Anto Budiharjo
Departemen Biologi, Fakultas Sains Dan Matematika, Universitas Diponegoro, Semarang, Indonesia

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Molecular Characterization of Zinc (Zn) Resistant Bacteria in Banger River, Pekalongan, Indonesia Sasi, Fitri Arum; Kusumaningrum, Hermin Pancasakti; Budiharjo, Anto
Biosaintifika: Journal of Biology & Biology Education Vol 10, No 3 (2018): December 2018
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (303.216 KB) | DOI: 10.15294/biosaintifika.v10i3.15835

Abstract

Indigenous bacteria are able to remove the metals contamination in environment. This study aimed to assess the resistance of bacterial species to Zinc (Zn) in Banger River, Pekalongan City. The bacteria from three different parts of Banger River were isolated and inoculated in Zn-selective medium. Then, molecular identification to determine the bacteria species was conducted using polymerase chain reaction (PCR) by applying forward-reverse 16SrRNA gene primers. The sequences analysis was conducted using MUSCLE and MEGA6. There were seven dominant species that possibly resistant to Zn. Approximately, every isolate could reach more than 95 % from 2000 ppm of Zn in the medium. The higher absorption of Zn was found in Z5 isolate. The seven bacteria species were clustered into nine genera i.e. Klebsiela, Xenorhabdus, Cronobacter, Enterobacter, Escherichia, Shigella and Sporomusa known as Gram Negative bacteria and Clostridium and Bacillus as Gram Positive bacteria. In Gram Positive bacteria, especially Bacillus sp, carboxyl group in peptidoglycan play a role as metal binder. In Gram-negative bacteria, lipopolysaccharide (LPS) which is highly anionic component on the outer membrane, able to catch the Zn. Besides that, Enterobacter activates endogen antioxidants such as glutathione peroxidase (GSHPx), glutathione reductase (GR), catalase (CAT) and superoxide dismutase (SOD). The research found there was possible seven novel indigenous bacteria species in Banger that able to remove Zn from the sediment extremely. This finding can be developed as an eco-friendly approach to reduce metals pollution using local microorganisms.
Produksi Bioetanol Dari Rumput Laut dan Limbah Agar Gracilaria sp. dengan Metode Sakarifikasi Yang Berbeda Adini, Saniha; Kusdiyantini, Endang; Budiharjo, Anto
Bioma : Berkala Ilmiah Biologi Vol. 16, No.2, Tahun 2014
Publisher : Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (206.041 KB) | DOI: 10.14710/bioma.16.2.65-75

Abstract

The Indonesia needs of Bioethanol were 390.000 kL in 2012, but the local ethanol production only able to cover less than 4% from the needed. The high demand of the bioethanol encourage for another innovation in ethanol production more efficient and effectively. Seaweeds and the residual pulp of Gracilaria sp. could be useful as substrate for bioethanol production, because of the high amount of polysaccharide, cellulose and galactan type. Unfortunately, this cellulose and galactan had through the saccharification process first, before they can be used as substrates in bioethanol production. This study examined the difference between two saccharification process which are acid hydrolisis using H2SO4 1% and enzymatic process using Aspergillus niger on the use seaweed and the residual pulp of Gracilaria sp. for bioethanol production. Bioethanol production been conducted for 5 days and in each 24 hour, the sampling for cell number variable, reduction sugar amount variable, and medium fermentation pH variable had been retrieved. The ethanol amount calculation in the last incubation phase conducted using distillate fermentation spesific gravity methode. The highest ethanol was obtained 5,50%  by treatment using seaweed medium with acid hydrolisis. The anova analysis result showed that interaction between medium variable and hydrolisis didn’t have signifficant influence toward ethanol product. It showed that seaweed and the residual pulp of Gracilaria sp. had same quality and they can be useful as main component of bioethanol production which are hydrolisis by enzymatic or acid hydrolisis.   Key Words :  Gracilaria sp., the residual pulp, saccharification, reducing sugar, ethanol
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
Kloning Gen pcbC dari Penicillium chrysogenum ke dalam Plasmid pPICZA untuk Pengembangan Produksi Penisilin G Wiharyani, Risma; Hardianto, Dudi; 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 (401.015 KB) | DOI: 10.14710/bioma.16.1.33-38

Abstract

Availability of drugs in Indonesia is still limited by the high prices of drugs due to on the imported raw materials that reaches 95%. Developing antibiotic raw materials can be achieved by increasing of penicillin G production, which is the raw material for the formation of semisynthetic penicillin derivatives through the production of 6-aminopenisillanic acid (6-APA). One of the important enzyme in the penicillin G biosynthesis is Isopenisilin N Synthase (IPNS) that encodes by pcbC gene on Penicillium chrysogenum. This study aimed to obtain a recombinant of pcbC gene fragments that is inserted into pPICZA plasmid. Amplification of pcbC gene used pcbC-F and pcbC-R primers. The pcbC gene fragment was inserted into pPICZA vector and then transformed into TOP 10 F’. The results showed that the recombinant of the pcbC gene fragment from P. chrysogenum has been obtained. Analysis of DNA sequences using the BLAST program showed that the pcbC gene fragment has high homology (99%) with the  pcbC gene from P. chrysogenum Wisconsin 54-1255 and P. chrysogenum AS-P-78 which encodes IPNS   Keywords: pcbC Gene, Penicillium chrysogenum, cloning, penicillin G
Pelacakan Gen Sitokrom Oksidase Subunit 1 (Co1) DNA Mitokondria Pada Itik Tegal (Anas sp.) Rahayu, Annisa Rizky; Kusumaningrum, Hermin Pancasakti; Budiharjo, Anto
Bioma : Berkala Ilmiah Biologi Vol. 18, No.2, Tahun 2016
Publisher : Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (119.763 KB) | DOI: 10.14710/bioma.18.2.114-122

Abstract

Itik Tegal adalah salah satu sumber plasma nutfah ternak Indonesia yang belum memiliki informasi asal usul dan identitas genetik, sedangkan ini sangat diperlukan sebagai dasar dalam usaha persilangan dan pemuliaan untuk menghasilkan itik hibrida unggul. Penelitian ini bertujuan untuk mengetahui identitas genetik itik Tegal menggunakan gen sitokrom oksidase subunit 1 (CO1) dengan primer BirdF1 dan BirdR1. Penelitian dilakukan dengan cara isolasi DNA dari otot paha itik, diikuti amplifikasi gen CO1, dan sekuensing. Sekuen gen CO1 digunakan untuk analisis hubungan kekerabatan dengan mengkonstruksi pohon filogenetik menggunakan metode neighbor-joining dengan analisis bootstrap 1.000 ulangan. Model Kimura 2-parameter digunakan untuk menghitung jarak genetik dengan pairwise distance. Hasil penelitian memperoleh fragmen gen CO1 itik Tegal. Fragmen tersebut homolog dengan sekuen gen CO1 Anas platyrhynchos voucher NHMO-BC400. Analisis filogenetik menunjukkan itik Tegal memiliki hubungan kekerabatan paling dekat dengan A. platyrhynchos yang terdistribusi di Skandinavia dan Amerika Utara, A. poecilorhyncha yang terdistribusi di Asia tropis dan timur, serta Tadorna tadorna yang terdistribusi di China. Kata kunci: gen CO1, genetik, itik Tegal
Seleksi Primer LCO – HCO, Primer bird-f1 – HCO Dan Primer bch – bcl Untuk Amplifikasi Gen COI DNA Mitokondria Itik Magelang (Anas javanica) Setiyawan, Sonny Abdi; Budiharjo, Anto; Kusumaningrum, Hermin Pancasakti
Bioma : Berkala Ilmiah Biologi Vol. 16, No.2, Tahun 2014
Publisher : Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (671.668 KB) | DOI: 10.14710/bioma.16.2.83-89

Abstract

Magelang duck is a wild type of local duck from Indonesia. The advantagesof Magelangduckcompare tootherlocalduck from Indonesiaareabilityto livein the highlandsandlowlands and high production of egg and meat. Geneticcharacterization of Magelangduck still not available until now.The aim of the research is selectprimers forampliflying COIgeneof mitochondrialDNAof MagelangduckusingLCO-HCO, bird-f1 -HCO, andbcl-bch primers.The research methodwas DNAisolationfrom Magelangduck. Followed by, selection of primer in silicoto find homologywithin COIsequenceusing ClustalX, Genedoc, and FastPCR programs. Amplification of COIgenewas performedusing PCRwith all primerpairs. Result showed partial homology with all primer in COI sequence. TheamplificationusingtheLCO-HCO primer produced  primerdimer.Primerbirdf1-HCOand bch-bcl primers showed no amplification.   Key words: Magelang duck, COI gene, mitochondrial DNA, primer
Prediksi Resistensi Udang Vaname (Litopenaus vannamei) terhadap Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV) dari Tambak Intensif dan Semi Intensif Jepara Menggunakan Marka RAPD Mulyadi, Muhammad; Handayani, Christina Ratna; Kusumaningrum, Hermin Pancasakti; Budiharjo, Anto
Bioma : Berkala Ilmiah Biologi Vol. 15, No.2, Tahun 2013
Publisher : Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (91.931 KB) | DOI: 10.14710/bioma.15.2.73-80

Abstract

Infectious Hypodermal and Hematopoietic Necrosis Infectious Virus (IHHNV) is the most important DNA virus which can lead to Runt Deformity Syndrome (RDS) in vaname shrimp. The RAPD technique can be used to determine the resistance of a species to a disease. This research aimed to screen and identify RAPD markers which could distinguish the resistance of vaname shrimp to IHHNV reared at intensive and semi-intensive pond. The DNA template was amplified by PCR using 5 primers : OPA 06, OPA 08, OPA 19, OPD-02 and OPZ-15. The results showed that only the primer OPA-19 and OPZ-15 were able to produce 100% polymorphic bands with sizes from 400-1700 bp as well as showing the resistance IHHNV in vaname shrimp. Based on these results, vaname shrimp which reared at the intensive pond were more resistant to IHHNV compared with the semi-intensive pond.   Key words: RAPD, shrimp vaname, IHHNV, intensive & semi-intensive pond  
Kloning dan Sekuensing Gen Xilanase dengan Produk Gen Berukuran 30 kDa dari Bacillus halodurans CM1 pada Escherichia coli DH5α Safirah, Dearesty; Helianti, Is; Kusumaningrum, Hermin Pancasakti; Budiharjo, Anto
Bioma : Berkala Ilmiah Biologi Vol. 18, No.2, Tahun 2016
Publisher : Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (98.71 KB) | DOI: 10.14710/bioma.18.2.167-172

Abstract

The paper industry contributed the environment pollution due to chlor substances. Utilization of alkalothermophilic xylanase enzyme as a biocatalyst in the production of paper may become an environmentally friendly biobleaching alternative. Bacillus halodurans CM1 produces xilanase enzyme that had optimal activity at pH 9 and temperature 70°C. Previous study showed that this CM1 strains has several xilanase genes. The cloning of one of these alkalothermophiic xylanase (alkxyn) gene has been already conducted. This study aimed to clone alkxyn gene that encode alkalothermophilic xylanase enzyme from B. halodurans CM1 into Escherichia coli DH5α. Amplification of alkxyn has been carried out using primers for amplification xylanase 30 kDa. The alkxyn gene fragment was inserted into pGEM-T Easy vector and then transformed into E. coli DH5α. The results showed that the recombinant of E. coli DH5α harboring alkxyn gene from B. halodurans CM1 has been obtained. The sequences analysist based on BLAST showed that alkxyn fragment has homology (99%) with the alkaliphilic xylanase gene from Bacillus sp. 31 which encodes alkaliphilic xilanase (Genebank assession number: JF912895.1). Keywords: cloning, Bacillus halodurans CM1, xylanase, alkalothermophilic.
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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (724.895 KB)

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%.
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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (3251.83 KB)

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