fragmen ORF100 dan ORF29 sebagai penanda untuk mengidentifikasi tipe indica atau japonica. Pemanfaatan marka molekuler fragmen ORF100 dan ORF29 dalam mendeteksi jenis padi diharapkan dapat melengkapi hasil karakterisasi dan pengelompokkan varietas padi berdasar karakter morfologi dan fisiologi.   Keywords: chloroplast DNA, ORF100, ORF29, indica-japonica differentiation
THE ANTIOXIDANT GROWTH AND POTENCY OF YEAST RHODOSPORIDIUM PALUDIGENUM DUCC Y-007 ON DIFFERENT MEDIUMS Kusdiyantini, Endang; Budiharjo, Anto
JURNAL SAINS DAN MATEMATIKA Volume 22 Issue 4 Year 2014
Publisher : JURNAL SAINS DAN MATEMATIKA

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Abstract

The antioxidant growth and potency of yeast Rhodosporidium paludigenum DUCC Y-007 have been studied on two treatment mediums. The yeast could grow on two treatment mediums and the dry weight results obtained during the incubation period of 120 hours were 7.17 g/L and 7.33 g/L. The concentration of reducing sugars in stabilized medium were 3.14 g/L and 3.30 g/L at 72-120 hours incubation time respectively. There were differences in pH changes during incubation time which at YPG medium, it tended to increase whereas at semi synthetic medium, the pH tended to decline. Total carotenoid on YPG medium was 50.13 µg/g cell and on the semi-synthetic medium was 197.50 µg/g cell. Antioxidant activity measured by DPPH reagent showed the results at YPG medium was 50% and at semi-synthetic medium was 61%.
ISOLASI, KARAKTERISASI BAKTERI ASAM LAKTAT, DAN ANALISIS PROKSIMAT DARI PANGAN FERMENTASI RUSIP IKAN TERI (STOLEPHORUS SP.) Mergypta, Deverina; Budiharjo, Anto; Kusdiyantini, Endang
Jurnal Akademika Biologi Vol. 3 No. 2 April 2014
Publisher : Departemen Biologi, Fakultas Sains dan Matematika Undip

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Abstract

Rusip is a traditional food from Bangka-Belitung made from fresh anchovy with salt and palm sugar that is brooded for seven days. Rusip fermentation process is caused by microbial activity mainly from lactic acid bacteria. The purpose of this study was to isolate lactic acid bacteria from rusip, to characterize isolates obtained based on common characteristic of lactic acid bacteria, and to carry out proximate analysis of rusip anchovy. Isolation from rusip fermented food obtained eight bacterial isolates, five isolates were circular and three isolates were rod-shaped. Characterization and identification of lactic acid bacterial were performed using tests that led to the common characteristic of lactic acid bacteria, i.e the gram staining, motility test, acid formation test, catalase test, and proteolytic test. The result showed that eight bacterial isolates were gram-positive, non-motile, catalase-negative, positive to produce acid, and had proteolytic activity. Rusip anchovy had 0,64% of total lactic acid and the pH 5,40. Nutrient content of rusip fermentation had 10,3644% moisture content; 50,0702% ash content; 0,9524% crude fat content; 0,3764% crude fiber content; 34,8603% crude protein content; and 14,1171% carbohydrate content. Keywords: rusip, isolation, characterization, lactic acid bacteria, proximate analysis
DETEKSI GEN TLH DAN TDH PADA BAKTERI VIBRIO PARAHAEMOLYTICUS DARI AIR TAMBAK UDANG VANNAME (LITOPENAEUS VANNAMEI) DI KABUPATEN REMBANG Hasrimi, Adila Nawan; Budiharjo, Anto; Jannah, Siti Nur
Jurnal Akademika Biologi Vol. 6 No. 3 Juli 2017
Publisher : Departemen Biologi, Fakultas Sains dan Matematika Undip

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Abstract

Vibrio parahaemolyticus is hallophilic gram-negative bacteria that live as natural inhabitant in aquatic environment. All Vibrio parahaemolyticus strain known to have thermolabile hemolysin encoded by tlh gene as species marker. Thermostable direct hemolysin encoded by tdh gene is responsible for regulating one of the virulence factors in Vibrio parhaemolyticus. The aim of this research is to detect tlh gene and tdh gene from water of vanname shrimp?s aquaculture in Rembang regency. Colonies of green-blueish bacteria grew from the isolation of  vanname shrimp?s aquaculture water in CD-VP media which is identified as Vibrio parahaemolyticus. The isolated bacteria is specifically identified as Vibrio parahaemolyticus bacteria by the detection of tlh gene. Molecular analysis shows tdh negative result that indicates tdh gene is not present in the isolated bacteria. Vibrio parahaemolyticus isolate were cultured in Wagatsuma agar for the tdh gene confirmation test that showed Kanagawa negative result, in which indicated that V. parahaemolyticus did not produce thermostable direct hemolysin. Vibrio parahaemolyticus isolate did not show any virulence factors to initiate host colonization in the aquatic environment. Keywords: Vibrio parahaemolyticus, tdh gene, tlh gene
ISOLASI DAN KARAKTERISASI MORFOLOGI KOLONI BAKTERI ASOSIASI ALGA MERAH (RHODOPHYTA) DARI PERAIRAN KUTUH BALI Sabdaningsih, Aninditia; Budiharjo, Anto; Kusdiyantini, Endang
Jurnal Akademika Biologi Vol. 2 No. 2 April 2013
Publisher : Departemen Biologi, Fakultas Sains dan Matematika Undip

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Abstract

Kutuh Beach in Bali is an area established as the Minapolitan algae with a high diversity. Microorganisms associated with marine organisms, usually have secondary metabolites that can be used as a source of drugs, antibiotics, enzymes, and cosmetics. The aimed of this research was to isolate and characterize colony morphology of bacteria associated with red algae based on colony morphology. Seven bacteria were isolated from three samples of red algae that were Kappapycus alvarezii, Gelidiella acerosa and Eucheuma spinosum. The isolates had pigmentation of beige, white and orange. Based on Gram's staining, seven isolates were Gram positive with bacilli and cocci in shape. Keywords : associated bacteria, morphological colony, pigmentation, red algae
HUBUNGAN KEBERADAAN BREEDING PLACE DENGAN KEJADIAN DEMAM BERDARAH DENGUE DI KOTA SEMARANG DAN SEKITARNYA Mubarok, Muhammad Adib; Wahyuningsih, Nur Endah; Budiharjo, Anto
Jurnal Kesehatan Masyarakat (e-Journal) Vol 5, No 5 (2017): Jurnal Kesehatan Masyarakat (E-Journal)
Publisher : Fakultas Kesehatan Masyarakat

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Abstract

Dengue Hemorrhagic Fever is an infectious disease caused by dengue virus that is transmitted through Aedes mosquito bites, both Aedesaegypti and Aedesalbopictus. DHF is one of the major public health problem in Indonesia.The Incidence Rate (IR) of DHF in Semarang City from 2006 to 2016 are always much higher than IR DHF of Central Java and IR DHF of National Indonesia.The cases of Dengue Hemorrhagic Fever (DHF) in Semarang City has increased significantly and cause death.This study aims to see the Breeding Places description and its relation to the incidence of Dengue Hemorrhagic Fever in Semarang city and surrounding areas.The type of research was an observational analytic study using Case-control design. The cases sample in this study were hospitalized DHF patients from the period of March to May 2017 in three hospitals in Semarang City.The control samples were health people and live around the cases with the same characteristics. Total sample were 27 cases and 27 controls. The data was analyzed by Mann Whitney test.The result showed that insignificant factors were existence of daily necessities containers (p=0,383), existence of containerswhat are not daily necessities (p=0,307), existence of total containers (p=0,142), opened containers condition (p=0,199), closed containers condition (p=0,683), and containers infested with larvae (p=0,253).  In conclusion, there is no association between breeding places factors with DHF incidence in Semarang city and surrounding areas.