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Cloning ORF2 Membrane Protein of Koi Herpesvirus Lake Toba, Indonesian Isolate

HAYATI Journal of Biosciences Vol 16, No 2 (2009): June 2009
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Koi herpesvirus (KHV) caused significant morbidity and mortality in koi and common carp. KHV which showed strong antigenic property implied that KHV virion or proteins may be used as antigen to raise antibody or vaccine to increase the resistance. The objectives of this research were to (i) clone KHV membrane protein ORF2, (ii) analysis on immunogenicity, and (iii) genetic tracing. Based on genbank data, one pair of primers was designed to amplify KHV ORF2. The KHV ORF2 can be amplified using infected fish DNA which originally from Toba Lake, Sumatera, Indonesia. The KHV ORF2 composed of 699 nucleotides encoded for 292 amino acids. BLAST analysis showed that KHV ORF2 had 100% homology with KHV-J and KHV0301 strains from Japan; 98 and 91% homology on nucleotides and amino acids respectively with both KHV-U strain from Unites State and KHV-I strain from Israel. KHV in Indonesia was most likely to have originated from Japan via spreading directly or not directly to China or Hongkong. Based on T- and B-cell epitopes prediction, membrane protein ORF2 was proposed has a potency to be used in development vaccine and immunodetection. Key words: genetic tracing, koi herpesvirus (KHV), membrane protein, ORF2

Metode Loop-Mediated Isothermal Amplification (LAMP) dan Aplikasinya untuk Deteksi Penyakit Ikan

Jurnal Perikanan Universitas Gadjah Mada Vol 8, No 1 (2006)
Publisher : Universitas Gadjah Mada

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Abstract

Polymerase chain reaction (PCR) is a method that amplifies DNA which have been widely used in molecular biology technique. Based on the PCR, many methods have been developed on isothermal condition and the useful one is loop-mediated isothermal amplification of DNA (LAMP). LAMP reaction employs a Bst DNA polymerase and a set of four specific primers that recognizes a total of six distinct sequences of the target DNA and produces amount of different size of DNA. Many advantages have been achieved in LAMP such as the simple equipment for reaction and observation, short time, highly specific and sensitive procedure. LAMP has been used as a tools for detection many pathogens for human, animals and plants. Some fish pathogens as parasites, bacteria and viruses have been detected by LAMP. The principles and application of LAMP method are discussed in this paper.

ISOLASI, KARAKTERISASI, DAN PATOGENITAS BAKTERI PENYEBAB PENYAKIT PADA GURAMI (Osphronemus goramy) DI KABUPATEN BANTUL

Jurnal Perikanan Universitas Gadjah Mada Vol 15, No 2 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

Gouramy (Osphronemusgoramy) is an important fish comodity and preferred to be consumed by people. One of the limiting factor in freshwater aquaculture is bacterial infections. The objective of this research was to identify the species of pathogenic bacteria on gourami from Bantul Regency and to determine their pathogenicity. Eighteen diseased gouramy were collected from seven different fi sh farms. Bacteria were isolated from kidney and purifyon TSA medium. Characterization was conducted on the morphology of bacterial colonies and cells, biochemical tests. Koch Postulate Test was done to confirm pathogenic properties of the isolated bacteria. Pathogenicity test was performed by intraperitoneal injection of a serial doses of bacteria into gouramy and the Lethal Dosage 50 (LD50) was calculated. Twenty isolates of Aeromonas hydrophila, 5 isolates of Aeromonas salmonicida and one isolate of Vibrio cholerae,Vibrio anguillarum and Pseudomonas fluorescens respectively were isolated from and confi rmed as pathogen ingouramy. Pathogenic diversity was found among isolated bacteria, which a group of virulent bacteria as Aeromonas hydrophila GBNB, GGRB, and GCMA3 with LD50 values of 6.28 x 105, 2.09 x 105 and 5.37 x 105 CFU /fish; and a group of non virulent bacteria as A. hydrophila GKRA isolate and Vibrio cholera GPDA isolat with LD50 value of 7.14 x 107 and 3.45 x 107 CFU/fish respectively.

GENETIC GAIN DAN DIFFERENTIAL SELECTION CALON INDUK NILA PUTIH (Oreochromis sp.) JANTI STRAIN SINGAPURA F5 UMUR 5 BULAN YANG DIPELIHARA DI KOLAM AIR DERAS

Jurnal Perikanan Universitas Gadjah Mada Vol 15, No 1 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

The purpose of this research was to observe the genetic gain value of 5 months white tilapia breeders of fi fth generation (F5) Singapore strain (ss) Janti compared with fourth generation (F4) and to revealed the differential selection value of 5 months white tilapia breeders of F5 ss Janti from average weight of top 100 compared to average weight of the population. Research was done for 5 months white tilapia (Oreochromis sp.) breeders of F5 ss Janti. The tilapia cultured in running water system for a month. The research performed for 5 months white tilapia breeders of ss Janti through individual selection method (selective breeding). The white tilapia breeders ss strain used in this research consisted of 400 male and 400 female. The selection of the white tilapia was done randomly. Parameter measured included total weight, length, survival rate, feed amount and water quality for culturing. The result showed that the F5 had increased growth weight of each individual with genetic gain value against the F4 was 30.12 % for the male and 27.92 % for female. The genetic gain value was better than several other selective breeding of tilapia before. The top 100 average weight of the 5 months white tilapia Janti breeders of F5 ss strain (184.03 ± 22.87 g to 224.88 ± 24.31 g) was  higher than average weight of the population (131.27 ± 38.98 g to 163.31 ± 47.17 g). The differential selection value of white tilapia breeders was 37.70 g for male and 40.19 g for female. The weight of male tilapia population was less various than female ones.

ISOLASI DAN IDENTIFIKASI BAKTERI Aeromonas sp. DARI LELE DUMBO (Clarias sp.) DI KABUPATEN NGAWI

Jurnal Perikanan Universitas Gadjah Mada Vol 18, No 2 (2016)
Publisher : Universitas Gadjah Mada

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Abstract

Lele dumbo (Clarias sp.) merupakan satu jenis ikan air tawar penting yang digemari oleh masyarakat karena memiliki banyak kelebihan. Bakteri.Aeromonas merupakan  penyakit berbahaya pada budidaya air tawar. Penelitian ini bertujuan untuk mengisolasi, mengidentifikasi dan mengetahui pathogenisitas bakteri Aeromonas spp. dari lele dumbo dari Kabupaten Ngawi.  Sampel ikan lele berukuran 20-25 cm yang menunjukkan gejala sakit diperoleh dari kolam pembesaran di 3 kecamatan. Bakteri disisolasi dari ginjal diinokulasikan pada medium GSP. Karakterisasi dan identifikasi bakteri melalui pengamatan morfologi koloni, sel, dan sifat biokimia. Pembuktian sifat patogen dengan uji Postulat Koch. Tingkat patogensitas dianalisis dengan mengukur nilai Lethal Dosage 50  pada benih  lele ukuran 7-9 cm. Hasil pengamatan menunjukkan gejala penyakit pada ikan yang terserang bakteri berupa luka borok pada kulit, pembengkakan pada bagian perut dan kerusakan ginjal. Isolasi bakteri yang diperoleh berjumlah 15 yang terdiri dari lima, enam dan empat isolat yang masing masing berasal dari Kecamatan Karang Jati, Geneng dan Paron. Hasil identifikasi menunjukkan bahwa 12 isolat (GKJ1, GKJ3, GKJ4, GGN1, GGN2, GGN3, GGN4, GGN5, GGN6, GPR2, GPR3 dan GPR4 teridentifikasi sebagai bakteri Aeromonas hydrophila. Tiga isolat (GKJ2, GKJ5 dan GPR1) teridentifikasi sebagai bakteri A. salmonicida. Isolat A. hydrophila GKJ1, GKJ4, GGN2, GGN5, GPR2 dan GPR4 bersifat virulen terhadap lele dumbo dengan LD50 1,55 x 105, 3,89 x 105, 7,24 x 105, 2,39 x 105, 6,61 x 104 dan 1,95 x 104 cfu/ikan.   

Cloning ORF2 Membrane Protein of Koi Herpesvirus Lake Toba, Indonesian Isolate

HAYATI Journal of Biosciences Vol 16, No 2 (2009): June 2009
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Original Source | Check in Google Scholar | Full PDF (88.532 KB)

Abstract

Koi herpesvirus (KHV) caused significant morbidity and mortality in koi and common carp. KHV which showed strong antigenic property implied that KHV virion or proteins may be used as antigen to raise antibody or vaccine to increase the resistance. The objectives of this research were to (i) clone KHV membrane protein ORF2, (ii) analysis on immunogenicity, and (iii) genetic tracing. Based on genbank data, one pair of primers was designed to amplify KHV ORF2. The KHV ORF2 can be amplified using infected fish DNA which originally from Toba Lake, Sumatera, Indonesia. The KHV ORF2 composed of 699 nucleotides encoded for 292 amino acids. BLAST analysis showed that KHV ORF2 had 100% homology with KHV-J and KHV0301 strains from Japan; 98 and 91% homology on nucleotides and amino acids respectively with both KHV-U strain from Unites State and KHV-I strain from Israel. KHV in Indonesia was most likely to have originated from Japan via spreading directly or not directly to China or Hongkong. Based on T- and B-cell epitopes prediction, membrane protein ORF2 was proposed has a potency to be used in development vaccine and immunodetection. Key words: genetic tracing, koi herpesvirus (KHV), membrane protein, ORF2

Polikromatik, dimorfisme seksual, dan redeskripsi spesies ikan red devil, Amphilophus amarillo [Stauffer & McKaye, 2002] di Waduk Sermo Yogyakarta

Jurnal Iktiologi Indonesia Vol 18, No 1 (2018): Februari 2018
Publisher : Masyarakat Iktiologi Indonesia (MII )

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Abstract

Red devil has been extensively researched due to extremely high morphometric and chromatophore variations, including the phenomena of polychromatic and trophic polymorphism. The purpose of this study was to identify and observe the phenomenon of sex dimorphism that occurs in polychromatic red devil species which caught in Sermo Reservoir. Fish sample as much as 240 individual was collected from fishermen catch during November 2016-September 2017 by using gill nets, cest nets, and fishing rods. Subsequently, the fish sample was grouped based on color and sex, the namely group of red devil red, red devil black, and red devil reddish black. The morphometric character data of 21 units were measured in each fish sample, whereas the DNA samples were taken from the gill tissue on each species of two individuals. The morphometric character data was analyzed for discriminant distance, while DNA was analyzed by BLAST (Basic Local Allignment Search Tools) from NCBI. The result of the principal component analysis and discriminant function showed the three group of fish can be distinguished by the characters around the head. The T-test of male and female morphometric characters in each fish group showed the phenomenon of sex dimorphism. Canonical and dendrogram diagrams consistently classify the three group of fish as the same species but are segregated by sex so that significantly dimorphism occurs. The mitochondrial sequencing results of the DNA control region show that among the red devil fish group found in the Sermo Reservoir is a species of A. amarillo.AbstrakRed devil telah banyak diteliti karena variasi morfometrik dan kromatofora yang sangat tinggi, termasuk di dalamnya fenomena polikromatisme dan trofik polimorfisme. Penelitian ini bertujuan untuk mengamati polikromatik dan dimor-fisme seksual serta mengidentifikasi spesies red devil di perairan Waduk Sermo Yogyakarta. Contoh ikan sebanyak 240 ekor diambil dari hasil tangkapan nelayan selama bulan November 2016-September 2017 dengan menggunakan jaring insang, jala dan pancing. Selanjutnya contoh ikan dikelompokkan berdasarkan warna dan jenis kelamin, yaitu kelompok red devil merah, red devil hitam, dan red devil merah kehitaman. Data karakter morfometrik sebanyak 21 unit diukur pada setiap contoh ikan, sedangkan contoh DNA diambil dari jaringan insang pada masing-masing kelompok ikan seba-nyak dua ekor. Data karakter morfometrik dianalisis pembedanya, sedangkan DNA dianalisis dengan BLAST (Basic Local Allignment Search Tools) dari NCBI. Hasil analisis komponen utama dan fungsi diskriminan menunjukkan ketiga kelompok ikan dapat dibedakan berdasarkan karakter yang berada di sekitar kepala. Uji t terhadap karakter morfome-trik jantan dan betina pada masing-masing kelompok ikan menunjukkan fenomena dimorfisme seksual. Diagram kanonikal dan dendrogram konsisten mengelompokkan ketiga kelompok ikan tersebut sebagai spesies yang sama, namun terpisah berdasarkan jenis kelamin sehingga sangat nyata terjadi dimorfisme. Hasil sekuensing mitokondria DNA control region menunjukkan seluruh kelompok ikan red devil yang ditemukan di Waduk Sermo merupakan spesies Amphilophus amarillo.

Reproductive biology of largehead hairtails, Trichiurus lepturus Linnaeus, 1758 in the coastal area of Bantul Regency

Jurnal Iktiologi Indonesia Vol 17, No 2 (2017): June 2017
Publisher : Masyarakat Iktiologi Indonesia (MII )

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Abstract

Largehead hairtail (Trichiurus lepturus) is one commodity fish catches with high production and value in Yogyakarta. The purpose of this research is to analyse reproductive aspects of this fish in coastal area of Bantul Regency. Yogyakar-ta. Those aspects are gonadal maturity level, fecundity, and the length at the first gonadal maturity. Fish samples are taken from the catch of fisherman using gillnet with a mesh sizes of 1.75 and 2 inches in the coastal fishing port of Depok and Samas. The fish collected from January to April 2016 with at least 30 individuals every two weeks. The samples are identified to find their sex and measured to know the length, weight, and gonadal maturity level (TKG). The data analyzed include length distribution, weight, sex ratio, gonadosmoatic index, length at the first gonadal maturity (Lm), fecundity and oocyte diameter. The result shows the fish length varies between 52.8 and 86.2 cm, and weight 115 and 567.2 g. The sex ratio between male and female was 1:0.6. Gonad maturity stage II and III are found every month observation while gonad maturity stage IV found in April. Oocyte diameter in the stage of gonadal ma-turity IV was 0.35-1.02 mm, there were two distribution modus so that the spawning expected partial spawner with fec-undity of 24.601 eggs with range was 12.873-33.534 eggs. Fecundity increased as parent’s body length with equation F= 0,434L2.60. Hairtail expected reaching the length of the first gonadal maturity in 65.55 cm, higher than the average captured, namely 63.4 cm. AbstrakIkan layur (Trichiurus lepturus) merupakan salah satu komoditas hasil tangkapan ikan di Daerah Istimewa Yogyakarta dengan jumlah produksi dan nilai yang tinggi. Penelitian ini bertujuan untuk mengkaji aspek reproduksi yang meliputi: tingkat kematangan gonad, fekunditas, dan ukuran ikan kali pertama matang gonad layur di perairan pantai Kabupaten Bantul, Daerah Istimewa Yogyakarta. Sampel ikan dikumpulkan dari hasil tangkapan nelayan yang menggunakan jaring insang dengan ukuran mata jaring 1,75 dan 2 inci di Tempat Pelelangan Ikan Depok dan Samas. Pengumpulan sampel ikan dilakukan pada bulan Januari hingga April 2016 setiap dua minggu sekali minimal 30 ekor. Sampel ikan diidentifikasi jenis kelamin, diukur panjang, bobot tubuh, bobot gonad, dan tingkat kematangan gonad (TKG). Data yang dianalisis meliputi sebaran panjang, bobot, nisbah kelamin, indeks kematangan gonad, ukuran ikan kali pertama matang gonad (Lm), fekunditas, dan diameter telur. Hasil pengamatan menunjukkan kisaran panjang ikan 52,8-86,2 cm dan bobot 115-567,2 g, nisbah betina dan jantan sebesar 1 : 0,6. TKG II dan III ditemukan pada setiap bulan pengamat-an sedangkan TKG IV banyak ditemukan pada bulan April. Diameter telur ikan TKG IV berkisar 0,35-1,02 mm, terda-pat dua modus persebaran sehingga pemijahan diduga bertahap dan fekunditas sebanyak 24.601 butir dengan kisaran 12.873-33.534 butir. Fekunditas meningkat seiring panjang tubuh induk dengan persamaan F = 0,434L2,60. Ukuran ikan layur kali pertama matang gonad diperkirakan pada panjang 65,55 cm, lebih panjang daripada ukuran rata-rata tertangkap, yaitu pada 63,4 cm.

Biologi reproduksi ikan layur, Trichiurus lepturus Linnaeus, 1758 di perairan pantai Kabupaten Bantul

Jurnal Iktiologi Indonesia Vol 17, No 2 (2017): Juni 2017
Publisher : Masyarakat Iktiologi Indonesia (MII )

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Abstract

Largehead hairtail (Trichiurus lepturus) is one commodity fish catches with high production and value in Yogyakarta. The purpose of this research is to analyse reproductive aspects of this fish in coastal area of Bantul Regency. Yogyakar-ta. Those aspects are gonadal maturity level, fecundity, and the length at the first gonadal maturity. Fish samples are taken from the catch of fisherman using gillnet with a mesh sizes of 1.75 and 2 inches in the coastal fishing port of Depok and Samas. The fish collected from January to April 2016 with at least 30 individuals every two weeks. The samples are identified to find their sex and measured to know the length, weight, and gonadal maturity level (TKG). The data analyzed include length distribution, weight, sex ratio, gonadosmoatic index, length at the first gonadal maturity (Lm), fecundity and oocyte diameter. The result shows the fish length varies between 52.8 and 86.2 cm, and weight 115 and 567.2 g. The sex ratio between male and female was 1:0.6. Gonad maturity stage II and III are found every month observation while gonad maturity stage IV found in April. Oocyte diameter in the stage of gonadal ma-turity IV was 0.35-1.02 mm, there were two distribution modus so that the spawning expected partial spawner with fec-undity of 24.601 eggs with range was 12.873-33.534 eggs. Fecundity increased as parent’s body length with equation F= 0,434L2.60. Hairtail expected reaching the length of the first gonadal maturity in 65.55 cm, higher than the average captured, namely 63.4 cm. AbstrakIkan layur (Trichiurus lepturus) merupakan salah satu komoditas hasil tangkapan ikan di Daerah Istimewa Yogyakarta dengan jumlah produksi dan nilai yang tinggi. Penelitian ini bertujuan untuk mengkaji aspek reproduksi yang meliputi: tingkat kematangan gonad, fekunditas, dan ukuran ikan kali pertama matang gonad layur di perairan pantai Kabupaten Bantul, Daerah Istimewa Yogyakarta. Sampel ikan dikumpulkan dari hasil tangkapan nelayan yang menggunakan jaring insang dengan ukuran mata jaring 1,75 dan 2 inci di Tempat Pelelangan Ikan Depok dan Samas. Pengumpulan sampel ikan dilakukan pada bulan Januari hingga April 2016 setiap dua minggu sekali minimal 30 ekor. Sampel ikan diidentifikasi jenis kelamin, diukur panjang, bobot tubuh, bobot gonad, dan tingkat kematangan gonad (TKG). Data yang dianalisis meliputi sebaran panjang, bobot, nisbah kelamin, indeks kematangan gonad, ukuran ikan kali pertama matang gonad (Lm), fekunditas, dan diameter telur. Hasil pengamatan menunjukkan kisaran panjang ikan 52,8-86,2 cm dan bobot 115-567,2 g, nisbah betina dan jantan sebesar 1 : 0,6. TKG II dan III ditemukan pada setiap bulan pengamat-an sedangkan TKG IV banyak ditemukan pada bulan April. Diameter telur ikan TKG IV berkisar 0,35-1,02 mm, terda-pat dua modus persebaran sehingga pemijahan diduga bertahap dan fekunditas sebanyak 24.601 butir dengan kisaran 12.873-33.534 butir. Fekunditas meningkat seiring panjang tubuh induk dengan persamaan F = 0,434L2,60. Ukuran ikan layur kali pertama matang gonad diperkirakan pada panjang 65,55 cm, lebih panjang daripada ukuran rata-rata tertangkap, yaitu pada 63,4 cm.

Penapisan Kapang Laut Penghasil Senyawa Sitotoksik dari Beberapa Perairan di Indonesia

Jurnal Pascapanen dan Bioteknologi Kelautan dan Perikanan Vol 6, No 1 (2011): Juni 2011
Publisher : Balai Besar Riset Pengolahan Produk dan Bioteknologi Kelautan dan Perikanan

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Abstract

ABSTRACTMarine-derived fungi have proven to be a rich source of cytotoxic compounds for the development of new anti cancer drugs. The aims of this research were to: 1) screen cytotoxic activity of marine fungi from Indonesian waters, 2) indentify marine fungus that produced thatproduced the most active cytotoxic compound and 3) investigate inhibition concentration 50 (IC50) value of cytotoxic compound. The fungi were isolated from marine organism collected fromWakatobi Marine National Park-South East Sulawesi, Binuangeun Beach-Banten, Manado watersNorth Sulawesi and Kepulauan Seribu Marine National Park-Jakarta. Liquid cultures of the fungiwere carried out in Malt Extract Broth and Soluble Starch Soytone medium for 4 weeks at 27–28oC without shaking. Molecular identification of fungus was conducted through PCR amplificatin usingprimers of ITS1 and ITS4 primer. Cytotoxic activity of the extract was tested by using MTT (3-(4.4-dimethylthiazol-2-yl)-2.5-diphenyl-tetrazolium bromide) method. The MTT test showed that MFW39strain exhibited the strongest cytotoxic activity. Molecular identification revealed that MFW39 marine fungus was similar to Emericella nidulans with precent identity of 99%. Mycelium and broth extract of MFW39 fungus inhibited the growth of T47D cell with IC 50 values of 21.9 and 169.3 µg/mL, respectively. Further research will be focus on to the strain of MFW39 marine fungi.