Makara Journal of Science
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Identification of Gene Resistance to Avian Influenza Virus (Mx Gene) among Wild Waterbirds
No full textThe Mx gene is an antiviral gene used to determine the resistance or the susceptibility to different types of viruses, including the Avian Influenza (AI) virus subtype H5N1. The AI virus subtype H5N1 infection in chickens causes Mx gene polymorphism. The Mx+ gene shows resistant to the AI virus subtype H5N1, whereas the Mx- gene shows signs of susceptible. The objective of this research was to detect the Mx gene in wild aquatic birds using the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method with the primer pairs F2 and NE-R2/R and the RsaI restriction enzyme. DNA samples were obtained from eight species of wild waterbirds with positive and negative exposure to the AI virus subtype H5N1. DNA amplification results showed that the Mx gene in wild aquatic birds is found in a 100 bp fragment, which is the same as the Mx gene found in chickens. However, unlike chickens, the Mx gene in wild aquatic birds did not show any polymorphism. This study proves that Mx- based resistance to AI virus subtype H5N1 in different in wild birds than in chickens. Keywords: Mx gene, wild waterbirds, exposure, AI virus subtype H5N1, resistance Keywords: Mx gene, wild waterbirds, exposure, AI virus subtype H5N1, resistance 
Distribution Patterns of the Morphology, Species, and Sex in the Stingray Species Complex of Himantura uarnak, Himantura undulata,and Himantura leopardain Indonesia
No full textAbstract The assessment of the morphology and stingray species distribution of the Himantura uarnak species complex covers eight sampling sites in western and eastern Indonesia as many as 113 individuals. The observation of the reticulate pattern was accomplished by directly checking the dorsal side of the stingrays, and growth observations also carried out. The distribution patterns were analyzed using the principal component analysis (PCA), while the growth patterns were evaluated using correlation analyses. The reticulation patterns of the H. uarnak species complex were highly variable, and the distribution patterns based on the morphological parameters, species, and sex produced four groups. The distribution of the length frequency of H. undulata and H. uarnak showed a range of different sizes. The body length of the female in the western region is relatively longer than the male, while in the eastern region the female revealed a range in relative size showing that the male was longer than the female. The length-weight relationships of the stingrays were negative allometric, indicating a b-value of less than 3. The b-values of both the male and female H. undulata were 1.5860 and 0.4380, respectively; while the male and female H. uarnak were 0.2956 and 0.4376, respectively. Abstrak Pola Distribusi dari Morfologi, Spesies dan Jenis Kelamin pada Kompleks Spesies Ikan Pari Himantura uarnak, Himantura undulata dan Himantura leoparda di Indonesia. Penilaian terhadap morfologi dan distribusi spesies dari ikan pari kompleks spesies H. uarnak meliputi delapan lokasi pengambilan sampel di barat dan timur Indonesia sebanyak 113 individu. Identifikasi spesimen mengikuti kunci family Dasyatidae, untuk genus Himantura. Pengamatan pola retikulasi dilakukan dengan pengecekan langsung pada punggung ikan pari dan observasi pertumbuhan juga dilakukan. Pola distribusi ikan pari dianalisis dengan principal component analysis (PCA), sedangkan pola pertumbuhan menggunakan analisis korelasi. Pola retikulasi kompleks spesies H. uarnak sangat bervariasi. Pola distribusi berdasarkan parameter morfologi, spesies dan jenis kelamin ikan pari menghasilkan empat kelompok. Distribusi panjang frekuensi H. undulata dan H. uarnak menunjukkan berbagai ukuran yang berbeda. Panjang tubuh dari betina di wilayah barat relatif lebih panjang dari jenis kelamin jantan, sedangkan wilayah timur menunjukkan bahwa ukuran tubuh dari jenis kelamin jantan relatif lebih panjang dari betina. Hubungan panjang-berat ikan pari menunjukkan alometrik negatif dengan nilai b kurang dari 3. Nilai b pada masing-masing jantan dan betina dari H. undulata adalah 1,5860 dan 0,4380, sedangkan masing-masing jantan dan betina H. uarnak adalah 0,2956 dan 0,4376. Keywords: distribution pattern, Himantura uarnak species complex, morphology, reticulation, stingra
The Relationship between the Harmful Algal Blooms (HABs) Phenomenon with Nutrients at Shrimp Farms and Fish Cage Culture Sites in Pesawaran District Lampung Bay
No full textThe phenomenon of harmful algal blooms (HABs) in the Lampung Bay has been reported by many researchers. The occurrence of HABs may be due to the increase of nutrient (N and P) as results of waste water of aquaculture (shrimp farms, hatcheries and fish cage farms). This study aim to determine the relationship between N and P concentrations in some aquaculture sites with harmful algal blooms. The analysis revealed the differences concentration of N and P at each different shrimp farms and fish cage farms sites (Hurun, Sidodadi, Ringgung, and Cikunyinyi Bay). The result showed that the increase of N and P concentration were followed by the increase of harmful phytoplankton populations. High density HABs were found in this study, such as: Ceratium furca with the highest density at 5.314x106 cells l-1, Trichodesmium erithraeum 1.05x105 cells l-1 and Noctiluca scintilans 5.99x104 cells l-1. The Multiple regression and canonical corelation analysis (CCA) also indicated a strong positive relationship between N and P with the HABs at the shrimp farms and fish cage farms sites in the Lampung Bay. Keywords: phytoplankton, harmful, nutrients, Lampung ba
Phylogeny of Indonesian Nostoc (Cyanobacteria) Isolated from Paddy Fields as Inferred from Partial Sequence of 16S rRNA Gene
No full textIn order to collect Indonesian Nostoc, isolation of soil microflora from several paddy fields in West Java, Bali, and South Celebes was carried out. Fast-growing isolates of Nostoc were selected to describe and perform molecular identification using partial sequences of 16S rRNA. The results showed that partial sequences of 16S rRNA could not resolve the phylogeny of the isolates. However, it supported the morphological studies that recognize isolates as different species of Nostoc. Potential use of Nostoc as a nitrogen source for paddy growth was carried out using six strains as single inoculums. A total biomass of 2 g (fresh weight) for each strain was inoculated, respectively, into the pot planted with three paddy plants. This experiment was conducted in the green house for 115 days. Statistical analyses (ANOVA; α = 0.05) showed that of six strains tested in this study, only strain GIA13a had influence on the augmentation of root length and the total number of filled grains. Keywords: biofertilizer, diversity, inoculum, Nostoc, padd
Multilocus Sequence Analysis of Cercospora spp. from Different Host Plant Families
No full textAbstract Identification of the genus Cercospora is still complicated due to the host preferences often being used as the main criteria to propose a new name. We determined the relationship between host plants and multilocus sequence variations (ITS rDNA including 5.8S rDNA, elongation factor 1-α, and calmodulin) in Cercospora spp. to investigate the host specificity. We used 53 strains of Cercospora spp. infecting 12 plant families for phylogenetic analysis. The sequences of 23 strains of Cercospora spp. infecting the plant families of Asteraceae, Cucurbitaceae, and Solanaceae were determined in this study. The sequences of 30 strains of Cercospora spp. infecting the plant families of Fabaceae, Amaranthaceae, Apiaceae, Plumbaginaceae, Malvaceae, Cistaceae, Plantaginaceae, Lamiaceae, and Poaceae were obtained from GenBank. The molecular phylogenetic analysis revealed that the majority of Cercospora species lack host specificity, and only C. zinniicola, C. zeina, C. zeae-maydis, C. cocciniae, and C. mikaniicola were found to be host-specific. Closely related species of Cercospora could not be distinguished using molecular analyses of ITS, EF, and CAL gene regions. The topology of the phylogenetic tree based on the CAL gene showed a better topology and Cercospora species separation than the trees developed based on the ITS rDNA region or the EF gene. Abstrak Analisis Sequence Multilokus Cercospora spp. dari Beberapa Famili Tanaman Inang yang Berbeda. Identifikasi genus Cercospora masih menjadi perdebatan karena preferensi tanaman inang sering digunakan sebagai kriteria utama untuk mengusulkan spesies baru. Penelitian bertujuan menguji host specificity Cercospora spp. dengan tanaman inangnya. Pengujian dilakukan dengan melihat hubungan kekerabatan antara tanaman inang dan variasi sequence multilokus (daerah ITS rDNA, gen elongation factor 1-α (EF), dan gen calmodulin (CAL) pada Cercospora spp. Analisis filogenetik menggunakan 53 strain Cercospora spp. yang menginfeksi 12 famili tanaman inang. Sequence dari 23 strain Cercospora spp. pada penelitian menginfeksi famili tanaman Asteraceae, Cucurbitaceae, dan Solanaceae, dan sequence dari 30 strain Cercospora spp. berasal dari GenBank menginfeksi famili tanaman Fabaceae, Amaranthaceae, Apiaceae, Plumbaginaceae, Malvaceae, Cistaceae, Plantaginaceae, Lamiaceae, dan Poaceae. Analisis filogenetik menunjukkan bahwa mayoritas spesies Cercospora tidak host specific, hanya C. zinniicola, C. zeina, C. zeae-maydis, C. cocciniae, dan C. mikaniicola yang menunjukkan host specificity. Spesies-spesies Cercospora yang memiliki hubungan kekerabatan sangat dekat, tidak dapat dipisahkan menggunakan analisis filogenetik secara molekuler berdasarkan daerah ITS rDNA, gen EF, dan gen CAL. Gen CAL menunjukkan topologi pohon yang lebih baik dibandingkan daerah ITS rDNA dan gen EF. Topologi pohon filogenetik gen CAL tersebut dapat memisahkan spesies-spesies Cercospora lebih baik dibandingkan dengan dua lokus yang lain. Keywords: Cercospora, host specificity, leaf spot, multilocus sequence, phylogenetic analysi
Synthesis of Fe3O4 Nanoparticles from Ironstone Prepared by Polyethylene Glycol 4000
No full textAbstract This study reports the modification of the preparation method of Fe3O4 nanoparticles, which consists of two stages, beginning with the destruction and separation of iron ore from ironstone. Then, the Fe3O4 nanoparticles are synthesized using the coprecipitation method with magnetite (Fe3O4). Polyethylene glycol (PEG) 4000, a readily available chemical, was introduced in varying amounts into the reactions. The ratio of Fe3O4 powder and PEG 4000 is 1:3, 1:4, and 1:5, respectively, and the effects of the PEG 4000 on the morphology, crystalline size, and magnetic properties of the products were studied. It was shown that the particle and crystalline sizes decreased when the concentration of PEG 4000 increased. Additionally, the smallest Fe3O4 nanoparticles were around 50-60 nm, and semispherical nanoparticles were formed. The reduction of the crystalline size with the increase in PEG 4000 was shown by using XRD patterns, with the crystalline size being about 30 nm at a ratio of 1:5 Fe3O4 and PEG 4000, respectively. The hysteresis loop showed low coercivity, indicating that all products were soft magnetic. Abstrak Sintesis Nanopartikel Fe3O4 dari Batuan Besi dibantu oleh Polietilen Glikol 4000. Pada penelitian ini dilakukan modifikasi metode pembuatan nanopartikel Fe3O4. Sintesis nanopartikel Fe3O4 terdiri atas dua tahap, diawali dengan destruksi dan pemisahan biji besi dari batuan besi yang terdiri dari unsur-unsur lain selain besi (Fe). Selanjutnya nanopartikel Fe3O4 disintesis menggunakan metode kopresipitasi. Polietilen Glikol 4000 (PEG 4000) yang mudah diperoleh, digunakan sebagai cetakan pada sintesis nanopartikel Fe3O4. Variasi penggunaan PEG 4000 terhadap serbuk Fe3O4 adalah 1:3, 1:4, dan 1:5. Ukuran partikel dan ukuran kristal menurun dengan peningkatan jumlah PEG 4000. Ukuran partikel terkecil sekitar 50-60 nm, dan partikel berbentuk semi bulat. Ukuran kristal menurun dengan peningkatan jumlah PEG 4000 yang terlihat pada pola difraksi XRD, dengan ukuran kristal terkecil sebesar 30 nm pada perbandingan serbuk Fe3O4 dengan PEG 4000 yaitu 1:5. Berdasarkan kurva hysteresis yang diperoleh, medan koersivitas untuk semua nanopartikel Fe3O4 cukup kecil, hal tersebut mengindikasikan bahwa nanopartikel Fe3O4 bersifat magnetik lemah. Keywords: coprecipitation, Fe3O4, ironstone, nanoparticles, PEG 400
Investigation on the Synergistic Complexation of Ni(II) with 1,10-Phenanthroline and Dithizone at Hexane-Water Interface Using Centrifugal Liquid Membrane-Spectrophotometry
No full textComplex formation of Ni(II) and 1,10-phenanthroline (C12H8N2/Phen) with the addition of dithizone (C13H12N4S/HDz) at the hexane-water interface has been studied by direct measurement spectrophotometry using the centrifugal liquid membrane (CLM) method. Ni(II) ion with Phen formed a cationic complex of Ni(C12H8N2)22+ or NiPhen22+. That complex dissolved in the aqueous phase and had two UV absorption spectrum maxima wavelengths, lmax 270 and 292 nm. Observation of complex formation was performed variations of pH and ligand concentration. The pH caused protonation that affected the amount of the formed complex. With the variations of ligand concentrations, the greater was the concentration of ligands the greater was the formed complex. Based on the Batch method, the HDz ligand addition into the NiPhen22+ cationic complex produced ion association complex of Ni(C13H11N4S)2(C12H8N2) or NiDz2Phen at lmax 403 nm, and is extracted in the organic phase. Measurement results using CLM method showed that NiDz2Phen complex was formed at hexane-water interface with lmax 523 nm. Comparison of Phen with HDz ligand concentrations affected the initial formation rate of NiDz2Phen complex. The greater concentration of Phen ligand increased the initial rate of formation for synergistic complex. The obtained data using CLM method indicated that the synergistic complex formation rate constant of NiDz2Phen at the interface, k was 0.30 s-1. Keywords: 1,10-Phenanthroline, centrifugal liquid, dithizone, interfacial complexation, membrane method, synergistic extractio
Design A Prototype of Temperature Logging Tools for Geothermal Prospecting Areas
No full textAbstract The costs of geothermal exploration are very high because technology is still imported from other countries. The local business players in the geothermal sector do not have the ability to compete with global companies. To reduce costs, we need to develop our own equipment with competitive prices. Here in Indonesia, we have started to design a prototype of temperature logging tools for geothermal prospecting areas. This equipment can be used to detect temperature versus depth variations. To measure the thermal gradient, the platinum resistor temperature sensor is moved slowly down along the borehole. The displacement along the borehole is measured by a rotary encoder. This system is controlled by a 16-bit H8/3069F microcontroller. The acquired temperature data is displayed on a PC monitor using a Python Graphical User Interface. The system has been already tested in the Gunung Pancar geothermal prospect area in Bogor. Abstrak Perancangan Prototipe Alat Logging Temperatur untuk Area Prospek Panasbumi. Biaya eksplorasi panasbumi tinggi dikarenakan teknologi yang masih diimpor dari luar negeri. Akibatnya, pelaku bisnis panasbumi dari dalam negeri sulit bersaing dengan perusahaan asing bermodal besar. Dalam upaya menekan biaya eksplorasi, kami merancang alat ukur gradien suhu di lubang sumur eksplorasi panasbumi dengan biaya produksi yang relatif terjangkau. Alat ini berfungsi untuk mengukur peningkatan suhu sebagai variasi terhadap kedalaman. Untuk mengukur gradien suhu, sensor Pt-100 diturunkan ke dalam lubang sumur secara perlahan-lahan. Penambahan kedalaman posisi sensor Pt-100 diukur menggunakan sensor rotary encoder. Alat ini dikendalikan sepenuhnya oleh mikrokontroler 16-bit H8/3069F. Data suhu hasil pengukuran ditampilkan pada layar monitor menggunakan Graphical-User Interface dengan bahasa pemrograman Python. Alat ukur gradien suhu ini telah diujicoba di daerah prospek panasbumi Gunung Pancar, Bogor. Keywords: borehole, geothermal, gradient temperature, logging, prototyp
Non-Saponifiable Lipid Composition of Four Salt-Secretor and Non-Secretor Mangrove Species from North Sumatra, Indonesia
No full textNon-saponifiable lipid (NSL) of the fresh leaves and roots from two salt-secretor mangrove species, namely Aegiceras corniculatum (L.) Blanco and Avicennia alba Bl. and two non-secretor mangroves, i.e. Acrostichum aureum L. and Excoecaria agallocha L. was analyzed with special emphasize to triterpenoids and phytosterols. Identification of the triterpenoids and phytosterols was confirmed by comparison of their retention time on the GC column with those of authentic standards and on the interpretation of GC-MS spectra. Triterpenoids and phytosterols comprised the major proportion of NSL. The triterpenoids and phytosterols mainly consisted of 7 and 4 compounds. Triterpenoids were the largest constituent of Ac. aureum and Ae. corniculatum leaves and roots, and E. agallocha roots. In contrast to these triterpenoids-rich species, phytosterols were relatively dominant in the roots of Av. alba. The species of Av. alba and E. agallocha in the leaves were distinguished from the others in that both species contained a larger quantity of phytol. Ae. corniculatum contained a large amount of betulin and α-amyrin in the roots, as well as lupeol in the roots of Av. alba. The diversity in the NSL composition noted with mangrove species in both the leaves and roots suggested that NSL of mangroves was chemotaxonomically significant between the species. Keywords: leaf, mangrove, phytosterol, triterpenoid, roo
Cultivation of Uncultured Bacteria of the Class Ktedonobacteria in the Phylum Chloroflexi
No full textThe class Ktedonobacteria in the phylum Chloroflexi is known to contain a large number of uncultured, environmental 16S rRNA gene clones, and cultured representatives are a limited number. In this review, recent findings on the taxonomical and ecological significance of the class Ktedonobacteria in the phylum Chloroflexi are discussed based on the findings from both the characteristics of the cultured Ktedonobacteria and molecular-based analysis. The microorganisms characterized so far include four species in three genera, Ktedonobacter, Thermosporothrix and Thermogemmatispora, and were proposed to represent three families, Ktedonobacteraceae, Thermosporotricaceae, and Thermogemmatisporaceae, and two orders, Ktedonobacterales and Thermogemmatisporales. Ktedonobacteria strains showed a common property of gram-positive, aerobic organisms that produce branched vegetative mycelia and form spores by budding. Keywords: blastospore, Chloroflexi, Ktedonobacteria, Thermosporothrix, Thermogemmatispor