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"Molecular Phylogenetic Studies in Providing Basic Knowledge to Improve Quality of Genetic Resources of Orchid. Topik Hidayat and Adi Pancoro. Early information resulted from molecular phylogenetic studies of many im-portant ornamental crops is often less attention to many growers and farmers. Phylogenetics is one of the most pre-ferable method in systematics to reconstruct evolutionary relationships of groups of biological organisms in order to understand their biodiversities. This has been revolutionized by DNA sequences data. In this method, a group of organ-isms that shares many identical characteristics are con-sidered to be closely related; deriving from a common ancestor and is assumed to have similar genetic patterns and biochemical properties. By these basic principles, molecular phylogenetics plays important roles in revealing a basic knowledge on pattern of relationships to which genetic resources can be improved. Over the past decade, botanists have done several thousand phylogenetic analyses based on molecular data of economically and horticulturally important crops. Orchids are the best example for this. There is no doubt that most orchid plants had played roles in horticulture and hybridization. At present, many infrageneric and intergeneric hybrids are available commercially. Suc-cessful hybridization can be achieved if two or more individ-ual plants understudy are closely related in respect to their genetics and evolution."

"Osteogenesis imperfecta (OI) is a heritable disorder of connective tissue that mainly affects the bones. Being always associated with bone fragility, it is also known as "brittle bone" disease. Multiple bone fractures are common, and in severe cases can occur even before birth. The condition is characterized by fractures with minimal or absent trauma, dentinogenesis impercta, short stature, blue sclerae, and in adult years, hearing loss. Most cases of OI, which is inherited in an autosomal dominant manner, result from mutations affecting the genes COLIA1 (collagen type 1 alpha 1) and COLIA2 (collagen type 1 alpha 2) that encode pro-a 1 and pro-a 2 chains of type 1 collagen. The type 1 collagen molecule accounts for about 90% of the organic matrix of the bone. In addition, collagen forms a family of proteins that strengthen and support many tissues in the body, including cartilage, tendons, skin, and the white part of the eye (sclera). This paper aims to review the genetic contribution to OI."

"Konvensi keanekaragaman hayati pada dasarnya berisi ketentuan yang meminta negara-negara untuk melestarikan keanekaragaman hayati memanfaatkan dan mengembangkan komponen-komponennya secara berkelanjutan dan membagi keuntungan dari hasil pemanfaatan sumber daya gen secara adil dan merata. Indonesia yang memiliki keanekaragaman hayati yang sangat tinggi tenyata belum memanfaatkan secara maksimal justru negara lain yang memanfaatkannya.Tulisan ini menyoroti hal tersebut dalam perspektif hubungan internasional."

"Perkembangan dari produk rekayasa genetik ibarat dua sisi mata uang: ada potensi manfaat, ada juga potensi risiko. Kedua sisi ini sendiri masih sarat dengan ketidakpastian ilmiah. Oleh sebab itu, penting untuk menerapkan prinsip kehatihatian. Dalam Protokol Cartagena, salah satu instrumen yang digunakan untuk mendorong prinsip kehati-hatian adalah kajian risiko. Di Indonesia, instrumen ini digunakan untuk dasar pengambilan keputusan terkait pelepasan dan peredarannya. Agar dapat menjelaskan potensi, kemungkinan, dan konsekuensi dari pemanfaatan dan pelepasan produk rekayasa genetik, maka kajian risiko perlu menggunakan data yang bersifat langsung (direct) sehingga memenuhi posisi ‘risiko’ di kerangka kerja incertitude. Mengingat pentingnya kajian risiko dalam kerangka perizinan atas pelepasan dan/atau peredaran produk rekayasa genetik di Indonesia, maka tulisan ini menganalisis bagaimana penerapan peraturan mengenai produk rekayasa genetik, khususnya terkait kajian risiko terhadap keamanan lingkungan. Dengan menggunakan contoh dari hasil kajian risiko dari jagung event Bt11 dan GA21, tulisan ini juga membahas bagaimana implementasi kajian risiko di Indonesia. Lebih lanjut, tulisan ini juga menjelaskan kualitas dari implemetasi kajian risiko keduanya dengan menggunakan kerangka kerja incertitude. Penelitian ini menemukan kajian risiko sudah diatur dan dilaksanakan berdasarkan peraturan perundang-undangan yang berlaku. Sayangnya, hasil kajian risiko yang dilakukan tidak menunjukkan posisi atau ranah risiko (risk). Di samping itu, regulasi yang berlaku belum cukup memadai untuk menjadi landasan terciptanya kajian risiko yang berkualitas. Oleh sebab itu, penting untuk menegakkan peraturan yang sudah berlaku, serta melihat alternatif instrumen pengambilan keputusan sesuai dengan posisi incertitude yang dihasilkan.

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The development of genetically modified organisms brings both potential benefits and risks. This issue is still debatable because of the lack of scientific certainty. Therefore, the precautionary principle plays an important role. One of the instruments used to promote the precautionary principle is risk assessment. In Indonesia, this instrument is used as a basis for decision-making related to its release and/or distribution of genetically modified organisms. In order to explain the potential, likelihood, and outcome of the use and/or release of genetically modified organisms, a risk assessment needs to use direct evidence. Within the incertitude framework, this condition known as 'risk': the expected result that indicates a correct risk assessment. Given the importance of risk assessment for release and/or the distribution of genetically modified organisms in Indonesia, this thesis identifies the regulatory framework and the implementation of risk assessment's regulation, especially on environmental safety, using the RA results from GM Maize (Bt11 and GA21). Moreover, this thesis also examines the quality of both risk assessments quality using an incertitude framework. This research found that the risk assessment has been regulated and carried out based on the governing laws and regulations. Unfortunately, the results of the risk assessment carried out do not show a risk position. It is also concluded that the applicable governing regulations are insufficient as a basis to create a risk assessment. Therefore, it is important to strengthening the governing regulations. It is also suggested to look for more alternative decision-making instruments according to the incertitude position."

"Ikan mujair (Oreochromis mossambicus) merupakan salah satu jenis ikan air tawar dari famili Cichlidae dan genus Oreochromis yang memiliki bentuk adaptasi serta tingkat toleransi yang tinggi terhadap kondisi habitatnya, misalnya pada tingkat salinitas yang tinggi. Danau Laut Mati Oemasapoka di Perairan Pulau Rote merupakan salah satu danau air asin yang menjadi habitat ikan mujair. Penelitian ini dilakukan untuk mengetahui hubungan kekerabatan spesies ikan mujair yang diperoleh dari Danau Laut Mati Oemasapoka dengan ikan mujair dari danau air tawar, Danau Ledulu yang berada pada perairan yang sama dengan melakukan identifikasi molekuler menggunakan metode DNA barcoding dengan gen CO1. Tahapan DNA barcoding terdiri atas ekstraksi DNA, amplifikasi gen CO1 melalui reaksi PCR, dan sekuensing. Hasil penelitian menunjukkan gen CO1 mampu mengidentifikasi bahwa ikan mujair yang hidup di danau air asin, Danau Laut Mati Oemasapoka merupakan jenis spesies yang sama dengan ikan mujair yang hidup di danau air tawar, Danau Ledulu dengan persentase kemiripan sebesar 99,53—100%. Rekonstruksi pohon filogenetik yang dibentuk dengan metode Maximum Likelihood, model evolusi Kimura 2-Parameter, dan uji bootstrap 1000x menunjukkan bahwa ikan mujair dari Danau Laut Mati Oemasapoka dan Danau Ledulu berada dalam satu klade yang sama dengan jarak genetik sebesar 0,000—0,004. Analisis keragaman haplotipe dari ikan mujair yang diperoleh dari Danau Laut Mati Oemasapoka dan Danau Ledulu terdapat satu haplotipe dengan nilai keragaman sebesar 0,0824. Rendahnya nilai keragaman haplotipe tersebut dapat disebabkan karena ikan mujair Danau Laut Mati Oemasapoka dan Danau Ledulu memiliki tingkat migrasi yang rendah.

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Tilapia fish (Oreochromis mossambicus) is one type of freshwater fish from the family Cichlidae and genus Oreochromis which has a form of adaptation and a high level of tolerance to habitat conditions, for example at high salinity levels. Dead Sea Lake Oemasapoka, Rote Island is one of the saltwater lakes that is a habitat for tilapia fish. This study was conducted to determine the relationship between tilapia species obtained from Dead Sea Lake Oemasapoka and tilapia fish from freshwater lake, Lake Ledulu which are in the same waters by conducting molecular identification using DNA barcoding method with CO1 gene. The DNA barcoding stages consist of DNA extraction, CO1 gene amplification through PCR reactions, and sequencing. The results of this study indicate that the CO1 gene is able to identify that tilapia fish that live in saltwater lakes, Dead Sea Lake Oemasapoka are the same species as tilapia fish that live in freshwater lakes, Lake Ledulu with a similar percentage of 99,53-100%. Reconstruction of the phylogenetic tree using the Maximum Likelihood method Kimura 2-Parameter evolution model, and 1000x bootstrap test showed that tilapia fish from Dead Sea Lake Oemasapoka and Lake Ledulu were in the same clade with a genetic distance of 0.000-0.004. Analysis of haplotype diversity of tilapia fish obtained from Dead Sea Lake Oemasapoka and Lake Ledulu there is one haplotype with a diversity value of 0.0824. The low value of this haplotype diversity can be caused by a low migration rate."

"Penelitian bertujuan untuk memperoleh dan mengidentifikasi isolat-isolat bakteri endofit yang potensial senyawa bioaktif antidiare dari tanaman N. altissima; mendeteksi, memurnikan dan mengidentifikasi senyawa bioaktif antidiare yang dihasilkan; serta menganalisis mekanisme kerjanya dalam menghambat pertumbuhan bakteri uji. Bakteri endofit diisolasi dari bagian akar, kulit batang, dan daun tanaman N. altissima. Bakteri endofit diisolasi dan dimurnikan menggunakan medium Nutrient Agar NA dan Luria Bertani LB agar. Aktinomisetes endofit diisolasi dan dimurnikan menggunakan medium Starch Casein Agar SCA dan International Streptomyces Project ISP 2 agar. Identifikasi bakteri dan aktinomisetes endofit dilakukan secara molekuler dengan melakukan analisis filogenetik sekuen nukleotida bakteri dari daerah 16S rRNA dengan metode Neighbour Joining NJ . Isolasi dan purifikasi senyawa dilakukan dengan metode maserasi menggunakan pelarut etil asetat dan kromatografi kolom. Senyawa bioaktif dideteksi dengan teknik Kromatografi Lapis Tipis KLT bioautografi. Senyawa bioaktif yang dihasilkan oleh bakteri dan aktinomisetes endofit diidentifikasi dengan menggunakan KLT, spektroskopi Resonansi Magnetik Inti NMR dan Spektroskopi Massa LC-MS . Mekanisme aksi dari senyawa bioaktif antidiare dianalisis dengan menggunakan mikroskop elektron scanning SEM . Dari 185 isolat bakteri endofit yang diperoleh, 104 isolat 56,21 dari bagian daun; 51 isolat 27,56 dari bagian kulit batang; dan 30 isolat 16,21 dari bagian akar. Sedangkan dari 33 isolat aktinomisetes endofit yang diperoleh, dua isolat 6,06 dari bagian kulit batang, 31 isolat 93,94 dari bagian akar, dan tidak diperoleh isolat aktinomisetes dari daun. Spesies bakteri endofit potensial ialah Pseudomonas aeruginosa strain UICC B-40, P. aeruginosa strain UICC B-93, dan P. azotoformans strain UICC B-91. Sedangkan aktinomisetes endofit potensial diidentifikasi sebagai Streptomyces sp. strain UICC B-92 dan Nonomuraea sp. strain UICC B-94. Hasil identifikasi senyawa menunjukkan bahwa senyawa bioaktif yang diperoleh dari P. aeruginosa strain UICC B-40 diduga merupakan senyawa metabolit baru, terdiri atas 2E,5E -phenyl tetradeca-2,5-dienoate C20H28O2 . Senyawa bioaktif aktinomisetes Streptomyces sp. strain UICC B-92 ialah 4-O-glucocyl, 1-carboxyl-phenazine C19H18N2O8 . Senyawa turunan phenazine dengan adanya gugus gula dari isolat Streptomyces sp. strain UICC B-92 diduga merupakan senyawa bioaktif baru. Hasil bioassai aktivitas antibakteri menunjukkan baik senyawa bioaktif dari P. aeruginosa strain UICC B-40 maupun Streptomyces sp. strain UICC B-92 menghambat bakteri Gram positif Bacillus cereus strain ATCC 10876 dan Staphylococcus aureus strain ATCC 25923. Mekanisme penghambatan dari kedua senyawa menunjukkan adanya aktivitas lisis terhadap membran sel bakteri uji, ditunjukkan dengan terjadinya pemanjangan ukuran sel, kerusakan dan kebocoran membran sel sehingga mengganggu permeabilitas membran sel dan akhirnya menyebabkan kematina sel. Senyawa metabolit P. aeruginosa strain UICC B-40 lebih potensial sebagai senyawa antidiare dibandingkan senyawa metabolit dari Streptomyces sp. strain UICC B-92.Kata kunci : antidiare, bakteri endofit, 16S rRNA, lisis, Neesia altissima, spektroskopi.

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The aims of this study were to obtain potential endophytic bacteria and actinomycetes from N. altissima as anti diarrhea bioactive producer and to screen and identify their anti diarrhea bioactive compound and to investigate the mechanism of action of the bioactive compound in inhibiting the growth of diarrhea causing bacteria. Media for endophytic bacteria isolation and purification were NA and LB agar, while media for endophytic actinomycetes isolation and purification were SCA and ISP2 agar. Identification of endophytic bacteria and actinomycetes was carried out based on phylogenetic analysis of DNA sequence generated from 16S rRNA region. Isolation, purification, and detection of bioactive compounds were carried out using maceration process, column chromatography and Thin Layer Chromatography TLC bioautography, respectively. Identification were elucidated using Nuclear Magnetic Resonance NMR and Liquid Chromatography Mass Spectroscopy LC MS analyses. The mechanism of action of bioactive compound were morphologically observed using scanning electron microscope SEM . In this study, from a total 185 endophytic bacteria obtained, 104 isolates 56.21 obtained from leaves, 30 isolates 16.21 from roots, and 51 isolates 27.56 from stem barks. From a total 33 endophytic actinomycetes isolates obtained, 31 isolates 93.94 from roots, two isolates 6.06 from stem barks, and no isolates obtained from leaves. Based on phylogenetic analysis of nucleotide sequence generated from 16S rRNA region, two isolates of endophytic bacteria determined as P. aeruginosa strain UICC B 40 and one isolate belongs to P. azotoformans strain UICC B 91 two isolates of endophytic actinomycetes determined as Streptomyces sp. strain UICC B 92 and Nonomuraea sp. strain UICC B 94 . On the basis of 1H NMR spectral data and supported with molecular weight data from LC MS analysis, bioactive compound from P. aeruginosa strain UICC B 40 was identified as growth associated metabolite, and determined as 2E,5E phenyl tetradeca 2,5 dienoate C20H28O2 . In addition, bioactive compound from Streptomyces sp. strain UICC B 92 was identified as 4 O glucocyl, 1 carboxyl phenazine C19H18N2O8 . The bioactive compound from Streptomyces sp. strain UICC B 92 is suggested as novel type of phenazine derivative. All of bioactive compounds showed high in vitro antibacterial activity against two Gram positive bacteria, Bacillus cereus strain ATCC 10876 and Staphylococcus aureus strain ATCC 25923. The bioactive compounds from P. aeruginosa strain UICC B 40 and Streptomyces sp. strain UICC B 92 showed membrane cell walls lysis mechanism. The cell walls of S. aureus strain ATCC 25923 and B. cereus strain ATCC 10876 were apparently damaged after treated by the antibacterial compound. Occurrence of local rupture or pore formation in the cell membranes was also found and causing leakage of essential intracellular constituents from the cells. The bioactive compound from P. aeruginosa strain UICC B 40 is more potential as anti diarrhea compound than that from Streptomyces sp. strain UICC B 92.Key words antidiarrhea, endophyte bacteria, 16S rRNA, lysis, Neesia altissima, spectroscopy."