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Isolasi dan identifikasi Khamir dari bunga Jatropha integerrima Jack. Asal Kampus Unversitas Indonesia
Abstrak :
Penelitian bertujuan untuk memperoleh informasi keanekaragaman khamir dari bunga Jatropha integerrima Jacq. di kampus Universitas Indonesia, Depok. Khamir diisolasi dari 30 bunga (15 bunga jantan dan 15 bunga betina). Hasil elektroforesis menunjukkan terdapat polimorfisme panjang (300--700 pb) daerah ITS rDNA 26 isolat khamir representatif yang mengindikasikan adanya keragaman genetik di antara isolat tersebut. Berdasarkan data sequence, 26 isolat khamir representatif tersebut secara taksonomi beragam, yaitu terdiri dari 13 species yang berasal dari phylum Ascomycota (class Hemiascomycetes (Candida)) dan dari phylum Basidiomycota (class Urediniomycetes (Sporidiobolus), Ustilaginomycetes (Pseudozyma & Ustilago), dan Hymenomycetes (Bullera & Cryptococcus)).
Universitas Indonesia, 2010
S31632
UI - Skripsi Membership  Universitas Indonesia Library
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Eka Nurhangga
Identifikasi Khamir dari Saluran Pencernaan Lebah Pejantan dan Lebah Pekerja Pengumpul Polen Apis mellifera L. Berdasarkan Data Sequence Daerah ITS rDNA = Identification of Yeasts from Digestive Track of Drone and Pollen Collecting Bees of Apis mellifera L. Based on ITS Region of rDNA Sequence Data
Abstrak :
Penelitian bertujuan untuk mengetahui identitas khamir dari saluran pencernaan lebah madu Apis mellifera L. yang mengunjungi bunga kapuk (Ceiba pentandra (L.) Gaertn) di Jepara. Sebanyak 12 isolat khamir yang terdiri atas 3 isolat dari saluran pencernaan lebah pejantan (drone) dan 9 isolat dari lebah pekerja pengumpul polen (pollen collecting bees, PCB) diidentifikasi berdasarkan data sequence daerah internal transcribed spacer (ITS) rDNA. Primer yang digunakan untuk amplifikasi daerah ITS adalah primer forward ITS1 atau primer reverse ITS4. Hasil elektroforesis produk PCR menunjukkan daerah ITS rDNA khamirkhamir tersebut bervariasi antara 400 pb hingga 750 pb. Berdasarkan hasil pencarian homologi sequence daerah ITS rDNA melalui program basic local alignment search tool (BLAST), analisis filogenetik dengan metode Neighbor Joining, dan pengamatan karakter morfologi, 12 isolat tersebut diidentifikasi ke dalam empat genus dan tujuh spesies. Berdasarkan taksonomi, khamir-khamir tersebut termasuk kedalam family Candidaceae dan Saccharomycetaceae, order Saccharomycetales, class Hemiascomycetes dari phylum Ascomycota. Isolat-isolat tersebut diidentifikasi ke dalam spesies Candida magnoliae (isolat JZ078), C. orthopsilosis (isolat JZ068 dan JZ069), C. parapsilosis (isolat JZ067 dan JZ095), Debaryomyces hansenii (isolat JZ083 dan JZ096), Meyerozyma caribbica (isolat JZ094), Zygosaccharomyces mellis (isolat JZ075), dan Z. siamensis (isolat JZ054,JZ055, dan JZ056). ......The aim of this research was to determine the identity of the yeasts isolated from the digestive tract of honey bee Apis mellifera that visit flowers of kapok (Ceiba pentandra (L.) Gaertn) in Jepara. A total of 12 yeast isolates consist of 3 isolates from digestive tract of drones and 9 isolates from digestive tract of pollen collecting bees (PCB) were identified based on sequence data of internal transcribed spacers regions of ribosomal DNA (ITS rDNA). The primer set of ITS1 (forward primer) and ITS4 (reverse primer) were used to amplify the ITS rDNA of yeasts. The results of electrophoresis of PCR products showed ITS region rDNA of yeast isolates varied between 400bp--750 bp. Based on sequence homology search results by basic local alignment search tool (BLAST) program, phylogenetic analysis by Neighbor Joining method, and morphological characterization, those 12 isolates were identified into four genera and seven species. Taxonomically, 11 isolates belong to family Candidaceae and Saccharomycetaceae, order Saccharomycetales, class Hemiascomycetes of the phylum Ascomycota. Those isolates were identified as species Candida magnoliae (isolat JZ078), C. orthopsilosis (isolat JZ068 and JZ069), C. parapsilosis (isolat JZ067 and JZ095), Debaryomyces hansenii (isolat JZ083 and JZ096), Meyerozyma caribbica (isolat JZ094), Zygosaccharomyces mellis (isolat JZ075), and Z. siamensis (isolat JZ054, JZ055, and JZ056).
Depok: Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Indonesia, 2013
S47074
UI - Skripsi Membership  Universitas Indonesia Library
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Dyah Restu Pamuji
Identifikasi Khamir dari Saluran Pencernaan Lebah Pekerja Pengumpul Polen Apis mellifera L. Berdasarkan Data Sequence Daerah ITS rDNA = Identification of Yeasts Isolated from Digestive Tract of Pollen Collecting Bees Apis mellifera L. Based on ITS Region rDNA Sequence Data
Abstrak :
Penelitian bertujuan mengetahui identitas khamir dari saluran pencernaan lebah pekerja pengumpul polen (pollen collecting bees, PCB) Apis mellifera. Sebanyak 12 isolat khamir dari saluran pencernaan PCB yang mengunjungi bunga kapuk Ceiba pentandra di Jepara, Jawa Tengah, diidentifikasi berdasarkan data sequence daerah internal transcribed spacer (ITS) rDNA. Amplifikasi daerah ITS rDNA menggunakan primer forward ITS1 dan primer reverse ITS4. Elektroforesis produk PCR menunjukkan bahwa daerah ITS rDNA khamir-khamir tersebut berukuran antara 400--900 pb. Berdasarkan hasil pencarian homologi sequence menggunakan program basic local alignment search tool (BLAST), analisis filogenetik menggunakan metode Neighbor Joining (NJ), dan karakterisasi morfologi, 12 isolat khamir tersebut terdiri dari tujuh spesies yang termasuk dalam lima genus. Secara taksonomi, seluruh khamir tersebut termasuk phylum Ascomycota, class Hemiascomycetes, dan order Saccharomycetales. Isolat-isolat tersebut diidentifikasi sebagai Candida magnoliae (isolat JZ002), Candida orthopsilosis (isolat JZ003, JZ008, JZ011, dan JZ034), Candida rugosa (isolat JZ010); Debaryomyces hansenii (isolat JZ001); Meyerozyma caribbica (isolat JZ013 dan JZ014), Pichia guilliermondii (isolat JZ015), dan Zygosaccharomyces siamensis (isolat JZ005 dan JZ006). ......The aim of this study was to obtain the identity of yeasts from digestive tracts of pollen collecting bees (PCB) Apis mellifera. A total of 12 yeast isolates obtained from digestive tract of PCB foraging on flowers Ceiba pentandra in Jepara, Central Java, were identified based on sequence data of internal transcribed spacer of ribosomal DNA (ITS rDNA). The primer set of ITS1 (forward primer) and ITS4 (reverse primer) were used to amplify the ITS region rDNA. Gel electrophoresis result showed that the size of ITS rDNA of those yeast were varied between 400--900 base pairs. Based on sequence homology search using basic local alignment search tool (BLAST) program, phylogenetic analysis by Neighbor Joining method, and morphological characterization, those 12 isolates belong to five genera and seven species. Taxonomically, all of those isolates belong to order Saccharomycetales, class Hemiascomycetes from the phylum Ascomycota. Those 12 isolates were identified as species Candida magnoliae (isolate JZ002); Candida orthopsilosis (isolates JZ003, JZ008, JZ011, and JZ034); Candida rugosa (isolate JZ010); Debaryomyces hansenii (isolate JZ001); Meyerozyma caribbica (isolates JZ013 and JZ014); Pichia guilliermondii (isolate JZ015); and Zygosaccharomyces siamensis (isolates JZ005 and JZ006).
Depok: Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Indonesia, 2013
S46972
UI - Skripsi Membership  Universitas Indonesia Library
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Madinna Rahmadewi
Identifikasi kapang dari manuskrip Cina lama yang mengalami deteriorasi asal plot 1 Perpustakaan Pusat UI berdasarkan daerah ITS rDNA = Moulds identification from deteriorated old Chinese manuscripts from plot 1 Central Library UI based on ITS rDNA region
Abstrak :
Penelitian ini bertujuan untuk mengidentifikasi kapang dari dua manuskrip Cina lama yang mengalami deteriorasi asal plot 1 Ruang Naskah PP-UI Depok berdasarkan data sekuens daerah internal transcribed spacers ribosomal DNA ITS rDNA . Pengambilan sampel kapang dari manuskrip dengan metode swab dan isolasi kapang dengan metode culture-dependent. Amplifikasi daerah ITS rDNA dan DNA sequencing menggunakan primer forward ITS5 dan primer reverse ITS4. Pencarian homologi sekuens daerah ITS rDNA menggunakan program basic local alignment search tool BLAST. Pembuatan pohon filogenetik menggunakan metode Neighbor Joining, model dua parameter Kimura dan bootstrap sebanyak 1.000 kali replikasi. Lima isolat kapang terpilih diperoleh berdasarkan tipe morfologi yang berbeda dengan kapang dari manuskrip Cina lama asal plot 2, 4, 5, dan 6. Hasil elektroforesis gel produk PCR daerah ITS rDNA menunjukkan lima strain memiliki ukuran fragmen ITS rDNA dengan kisaran 500--700 pb dan DNA sequencing menunjukkan panjang daerah ITS rDNA berkisar 579--610 pb. Lima strain UICC merupakan anggota dari dua kelas Class Eurotiomycetes dan Dothideomycetes , dua ordo Order Eurotiales dan Capnodiales serta tiga famili Family Aspergillaceae, Cladosporiaceae dan Trichocomaceae. Strain UICC 1099 dan UICC 1102 memiliki homologi 99,4 dan 99,8 dengan type strain Aspergillus pseudodeflectus NRRL 6135T. Strain UICC 1103 memiliki homologi 99,7 dengan type strain Cladosporium colocasiae ATCC 200944 T. Strain UICC 1101 memiliki homologi 99,8 dengan type strain Penicillium coffeae NRRL 35363T. Strain UICC 1100 memiliki homologi 99,4 dengan type strain Penicillium mallochii DAOM 239917T. Lima strain UICC merupakan fungi anamorf dan bersifat xerofilik. ......The objective of this study was to identify moulds isolated from two deteriorated old Chinese manuscripts from plot 1 Ruang Naskah Central Library Universitas Indonesia Depok based on sequence data of internal transcribed spacer regions of ribosomal DNA ITS rDNA . Sterile cotton swab was used to obtain samples and culture dependent method was used to isolate moulds. Forward primer ITS5 and reverse primer ITS4 were used to amplify ITS rDNA region and sequencing the DNA. Basic Local Alignment Search Tool BLAST program was used to determine the sequence homology of ITS rDNA region. A phylogenetic tree was constructed by Neighbor Joining method with Kimura rsquo s two parameter model and bootstrap with 1,000 replicates. Five selected mould isolates were obtained based on the morphological type differences compared to moulds from old Chinese manuscripts from plot 2, 4, 5, and 6. Gel electrophoresis showed that the fragment lengths of ITS rDNA region from five strains were on the range of 500 700 bp and DNA sequencing showed that the length variations of ITS DNA fragments were 579 to 610 bp. The five UICC strains belonged to two classes Class Eurotiomycetes and Dothideomycetes , two orders Order Eurotiales and Capnodiales and three families Family Aspergillaceae, Cladosporiaceae and Trichocomaceae. UICC 1099 and UICC 1102 strains showed 99.4 and 99.8 homologies with their type strain Aspergillus pseudodeflectus NRRL 6135T. UICC 1103 strain has 99.7 homology with its type strain Cladosporium clocasiae ATCC 200944T. UICC 1101 strain has 99.8 homology with its type strain Penicillium coffeae NRRL 35363T. UICC 1100 strain has 99.4 homology with its type strain Penicillium mallochii DAOM 239917T. The five UICC strains are anamorphic and xerophilic fungi.
Depok: Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Indonesia, 2017
S69876
UI - Skripsi Membership  Universitas Indonesia Library
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Mazytha Kinanti Rachmania
Identifikasi kapang dari manuskrip cina lama yang mengalami deteriorasi asal plot 5 Perpustakaan Pusat UI berdasarkan daerah ITS RDNA = moulds identification from deteriorated old chinese manuscripts from plot 5 central library ui based on ITS region of RDNA
Abstrak :
ABSTRAK
Penelitian ini bertujuan untuk memperoleh identitas spesies kapang dari dua manuskrip Cina lama yang mengalami deteriorasi asal plot 5 Ruang Naskah Perpustakaan Pusat Universitas Indonesia PP-UI , Depok berdasarkan data sekuens daerah internal transcribed spacers ribosomal DNA ITS rDNA . Pengambilan sampel pada manuskrip menggunakan metode swab dengan cotton bud steril. Isolasi kapang menggunakan metode culture-dependent. Polymerase chain reaction PCR dan DNA sequencing menggunakan primer forward ITS5 dan primer reverse ITS4. Pencarian homologi sekuens daerah ITS rDNA menggunakan program basic local alignment search tool BLAST dan pembuatan pohon filogenetik menggunakan metode Neighbor Joining, model dua parameter Kimura, serta bootstrap sebanyak 1.000 kali replikasi. Penentuan spesies terdekat dan posisi taksonomi menggunakan analisis filogenetik dan didukung oleh data morfologi. Isolasi kapang menghasilkan enam isolat kapang terpilih berdasarkan tipe morfologi yang berbeda dengan kapang dari manuskrip Cina lama asal plot 1, 2, 4, dan 6 Ruang Naskah PP-UI, Depok. Berdasarkan elektroforesis gel, panjang fragmen daerah ITS rDNA dari enam isolat kapang bervariasi antara 600--700 pb. Hasil DNA sequencing lengkap menunjukkan panjang daerah ITS rDNA enam isolat berkisar 582--625 pb. Enam strain UICC merupakan anggota dari tiga kelas Dothideomycetes, Eurotiomycetes dan Sordariomycetes , tiga ordo Capnodiales, Eurotiales dan Hypocreales , dan empat famili Cladosporiaceae, Nectriaceae, Ophiocordycipitaceae, dan Pleosporaceae . Strain UICC 1107 memiliki homologi 99,32 dengan type strain Purpureocillium lilacinum sin. Paecilomyces lilacinus ATCC 10114T. Lima strain UICC tidak dapat ditentukan spesiesnya. Strain UICC 1106 adalah Cladosporium sp. dengan homologi 100 terhadap type strain Cladosporium oxysporum CBS 125991T dan Cla. tenuissimum CPC 14235T. Strain UICC 1105 adalah Curvularia sp.1 dengan homologi 93,80 dan strain UICC 1108 adalah Curvularia sp.2 dengan homologi 94,70 terhadap type strain Curvularia carica-papayae CBS 135941T. Strain UICC 1109 adalah Rectifusarium sp. dengan homologi 85,87 terhadap type strain Rectifusarium robinianum CBS 430.91T. Strain UICC 1104 adalah Sarocladium sp. dengan homologi 97,13 terhadap type strain Sarocladium bifurcatum UTHSC 05-3311T. Enam strain UICC merupakan fungi anamorf dan bersifat xerofilik.
ABSTRACT The aim of this study was to determine the species identity of moulds from two deteriorated old Chinese manuscripts from plot 5 Ruang Naskah Central Library Universitas Indonesia, Depok based on internal transcribed spacers region of ribosomal DNA ITS rDNA . Samples from the manuscripts were collected by using swab method with sterile cotton swabs. Mould isolates were obtained by culture dependent method. Polymerase chain reaction PCR and DNA sequencing were performed using forward primer ITS5 and reverse primer ITS4. Homology search of ITS rDNA sequences was carried out using basic local alignment search tool BLAST program and phylogenetic tree construction was performed using Neighbor Joining method, Kimura rsquo s two parameter model, and bootstrap 1,000 replicates. The closest species and taxonomic position were obtained by phylogenetic analysis and supported by morphological data. Six mould isolates were selected based on morphological type differences compared to mould isolates from old Chinese manuscripts from plot 1, 2, 4, and 6 Ruang Naskah Central Library UI, Depok. Based on gel electrophoresis, the lengths of ITS rDNA fragments of six mould isolates varied between 600 700 bp. Full sequence data of ITS rDNA of six isolates showed that the lengths of their ITS rDNA varied between 582 625 bp. Six UICC strains belonged to three classes Dothideomycetes, Eurotiomycetes and Sordariomycetes , three orders Capnodiales, Eurotiales and Hypocreales , and four families Cladosporiaceae, Nectriaceae, Ophiocordycipitaceae, and Pleosporaceae . UICC 1107 strain showed 99.32 homology to the type strain, Purpureocillium lilacinum syn. Paecilomyces lilacinus ATCC 10114T. Five UICC strains were not able to be determined to the species level. UICC 1106 strain was identified as Cladosporium sp., with 100 homology to the type strains, Cladosporium oxysporum CBS 125991T and Cla. tenuissimum CPC 14235T. UICC 1105 strain was identified as Curvularia sp.1, with 93.80 homology and UICC 1108 strain was identified as Curvularia sp.2, with 94.70 homology to the type strain, Curvularia carica papayae CBS 135941T. Strain UICC 1109 was identified as Rectifusarium sp., with 85.87 homology to the type strain, Rectifusarium robinianum CBS 430.91T. Strain UICC 1104 was identified as Sarocladium sp., with 97.13 homology to the type strain, Sarocladium bifurcatum UTHSC 05 3311T. Six UICC strains were anamorphic and xerophilic fungi.
Depok: Universitas Indonesia, 2016
S66193
UI - Skripsi Membership  Universitas Indonesia Library
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Floreta Fiska Yuliarni
Studi filogenetik dan analisis host specificity cercospora spp berdasarkan data sequence daerah its rdna gen elongation factor 1 dan gen calmodulin = Phylogenetic study and host specificity analysis of cercospora spp based on its region of rdna elongation factor 1 gene and calmodulin gene sequences / Floreta Fiska Yuliarni
Abstrak :
ABSTRAK
Penelitian bertujuan menganalisis hubungan kekerabatan spesies-spesies Cercospora berdasarkan data sequence daerah Internal Transcribed Spacers (ITS) rDNA, gen elongation factor 1-α (EF), dan gen calmodulin (CAL); mengetahui lokus yang paling baik dalam memisahkan spesies-spesies Cercospora; dan menguji host specificity Cercospora spp. dengan tanaman inangnya. Pada penelitian ini telah dilakukan amplifikasi dan sequencing daerah ITS rDNA, gen EF, dan gen CAL pada 14 spesies dari 23 strain Cercospora yang berasal dari tiga famili tanaman inang (Asteraceae, Cucurbitaceae, dan Solanaceae). Pohon filogenetik dibangun menggunakan metode Neighbor-Joining, Maximum Parsimony, dan Bayesian. Hasil penelitian menunjukkan bahwa pohon filogenetik berdasarkan data sequence daerah ITS rDNA tidak dapat menjelaskan hubungan kekerabatan antarspesies pada genus Cercospora; sebagian besar Cercospora (57 dari 61 OTU) berada dalam satu kelompok besar yang jarak cabangnya berimpit satu dengan lainnya. Pohon filogenetik berdasarkan data sequence gen EF dapat menjelaskan hubungan kekerabatan beberapa spesies Cercospora, walaupun sebagian spesies Cercospora (24 OTU) berada dalam satu kelompok yang jarak cabangnya berimpit satu dengan lainnya. Pohon filogenetik berdasarkan data sequence gen CAL dapat menjelaskan hubungan kekerabatan sebagian besar spesies Cercospora, jarak cabang terlihat lebih panjang dibandingkan pada pohon filogenetik berdasarkan data sequence gen EF, walaupun beberapa spesies Cercospora (16 OTU) belum dapat dipisahkan. Hasil analisis filogenetik menunjukkan bahwa spesies-spesies Cercospora tidak dapat dipisahkan berdasarkan data sequence daerah ITS rDNA, akan tetapi sebagian spesies dapat dipisahkan berdasarkan data sequence gen EF dan gen CAL. Pohon filogenetik berdasarkan data sequence gen CAL menunjukkan bahwa gen tersebut dapat digunakan untuk memisahkan spesies-spesies Cercospora lebih baik daripada daerah ITS rDNA dan gen EF. Hasil analisis filogenetik berdasarkan data sequence multilokus menunjukkan bahwa 11 dari 14 spesies Cercospora yang digunakan dalam penelitian tidak host-specific, hanya tiga spesies yaitu C. zinniicola, C. cocciniae, dan C. mikaniicola yang spesifik terhadap inangnya.
ABSTRACT
The aims of this study were to analyze the phylogenetic relationships of Cercospora spp. based on sequence data of the internal transcribed spacer (ITS) region of rDNA, elongation factor 1-α (EF), and calmodulin (CAL) genes; to determine the best locus in separating Cercospora species; and to investigate the host specificity of Cercospora spp. In this study, the sequences of the ITS region of rDNA, EF, and CAL genes of 23 strains which belong to 14 species of Cercospora from three host plants families were amplified and sequenced. The phylogenetic trees of the Cercospora spp. were constructed by Neighbor-Joining, Maximum Parsimony, and Bayesian methods. Our result showed that phylogenetic relationship of Cercospora at the species level could not be resolved by ITS rDNA; most of Cercospora species (57 OTU) were grouped in one major clade with no branch length differences among species. The EF phylogenetic tree, showed that some species of Cercospora could be separated, although 24 OTU were grouped into one clade with no branch length differences. The CAL phylogenetic tree showed that the majority of Cercospora species could be separated with longer branch compared to the EF phylogenetic tree, although several species (16 OTU) could not be separated. The phylogenetic analyses showed that most of Cercospora species could not be separated in the ITS rDNA tree, however those species could be separated in the EF and CAL phylogenetic trees. The results showed that CAL gene was the best locus in separating Cercospora species compared to ITS rDNA and EF gene. Molecular phylogenetic analysis from multiloci (ITS regions of rDNA, EF gene, and CAL gene) revealed that 11 out of 14 species of Cercospora have no host specificity (have a wide host range) and only three species e.g., C. zinniicola, C. cocciniae, and C. mikaniicola showed host specificity.
Depok: Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Indonesia, 2014
T42002
UI - Tesis Membership  Universitas Indonesia Library