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"Biofuling is the undesirable accumulation of microorganisms, plants, algae and animals on submerged structures espicially ship hulls...."

"ABSTRAKHelicobacter pylori diperkirakan menginfeksi lebih dari setengah populasi orang dewasa. Deteksi dini H.pylori sangat diperlukan untuk mencegah berkembangnya infeksi menjadi keganasan lambung. Bentuk coccoid dari H. pylori sulit dideteksi dengan kultur dan histopatologi, namun dapat terdeteksi dengan metode molekuler seperti real-time PCR. Salah satu gen yang dapat digunakan sebagai gen target real-time PCR yaitu 16S rRNA, yang diketahui spesifik dan juga digunakan untuk menganalisis kekerabatan antar strain. Analisis ini bermanfaat untuk melihat penyebaran infeksi H.pylori di dunia. Penelitian ini merupakan penelitian eksperimental laboratorium. Metode pengambilan sampel yang digunakan yaitu, metode consecutive sampling. Biopsi diambil dari 2 antrum dan 2 korpus pada 42 penderita dispepsia untuk pemeriksaan real-time PCR dan histopatologi. Optimasi kondisi real-time PCR meliputi uji volume cetakan DNA, sensitifitas dan spesifisitas teknik, kemudian dilanjutkan aplikasi pada sampel klinis dari biopsi lambung. Delapan dari 11 sampel yang positif dilakukan sekuensing dan analisis filogenetik. Hasil optimasi diperoleh suhu annealing 64?C, konsentrasi primer 0,8 ?M dan konsentrasi probe 0,6 ?M. Ambang batas deteksi real-time PCR untuk mendeteksi jumlah DNA minimal H.pylori yaitu 46 bakteri. Spesifisitas uji reaksi silang real-time PCR ini tidak menunjukkan adanya reaksi silang dengan mikroorganisme lain. Proporsi positif hasil pemeriksaan real-time PCR sebesar 26,2 , sedangkan histopatologi sebesar 11,9 . Pemeriksaan real-time PCR mampu meningkatkan diagnosis sebesar 14,3 dibandingkan pemeriksaan histopatologi. Hasil sekuensing dan analisis filogenetik menunjukkan bahwa strain H.pylori dari sampel memiliki kekerabatan dengan strain Taiwan, India, dan Australia. Kata kunci : H.pylori, histopatologi, real-time PCR, analisis filogenetik

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ABSTRACTHelicobacter pylori infection is estimated infect almost half of the adult population in the world. Early detection of H.pylori is needed to prevent the development of infections into gastric malignancies. The coccoid form of H. pylori is difficult to detect using culture and histopathology but it can be detected by molecular methods such as real time PCR. One of the genes that can be used as a real time PCR target gene is 16S rRNA, which is known to be specific and also used to analyze closely related strain. This analysis were useful to showed the spread of H.pylori infection in the world.This study is an experimental laboratory. The sampling method used is the consecutive sampling method. Biopsy was taken from 2 antrum and 2 corpus in 42 patients with dyspepsia for real time PCR and histopathology examination. Optimization real time PCR conditions include DNA template volume testing, sensitivity and specificity of the technique, followed by application of clinical samples from gastric biopsy. Eight of the 11 positive samples were sequenced and analyzed for phylogenetics pattern. The optimization result obtained annealing temperature 64 C, primer concentration was 0,8 M and probe concentration was 0,6 M. Limit detection of the DNA was 46 bacteria. The specificity of the PCR 39 s real time indicate that there was no cross reaction with other microorganisms. The positive proportion of PCR real time examination was 26.2 , while histopathology was 11.9 . A real time PCR examination was able to improve the diagnosis by 14,3 compared to histopathology examination. Sequencing and phylogenetic analysis results showed that our strain were closely related to Taiwan, India and Australia strains. Keywords H.pylori, histopathology, real time PCR, phylogenetic analysis"

"Molecular biological techniques support the identification of microalgae of Vietnam.Prprocentrum,Alexandrium and Pseudo-nitzschia are main harmful and toxic microalgal genera found in Vietnam coastal waters...."

"Universitas Indonesia Culture Collection (UICC) memiliki koleksi strain-strain Rhizopus oryzae Went dan Prinsen Geerligs yang diisolasi dari tempe dan telah diidentifikasi berdasarkan karakter fenotipik (morfologi dan fisiologi). Tujuan penelitian adalah melakukan re-identifikasi lima strain R. oryzae (UICC 10, UICC 85, UICC 119, UICC 120, dan UICC 135) berdasarkan data sequence daerah internal transcribed spacers ribosomal DNA dan analisis filogenetik untuk memperoleh identitas spesies yang akurat. Amplifikasi dan sequencing daerah ITS rDNA dilakukan menggunakan primer forward ITS 5 dan primer reverse ITS 4. Data sequence dikirim ke database DNA GenBank untuk pencarian homologi dengan program BLAST. Sequence alignment dilakukan menggunakan program Clustal X. Konstruksi pohon filogenetik dilakukan menggunakan metode Neighbor Joining, model dua parameter Kimura, dan nilai bootstrap 1000 kali pengulangan. Karakterisasi morfologi dan pengujian kemampuan tumbuh pada variasi suhu dilakukan untuk mendukung hasil re-identifikasi dan melengkapi deskripsi strain masing-masing. Hasil amplifikasi daerah ITS rDNA menunjukkan bahwa kelima strain R. oryzae UICC memiliki panjang fragmen dengan ukuran 600--700 pb. Hasil pencarian homologi BLAST menunjukkan bahwa kelima strain memiliki homologi 99,8% terhadap type strain R. oryzae CBS 112.07T. Hasil analisis filogenetik menunjukkan bahwa kelima strain berada dalam satu grup yang monofiletik dengan strain tipe R. oryzae CBS 112.07T dan strain-strain R. oryzae dari database DNA GenBank, dengan dukungan nilai bootstrap yang tinggi (84%). Re-identifikasi lima strain R. oryzae UICC secara molekuler menghasilkan identitas spesies yang sama, yaitu sebagai R. oryzae, dan didukung oleh karakter morfologi dan fisiologi.

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Universitas Indonesia Culture Collection (UICC) has collection of Rhizopus oryzae Went and Prinsen Geerligs strains, which were isolated from tempeh. These strains were identified based on phenotypic characters (morphology and physiology). The aim of this study was to re-identify five strains of R. oryzae (UICC 10, UICC 85, UICC 119, UICC 120, and UICC 135), based on internal transcribed spacers (ITS) region of ribosomal DNA sequence data to obtain accurate identification at species level.

Amplification and sequencing of ITS region of rDNA were performed using primer set, forward primer ITS 5 and reverse primer ITS 4. The sequence data was sent to GenBank DNA database for homology search using BLAST. Sequence alignment was carried out using Clustal X. Construction of phylogenetic tree was performed using Neighbor Joining method, Kimura's two parameter model and bootstrap values of 1000 iterations. Characterization of the five strains based on morphology and growth ability at temperature variations were carried out to support the description of each strain.

Amplification result showed that the strains have fragment length of ITS region of rDNA about 600--700 bp. Results of BLAST homology search of the strains showed a very high similarity (99.8%) to the type strain R. oryzae CBS 112.07T. Phylogenetic tree showed that the five strains were clustered together in a monophyletic group with the type strain R. oryzae CBS 112.07T and other R. oryzae strains from GenBank DNA database, and supported by high bootstrap value (84%). Re-identification of five strains of R. oryzae UICC based on molecular method showed that they were identified as R. oryzae, similar to previous identification, and supported by morphological and physiological characterization."

"Universitas Indonesia Culture Collection UICC memiliki koleksi Rhizopus spp. yang diisolasi dari tempe dan telah diidentifikasi berdasarkan karakter morfologi dan fisiologi. Tujuan penelitian adalah re-identifikasi lima strain R. oligosporus koleksi UICC UICC 27, UICC 40, UICC 51, UICC 67, dan UICC 116 berdasarkan data sequence daerah internal transcribed spacers rDNA dan analisis filogenetik. Amplifikasi dan sequencing daerah ITS rDNA menggunakan pasangan primer forward ITS5 dan primer reverse ITS4. Data sequence daerah ITS rDNA Rhizopus koleksi UICC dikirim ke database GenBank untuk pencarian homologi BLAST terhadap spesies terdekat dengan pembatasan pencarian hanya pada type material. Pembuatan pohon filogenetik menggunakan metode neighbor joining dengan model evolusi dua parameter Kimura, serta bootstrapping dilakukan sebanyak 1000 kali pengulangan. Karakterisasi morfologi makroskopik dan mikroskopik dan fisiologi pertumbuhan pada variasi suhu dilakukan untuk menunjang hasil identifikasi molekuler. Hasil elektroforesis gel produk PCR daerah ITS rDNA menunjukkan kelima strain memiliki ukuran fragmen ITS rDNA pada kisaran 500--700 pb, dan hasil sequencing lengkap daerah ITS rDNA kelima strain menunjukkan panjang berkisar antara 655--658 pb. Hasil BLAST menunjukkan strain UICC 27, UICC 40, UICC 51, dan UICC 67 memiliki homologi 99,2 ; sedangkan strain UICC 116 memiliki homologi 99,8 terhadap type strain R. oryzae CBS 112.07T. Berdasarkan konsep spesies filogenetik, strain UICC 27, UICC 40, UICC 51, dan UICC 67 dapat diidentifikasi sebagai R. delemar karena pada pohon filogenetik berada dalam satu kelompok yang monofiletik dengan type strain R. delemar CBS 120.12T, dengan dukungan nilai bootstrap 90 ; sedangkan strain UICC 116 diidentifikasi sebagai R. oryzae karena pada pohon filogenetik berada dalam satu kelompok yang monofiletik dengan type strain R. oryzae CBS 112.07T , dengan dukungan nilai bootstrap 82 . Hasil penelitian menunjukkan bahwa kedua spesies tidak dapat dibedakan secara morfologi, kelima strain menunjukkan karakter morfologi yang sesuai dengan R. oryzae. Namun demikian, terdapat perbedaan karakter fisiologi antara R. oryzae dan R. delemar, yaitu pertumbuhan pada variasi suhu.

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Universitas Indonesia Culture Collection UICC has strains collection of Rhizopus spp. which were isolated from tempeh and identified based on phenotypic characters morphology and physiology . The aim of this study was to re identify five strains of R. oligosporus UICC 10, UICC 85, UICC 119, UICC 120, and the UICC 135 , based on internal transcribed spacers region of ribosomal DNA sequence data and phylogenetic analysis. Amplification and sequencing of ITS region of rDNA were performed using primer set forward primer ITS 5 and reverse primer ITS 4. The sequence data was sent to GenBank for homology search using basic local alignment search tool BLAST program, restricted only to type materials. Construction of phylogenetic tree was performed using Neighbor Joining method with Kimura's two parameter evolution model and bootstrapping with 1,000 replicates. Characterization of morphological and physiological growth at variation of temperature data was carried out to support molecular identification results. Gel electrophoresis showed that five strains have fragment length of ITS region of rDNA, about 500 700 bp. Full sequence data of ITS rDNA of five strains showed the length of their ITS rDNA was ranged 655 658 bp. BLAST homology search results showed that UICC 27, UICC 40, UICC 51, and UICC 67 strain have similarity 99,2 to the type strain of R. oryzae CBS 112.07T, whilst UICC 116 strain showed a higher similarity 99,8 to the type strain of R. oryzae CBS 112.07T. Based on phylogenetic species concept, four strains UICC 27, UICC 40, UICC 51, and UICC 67 were identified as R. delemar. They were clustered with the type strain of R. delemar CBS 120.12T in a monophyletic group, and supported by 90 bootstrap value. Another one strain UICC 116 was identified as R. oryzae. It was clustered with the type strain of R. oryzae CBS 112.07T in a monophyletic group and supported by 82 bootstrap value. Morphological characterization results indicated that the two species are indistinguishable and they showed morphological characters that correspond to R. oryzae. However, the physiological characters i.e. growth at temperature variations differ between of R. delemar and R. oryzae."

"Aspergillus section Nigri adalah salah satu kelompok kapang yang memiliki peran penting dalam bidang mikologi pangan, kedokteran, dan bioteknologi. Kapang tersebut merupakan kandidat yang sering digunakan untuk rekayasa genetika dan pemerintah Amerika Serikat melalui Food and Drug Administration (FDA) memberikan status GRAS (Generally Regarded As Safe) dalam penggunaannya di bidang industri dan bioteknologi. Secara sistematika dan taksonomi, kapang Aspergillus section Nigri memiliki sejumlah permasalahan karena kapang tersebut sukar untuk diidentifikasi dan diklasifikasi. Dalam penelitian ini dilakukan identifikasi dan analisis filogenetik terhadap 20 strain Aspergillus section Nigri terseleksi asal Kebun Raya Eka Karya, Bedugul Bali. Identifikasi kapang terseleksi dilakukan melalui pendekatan morfologi dan molekuler. Karakterisasi morfologi dilakukan dengan mengamati karakter fenotip di media CzA, MEA, CYA, MEA37, dan CY20S. Adapun analisis molekuler dilakukan melalui analisis sekuensing gen pada lokus ITS rDNA, gen ß-tubulin dan calmodulin. Analisis filogenetik dilakukan menggunakan analisis statistik neighbor-joining (NJ). Hasil analisis morfologi dalam penelitian ini belum dapat digunakan untuk mengidentifikasi dan membedakan ke-20 strain pada tingkat takson spesies. Hasil analisis molekuler menunjukkan 7 strain memiliki kedekatan secara genotip dengan A. aculeatus pada kisaran homologi 97-99%, 4 strain memiliki kedekatan dengan A. niger pada kisaran homologi 99-100%, dan 9 strain memiliki kedekatan genotip dengan A. tubingensis pada kisaran homologi 97-100%. Hasil analisis molekuler juga menunjukkan 10 strain yaitu P03, P08, P09,P10, P12, P15, P16, P18, P19, dan P20 memiliki homologi yang rendah pada lokus gen ß-tubulin dan calmodulin sehingga secara genotip strain tersebut kemungkinan merupakan kandidat spesies yang berbeda. Hasil tersebut diperkuat oleh hasil analisis filogenetik NJ pada ketiga lokus. Berdasarkan hasil analisis filogenetik multilokus strain P01, P02, P11, dan P17 adalah takson A. tubingensis, strain P04, P05, P06, dan P07 adalah takson A. niger, dan strain P13 dan P14 adalah takson A. aculeatus. Hasil analisis filogenetik juga menunjukkan adanya spesies tersembunyi (cryptic species) dari beberapa strain Aspergillus hitam yang disolasi dari rhizosfer Piper asal Kebun Raya Eka Karya, Bedugul Bali, yaitu strain P03, P08, P09, P10, P12, P15, P16, P18, P19, dan P20.

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The black aspergilli (Aspergillus section Nigri ) are an important group of species in food mycology, medical mycology, and biotechnology. They are also candidates for genetic manipulation in the biotechnolology industries since A. niger used under certain industrial condition has been granted the GRAS (Generally Regarded As Safe) status by the Food and Drug Administration of the US government. Black aspergilli are one of the more difficult groups regarding classification and identification. In spite of the taxonomy of the Aspergillus species of the Nigri section being regarded as troublesome. This work aimed to identify and analyse the phylogeny of 20 selected strains of black aspergilli from Eka Karya Botanical Garden, Bedugul Bali. Morphological character were observed from culture were grown on CzA, MEA, CYA, MEA37, and CY20S. Meanwhile, molecular analysis have been conducted based on the ITS rDNA, ß-tubulin, and calmodulin genes. Morphological data result are useful for preliminary identification but it did not having been totally effective in describing and elucidating 20 selected strains into species level. Further molecular analysis showed that from 20 selected strains, seven strains have 97-99% similarity with A. aculeatus, four strains have 99-100% similarity with A. niger, and nine strains have 97-100% similarity with A. tubingensis. Based on molecular analysis particularly ß-tubulin and calmodulin genes, 10 strains (P03, P06, P08, P09, P10, P12, P15, P16, P18, P19, and P20) can be presumed as new species because of the low homology value to their closest related species. Based on the phylogenetic analysis strains of P01, P02, P11, and P17 were identified as A. tubingensis; strain P04, P05, P06, and P07 were identified as A. niger, and strain P13 and P14 were identified as A. aculeatus. Ten strains, namely, P03, P08, P09, P10, P12, P15, P16, P18, P19, and P20, form distinct lineage separated from other recognized Aspergillus in this section. Cryptic species probably exist among the Aspergillus section Nigri strains inhabiting Piper rhizosphere from Eka Karya Botanical Garden, Bedugul Bali."

"Bacopa sp. merupakan genus tanaman air yang umumnya digunakan sebagai tanaman hias akuarium. Sekitar 60 spesies Bacopa tersebar di seluruh dunia. Namun, data molekuler dan analisis filogenetik terhadap spesies-spesies tersebut masih sangat terbatas. Studi ini dilakukan untuk mengidentifikasi tujuh spesies Bacopa menggunakan penanda molekuler dan mengetahui hubungan kekerabatan antar spesies melalui nilai jarak genetik. Sebanyak tujuh spesies Bacopa diamati secara morfologi dan diidentifikasi secara molekuler menggunakan sekuens rbcL melalui metode DNA Barcoding dan RAPD marker. Hasil amplifikasi DNA Bacopa sp. divisualisasikan pada gel agarosa dengan konsentrasi 1,5% (rbcL) dan 2% (RAPD marker). Data yang didapatkan kemudian diolah menggunakan aplikasi MEGA (rbcL) dan NTSys (RAPD marker) untuk diketahui hubungan kekerabatannya. Amplifikasi tujuh spesies Bacopa sp. menggunakan rbcL menghasilkan tujuh amplikon yang berukuran sekitar 600 bp. Selain itu, amplifikasi menggunakan delapan primer RAPD juga berhasil dilakukan pada lima spesies Bacopa sp. dan menunjukkan tingkat polimorfisme sebesar 100%. Bacopa rotundifolia dan B. myriophylloides tidak berhasil diamplifikasi oleh delapan primer RAPD karena ketidakcocokan cetakan DNA dengan primer. Analisis filogenetik berdasarkan sekuens rbcL menggunakan metode UPGMA menunjukkan bahwa tujuh spesies Bacopa memiliki rentang jarak genetik 0,000—0,024, sedangkan berdasarkan RAPD, tujuh spesies Bacopa memiliki rentang jarak genetik 0,000—0,625. Identifikasi menggunakan sekuens rbcL lebih dianjurkan karena hasil RAPD sulit untuk diinterpretasikan dan dapat menimbulkan salah tafsir.

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Bacopa sp. is a genus of aquatic plants commonly used as aquarium ornamental plants. About 60 species of Bacopa are distributed throughout the world. However, data on molecular identification and phylogenetic analysis of this species are still limited. This study was conducted to identify seven species of Bacopa using molecular markers and determine the relationship among species through the value of genetic distance. A total of seven species of Bacopa were observed morphologically and identified molecularly using rbcL sequences through DNA barcoding and RAPD marker methods. The results of Bacopa DNA amplification were visualized on agarose gel with a concentration of 1.5% (rbcL) and 2% (RAPD marker). The data obtained then processed using the MEGA (rbcL) and NTSys (RAPD marker) applications to determine the relationship among them. Amplification of seven species Bacopa sp. using rbcL resulted in an amplicon measuring about 600 bp. In addition, amplification using eight RAPD primers was also successfully carried out on five species of Bacopa and showed a polymorphism rate of 100%. Bacopa rotundifolia and B. myriophylloides were not successfully amplified by eight RAPD primers due to a mismatch of DNA templates with primers. Phylogenetic analysis based on rbcL sequences using the UPGMA method showed that seven Bacopa species had a genetic distance range of 0.000-0.024, while based on RAPD, seven Bacopa species had a genetic distance range of 0.000-0.625. Identification using the rbcL sequence is recommended because RAPD results are difficult to interpret and can lead to misinterpretation."

"Universitas Indonesia Culture collection (UICC) memiliki koleksi strain-strain Rhizopus arrhizus Fischer yang diisolaasi dari tempe dan telah diidentifikasi berdasarkan karakter morfologi dan fisiologi. Penelitian bertujuan memperoleh identitas yang akurat pada tingkat spesies dari lima strain R. arrhizus (UICC 26, UICC 36, UICC 39, UICC 55, dan UICC 121) berdasarkan data sequence daerah internal transcribed spacers ribosomal DNA dan analisis filogenetik. Amplifikasi dan sequencing daerah ITS rDNA dilakukan menggunakan primer forward ITS5 dan primer reverse ITS4. Pencarian homologi sequence dilakukan dengan program BLAST. Sequence alignment dilakukan menggunakan program Clustal X. Konstruksi pohon filogenetik dilakukan menggunakan metode neighbor joining dengan model dua parameter Kimura dan nilai bootstrap 1000 pengulangan. Karakterisasi morfologi dan fisiologi (pengujian pertumbuhan pada variasi suhu) dilakukan untuk melengkapi deskripsi strain. Panjang fragmen daerah ITS rDNA kelima strain R. arrhizus sekitar 600--700 pb. Hasil BLAST menunjukkan kelima strain UICC memiliki homologi dengan type strain R. oryzae CBS 112.07T pada kisaran 98,9--99,8%. Pohon filogenetik menunjukkan strain UICC 36 dan strain UICC 55 berada dalam satu grup yang monofiletik dengan type strain R. oryzae CBS 112.07T dan neo type R. arrhizus NRRL 1469NT. Saat ini R. arrhizus merupakan sinonim dari R. oryzae, sehingga kedua strain tersebut diidentifikasi sebagai R. oryzae. Strain UICC 26, UICC 39, dan UICC 121 berada dalam satu grup yang monofiletik dengan type strain R. delemar CBS 120.12T, sehingga ketiga strain diidentifikasi sebagai R. delemar. Rhizopus oryzae dan R. delemar merupakan dua spesies yang berkerabat sangat dekat, sehingga secara morfologi tidak dapat dibedakan. Re-identifikasi lima strain R. arrhizus UICC secara molekuler menghasilkan identitas spesies yang berbeda menjadi R. oryzae dan R. delemar, namun karakter morfologi dan fisiologi lima strain tersebut menunjukkan karakter sebagai R. oryzae.

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Universitas Indonesia Culture Collection (UICC) has collection of Rhizopus arrhizus Fischer strains, which were isolated from tempeh and were identified based on morphological and physiological characters. The aim of this study was to obtain accurate identification at species level of five strains of R. arrhizus (UICC 26, UICC 36, UICC 39, UICC 55, and UICC 121) based on internal transcribed spacers (ITS) region of ribosomal DNA (rDNA) sequence data and phylogenetic analysis. Amplification and sequencing of ITS region of rDNA were performed using forward primer ITS5 and reverse primer ITS4. Sequence homology search was performed using BLAST. Sequence alignment was carried out using Clustal X. Construction of phylogenetic tree was performed using neighbor joining method, Kimura?s two parameter model and bootstrap values of 1000 iterations. Characterization of morphological features and growth at variation of temperature were carried out to support the description of the strains. The fragment length of ITS region rDNA from five strains of R. arrhizus was about 600--700 bp.

Results of BLAST homology search of the strains showed 98.9--99.8% similarities to the type strain R. oryzae CBS 112.07T. Phylogenetic tree showed that UICC 36 and UICC 55 were clustered together in a monophyletic group with the type strain R. oryzae CBS 112.07T and neo type strain R. arrhizus NRRL 1469NT. Currently, R. arrhizus is a synonym of R. oryzae, therefore both strains were identified as R. oryzae. Strains UICC 26, UICC 39, and UICC 121 were clustered together in a monophyletic group with the type strain R. delemar CBS 120.12T, therefore they were identified as R. delemar. Rhizopus oryzae and R. delemar are very closely related species and morphologically similar. Re-identification of five strains R. arrhizus UICC based on molecular has difference of species identity as R. oryzae and R. delemar, but the five strains show similar morphological and physiological characters as R. oryzae."

"Berdasarkan data WHO pada pertengahan Juli 2021 lebih dari 185,2 juta orang di seluruh dunia terinfeksi virus corona atau Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Virus ini menyerang penapasan manusia yang dapat mengakibatkan infeksi paru-paru pada manusia dan bahkan dapat menyebabkan kematian. Tercatat bahwa lebih dari 4 juta orang di seluruh dunia meninggal akibat terinfeksi virus corona. Di Indonesia sendiri pada pertengahan Juli 2021 tercatat lebih dari 2,4 juta orang ternfeksi virus corona dan lebih dari 65,4 ribu orang meninggal akibat terinfeksi virus corona. Berdasarkan data tersebut, perlu dilakukan analisis kekerabatan virus SARS-CoV-2 untuk mengurangi penyebaran dan memberikan batasan sosial dari negara satu dengan negara lainnya. Identifikasi kekerabatan dari virus covid-19 dan penyebarannya dapat dilakukan dengan cara pembentukan pohon filogenetik dan clustering. Pada penelitian ini pohon filogenetik akan dibangun berdasarkan metode Hierarchical Clustering dengan menggunakan metode Multiple Encoding Vector dan K-Mer berdasarkan translasi DNA kodon menjadi asam amino. Jarak Euclidean akan digunakan untuk menentukan matriks jarak. Penelitian ini selanjutnya menggunakan metode K- Means Clustering untuk melihat penyebarannya, dimana nilai k ditentukan dari jumlah centroid yang dihasilkan dari metode Hierarchical Clustering. Penelitian ini mengambil sampel barisan DNA SARS-CoV-2 dari beberapa negara yang tertular. Dari hasil simulasi, nenek moyang SARS-CoV-2 berasal dari China. Hasil analisis juga menunjukkan bahwa leluhur covid-19 yang paling dekat dengan Indonesia berasal dari India, Australia dan Spanyol. Selain itu dari hasil simulasi dihasilkan bahwa barisan DNA SARS-CoV-2 terdiri dari 9 cluster dan cluster keenam adalah kelompok yang memiliki anggota paling banyak. Hasil analisis juga menunjukkan bahwa metode ini sangat opitimal dalam pengelompokan data dengan nilai 97.4%.

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Based on WHO data in middle of July 2021, Coronavirus or Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is infecting more than 185.2 million people worldwide. The virus attacks human breathing, which can cause lung infections and can even cause death. More than 4 million people worldwide have died due to being infected with the coronavirus. In Indonesia alone, in mid-July 2021, there were more than 2.4 million people infected with the corona virus and more than 65.4 thousand people died from being infected with the corona virus. Based on those covid-19 survivor data, it is necessary to carry out a kinship analysis of the coronavirus to reduce its spreading. Identification of the kinship of the covid- 19 virus and its spread can be done by forming a phylogenetic tree and clustering. This study uses the Multiple Encoding Vector method and K-mer based on translation DNA codon to amino acid in analyzing sequences and Euclidean Distance to determine the distance matrix. This research will then use the Hierarchical Clustering method to determine the number of initial centroids and cluster, which will be used later by the K-Means Clustering method kinship in SARS-CoV-2 DNA sequence. This study took samples of DNA sequences of SARS-CoV-2 from several infected countries. From the simulation results, the ancestors of SARS-CoV-2 came from China. The results of the analysis also show that the closest ancestors of covid-19 to Indonesia came from India, Australia and Spain. In addition, the ancestors of SARS-CoV-2 came from China. The SARS- CoV-2 DNA sequence is also consisted of 9 clusters, and the sixth cluster is the group that has the most members. The results also show that this method is very optimal in a grouping of data with a value of 97.4%."

"ABSTRAKPenelitian bertujuan menganalisis hubungan kekerabatan spesies-spesiesCercospora berdasarkan data sequence daerah Internal Transcribed Spacers (ITS)rDNA, gen elongation factor 1-α (EF), dan gen calmodulin (CAL); mengetahuilokus yang paling baik dalam memisahkan spesies-spesies Cercospora; danmenguji host specificity Cercospora spp. dengan tanaman inangnya. Padapenelitian ini telah dilakukan amplifikasi dan sequencing daerah ITS rDNA, genEF, dan gen CAL pada 14 spesies dari 23 strain Cercospora yang berasal dari tigafamili tanaman inang (Asteraceae, Cucurbitaceae, dan Solanaceae). Pohonfilogenetik dibangun menggunakan metode Neighbor-Joining, MaximumParsimony, dan Bayesian. Hasil penelitian menunjukkan bahwa pohonfilogenetik berdasarkan data sequence daerah ITS rDNA tidak dapat menjelaskanhubungan kekerabatan antarspesies pada genus Cercospora; sebagian besarCercospora (57 dari 61 OTU) berada dalam satu kelompok besar yang jarakcabangnya berimpit satu dengan lainnya. Pohon filogenetik berdasarkan datasequence gen EF dapat menjelaskan hubungan kekerabatan beberapa spesiesCercospora, walaupun sebagian spesies Cercospora (24 OTU) berada dalam satukelompok yang jarak cabangnya berimpit satu dengan lainnya. Pohon filogenetikberdasarkan data sequence gen CAL dapat menjelaskan hubungan kekerabatansebagian besar spesies Cercospora, jarak cabang terlihat lebih panjangdibandingkan pada pohon filogenetik berdasarkan data sequence gen EF,walaupun beberapa spesies Cercospora (16 OTU) belum dapat dipisahkan. Hasilanalisis filogenetik menunjukkan bahwa spesies-spesies Cercospora tidak dapatdipisahkan berdasarkan data sequence daerah ITS rDNA, akan tetapi sebagianspesies dapat dipisahkan berdasarkan data sequence gen EF dan gen CAL. Pohonfilogenetik berdasarkan data sequence gen CAL menunjukkan bahwa gen tersebutdapat digunakan untuk memisahkan spesies-spesies Cercospora lebih baikdaripada daerah ITS rDNA dan gen EF. Hasil analisis filogenetik berdasarkandata sequence multilokus menunjukkan bahwa 11 dari 14 spesies Cercosporayang digunakan dalam penelitian tidak host-specific, hanya tiga spesies yaitu C.zinniicola, C. cocciniae, dan C. mikaniicola yang spesifik terhadap inangnya.

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ABSTRACTThe aims of this study were to analyze the phylogenetic relationships ofCercospora spp. based on sequence data of the internal transcribed spacer (ITS)region of rDNA, elongation factor 1-α (EF), and calmodulin (CAL) genes; todetermine the best locus in separating Cercospora species; and to investigate thehost specificity of Cercospora spp. In this study, the sequences of the ITS regionof rDNA, EF, and CAL genes of 23 strains which belong to 14 species ofCercospora from three host plants families were amplified and sequenced. Thephylogenetic trees of the Cercospora spp. were constructed by Neighbor-Joining,Maximum Parsimony, and Bayesian methods. Our result showed thatphylogenetic relationship of Cercospora at the species level could not be resolvedby ITS rDNA; most of Cercospora species (57 OTU) were grouped in one majorclade with no branch length differences among species. The EF phylogenetic tree,showed that some species of Cercospora could be separated, although 24 OTUwere grouped into one clade with no branch length differences. The CALphylogenetic tree showed that the majority of Cercospora species could beseparated with longer branch compared to the EF phylogenetic tree, althoughseveral species (16 OTU) could not be separated. The phylogenetic analysesshowed that most of Cercospora species could not be separated in the ITS rDNAtree, however those species could be separated in the EF and CAL phylogenetictrees. The results showed that CAL gene was the best locus in separatingCercospora species compared to ITS rDNA and EF gene. Molecularphylogenetic analysis from multiloci (ITS regions of rDNA, EF gene, and CALgene) 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."