Donny Widianto

Creating a Saccharomyces cerevisiae haploid strain having 21 chromosomes

Chromosome engineering techniques that can manipulate a large segment of chromosomal DNA are useful not only for studying the organization of eukaryotic genomes but also for the improvement of industrially important strains. Toward the development of techniques that can efficiently manipulate a large segment of chromosome, we have previously reported a one-step chromosome splitting technique in a haploid Saccharomyces cerevisiae cell, with which we could successfully split yeast chromosome 11, XIII, or XI into two halves to create a haploid strain having 17 chromosomes. We have now constructed chromosome splitting vectors bearing ADE2, HIS3, LEU2, or TRP1 marker, and by using these vectors, we could successively split yeast chromosomes to create a novel yeast haploid strain having up to 21 chromosomes. The specific growth rates of yeast strains carrying more than 16 chromosomes up to 21 did not differ significantly, suggesting that yeast cells can harbor more chromosomes than they do in their natural state, that is, 16 chromosomes, without serious effects on their growth.

One-step splitting of a chromosome in haploid cells of Saccharomyces cerevisiae and its effect on the cell proliferation

Abstract A simple method has been developed for splitting a chromosome in Saccharomyces cerevisiae into two replicating halves. Haploid yeast cells of an ura3 mutant were transformed with a linear molecule bearing an S. cerevisiae DNA fragment for targeted integration into a chromosome, the URA3 and CEN4 DNA sequences of S. cerevisiae , and a pair of inverted repeats (IRs) of the terminal 0.7 kbp of Tetrahymena ribosomal DNA (Tr). The integrated IRs of Tr ends of the molecule at a site on a chromosome in an ura3 mutant cell of S. cerevisiae subsequently resolved and the chromosome was split into two monocentric chromosomes in the Ura + transformant. Using this procedure, chromosomes XI, VIII, and II were each split into two halves, at the GCN3 , YHR088 , and VPS15 loci, respectively. Occurrence of the split chromosomes was confirmed by examination of their electrophoretic karyotypes. Some of the clones with the split chromosomes proliferated more quickly than the parental strain.

Soil Bacterial Diversity and Productivity of Coffee - Shade Tree Agro-ecosystems

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.

A method for fusing chromosomes in Saccharomyces cerevisiae

Abstract A method was developed for fusing chromosomes in Saccharomyces cerevisiae by employing the site-specific recombination system of pSR1, a circular DNA plasmid originating from Zygosaccharomyces rouxii , and a conditional centromere. 58-bp DNA fragments bearing the specific recombination sites (RSs) of pSR1 were inserted in the subtelomeric regions of chromosomes I (231 kbp) and XI (666 kbp) of a host strain in which chromosome I had a conditional centromere, i.e. , a centromere whose function can be switched off upon induction of the GAL1 promoter placed beside it. The resultant cells were then transformed with a plasmid bearing the R gene of pSR1 encoding the site-specific recombination enzyme connected downstream of the GAL1 promoter. When the transformant was cultivated in a galactose medium, the site-specific recombination enzyme catalyzed recombination between the two RSs inserted in the subtelomeric regions of chromosomes I and XI, generating a dicentric fusion chromosome (863 kbp) and an acentric one (46 kbp). Simultaneously, the function of the conditional centromere on the resultant fusion chromosome was switched off. The acentric chromosome was lost during cultivation, resulting in a yeast strain having 15 chromosomes. The fused chromosome was mitotically stable; its rate of loss was (1.68±0.24) × 10 −5 per cell division compared to a rate of loss of (1.09±0.54) × 10 −5 per cell division for a normal chromosome I.

Simultaneous Hydrolysis and Fermentation of Sweet Sorghum Varieties (FS501 and KCS105) into Bioethanol Using Saccharomyces steineri – A Kinetics Study

In this study, kinetics of bioethanol production by fermentation of three different substrates, which were artificial substrate and the juice of two sweet sorghum varieties (FS501 and KCS105) using Saccharomyces steineri, were examined using two proposed models by assuming that simultaneous hydrolysis and fermentation occurred. Fermentation of the substrate of FS501 and KCS105 juices showed better data fitting by using the modified version of the kinetics model while the fermentation of artificial substrate which was free of any other components followed Philippidis’s kinetics model. This difference was caused by the change of the yeast behavior in the form of the reduction of both the rate of fructose and/or glucose consumption by the yeast and the rate of fructose and or glucose conversion into ethanol during lag phase. As the consequence, sucrose hydrolysis seems very dominant in the FS501 and KCS105 juices fermentation during the lag phase. The change of behavior of the yeast was estimated being caused by the existence of “impurities” such as acetic acid, glycerol, nitrogen, phosphor, and potassium in the FS501 and KCS105 juices. From statistical analysis using correlation coefficient (between kinetics parameters and “impurities”), acetic acid was the most influential component to change the behavior.

The Effect of Rock Phosphate and Level of Inoculums on The Survivability of Aspergillus niger and Its Solubilization Ability When Pelleted With Rock Phosphate

The objectives of this research were to explore methanol utilizing microbes by isolation. selection and collection of methanol utilizing microbes from soil and dung. further it will be produced as single cell protein. The experiment covers two steps. i.e. I) Sampling of soil and dungfrom Bogor. Cianjur and Karawang. 2) Laboratory activity. consisted of: isolation. selection. identification and collection. The microbes were isolated by using the medium of Tani. et al (/982) and its modification. whereas the methanol utilizing microbes were identified by using standard method of Bergeys Manual of Determinative Bacteriology edition Ijh (/994) and Balow et al. (/99 I). The microbes were then proliferated by using Medium of Mimura et al. (1978) and its modification. Furthermore the cell were harvested and measured its nitrogen content. The collection of methanol utilizing microbes was conducted with the standard procedure of soil microbiology. This research indicated that from 72 samples of soil and dung were obtained 56 isolates of methanol utilizing microbes that diverse in number and types. Most of methanol utili:ing microbes were isolated from soil and dung by methanol medium 1% and /.5 % in pH 5 and 7. From 56 isolates were chosen 12 isolates to be identified and made as a data base. and then upt as culture collection at Indonesian Center for Biodiversity and Biotechnology (ICBB). Laboratory of Microbiology and Environmental Biotechnology PPLH. and Laboratory of Soil Biology. IPB. From the 12 isolates. 2 isolates were classified into methylotrophic group and they have big potency to be exploited in producing single cell protein. i.e. MelhylococCJIS capsulatus and Acidomonas methanolica. Between 2 isolates. Methylococcus capsulatus (T2M 1 P 1 Cianjur) have a big potency to be used as a source of single cell protein. due to their high content of protein. i.e. 6.4%. Both of the microbes were not pathogenic for human and animal.