Coffee is an important commodity and one of the most popular beverages in the world. Over 2.25 billion cups of coffee are consumed in the world every day (Ponte 2002). In 2012, Indonesia ranked third after Brazil and Vietnam in the global production of green coffee beans (USDA 2012). Five species of coffee that are commonly cultivated in the world include Coffea arabica, C. canephora, C. robusta, C. liberica, and C. excelsa (Doyle et al., 2001). In Indonesia C. robusta and C. arabica are the species mostly planted (Neilson, 2008). Due to its high market demand, coffee processing has developed to produce various flavors to satisfy the consumers. One type of coffee that is increasingly popular is luwak coffee (Kopi Luwak) which is produced exclusively by the Indonesian palm civet or luwak (Paradoxurus hermaphrodites ssp.). Luwak is a small mammal (Carnivora, Viverridae) living in the rain forests of Java and Sumatera, although its various subspecies are intensely distributed in South East Asia (Patou 2010). The distinctive taste of this coffee has been recognized since coffee plantation started in Indonesia during the Dutch colonial era. The luwak eats fruits, including coffee fruits or coffee cherries. Only the best and mature coffee cherries would be eaten by the luwak. This process will produce coffee with distinctive flavor. The price of luwak coffee is relatively high because only a small quantity of this coffee is produced (Marcone 2004). Once ingested by luwak, coffee cherries will pass through its entire digestive system. This process removes the outer layers of the fruit. After digestion, the remaining coffee beans were collected from the forest floor, cleaned, roasted, and ground; with the same process as the harvested coffee beans. Thus the unique flavor of Kopi Luwak comes from the digestion process in luwak, which includes mechanical, biochemical, and fermentation processes (Marcone 2004). Microorganisms, especially bacteria, are closely associated with the digestive process in monogastric animals (Kraatz 2010). Several studies have been conducted to determine the types of bacteria involved in the fermentation process, for example by trying to isolate the bacteria from faeces of civet and the luwak's coffee beans (Fauzi 2014). Currently, there is no information about the bacterial diversity in parts of Luwak coffee is a highly-priced coffee produced exclusively by the palm civet or luwak (Paradoxurus hermaphrodites ssp.). The purpose of this study was to determine the diversity of culturable bacteria in the gastro intestinal tract of luwak. The bacterial isolates were phenotypically characterized by their morphology and molecularly by analysis of their 1 500 bp 16s rDNA sequence. The results showed that Enterobacter cloacae and Lactobacillus brevis were found all over luwak's digestive tract. E. cloacae was the most common species. The most diverse bacterial population was found in small intestine. Seven bacterial genera were successfully identified from the small intestine and colon, compared to only ...
The development of molecular biology techniques nowadays has enabled to engineer drought tolerant sugarcane by genetic engineering to accelerate the breeding program. Dehydrin (DHN) is known to have an important role in plant response and adaptation to abiotic stresses (drought, high salinity, cold, heat, etc.). While plant tissues are subjected to drought stress (dehydration), DHN protein is accumulated to high content throughout all vegetative or generative tissues. The research aimed to isolate and characterize the DHN promoter from sugarcane that can be used as transformation material in generating drought tolerant sugarcane. Specific primers for DHN promoter amplification were designed and DHN promoter region was successfully isolated by PCR cloning method. Two putative promoter sequences were identified namely Pr-1DHNSo and Pr-2DHNSo. In silicoanalyses were carried out and cis-regulatory elements motifs that play a role in adaptation on abiotic stress as well as biotic stress including ABRE, MBS, CGTCA-motif, TGACG-motif, GARE-motif, P-box TCA-element and Box-W1 were identified. The promoter Pr-1DHNSo was then cloned into pBI121 expression vector by Overlap Extention PCR (OE-PCR) for further characterization. Functional test of the promoter construct pBI- Pr-1DHNSo was conducted through Agrobacterium transformation into sugarcane calli. GUS assay and PCR analysis showed that the DHN promoter was transformed and expressed in the sugarcane calli.
Microbes in marine ecosystems are known to produce secondary metabolites. One of which are carotenoids, which have numerous industrial applications, hence their demand will continue to grow. This review highlights the recent research on natural carotenoids produced by marine microorganisms. We discuss the most recent screening approaches for discovering carotenoids, using in vitro methods such as culture-dependent and culture-independent screening, as well as in silico methods, using secondary metabolite Biosynthetic Gene Clusters (smBGCs), which involves the use of various rule-based and machine-learning-based bioinformatics tools. Following that, various carotenoids are addressed, along with their biological activities and metabolic processes involved in carotenoids biosynthesis. Finally, we cover the application of carotenoids in health and pharmaceutical industries, current carotenoids production system, and potential use of synthetic biology in carotenoids production.
Human papillomavirus (HPV) type 52 is the most prevalent type for causing cervical cancer in Indonesian population. Cervical cancer becomes the most common cancer suffered by Indonesian women. Prevention of HPV infection can be achieved using HPV virus-like particle (VLP) vaccine derived from L1 major capsid protein. This study aimed to clone and analyze HPV-52 L1 gene. DNA obtained from biopsy of a cervical cancer patient was amplified using specific primers designed from Asian originated HPV-52 L1 gene available in the GenBank. The isolated HPV-52 L1 gene sequence was submitted to GenBank with accession number KF225497. Expression of HPV-52 L1 gene was performed using pRSET/EmGFP expression vector. We Escherichia coli analyzed and compared the HPV-52 L1 gene expressions from recombinant BL21 (DE3) that had been E.coli induced for 3 hours with 1 mM IPTG and without induction. The protein was expressed in insoluble form. We performed the following bioinformatic analyses: construction of phlyogenetic tree, T-cell epitopes prediction and 3D proteins structure modelling. We utilized the following softwares: MEGA5 for phylogenetic tree, IEDBann for MHC prediction, CLC DNA Workbench 6.5 for hydrophobicity analysis, and PDB-Viewer Deep for 3D protein structure analysis. The phylogenetic tree which was developed based on KF225497 sequence showed that it shared a branch with Asian countries (Philippines and Thailand). The deduced amino acid sequences of the predicted epitopes that were consistent in all of the programs were 259GTLGDPVPGDLYIQGS274 and 345KKESTYKNE353. This information may be useful to design diagnostic strategies and vaccine suitable for Indonesian population.Key words: epitope, HPV-L1 52 gene, human papillomavirus L1 protein Human papillomavirus ( HPV ) tipe 52 merupakan jenis penyebab kanker serviks yang paling umum pada penduduk Indonesia, terutama kaum perempuan. Pencegahan infeksi HPV dapat dicapai dengan menggunakan vaksin ( VLP ) HPV yang berasal dari L1 protein kapsid utama. Penelitian ini bertujuan untuk virus like particle mengkloning dan menganalisa L1 gen HPV-52. DNA yang diperoleh dari biopsi pasien kanker serviks diamplifikasi menggunakan primer spesifik yang dirancang dari L1 gen HPV-52 berasal dari Asia yang tersedia di GenBank. Urutan L1 gen HPV-52 yang terisolasi didaftarkan ke GenBank dengan nomor akses [KF225497]. Ekspresi L1 gen HPV-52 dilakukan dengan menggunakan vektor ekspresi Escherichia coli pRSET/EmGFP. Kami menganalisis dan membandingkan L1 gen HPV-52 dari BL21 (DE3) rekombinan E.coli yang telah diinduksi selama 3 jam dengan 1 mM IPTG dan tanpa induksi. Protein diekspresikan dalam bentuk terlarut. Kami melakukan analisis bioinformatika: pembuatan pohon filogenetik, prediksi epitop sel T, dan modeling struktur 3D protein. Kami menggunakan software MEGA5 untuk pohon filogenetik, IEDBann untuk prediksi MHC, CLC DNA Workbench 6.5 untuk analisis hidrofobik dan PDB -Viewer Deep untuk 3D analisis struktur protein . Pohon filogenetik yang dihasilkan berdasarkan pada urutan KF225497 me...
Penelitian guru merupakan suatu kegiatan yang dapat membantu proses pembelajaran generasi Z agar siap dalam menghadai masa depannya.
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