Unsupervised AI reveals insect species-specific genome signatures.

Insects are a highly diverse phylogeny and possess a wide variety of traits, including the presence or absence of wings and metamorphosis. These diverse traits are of great interest for studying genome evolution, and numerous comparative genomic studies have examined a wide phylogenetic range of insects. Here, we analyzed 22 insects belonging to a wide phylogenetic range (Endopterygota, Paraneoptera, Polyneoptera, Palaeoptera, and other insects) by using a batch-learning self-organizing map (BLSOM) for oligonucleotide compositions in their genomic fragments (100-kb or 1-Mb sequences), which is an unsupervised machine learning algorithm that can extract species-specific characteristics of the oligonucleotide compositions (genome signatures). The genome signature is of particular interest in terms of the mechanisms and biological significance that have caused the species-specific difference, and can be used as a powerful search needle to explore the various roles of genome sequences other than protein coding, and can be used to unveil mysteries hidden in the genome sequence. Since BLSOM is an unsupervised clustering method, the clustering of sequences was performed based on the oligonucleotide composition alone, without providing information about the species from which each fragment sequence was derived. Therefore, not only the interspecies separation, but also the intraspecies separation can be achieved. Here, we have revealed the specific genomic regions with oligonucleotide compositions distinct from the usual sequences of each insect genome, e.g., Mb-level structures found for a grasshopper Schistocerca americana. One aim of this study was to compare the genome characteristics of insects with those of vertebrates, especially humans, which are phylogenetically distant from insects. Recently, humans seem to be the "model organism" for which a large amount of information has been accumulated using a variety of cutting-edge and high-throughput technologies. Therefore, it is reasonable to use the abundant information from humans to study insect lineages. The specific regions of Mb length with distinct oligonucleotide compositions have also been previously observed in the human genome. These regions were enriched by transcription factor binding motifs (TFBSs) and hypothesized to be involved in the three-dimensional arrangement of chromosomal DNA in interphase nuclei. The present study characterized the species-specific oligonucleotide compositions (i.e., genome signatures) in insect genomes and identified specific genomic regions with distinct oligonucleotide compositions.

The draft genome sequence of the Brahminy blindsnake Indotyphlops braminus.

Blindsnakes of infraoder Scolecophidia (order Squamata) are the most basal group of extant snakes, comprising of more than 450 species with ecological and morphological features highly specialized to underground living. The Brahminy blindsnake, Indotyphlops braminus, is the only known obligate parthenogenetic species of snakes. Although the origin of I. braminus is thought to be South Asia, this snake has attracted worldwide attention as an alien species, as it has been introduced to all continents except Antarctica. In this study, we present the first draft genome assembly and annotation of I. braminus. We generated approximately 480 Gbp of sequencing data and produced a draft genome with a total length of 1.86 Gbp and N50 scaffold size of 1.25 Mbp containing 89.3% of orthologs conserved in Sauropsida. We also identified 0.98 Gbp (52.82%) of repetitive genome sequences and a total of 23,560 protein-coding genes. The first draft genome of I. braminus will facilitate further study of snake evolution as well as help to understand the emergence mechanism of parthenogenetic vertebrates.

Whole-genome sequencing of endangered Zhoushan cattle suggests its origin and the association of MC1R with black coat colour.

Zhoushan cattle are an endangered cattle breed in the Zhoushan islands in China. Since Zhoushan cattle have been bred in isolation, they show unique characteristics, such as dark black coat colour. However, no studies have been conducted on the genome of Zhoushan cattle. Here, we performed whole-genome sequencing of seven individuals of Zhoushan cattle and nine cattle in Wenling, geographically close to the Zhoushan islands. By integrating our data and publicly-available data, we found that Zhoushan cattle are genetically highly similar to Bos indicus cattle in south-eastern China. Furthermore, by identifying the genomic regions shared between Zhoushan cattle and Angus cattle, a Bos taurus breed, we found that the p.F195L mutation in melanocyte-stimulating hormone receptor (MC1R) could be associated with their dark black coat colour. Taken together, our results provide a valuable resource for characterising the uniqueness of Zhoushan cattle.

Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation.

Large yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments.

A novel nuclear localization signal spans the linker of the two DNA-binding subdomains in the conserved paired domain of Pax6.

Paired box (Pax) 6, a member of the Pax family of transcription factors, contains two DNA-binding domains, called the paired domain (PD) and the homeodomain (HD), and plays pivotal roles in development of structures such as the eye, central nervous system and pancreas. Pax6 is a major developmental switching molecule because, for example, ectopic expression of the Pax6 gene can induce ectopic whole eye development. Intensive research has been devoted to elucidating the molecular mechanism(s) involved in the function(s) of Pax6, but many issues remain unexplained. One of the important issues is to identify the nuclear localization signal (NLS) in the PD of Pax6, which is predicted to have a stronger NLS activity than that in the HD. We produced expression plasmid constructs that encode the chick Pax6 protein modified to delete the entire PD except for fragments containing putative NLS sequences, and electroporated them in ovo into the developing chick midbrain to define the NLS of the PD. The results show that the NLS in the PD of chick Pax6 consists of an unusually long sequence of 36 amino acid residues. Within this long NLS motif, the central 18 amino acids comprising two consecutive nine-residue segments showed highest NLS activity; this central area corresponds to the C-terminal half of the third α-helix of the PAI subdomain and the subsequent 11 amino acids of a 16-residue linker between PAI and the adjacent RED subdomain. This information helps to elucidate the molecular mechanism by which Pax6 plays a pivotal role during ontogeny.

Highly water pressurized brown rice improves cognitive dysfunction in senescence-accelerated mouse prone 8 and reduces amyloid beta in the brain.

BACKGROUND: Alzheimer's disease (AD) is the most common form of dementia and the number of AD patients continues to increase worldwide. Components of the germ layer and bran of Brown rice (BR) help maintain good health and prevent AD. Because the germ layer and bran absorb little water and are very hard and difficult to cook, they are often removed during processing. To solve these problems, in this study, we tried to use a high-pressure (HP) technique. METHODS: We produced the highly water pressurized brown rice (HPBR) by pressurizing BR at 600 MPa, and then we fed it to an AD mouse model, senescence-accelerated mouse prone 8, to investigate the therapeutic effects of HPBR on cognitive dysfunction by Y-maze spatial memory test. RESULTS: HP treatment increased the water absorbency of BR without nutrient loss. HPBR ameliorated cognitive dysfunction and reduced the levels of amyloid-ß, which is a major protein responsible for AD, in the brain. CONCLUSIONS: These results suggest that HPBR is effective for preventing AD.

Otx2 is involved in the regional specification of the developing retinal pigment epithelium by preventing the expression of sox2 and fgf8, factors that induce neural retina differentiation.

The retinal pigment epithelium (RPE) shares its developmental origin with the neural retina (NR). When RPE development is disrupted, cells in the presumptive RPE region abnormally differentiate into NR-like cells. Therefore, the prevention of NR differentiation in the presumptive RPE area seems to be essential for regionalizing the RPE during eye development. However, its molecular mechanisms are not fully understood. In this study, we conducted a functional inhibition of a transcription factor Otx2, which is required for RPE development, using early chick embryos. The functional inhibition of Otx2 in chick eyes, using a recombinant gene encoding a dominant negative form of Otx2, caused the outer layer of the optic cup (the region forming the RPE, when embryos normally develop) to abnormally form an ectopic NR. In that ectopic NR, the characteristics of the RPE did not appear and NR markers were ectopically expressed. Intriguingly, the repression of Otx2 function also caused the ectopic expression of Fgf8 and Sox2 in the outer layer of the optic cup (the presumptive RPE region of normally developing eyes). These two factors are known to be capable of inducing NR cell differentiation in the presumptive RPE region, and are not expressed in the normally developing RPE region. Here, we suggest that Otx2 prevents the presumptive RPE region from forming the NR by repressing the expression of both Fgf8 and Sox2 which induce the NR cell fate.

Isolation and evaluation of the radical-scavenging activity of the antioxidants in the leaves of an edible plant, Mallotus japonicus.

The antioxidative properties of a hot water extract of the leaves of Mallotus japonicus were evaluated. The extract had a high phenolic content and strong antioxidative activity, compared with green tea, rooibos tea, and red wine. Six phenolic compounds were isolated as antioxidative components by HPLC. They were identified as mallotinic acid, mallotusinic acid, corilagin, geraniin, rutin, and ellagic acid. These antioxidative compounds were subjected to DPPH radical-scavenging, superoxide radical-scavenging, and hydroxyl radical-scavenging assays, and compared with other antioxidative compounds. Four of the compounds, mallotinic acid, mallotusinic acid, corilagin and geraniin, exhibited much stronger antioxidative activity than gallic acid, rutin, ellagic acid, quercetin, and chlorogenic acid, and were as active as epigallocatechin gallate (EGCG), a strong antioxidant in green tea. Mallotus japonicus leaves are an excellent source of strong natural antioxidative materials.

Screening for antioxidant activity in edible plant products: comparison of low-density lipoprotein oxidation assay, DPPH radical scavenging assay, and Folin-Ciocalteu assay.

Oxidation of low-density lipoprotein (LDL) has been implicated in atherogenesis. Antioxidants that prevent LDL from oxidizing may reduce atherosclerosis. This study investigated LDL antioxidant activity in edible plant products for development of dietary supplementation to prevent atherosclerosis. Fifty-two kinds of edible plants were extracted using 70% aqueous ethanol solution, and the antioxidant activity of the extracts, which inhibit human LDL oxidation induced by copper ion, was determined on the basis of the oxidation lag time and represented as epigallocatechin 3-gallate equivalent. 1,1-Diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity and total phenolic content were also measured for comparisons with antioxidant activity in LDL. Plant products showing the greatest activity in LDL oxidation assay were akamegashiwa (Mallotus japonicus) leaf, Japanese privet (Ligustrum japonicum) leaf, green tea [Camellia sinensis (L.) O. Kuntze], and astringent persimmon (Diospyros kaki). The present study revealed high levels of LDL antioxidant activity in plant products for which such activity levels are underestimated in the DPPH radical scavenging assay and Folin-Ciocalteu assay.