Articles

Found 11 Documents
Search

Pemetaan quantitative trait loci untuk sifat berskala kategorik

Jurnal Ilmu Pertanian Indonesia Vol 12, No 1 (2007): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Original Source | Check in Google Scholar | Full PDF (546.809 KB)

Abstract

Genes or regions on chromosome underlying a quantitative trait are called quantitative trait loci (QTL). Characterizing genes controlling quantitative trait on their position in chromosome and their effect on trait is through a process called QTL mapping. In estimating the QTL position and its effect, QTL mapping utilizes the association between QTL and DNA makers. However, many important traits are obtained in categorical scale, such as resistance from certain disease. From a theoritical point of view, QTL mapping method assuming continuous trait could not be applied to categorical trait. This research was facusing on the assessment of the performance of maximum likehood (ML) and regression (REG) approach employed in QTL mapping for binary trait by means of simulation study. The simulation study to evaluate the performance of ML and REG approach was conducted by taking into accounte several factors that may affecting the performance of both approaches. The factors are (1) maker density, (2) QTL effect, (3) sample size, and (4) shape of phenotypic distribution. Form simulation study, it was obtained that the two approaches showing comparable performance. Hence, QTL analysis could be performed using these two approaches due to their similar performance.

MODELLING INGREDIENT OF JAMU TO PREDICT ITS EFFICACY

FORUM STATISTIKA DAN KOMPUTASI Vol 15, No 2 (2010)
Publisher : FORUM STATISTIKA DAN KOMPUTASI

Show Abstract | Original Source | Check in Google Scholar | Full PDF (555.672 KB)

Abstract

Jamu is an Indonesian herbal medicine made from a mixture of several plants.  Nowadays, many jamu are  produced commercially by many industries in Indonesia.  Each producer may have their own jamu formula. However, one is certain; the efficacy of jamu is determined by the composition of the plants used.  Thus, it is interesting to model the ingredient of jamu which consist of plants and use it to predict efficacy of jamu.  In this analysis, Partial Least Squares Discriminant Analysis (PLSDA) is used in modeling jamu ingredients to predict  the  efficacy.  It  is  obtained  that  utilizing the prediction of  y ij obtained  from  PLSDA  directly  rather  than  use  it  to calculate probability of jamu i belong to efficacy j and then use the probability to predict efficacy produces lower False Positive Rate (FPR) in predicting efficacy group.  Keywords: Jamu, PLSDA

Pemetaan quantitative trait loci untuk sifat berskala kategorik

Jurnal Ilmu Pertanian Indonesia Vol 12, No 1 (2007): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Original Source | Check in Google Scholar | Full PDF (546.809 KB)

Abstract

Genes or regions on chromosome underlying a quantitative trait are called quantitative trait loci (QTL). Characterizing genes controlling quantitative trait on their position in chromosome and their effect on trait is through a process called QTL mapping. In estimating the QTL position and its effect, QTL mapping utilizes the association between QTL and DNA makers. However, many important traits are obtained in categorical scale, such as resistance from certain disease. From a theoritical point of view, QTL mapping method assuming continuous trait could not be applied to categorical trait. This research was facusing on the assessment of the performance of maximum likehood (ML) and regression (REG) approach employed in QTL mapping for binary trait by means of simulation study. The simulation study to evaluate the performance of ML and REG approach was conducted by taking into accounte several factors that may affecting the performance of both approaches. The factors are (1) maker density, (2) QTL effect, (3) sample size, and (4) shape of phenotypic distribution. Form simulation study, it was obtained that the two approaches showing comparable performance. Hence, QTL analysis could be performed using these two approaches due to their similar performance.

Simultaneous clustering analysis with molecular docking in network pharmacology for type 2 antidiabetic compounds

Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Show Abstract | Original Source | Check in Google Scholar

Abstract

The database of drug compounds and human proteins plays a very important role in identifying the protein target and the compound in drug discovery. Recently, a network pharmacology approach was established by updating the research paradigm from the current “one disease-one target-one drug” to a new “drug-target-disease network”. Ligand-protein interactions can be analyzed quantitatively using simultaneous clustering and molecular docking. The docking method offers the ability to quickly and cheaply predict the ligand-protein binding free energy (DG) in structure-based virtual screening. Meanwhile, simultaneous clustering was used to find subgroups of compounds that exhibit a high correlation with subgroups of target proteins. This study is focused on the interaction between the 306 compounds from medicinal plants (brotowali Tinospora crispa, ginger Zingiber officinale, pare Momordica charantia, sembung Blumea balsamifera, synthetic drugs (FDA-approved) and the 21 significant human proteins associated with type 2 diabetes. We found that brotowali (B018), sembung (S031), pare (P231), and ginger (J036, J033) were close to the synthetic drugs and can possibly be developed as antidiabetic drug candidates. Likewise, the proteins AKT1, WFS1, APOE, EP300, PTH, GCG, and UBC which assemble each other and which have a high association with INS can be seen as target proteins that play a role in type 2 diabetes.

Liquid Chromatography Mass Spectrometry (LC-MS) Fingerprint Combined with Chemometrics for Identification of Metabolites Content and Biological Activities of Curcuma aeruginosa

Indonesian Journal of Chemistry Vol 18, No 1 (2018)
Publisher : Universitas Gadjah Mada

Show Abstract | Original Source | Check in Google Scholar

Abstract

Curcuma aeruginosa is known as one of the components of herbal medicine with various biological activities. This research aims to identify the metabolites content of C. aeruginosa related to their biological activities using LC-MS fingerprint combined with chemometrics. C. aeruginosa from 3 areas in Java were collected and macerated with ethanol and then analyzed with LC-MS. Along with this analysis, the antioxidant activity of all samples was determined using CUPRAC method, and the toxicity was determined using Brine Shrimp Lethality Test (BSLT), and chemometric method was used Principle Component Analysis (PCA) and Partial Least square (PLS). Metabolites profiles showed 175 predicted compounds, in which the dominant compounds are from the sesquiterpene of Curcuma genus. The PCA metabolites profiles can separate the samples by their location of origin. Interpretation of the correlation between metabolites profiles and their bioactivities was determined using PLS technique. The results showed that the toxicity of samples was exerted by compounds with ion mass of 312.28 and 248.15, which have the highest antioxidant and toxicity potentials. Compounds with ion mass of 248.15 were predicted to be 9-Oxo-neoprocurcumenol, 7α,11α,-Epoxy-5β-hydroxy-9-guaiaen-8-one, Curcumenolactone A, or Curcumenolactone B. While compound with ion mass of 312.28 was predicted to tetrahydro-bisdemethoxycurcumin.

Pengaruh Spiritualitas Kerja terhadap Keterlekatan Karyawan melalui Kepuasan Kerja pada UKM Kota Bogor

Jurnal Manajemen dan Organisasi Vol 8, No 2 (2017): Jurnal Manajemen dan Organisasi
Publisher : Institut Pertanian Bogor

Show Abstract | Original Source | Check in Google Scholar | Full PDF (492.665 KB)

Abstract

The Quality human resources are needed in global economic competition. Spirituality in work becomes a solution developed by companies, because it can be created a conducive environment for employees to work as good as possible. The purpose of this study is to analyze the influence of work spirituality on employee engagement through job satisfaction in Small and Medium Enterprises cluster of food and beverages in the city of Bogor. This research used Structural Equation Modeling PLS for data analysis. Samples are SMEs that have at least 5 employees and have been registered in the Department of Industry and Trade (Disperindag) and the Department of Cooperatives and SMEs Bogor City. So that 25 SMEs are eligible, consisting of 65 people consisting of employees and owners of SMEs. Sampling method using purposive sampling. The results showed that the spirituality of work has a positive effect directly on employee engagement and indirectly influence through job satisfaction on employee engagement to the organization. Meanwhile, job satisfaction has a direct positive effect on employees'  engagement to the organization. Therefore, increased employee engagement to SMEs is suggested through several supporting activities such as: communicating and facilitating the need for spirituality in the workplace.

Efek Sinergis Bahan Aktif Tanaman Obat Berbasiskan Jejaring Dengan Protein Target

Jurnal Jamu Indonesia Vol 1 No 1 (2016): Jurnal Jamu Indonesia
Publisher : Pusat Studi Biofarmaka Tropika LPPM IPB; Tropical Biopharmaca Research Center - Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (1489.882 KB)

Abstract

Medicinal plants contain inherently active ingredients. Such ingredients are beneficial to prevent and cure diseases, as well as to perform specific biological functions. In contrast to synthetic drugs, which is based on one single chemicals, medicinal plants exert their beneficial effects through the additive or synergistic action of several chemical compounds. Those chemical compound act on single or multiple targets (multicomponent therapeutic) associated with a physiological process. Active ingredients combinations show a synergistic effect. This means that the combinational effect of several active ingredients is greater than that of individual one acting separately. A network target can be used to identify synergistic effects of plants active ingredients. The method of NIMS (Network target-based Identification of Multicomponent Synergy) is a computational approach to identify the potential synergistics effect of active ingredients. It also assessess synergistic strength of any active ingradients at the molecular level by synergy scores. We investigate these synergistic on a Jamu formula for diabetes mellitus type 2.  The Jamu formula is composed of four medicinal plants, namely Tinospora crispa , Zingiber officinale, Momordica charantia, and Blumea balsamivera. Our work succesfully demonstrates that the highest synergy scores on medicinal plants synergy can be seen in pairs of several active ingredients in Zingiber officinale. On the other hand, the synergy of pairs of active ingredients in Momordica charantia and Zingiber officinale posseses a relatively high score. The same occurs in Tinospora crispa and Zingiber officinale.

Analisis Gerombol Simultan dan Jejaring Farmakologi antara Senyawa dengan Protein Target pada Penentuan Senyawa Aktif Jamu Anti Diabetes Tipe 2

Jurnal Jamu Indonesia Vol 1 No 2 (2016): Jurnal Jamu Indonesia
Publisher : Pusat Studi Biofarmaka Tropika LPPM IPB; Tropical Biopharmaca Research Center - Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (1519.787 KB)

Abstract

Selama ini pembuatan obat untuk menyembuhkan suatu penyakit masih menargetkan hanya satu protein khusus yang menjadi penyebab penyakit tersebut, yang tentu hanya menggunakan satu senyawa aktif. Padahal selain menimbulkan efek samping, penanganan suatu penyakit perlu menyasar banyak protein sekaligus. Sehingga, baru-baru ini terjadi perubahan paradigma dari “one drug, one target” menjadi “multi-components, network target”. Paradigma baru ini telah melahirkan beberapa penelitian untuk menghasilkan formulasi jamu, hal ini dikarenakan konsep formulasi jamu memerlukan beberapa senyawa aktif yang terlibat. Formula jamu yang diteliti sebagai upaya menyembuhkan penyakit Diabetes Melitus (DM) tipe 2 terdiri dari 4 tanaman yaitu Pare (Momordica charantia), Sembung (Blumea balsamifera), bratawali (Tinospora crispa), dan jahe (Zingiber officinale) berdasarkan hasil penelitian Nurishmaya tahun 2014 serta berdasarkan ramuan jamu yang sedang dikembangkan di Pusat Studi Biofarmaka, Bogor. Evaluasi senyawa yang berkaitan dengan DM tipe 2 dilakukan dengan terlebih dahulu menambahkan 19 obat sintetis yang ditujukan untuk DM tipe 2 dari basis data Drug Bank. Sehingga terdapat total sebanyak 74 senyawa aktif yang terdiri dari 55 senyawa alami dari tanaman dan 19 senyawa sintetis obat. Sebanyak 100 protein yang berkaitan erat dengan masing-masing senyawa diperoleh melalui hasil skor konkordan DrugCHIPER. Skor konkordan tersebut kemudian digunakan dalam analisis gerombol simultan antara senyawa dan protein target. Plot komponen utama dan submatrix penggerombolan simultan menunjukkan 2 dari 3 senyawa dari bratawali sangat dekat dengan kelompok sintetis. Selain itu, ada 11 dari 44 senyawa dari Jahe terkumpul bersama dengan senyawa sintetis tetapi dalam jarak yang jauh. Sedangkan berdasarkan jejaring kemiripan, lebih spesifik lagi terdapat 17 dari 19 senyawa obat sintetis yang memiliki kemiripan berdasarkan protein target dengan 2 senyawa tanaman Bratawali dan 5 senyawa tanaman Jahe.

Prediksi Senyawa Aktif Pada Tanaman Obat Berdasarkan Kemiripan Struktur Kimiawi untuk Penyakit Diabetes Tipe II

Jurnal Jamu Indonesia Vol 1 No 3 (2016): Jurnal Jamu Indonesia
Publisher : Pusat Studi Biofarmaka Tropika LPPM IPB; Tropical Biopharmaca Research Center - Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (839 KB)

Abstract

Diabetes melitus merupakan penyakit metabolik yang dicirikan oleh tingginya kadar glukosa dalam darah. Di Indonesia jumlah penderita diabetes menempati urutan keempat di dunia setelah Amerika Serikat, India, dan Cina dengan jumlah penderita mencapai lebih dari 12 juta jiwa. Salah satu upaya yang dilakukan untuk mengatasi diabetes adalah mengkonsumsi obat herbal berupa jamu sebagai alternatif obat sintetik. Pusat Studi Biofarmaka Bogor sedang mengembangkan ramuan jamu untuk penyakit Diabetes Melitus Tipe II yang terdiri dari empat tanaman obat yaitu pare (Momordica charantia), sembung (Blumea balsamifera), bratawali (Tinospora crispa), dan jahe (Zingiber officinale). Kandungan senyawa keempat tanaman diduga memiliki aktivitas biologis yang mirip dengan senyawa sintetik. Pada prinsipnya, diasumsikan bahwa senyawa yang struktur kimiawinya mirip memiliki sifat biologis yang mirip. Kemiripan senyawa diukur menggunakan koefisien Modifikasi Tanimoto dengan sidik jari molekuler KR. Hasil penelitian menunjukkan bahwa tanaman Bratawali merupakan tanaman utama pada ramuan jamu untuk penyakit diabetes berdasarkan jumlah kandungan senyawa yang dominan mirip dengan senyawa sintetik yaitu senyawa N-trans-feruloyltyramine (B015) dan N-formylanonaine (B018). Selanjutnya, Senyawa-senyawa yang memiliki nilai kemiripan tinggi dengan senyawa sintetik diperoleh pula pada senyawa karaviloside I (P195) dari tanaman pare, senyawa xanthoxylin (S002) dari tanaman sembung, senyawa borneol (J207) dan (-)- isoborneol (J226) dari tanaman Jahe.

Penguraian Mekanisme Kerja Jamu Berdasarkan Jejaring Bahan Aktif-Protein Target-Gene Ontology

Jurnal Jamu Indonesia Vol 1 No 3 (2016): Jurnal Jamu Indonesia
Publisher : Pusat Studi Biofarmaka Tropika LPPM IPB; Tropical Biopharmaca Research Center - Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (1168.201 KB)

Abstract

Jamu merupakan obat tradisional Indonesia. Pada dasarnya obat herbal yang dibuat dari bahan-bahan alami yang diambil dari beberapa bagian dari tanaman obat yang mengandung beberapa zat dan senyawa yang penting dan bermanfaat bagi tubuh. Sejauh ini, khasiat untuk beberapa jenis jamu secara empiris telah terbukti. Dalam peneitian ini, kami bermaksud untuk menguraikan mekanisme kerja jamu menggunakan pendekatan komputasi. Penelitian ini berfokus pada ramuan jamu type 2 diabetesyang terdiri dari empat tanaman, yaitu: jahe, bratawali, sembung, dan pare. Kerangka analisis awal dengan membentuk 3 komponen jejaring yang terdiri dari: (1) bahan aktif tanaman (diperoleh dari Knapsack: 58 senyawa aktif), (2) protein target (diperoeh dari database pubchem: 416 protein target), dan (3) gene ontoogy(diperoeh dari database DAVID: 3104 GO). Selanjutnya, kami menerapkan analisis klaster-klasterdengan menggunakan konsep graf tri-partite. Graf tri-partite digunakan untuk mengelompokkan komponen-komponen penyusun jejaring dari empat tanaman yang disebutkandiatas, sehingga diperoleh system bagian-bagian penyusun ramuan jamu. Hal ini dilakukan untuk mengungkapkan mekanisme kerja jamu. Menggunakan metode fuzzy clustering pada data jejaring, kami memperoleh 15 senyawa aktif yang diduga potensial sebagai antidiabetes berada dalam kelompok berbeda. Pada 15 senyawa aktif memiliki nilai peluang cukup tinggi terbagi dalam kelompok yang berbeda, setiap kelompok terdiri dari pasangan bahan aktif yang memiliki efek sinergis tinggi. Berdasarkan koneksi antara klaster-klasterprotein dan GO-BP, penelitianini memperoleh informasi protein-protein yang menyebabkan T2D dan mekanisme proses biologis yang terkait. T2D bukan hanya disebabkan oleh protein kelainan sekresi insulin (insulin-merendahkan enzim isoform 1) saja, tetapi juga disebabkan oleh protein lain yang terlibat dalam penghambatan insulin di pankreas.