Growth and Fatty Acid Composition of Marine Microalga Nannochloropsis SP in Medium Enriched with Magnesium

Micro-algae are to be an attractive way to produce bio-diesel due to high photosynthetic yields and lipid accumulation in cells. This high productivity combined with possibility to uptake CO2 stimulated its utilization as a biological mitigation method of CO2, at once as an alternative renewable source of energy. Growth characteristics and chemical composition of micro-algae can be altered by culture environment. Nutrient sufficiency,included magnesium element (Mg2+) is important factors on overall biochemical composition. In study, Nannochloropsis sp was cultivated in Erlenmeyer 250 ml containing 200 ml f/2 medium. There are three groups of treatment with different levelof magnesium (Mg2+), i.e. 0 (M0); 0.1mgL-1 (M1); and 1.0 mgL-1 (M2). All treatment was designed triplicate in batch system. Culture was then aerated continuously with sterile atmospheric air (1.5 L.min-1). Cells were harvested on 25th day after inoculation and analyzed. Data showed that Chlorophyll-a increased linearly with time and maximum at 18th days of growth period, i.e. 23.57; 26.44; and 27.74mgL-1, for M0; M1; and M2,respectively. Chlorophyll-a content decreased significantly when pH dropped to 5-6.Enrichment with Mg2+ increased the chlorophyll-a content 12.2-17.7%. Dry cell reached 375-400mgL-1 in all treatment. Lipid content of Nannochloropsis sp in control (M0) is 55.3%, higher than M1 and M2. Saturated fatty acid tends to increase from 80.70 (M0)to 96.70 (M1) and 94.53% (M2). Fatty acid of M0 and M1 was composed dominantly by palmitic acid (C16:0), i.e. 49.19-70.75% total fatty acids. Meanwhile, M2 treatment was dominantly by lauric acid (C12:0), i.e. 32.98%

Zona Wisata Kawasan Wisata Alam Air Terjun Madakaripura, Kabupaten Probolinggo

Kabupaten Probolinggo memiliki keindahan wisata alam salah satunya berupa wisata air terjun. Wisata Alam Air Terjun Madakaripura termasuk dalam kawasan hutan lindung dan rawan bencana longsor sehingga pengembangannya membutuhkan pembagian zona wisata yang sesuai dengan karakteristik fisik kawasan wisata alam. Penelitian ini bertujuan menentukan zona wisata kawasan wisata alam Air Terjun Madakaripura, Kabupaten Probolinggo. Metode analisa yang digunakan dalam tahapannya adalah analisa Theoritical Deskriptif Kualitatif, teknik analisa Delphi dan analisa teknik Overlay. Hasil penelitian ini berupa zona wisata pada kawasan wisata alam Air Terjun Madakaripura, Kabupaten Probolinggo dengan melihat pada kondisi eksisting serta faktor-faktor yang mempengaruhi pengembangan kawasan wisata

Visual analysis of next-generation sequencing data to detect overlapping genes in bacterial genomes

Next generation sequencing (NGS) technologies are about to revolutionize biological research. Being able to sequence large amounts of DNA or, indirectly, RNA sequences in a short time period opens numerous new possibilities. However, analyzing the large amounts of data generated in NGS is a serious challenge, which requires novel data analysis and visualization methods to allow the biological experimenter to understand the results. In this paper, we describe a novel system to deal with the flood of data generated by transcriptome sequencing (RNA-seq) using NGS. Our system allows the analyzer to get a quick overview of the data and interactively explore interesting regions based on the three important parameters coverage, transcription, and fit. In particular, our system supports the NGS analysis in the following respects: (1) Representation of the coverage sequence in a way that no artifacts are introduced. (2) Easy determination of a fit of an open reading frame (ORF) to a transcript by mapping the coverage sequence directly into the ORF representation. (3) Providing automatic support for finding interesting regions to address the problems that the overwhelming volume of data comes with. (4) Providing an overview representation that allows parameter tuning and enables quick access to interesting areas of the genome. We show the usefulness of our system by a case study in the area of overlapping gene detection in a bacterial genome

Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces

BackgroundMultiple infection sources for enterohemorrhagic Escherichia coli O157:H7 (EHEC) are known, including animal products, fruit and vegetables. The ecology of this pathogen outside its human host is largely unknown and one third of its annotated genes are still hypothetical. To identify genetic determinants expressed under a variety of environmental factors, we applied strand-specific RNA-sequencing, comparing the SOLiD and Illumina systems.ResultsTranscriptomes of EHEC were sequenced under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes in strain EDL933 (genome and plasmid), a surprising minority of only 144 had null sequencing reads under all conditions. We therefore developed a statistical method to distinguish weakly transcribed genes from background transcription. We find that 96% of all genes and 91.5% of the hypothetical genes exhibit a significant transcriptional signal under at least one condition. Comparing SOLiD and Illumina systems, we find a high correlation between both approaches for fold-changes of the induced or repressed genes. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up-regulated on radish sprouts, cattle feces, or in the presence of antibiotics. Furthermore, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates.ConclusionsSince only a minority of genes (2.7%) were not active under any condition tested (null reads), we suggest that the assumption of significant genome over-annotations is wrong. Environmental transcriptomics uncovered hitherto unknown gene functions and unique regulatory patterns in EHEC. For instance, the environmental function of azoR had been elusive, but this gene is highly active on radish sprouts. Thus, NGS-transcriptomics is an appropriate technique to propose new roles of hypothetical genes and to guide future research

VisExpress : Visual exploration of differential gene expression data

Biologists are keen to understand how processes in cells react to environmental changes. Differential gene expression analysis allows biologists to explore functions of genes with data generated from different environments. However, these data and analysis lead to unique challenges since tasks are ill-defined, require implicit domain knowledge, comprise large volumes of data, and are, therefore, of explanatory nature. To investigate a scalable visualization-based solution, we conducted a design study with three biologists specialized in differential gene expression analysis. We stress our contributions in three aspects: first, we characterize the problem domain for exploring differential gene expression data and derive task abstractions and design requirements. Second, we investigate the design space and present an interactive visualization system, called VisExpress. Third, we evaluate the usefulness of VisExpress via a Pair Analytics study with real users and real data and report on insights that were gained by our experts with VisExpress.publishe

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA.publishe

Additional file 5: of Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

Prediction values for the novel and annotated proteins compared to their shuffled counterparts in dependence of the protein length. (PDF 443 kb

Additional file 8: Table S6. of Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

Data set of the 115 annotated ncRNAs and their properties, including blastp hits and proposed Shine-Dalgarno sequences. (XLSX 44 kb