NGS Expert Blog

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.

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 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!