Zebrafish behavior feature recognition using three-dimensional tracking and machine learning.

In this work, we aim to construct a new behavior analysis method by using machine learning. We used two cameras to capture three-dimensional (3D) tracking data of zebrafish, which were analyzed using fuzzy adaptive resonance theory (FuzzyART), a type of machine learning algorithm, to identify specific behavioral features. The method was tested based on an experiment in which electric shocks were delivered to zebrafish and zebrafish swimming was tracked in 3D simultaneously to find electric shock-associated behaviors. By processing the obtained data with FuzzyART, we discovered that distinguishing behaviors were statistically linked to the electric shock based on the machine learning algorithm. Moreover, our system could accept user-supplied data for detection and quantitative analysis of the behavior features, such as the behavior features defined by the 3D tracking analysis above. This system could be applied to discover new distinct behavior features in mutant zebrafish and used for drug administration screening and cognitive ability tests of zebrafish in the future.

Draft Genome Sequence of NYR20, a Red Pigment-Secreting Mutant of Saccharomyces cerevisiae.

A Saccharomyces cerevisiae mutant strain, NYR20, produces a red pigment owing to adenine auxotrophy. Unlike other yeast adenine biosynthetic mutants, this strain not only produces but also secretes this pigment. Here, we report the NYR20 draft genome sequence, thereby advancing our understanding of pigment secretion mechanisms.

Draft Genome Sequence of Glycoside Hydrolase-Producing Trichoderma asperellum Strain IC-1.

Glycoside hydrolases capable of degrading lignocellulose are important for effectively utilizing cellulosic biomass as a next-generation chemical resource. Trichoderma asperellum IC-1 produces various glycoside hydrolases. Here, we report a draft genome sequence of T. asperellum IC-1 to better understand its gene structures and gene regulatory mechanisms.

Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes.

Upstream open reading frames (uORFs) are present in the 5'-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously developed a novel pipeline, ESUCA, to comprehensively identify plant uORFs encoding functional peptides, based on genome-wide identification of uORFs with conserved peptide sequences (CPuORFs). Here, we applied ESUCA to diverse animal genomes, because animal CPuORFs have been identified only by comparing uORF sequences between a limited number of species, and how many previously identified CPuORFs encode regulatory peptides is unclear. By using ESUCA, 1517 (1373 novel and 144 known) CPuORFs were extracted from four evolutionarily divergent animal genomes. We examined the effects of 17 human CPuORFs on mORF translation using transient expression assays. Through these analyses, we identified seven novel regulatory CPuORFs that repressed mORF translation in a sequence-dependent manner, including one conserved only among Eutheria. We discovered a much higher number of animal CPuORFs than previously identified. Since most human CPuORFs identified in this study are conserved across a wide range of Eutheria or a wider taxonomic range, many CPuORFs encoding regulatory peptides are expected to be found in the identified CPuORFs.

Draft Genome Sequence of Saccharomyces cerevisiae Strain P-684, Isolated from Prunus verecunda.

Saccharomyces cerevisiae strain P-684 is a yeast isolated from the flowers of Prunus verecunda 'Antiqua,' producing high quantities of malic and succinic acids in sake brewing. Here, we report the draft genome sequence of P-684, enlightening the mechanisms of biosynthesis of these organic acids by this strain.

Draft Genome Sequence of the Aspergillus terreus High-Itaconic-Acid-Productivity Strain IFO6365.

Itaconic acid is an important organic acid used in the chemical industry. Aspergillus terreus strain IFO6365 is one of the highest-yielding itaconic acid-producing wild-type strains. Here, we report the draft genome sequence of IFO6365, enhancing the understanding of the role and biosynthesis of itaconic acid in this fungus.

Excess sterols disrupt plant cellular activity by inducing stress-responsive gene expression.

Sterols are important lipid constituents of cellular membranes in plants and other organisms. Sterol homeostasis is under strict regulation in plants because excess sterols negatively impact plant growth. HIGH STEROL ESTER 1 (HISE1) functions as a negative regulator of sterol accumulation. If sterol production exceeds a certain threshold, excess sterols are detoxified via conversion to sterol esters by PHOSPHOLIPID STEROL ACYL TRANSFERASE 1 (PSAT1). We previously reported that the Arabidopsis thaliana double mutant hise1-3 psat1-2 shows 1.5-fold higher sterol content than the wild type and consequently a severe growth defect. However, the specific defects caused by excess sterol accumulation in plants remain unknown. In this study, we investigated the effects of excess sterols on plants by analyzing the phenotypes and transcriptomes of the hise1-3 psat1-2 double mutant. Transcriptomic analysis revealed that 435 genes were up-regulated in hise1-3 psat1-2 leaves compared with wild-type leaves. Gene ontology (GO) enrichment analysis revealed that abiotic and biotic stress-responsive genes including RESPONSIVE TO DESICCATION 29B/LOW-TEMPERATURE-INDUCED 65 (RD29B/LTI65) and COLD-REGULATED 15A (COR15A) were up-regulated in hise1-3 psat1-2 leaves compared with wild-type leaves. Expression levels of senescence-related genes were also much higher in hise1-3 psat1-2 leaves than in wild-type leaves. hise1-3 psat1-2 leaves showed early senescence, suggesting that excess sterols induce senescence of leaves. In the absence of sucrose, hise1-3 psat1-2 exhibited defects in seedling growth and root elongation. Together, our data suggest that excess sterol accumulation disrupts cellular activities of vegetative organs including leaves and roots, resulting in multiple damages to plants.

Draft Genome Sequence of Aspergillus terreus High-Itaconic-Acid-Productivity Mutant TN-484.

Itaconic acid is an important organic acid used in the chemical industry. Aspergillus terreus strain TN-484 is a high-itaconic-acid-productivity mutant derived from strain IFO6365. Here, we report the draft genome sequence of strain TN-484, advancing the understanding of the biosynthesis of itaconic acid in filamentous fungi.

Draft Genome Sequence of Saccharomyces cerevisiae Strain Pf-1, Isolated from Prunus mume.

Saccharomyces cerevisiae strain Pf-1 is a yeast isolated from Prunus mume; it potentially can be used to produce wine and traditional Japanese sake. Here, we report the draft genome sequence of this strain. The genomic information will provide a deeper understanding of the brewing characteristics of this strain.