ISOLASI DAN IDENTIFIKASI BAKTERI PENAMBAT NITROGEN UNTUK PEMBUATAN BIOFERTILIZER

Nitrogen is a macro nutrient needed by plants. Generally, people use inorganic fertilizers to fulfill nitrogen nutrients in plants. The problem then is, the continuous use of synthetic nitrogen fertilizers has a direct negative impact on the soil and a derivative impact on human health. The use of microorganisms, in this case bacteria, to provide nitrogen to plants can be done by isolating it and making it a biological fertilizer agent. Nitrogen fixing bacteria was isolated on the land of the oil palm plantation of PT Astra Agro Lestari. The isolated nitrogen-fixing bacteria were then tested quantitatively for their ability to fix nitrogen. The bacteria with the highest nitrogen fixing ability were then identified by sequencing their DNA nucleotide bases so that the bacterial strains were identified. The result is that there are 13 bacteria that are able to fix nitrogen with the codes J1, J3, Q5, L1, L11, J31, D1, M6, M5, R1, P2, J4 and C7. The quantitative test shows that bacteria with code D1 are the best at fixing nitrogen in the form of NH4, namely 0.27 ppm. The results of D1 bacterial DNA nucleotide base sequencing showed that the putitive Bacillus aerius strain 24K with identical values ​​and query cover reach

CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing

Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P-values for CoolMPS (adjusted P-value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs.

Private haplotype barcoding facilitates inexpensive high-resolution genotyping of multiparent crosses

Inexpensive, high-throughput sequencing has led to the generation of large numbers of sequenced genomes representing diverse lineages in both model and non-model organisms. Such resources are well suited for the creation of new multiparent populations to identify quantitative trait loci that contribute to variation in phenotypes of interest. However, despite significant drops in per-base sequencing costs, the costs of sample handling and library preparation remain high, particularly when many samples are sequenced. We describe a novel method for pooled genotyping of offspring from multiple genetic crosses, such as those that that make up multiparent populations. Our approach, which we call "private haplotype barcoding” (PHB), utilizes private haplotypes to deconvolve patterns of inheritance in individual offspring from mixed pools composed of multiple offspring. We demonstrate the efficacy of this approach by applying the PHB method to whole genome sequencing of 96 segregants from 12 yeast crosses, achieving over a 90% reduction in sample preparation costs relative to non-pooled sequencing. In addition, we implement a hidden Markov model to calculate genotype probabilities for a generic PHB run and a specialized hidden Markov model for the yeast crosses that improves genotyping accuracy by making use of tetrad information. Private haplotype barcoding holds particular promise for facilitating inexpensive genotyping of large pools of offspring in diverse non-model systems.

Trichosporon guehoae sp.nov., an anamorphic basidiomycetous yeast

A morphological and physiological description of an anamorphic basidiomycetous yeast species, named Trichosporon guehoae (CBS 8521T), is presented. The ability to assimilate several aliphatic and aromatic compounds as sole source of carbon and energy is reported. The phylogenetic position within the genus, based on nuclear base sequencing of the D1/D2 region of the large subunit of rDNA is discussed.Key words: basidiomycetes, taxonomy, Trichosporon guehoae sp.nov., yeasts.