Dwi Andreas Santosa

Rapid Extraction and Purification of Environmental DNA for Molecular Cloning Applications and Molecular Diversity Studies

A rapid method for the extraction and purification of DNA from environmental samples for molecular cloning applications was developed. The indigenous cells from plant debris, organic materials, sediments, and soils were lysed directly by using DAS-IZ solution and the nucleic acids were precipitated with isopropanol. A simple purification step using DAS-IIZ solution without binding matrix produced highly pure, colorless and undegraded DNA with molecular weight of more than 20 kb. The superiority of this method was tested for wide applications in molecular cloning, i.e., construction of genomic library by using Lambda DASH(R)II Vector and Gigapack(R)III XL, plasmid library, cloning of gene encoding protease, and molecular microbial diversity analysis. An additional advantage of this method is that only 0.1 g of sample is required, if analysis of many samples in short time should be done. To extract large amounts of environmental DNA for molecular cloning lasts only 30 min and to purify it less than 1 h.

Limazepines A−F, Pyrrolo[1,4]benzodiazepine Antibiotics from an Indonesian Micrococcus sp.

In our screening of Indonesian microorganisms for novel bioactive natural products we have isolated seven new compounds, designated as limazepines A, B1 and B2 (isolated as an isomeric mixture), C, D, E, and F, from the culture broth of Micrococcus sp. strain ICBB 8177. In addition, the known natural products prothracarcin and 7-O-succinylmacrolactin A, as well as two previously reported synthetic compounds, 2-amino-3-hydroxy-4-methoxybenzoic acid methyl ester and 4-ethylpyrrole-2-carboxaldehyde, were obtained from the extract. Chemical structures were determined by spectroscopic methods and by comparison with the NMR data of structurally related compounds. The limazepines belong to the growing group of the pyrrolo[1,4]benzodiazepine antitumor antibiotics isolated from various soil bacteria. Limazepines B1/B2 mixture, C, and E were active against the Gram-positive bacterium Staphylococcus aureus and the Gram-negative bacterium Escherichia coli. Limazepine D was also active against S. aureus, but was not active against E. coli. Interestingly, only the limazepines B1/B2 mixture and D were active against Pseudomonas aeruginosa.

A rapid and highly efficient method for transformation of sugarcane callus

Modern sugarcane cultivars have complex genetic characteristics and low fertility that render their genetic improvement through traditional breeding difficult. Genetic engineering methodology to introduce foreign genes provides new opportunities for the genetic improvement of sugarcane cultivars. One of prerequisites for successful insertion of a gene cassette into the plant genome is the availability of an efficient transformation protocol. An improved protocol for Agrobacterium-mediated transformation of sugarcane is described. Between 85 and 100% of calli transformed using this procedure produced new calli, and 100% of them were positive for the inserted gene. The whole procedure permitted the production of transgenic calli in a short time (1.5 mo). The transformed calli can be cultured further for the production of the inserted geneencoded enzyme by using cell culture, or they can be regenerated into transgenic plants. This protocol may be implemented also for the generation of transgenic plants from other species.

Modified phenazines from an Indonesian Streptomyces sp.

Fractionation of the extract from the Indonesian Streptomyces sp. ICBB8198 as directed by the antibacterial activity delivered the known phenazine antibiotics griseoluteic acid (1a) and griseolutein A (1b), as well as two new phenazine derivatives (2 and 3). In addition, the known compounds spirodionic acid, dihydrosarkomycins, and 6-ethyl-4-hydroxy-3,5-dimethyl-2H-pyran-2-one (4a), along with the new pyrone 3,6-diethyl-4-hydroxy-5-methyl-2H-pyran-2-one (4b), were isolated. We report here the isolation, structure elucidation, and antibiotic activity of the new metabolites as well as a hypothetical pathway for the formation of the new phenazine derivatives.

Rearranged and Unrearranged Angucyclinones from Indonesian Streptomyces spp.

Two Indonesian Streptomyces strains, ICBB8309 and ICBB8415, were investigated for their ability to produce antibiotic compounds. In addition to the known antibiotics actiphenol, naramycin B, and sabaramycin, six new angucyclinones were identified. The isolation, structure elucidation and biological activities for the six new compounds are presented. The angucyclinones 7-deoxo-6-deoxy-7-hydroxy-8-O-methylrabelomycin, 1-deoxo-1-hydroxy-8-O-methylrabelomycin, and the angucycline 7-deoxo-7-hydroxy-1-O-α-rhamnosy1-8-O-methyltetrangulol have common angular backbones, while angucyclinone C, limamycin A, and limamycin B appear to be rearranged angucyclinones.

Apoptolidins A and C activate AMPK in metabolically sensitive cell types and are mechanistically distinct from oligomycin A

Apoptolidin A was first isolated as a secondary metabolite of a Nocardiopsis sp. and is the founding member of a family of potential selective cancer cell toxins. We now report the isolation, production and pharmacological characterization of apoptolidins A and C from an alternate actinomycete producer, an Amycolatopsis sp. from soil samples collected in Indonesia. We investigated the action of apoptolidins A and C in representative human glioblastoma cells, lung cancer cells and mouse embryonic fibroblasts (MEFs) to better understand the mechanism of action of the known apoptolidins. Shifts in cellular metabolism in intact cells and the status of the AMP-activated protein kinase (AMPK) stress pathway in response to apoptolidin A were entirely consistent with the actions of an ATP synthase inhibitor. We find the metabolic phenotype of the cell to be a critical determinant of apoptolidin sensitivity and the likely basis for cancer cell selectivity. The apoptolidins induce indirect activation of AMPK and trigger autophagy in sensitive cell types without significant inhibition of mTORC1. Human U87-MG glioblastoma cells and wild type MEFs showed increased phosphorylation of AMPK (Thr172), ACC (Ser79) and ULK1 (Ser555), whereas AMPKα-null MEFs and more glycolytic SF-295 glioblastoma cells lacked this response. Although both are reported to be selective inhibitors of mitochondrial ATP synthase, differences between apoptolidin- and oligomycin A-induced responses in cells indicate that the action of these macrolides is not identical.

DINAMIKA KELIMPAHAN ORIBATIDA PADA AREA PERKEBUNAN KELAPA SAWIT DI KECAMATAN BAJUBANG BATANGHARI JAMBI

Oribatids are one of the important fauna groups in the soil. They have an important role in the decomposition of organic matter in the soil. The objection of this research was to study population dynamics of Oribatids through determining the abundance and diversity of Oribatids and to know the effect of environmental factors on Oribatids in oil palm plantation at Bajubang, Batanghari, Jambi. Soil and litter samples were taken from four different locations (25 m x 25 m) and from each location three samples were taken from litter lanes and open lanes, respectively (the size was 16 x 16 cm with a depth of soil is 5 cm). The samples were extracted using Kempson extractor. Identification of Oribatids was done to the family level and the diversity of Oribatids was measured using Shannon’s diversity index. The population dynamic of Oribatids showed a fluctuation in the sampling period. When rainfall increased >200 mm did not follow by increasing abundance and diversity (number of the family) of Oribatid mites. When rainfall between 100 – 200 mm was the optimal condition for Oribatids so abundance and diversity (the number of the family) of Oribatids increased. But, when rainfall <100 mm especially in February 2014 (the lowest rainfall 1 mm), abundance and diversity (number of the family) of Oribatids was lowest (330 individual m-2; 7 families) compared to another month. It was assumed that Oribatids may migrate into the deep soil to avoid a harsh environmental condition. Abundance and diversity (number of the family) of oribatids were significantly higher in litter lanes (4,560 individual m-2; 25 families) than in open lanes (1,570 individual m-2; 14 families). The availability of litter in the litter lanes was higher than in open lanes. In this research, There are 3 families that most abundance and always found on the sampling period, they are Scheloribatidae, Mycobatidae and Galumniidae. Keywords: Abundance, diversity, oil palm plantation, Oribatids, soil fauna

The Diversity and Abundance of Springtail (Collembola) on Forests and Smallholder in Jambi

This research was completed using mixed qualitative and quantitative methods. Field surveys were executed in sugar cane plantation throughout South Sulawesi Indonesia. Land suitability analyses were performed using a parametric approach with Storie’s index equation followed up with correlation analysis using the Pearson correlation. Results revealed that the period for sugarcane crop growth in the humid tropic relatively dry regions of South Sulawesi Indonesia lasted for the months of November to July. The land suitability for sugar cane in the research location was moderately suitable (S2c) and marginally suitable (S3c, S3s, S3s,f and S3c,w) with limiting factors such as relative humidity during crop maturation phase, the duration of sunlight, soil depth, soil texture, soil pH and soil drainage. Land suitability index at the research location ranged from 25.2 to 55.0; sugar cane yields ranged from 30.3 to 62.0 Mg ha year. Pearson correlation coefficient (r) between LSI with cane and sugar productivity were 0.81 and 0.84 respectively, signifying the strength of the correlation between the two values. This also indicates that land suitability index can be estimating the potential crop yield in the humid tropicsthat relatively dry climate regions.Field experiment with a split plot design has been carried out in order to assess the growth characteristics and yields, and effectiveness of MVA upland rice which were given potassium fertilizer in two growing seasons. MVA inoculation consisted of three treatments (without MVA, Glomus sp. and Gigaspora sp.) while potassium fertilizer consisted of five levels (0, 12.5, 25, 37.5, and 50 kg ha-1 K). The results showed that plant growth variable which was inoculated by MVA at any levels of K fertilizer was higher in the dry season than that in the wet season, whereas the opposite occurred for net assimilation rate. Potassium content of leaf tissue, shoot/root ratio, and grain weight per hill was determined and mutually dependent on genus MVA, dosages of K fertilizer, and growing season. Harvest index and grain dry weight per hill were influenced by the growing season and the genus MVA but the effect did not depend on each other. At all dosages of K fertilizer and any MVA genera, Gigaspora sp. inoculation was better than that of Glomus sp. Dry weight of grains per hill was affected by the contribution of grain content per hill, weight of 1000 grains and number of productive seedlings per hill. The optimum dosage of K fertilizer in the dry season was 32.4 kg ha-1 K with grain yield 3.12 Mg ha-1 for inoculation of Gigaspora sp., whereas the optimum dosage in the wet season was 34.2 kg ha-1 K for the treatment Glomus sp. inoculation with Gigaspora sp. in the wet season did not reach dosages of optimum K fertilizer. Keywords: Harvest index, MVA, potassium fertilizer, upland rice [ How to Cite : Natawijaya D. 2012. Increasing Growth and Yield of Upland Rice by Application of Vesicular Arbuscular Mycorrhizae and Potassium Fertilizer. J Trop Soils 17 (1): 53-60. doi: 10.5400/jts.2012.17.1.53] [ Permalink/DOI: www.dx.doi.org/10.5400/jts.2012.17.1.53 ]This study aimed to examine Organonitrofos Plus fertilizer (OP) on sweet corn (Zea mays Saccharata L.) and its effect on changes in soil chemical properties of Ultisols. Organonitrofos Plus fertilizer is an enhancement of Organonitrofos fertilizer enriched with microbes at the beginning of the manufacturing process. Research was conducted in the greenhouse of Integrated Agricultural Laboratory of Lampung University. Treatment applied was a factorial of 4 t 2 t 3 with three replications in a randomized block design. The first factor was the dose of OP fertilizer (0, 10, 20, 30 Mg ha-1), the second factor was the dose of inorganic fertilizers (without inorganic fertilizers, and with inorganic fertilizers, namely Urea 0.44, 0.28 SP-36 and KCl 0.16 Mg ha-1), and the third factor was the dose of biochar (0, 10, 20 Mg ha-1). By a single OP fertilizers, inorganic fertilizers, and the interaction between the OP and the inorganic fertilizers increased the weight of dry stover, cob length, cob diameter, cob with husk and cob without husk of corn. OP fertilizers which are applied in Ultisols can improve soil fertility and increase corn production so that OP fertilizer can lessen the use of inorganic fertilizer and can be used as a substitute for inorganic fertilizer. RAE values were highest in treatment of O4K2B2 (30 Mg OP ha-1, with inorganic fertilizer, 10 Mg biochar ha-1) that was equal to 181%, followed by O2K2B3 (10 Mg OP ha-1, with inorganic fertilizer, 20 Mg biochar ha-1 ) with the difference in RAE value of 0.5%.[How to Cite: Dermiyati, SDn Utomo,n KF Hidayat, J Lumbanraja, S Triyono, H Ismono, NEn Ratna, NT Putri dan R Taisa. 2016. Pengujian Pupuk Organonitrofos Plus pada Jagung Manis (Zea mays Saccharata. L) dan Perubahan Sifat Kimia Tanah Ultisols. J Trop Soils 21: 9-17 Doi: 10. 10.5400/jts.2016.21.1.9][Permalink/DOI: www.dx.doi.org/10. 10.5400/jts.2016.21.1.9]Coco rind is a waste that if not used can cause environmental problem around the plantation. One way to utilize cocoa rind is by making it into compost which can be used as organic fertilizer. Different planting distance will affect on the number of plant population per unit area and will indirectly affect the absorption of nutrients, water and other growth factors. The purpose of this study was to determine the effect of the utilization of compost from cacao rind waste on the growth of Saccarum edule Hasskarl plant with different planting distance. The design used was to factor randomized block design with 2 replications, then there are 18 treatment combinations. In this research, the first factor of cacao rind composts comparison with cow manure consisted of three levels, they are: P1 = 50 kg; 10 kg; P2 =50 kg: 30 kg; P3 = 50 kg: 50. While the second factor uses the planting distance which consisted of three levels, they are: J1= 100 cm X 150 cm; J2= 100 cm X 100 cm; J3= 100 cm X 50 cm. Based on the research results, it shows that the best treatment of cocoa rind compost and cow manure, which affects on the number of buds is treatment P3 on 5 WAP, while the best used for the plants’ height is P2 on 3 WAP, and the best used for the leaves’ length is treatment P2 on 2 to 4 WAP.

KOMBINASI PUPUK ORGANIK HAYATI DAN PUPUK FOSFAT UNTUK PENINGKATAN KERAGAAN BIBIT KELAPA SAWIT (Elaeis guineensis Jacq)

Percobaan ini dilakukan untuk mengetahui pengaruh pupuk organik hayati diperkaya mikrob tanah terhadap keragaan tanaman, populasi total mikrob dan populasi mikrob pelarut fosfat di pembibitan kelapa sawit. Persiapan media tanam dilakukan dengan mengambil lapisan tanah atas (topsoil) dengan kedalaman maksimal 25 cm kemudian tanah tersebut dikering anginkan dan dimasukkan ke dalam setiap kantong plastik media tanam dengan volume masing-masing 5 kg. Pengukuran parameter keragaan tanaman bibit kelapa sawit dilakukan dari minggu ke-4 setelah tanam (MST) hingga ke-22 MST di rumah kaca kebun percobaan Cikabayan, Darmaga. Percobaan uji efektivitas mikrob pelarut fosfat (MPF) pada pupuk organik hayati menggunakan Rancangan Acak Kelompok (RAK), yang terdiri dari dua faktor dengan tiga ulangan. Hasil percobaan menunjukkan pengaruh penggunaan pupuk batuan fosfat terhadap tinggi tanaman memberikan hasil yang lebih baik dibandingan penggunaan SP-36 dan analisa statistik terhadap pengaruh tunggal pupuk organik hayati, pengaruh pupuk organik terhadap populasi total mikrob menunjukkan hasil terbaik.

PEMANFAATAN KONSORSIUM BAKTERI LOKAL UNTUK BIOREMEDIASI LIMBAH TEKSTIL MENGGUNAKAN SISTEM KOMBINASI ANAEROBIK-AEROBIK

The objective of this research is to study the potential use microorganisms which are identified as Aeromonas sp., Pseudomonas