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Revealed WGS of Oil Accumulating Diatom

bio-fuelMicroalgae are promising sources for biofuel production through the generation of carbon-neutral sustainable energy.

Biofuel from microalgae receives attention because it reduces CO2 emissions and does not use resources required for food production. A Japanese team revealed the whole genome sequence (WGS) of a marine diatom, Fistulifera solaris JPCC DA0580, which had been screened from their culture collection of microalgae (Tanaka et al., Plant Cell, 2015) as highly capable of oil accumulation. They said de novo assembly of this genome is so tough because it is alloploid, which means it has a very complex genome structure.

Finally, they could annotate about 20,000 genes on 42 chromosome pairs. They also identified a lot of genes which concern oil synthesis and, furthermore, they also analyzed activation patterns of these target genes.

I am sure this study will be a model case to highlight how NGS technologies can accelerate bioengineering!

The Common Marmoset as a Model Organism for the Study of Drug Metabolism

marmosetSeveral non-human primates including Macaca mulatta and Macaca fascicularis are well known as experimental animals in the field of neuroscience, stem cell research, drug toxicology, and other applications. The common marmoset (Callithrix jacchus) is also a non-human primate and is suitable as experimental animal because of the small size and highfecundity.

For developing a drug metabolism model, our collaborators and Eurofins Genomics (2014) performed transcriptome analysis of the common marmoset using in parallel long-read technology (Roche GS FLX+) and short-read sequencing (Illumina HiSeq 2000). This parallel NGS approach resulted in both, the identification and the quantitative analysis of transcripts and thus giving insight into gene expression during drug metabolism. Finally we obtained rich information about genes involved in drug-metabolism including 18 cytochrome P450- and 4 flavin-containing monooxygenase -like (FMO) genes, and their tissue-specific expression patterns.

The results of this study are the foundation for future studies not limited to drug metabolism & pharmacokinetics.

Possibility of Ideal Intestinal Remedy

I’m not able to keep intestinal condition without remedy which is prepared by Lactobacillus, Bifidobacterium, Lactococcus, and others. Eating yogurt is also okay for this purpose, ad personam I prefer to take these bacterial tablets and believe more effects. However, many people know these effects of current intestinal remedies are mild not fast-acting properties.

Several reports mentioned that intestinal bacterial flora and its regulation were not simple. It is starting discussion that natural immunity may regulate intestinal flora; e.g. antibacterial peptide α-defensins which is secreted from paneth cells on small-intestinal epithelium could regulate flora distribution (Salzman et al., 2010; Matsuda et al., 2011). By contrary, very simple strategy is reported as following: Clostridium difficile brings bad diarrhea that was resistant to antibiotic. Van Nood and co-workers (2013) injected healthy person’s feces into patient’s guts, and its curative effect was so good surprisingly, but we cannot call it a remedy!

Two NGS platforms, GS FLX/Junior and MiSeq, can perform distributional analysis via deep sequencing of 16S-rRNA amplicons. But it is still difficult for both platforms to do metagenome assembling for getting whole gene information in flora, because their read length is not long enough to make reliable contigs without chimeras between different bacteria one another. Therefore I strongly expect that super long read platforms including PacBio RS series and coming nano-pore technologies will break current limitations and will contribute to develop ideal intestinal remedy for my instable stomach.

Whole Genome Sequencing of Fukushima’s People

At the end of August, Mr. Hosono, the Japanese minister for the environment, announced, that the ministry aims to perform whole genome sequencing (WGS) of people who live around the disabled “Fukushima Daiichi Nuclear Power Station”. He said that the WGS project will not be able to relieve concerns immediately, but it will make an important provision for the future. According to Mr. Hosono the main target group for WGS will be children.

These genomic analyses face many problems including the aspect of experiments with humans, maintaining confidentiality, discovery of information according to need, and others. This story reminds me once more that NGS technologies start to have social impacts.

Sequencing than soaking in Hot Spring

There are many volcanoes and earthquakes in Japan, but it is not always a bad thing, they are also responsible for the many hot springs. Most Japanese people love soaking in a hot spring and they believe that this eliminates fatigue and improves health. Hot springs also had a great contribution to biotechnology via the heat resistant DNA polymerase from Thermus aquaticus (Taq) and its derivatives. Not only PCR, but also Sanger sequencing was accelerated by these heat resistant enzymes as we all know well.

Scientists have started to study the genome/transcriptome world in hot springs with NGS technologies. Murakami et al., peformed 16S-rRNA (Sanger sequencing) and meta-transcriptome analysis from small RNA (GS FLX sequencing) of groundwater (up to 1,000 m depth) from Yunohara hot spring, Japan. Their phylogenetic analysis using 16S rRNA showed the classification of 17 species including archaea and eubacteria.  There are only 2 or 3 dominant species in typical cases of other hot springs, but this one is rich in diversity. Furthermore, they found the very unique group “Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN)” which is a small organism/cell with only 200 nm size! Their small RNA analysis identified 64,194 (20,057 nonredundant) cDNA sequences, and they found several novel non coding RNAs which have a very stable secondary structure.

Therefore, hot springs may still be gold mines for useful genes and important biological knowledge of unknown underground ecosystems.



Nacreous Luster Spun by Gene Expression

Nacreous luster is held in high industrial value since ancient time. It is a jewelry which is generated in pearl oysters, so it is also called “biomineral”. Nacre consists of two kinds of layer structures: an “inorganic crystal layer by calcium carbonate” and a “protein layer”. The protein layer is made of a laminate structure, which comes up the characteristic luster by multilayer reflective. Recently, pearls are not only used as jewels but take on greater importance like as a new functional material for nano technology, as a CO2 fixation carrier for environmental science, and as a model of bone formation/bio-calcification for medical science.

However, molecular entity of the protein layer is not understood so much. To clarify it, Kinoshita et al. tried transcriptome analysis of the pearl oyster Pinctada fucata with 3’-fragment library and GS FLX sequencing. They could identify 29,682 novel genes, and clustering analysis of gene expression pattern with known nacreous genes revealed 20 candidates that most probably have an association with bio-mineralization. Furthermore, Takeuchi et al. determined the 1.15 Gb draft genome sequence of P. fukata. They found 23 257 complete gene models that included the candidate genes reported in the study from Kinoshita et al.

The spinning process of nacreous luster will be clarified by harmony of gene expression in near future!