Robotic data acquisition with deep learning enables cell image-based prediction of transcriptomic phenotypes.

Single-cell whole-transcriptome analysis is the gold standard approach to identifying molecularly defined cell phenotypes. However, this approach cannot be used for dynamics measurements such as live-cell imaging. Here, we developed a multifunctional robot, the automated live imaging and cell picking system (ALPS) and used it to perform single-cell RNA sequencing for microscopically observed cells with multiple imaging modes. Using robotically obtained data that linked cell images and the whole transcriptome, we successfully predicted transcriptome-defined cell phenotypes in a noninvasive manner using cell image-based deep learning. This noninvasive approach opens a window to determine the live-cell whole transcriptome in real time. Moreover, this work, which is based on a data-driven approach, is a proof of concept for determining the transcriptome-defined phenotypes (i.e., not relying on specific genes) of any cell from cell images using a model trained on linked datasets.

Polygenic risk score for bipolar disorder associates with divergent thinking and brain structures in the prefrontal cortex.

It has been hypothesized that a higher genetic risk of bipolar disorder (BD) is associated with greater creativity. Given the clinical importance of bipolar disorder and the importance of creativity to human society and cultural development, it is essential to reveal their associations and the neural basis of the genetic risk of bipolar disorder to gain insight into its etiology. However, despite the previous demonstration of the associations of polygenic risk score (PRS) of BD and creative jobs, the associations of BD-PRS and creativity measured by the divergent thinking (CMDT) and regional gray matter volume (rGMV) as well as regional white matter volume (rWMV) have not been investigated. Using psychological analyses and whole-brain voxel-by-voxel analyses, we examined these potential associations in 1558 young, typically developing adult students. After adjusting for confounding variables and multiple comparisons, a greater BD-PRS was associated with a greater total CMDT fluency score, and a significant relationship was found in fluency subscores. A greater BD-PRS was also associated with lower total mood disturbance. Neuroimaging analyses revealed that the BD-PRS was associated with greater rGMV in the right inferior frontal gyrus, which is a consistently affected area in BD, as well as a greater rWMV in the left middle frontal gyrus, which has been suggested to play a central role in the increased creativity associated with the risk of BD with creativity. These findings suggest a relationship between the genetic risk of BD and CMDT and prefrontal cortical structures among young educated individuals.

Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences.

SUMMARY: DNA sequence databases use compression such as gzip to reduce the required storage space and network transmission time. We describe Nucleotide Archival Format (NAF)-a new file format for lossless reference-free compression of FASTA and FASTQ-formatted nucleotide sequences. Nucleotide Archival Format compression ratio is comparable to the best DNA compressors, while providing dramatically faster decompression. We compared our format with DNA compressors: DELIMINATE and MFCompress, and with general purpose compressors: gzip, bzip2, xz, brotli and zstd. AVAILABILITY AND IMPLEMENTATION: NAF compressor and decompressor, as well as format specification are available at https://github.com/KirillKryukov/naf. Format specification is in public domain. Compressor and decompressor are open source under the zlib/libpng license, free for nearly any use. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Human short tandem repeat identification using a nanopore-based DNA sequencer: a pilot study.

Short tandem repeats (STRs) are repetitive DNA sequences that are highly polymorphic and widely used for personal identification in the field of forensic medicine. The standard method for determining the repeat number of STRs is capillary electrophoresis of PCR products; however, the use of DNA sequencing has increased because it can identify same-sized alleles with nucleotide substitutions (iso-alleles). In this study, we performed human STR genotyping using a portable nanopore-based DNA sequencer, the MinION, and evaluated its performance. Because the sequence quality obtained by MinION is considerably lower than those obtained with other DNA sequencers, we developed an original scoring scheme for judging the genotypes from MinION reads. Analysis of seven human samples for 21-45 STR loci yielded an average of 857 thousand reads per sample, and the accuracy of genotyping and iso-allele identification reached 75.7% and 82%, respectively. Although the accuracy is higher than that reported previously, further improvements are required before this method can be practically applied.

Molecular characterization of feline paramyxovirus in Japanese cat populations.

Feline paramyxovirus (FPaV) is a member of the family Paramyxoviridae that has been reported only in Germany and the United Kingdom. We detected FPaV for the first time in Japan by transcriptome sequencing of cat urine samples. We determined the genome structure of FPaV and conducted a phylogenetic analysis. It was found that FPaV belongs to the genus Jeilongvirus and forms a clade with Mount Mabu Lophuromys virus 1 (MMLV-1). FPaV lacks a small hydrophobic (SH) gene that is found in members of the genus Jeilongvirus; however, some jeilongviruses also do not have this gene. These results provide information about the diversity and evolution of paramyxoviruses.

Identification of a distinct lineage of aviadenovirus from crane feces.

Viruses are believed to be ubiquitous; however, the diversity of viruses is largely unknown because of the bias of previous research toward pathogenic viruses. Deep sequencing is a promising and unbiased approach to detect viruses from animal-derived materials. Although cranes are known to be infected by several viruses such as influenza A viruses, previous studies targeted limited species of viruses, and thus viruses that infect cranes have not been extensively studied. In this study, we collected crane fecal samples in the Izumi plain in Japan, which is an overwintering site for cranes, and performed metagenomic shotgun sequencing analyses. We detected aviadenovirus-like sequences in the fecal samples and tentatively named the discovered virus crane-associated adenovirus 1 (CrAdV-1). We determined that our sequence accounted for approximately three-fourths of the estimated CrAdV-1 genome size (33,245 bp). The GC content of CrAdV-1 genome is 34.1%, which is considerably lower than that of other aviadenoviruses. Phylogenetic analyses revealed that CrAdV-1 clusters with members of the genus Aviadenovirus, but is distantly related to the previously identified aviadenoviruses. The protein sequence divergence between the DNA polymerase of CrAdV-1 and those of other aviadenoviruses is 45.2-46.8%. Based on these results and the species demarcation for the family Adenoviridae, we propose that CrAdV-1 be classified as a new species in the genus Aviadenovirus. Results of this study contribute to a deeper understanding of the diversity and evolution of viruses and provide additional information on viruses that infect cranes, which might lead to protection of the endangered species of cranes.

VaDE: a manually curated database of reproducible associations between various traits and human genomic polymorphisms.

Genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms (SNPs) associated with the development of common diseases. However, it is clear that genetic risk factors of common diseases are heterogeneous among human populations. Therefore, we developed a database of genomic polymorphisms that are reproducibly associated with disease susceptibilities, drug responses and other traits for each human population: 'VarySysDB Disease Edition' (VaDE; http://bmi-tokai.jp/VaDE/). SNP-trait association data were obtained from the National Human Genome Research Institute GWAS (NHGRI GWAS) catalog and RAvariome, and we added detailed information of sample populations by curating original papers. In addition, we collected and curated original papers, and registered the detailed information of SNP-trait associations in VaDE. Then, we evaluated reproducibility of associations in each population by counting the number of significantly associated studies. VaDE provides literature-based SNP-trait association data and functional genomic region annotation for SNP functional research. SNP functional annotation data included experimental data of the ENCODE project, H-InvDB transcripts and the 1000 Genome Project. A user-friendly web interface was developed to assist quick search, easy download and fast swapping among viewers. We believe that our database will contribute to the future establishment of personalized medicine and increase our understanding of genetic factors underlying diseases.

Selection pressure on human STR loci and its relevance in repeat expansion disease.

Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases.

H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery.

H-InvDB (http://www.h-invitational.jp/) is a comprehensive human gene database started in 2004. In the latest version, H-InvDB 8.0, a total of 244 709 human complementary DNA was mapped onto the hg19 reference genome and 43 829 gene loci, including nonprotein-coding ones, were identified. Of these loci, 35 631 were identified as potential protein-coding genes, and 22 898 of these were identical to known genes. In our analysis, 19 309 annotated genes were specific to H-InvDB and not found in RefSeq and Ensembl. In fact, 233 genes of the 19 309 turned out to have protein functions in this version of H-InvDB; they were annotated as unknown protein functions in the previous version. Furthermore, 11 genes were identified as known Mendelian disorder genes. It is advantageous that many biologically functional genes are hidden in the H-InvDB unique genes. As large-scale proteomic projects have been conducted to elucidate the functions of all human proteins, we have enhanced the proteomic information with an advanced protein view and new subdatabase of protein complexes (Protein Complex Database with quality index). We propose that H-InvDB is an important resource for finding novel candidate targets for medical care and drug development.

Full-length transcriptome-based H-InvDB throws a new light on chromosome-centric proteomics.

H-Invitational Database (H-InvDB; http://hinv.jp/ ) is an integrated database of all human genes and transcripts that started in an international collaborative research project for establishing a functional annotation database of human full-length cDNAs. Because H-InvDB contains an abundance of information for human transcripts, including not only well-characterized protein-coding transcripts but also those without experimental evidence at the protein level, this will be a useful information resource for identifying novel and uncharacterized human proteins (so-called missing proteins). By extending predicted protein data in H-InvDB, we developed the H-Inv Extended Protein Database (H-EPD; http://hinv.jp/hinv/h-epd/ ). From now on, we plan to carry out a database-driven proteome research that makes full use of H-EPD to promote discoveries in the current and future C-HPP. Furthermore, we will push forward with the integration of genome, transcriptome, and proteome databases using a unique tool for connecting distributed databases and would like to develop a knowledge discovery system by incorporating data mining tools.

CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality.

The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includes original large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite of developmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and gene expression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36,034 unique sequences, but for higher usability it covers 89,683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10,000 proteins have been manually annotated. Furthermore, to establish a community-supported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http://cipro.ibio.jp/2.5.

Towards BioDBcore: a community-defined information specification for biological databases.

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases.

A prioritization analysis of disease association by data-mining of functional annotation of human genes.

Complex diseases result from contributions of multiple genes that act in concert through pathways. Here we present a method to prioritize novel candidates of disease-susceptibility genes depending on the biological similarities to the known disease-related genes. The extent of disease-susceptibility of a gene is prioritized by analyzing seven features of human genes captured in H-InvDB. Taking rheumatoid arthritis (RA) and prostate cancer (PC) as two examples, we evaluated the efficiency of our method. Highly scored genes obtained included TNFSF12 and OSM as candidate disease genes for RA and PC, respectively. Subsequent characterization of these genes based upon an extensive literature survey reinforced the validity of these highly scored genes as possible disease-susceptibility genes. Our approach, Prioritization ANalysis of Disease Association (PANDA), is an efficient and cost-effective method to narrow down a large set of genes into smaller subsets that are most likely to be involved in the disease pathogenesis.

Nanopore Sequencing Data Analysis of 16S rRNA Genes Using the GenomeSync-GSTK System.

With the development of nanopore sequencing technology, long reads of DNA sequences can now be determined rapidly from various samples. This protocol introduces the GenomeSync-GSTK system for bacterial species identification in a given sample using nanopore sequencing data of 16S rRNA genes as an example. GenomeSync is a collection of genome sequences designed to provide easy access to genomic data of the species as demanded. GSTK (genome search toolkit) is a set of scripts for managing local homology searches using genomes obtained from the GenomeSync database. Based on this protocol, nanopore sequencing data analyses of metagenomes and amplicons could be efficiently performed. We also noted reanalysis in conjunction with future developments in nanopore sequencing technology and the accumulation of genome sequencing data.

Donor cord blood aging accelerates in recipients after transplantation.

Cord blood stem cell transplantation is an important alternative for patients needing hematopoietic stem cell transplantation. However, it is unclear how cord blood cells, which are 0 years old, age in the recipient's body after allogeneic transplantation. We performed DNA methylation (DNAm) age analysis to measure the age of cells using post-transplant peripheral blood in 50 cases of cord blood transplantation. The median chronological age (the time elapsed from the date of the cord blood transplant to the day the sample was taken for DNAm analysis) of donor cells was 4.0 years (0.2-15.0 years), while the median DNAm age was 10.0 years (1.3-30.3 years), and the ratio of DNAm age to chronological age (AgeAccel) was 2.7 (1.2-8.2). When comparing the mean values of AgeAccel in cord blood transplant cases and controls, the values were significantly higher in cord blood transplant cases. The characteristics of patients and transplant procedures were not associated with AgeAccel in this analysis, nor were they associated with the development of graft-versus-host disease. However, this analysis revealed that transplanting 0-year-old cord blood into a recipient resulted in cells aging more than twice as quickly as the elapsed time. The results shed light on the importance of the mismatch between cord blood stem cells and donor environmental factors in stem cell aging.

H-DBAS: human-transcriptome database for alternative splicing: update 2010.

H-DBAS (http://h-invitational.jp/h-dbas/) is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. In this update, for better annotations of AS events, we correlated RNA-Seq tag information to the AS exons and splice junctions. We generated a total of 148,376,598 RNA-Seq tags from RNAs extracted from cytoplasmic, nuclear and polysome fractions. Analysis of the RNA-Seq tags allowed us to identify 90,900 exons that are very likely to be used for protein synthesis. On the other hand, 254 AS junctions of human RefSeq transcripts are unique to nuclear RNA and may not have any translational consequences. We also present a new comparative genomics viewer so that users can empirically understand the evolutionary turnover of AS. With the unique experimental data closely connected with intensively curated cDNA information, H-DBAS provides a unique platform for the analysis of complex AS.

H-InvDB in 2009: extended database and data mining resources for human genes and transcripts.

We report the extended database and data mining resources newly released in the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). H-InvDB is a comprehensive annotation resource of human genes and transcripts, and consists of two main views and six sub-databases. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs. 'Navigation search' is an extended search system that enables complicated searches by combining 16 different search options. HEAT is a data mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. H-InvDB now has web service APIs of SOAP and REST to allow the use of H-InvDB data in programs, providing the users extended data accessibility.

RELN rs7341475 Associates with Brain Structure in Japanese Healthy Females.

Although temperament has been regarded as an innate aspect of human personality, its association with proteins involved in embryonic development is unclear. Reelin, encoded by RELN, plays an important role in brain development. Herein, we investigated the association between the RELN rs7341475 (G/A) single nucleotide polymorphism, detected as a female-specific risk factor for schizophrenia, brain structure, and temperament to elucidate the role of RELN in the development of human personality. In this study, 1580 healthy young Japanese adults were genotyped for RELN rs7341475 and completed the Temperament and Character Inventory. Whole-brain analysis of covariance was conducted to investigate differences between genotypes in regional gray matter volume (rGMV) and cortical morphology. Additionally, multiple regression analysis was performed to examine the association of four temperaments with rGMV. Those statistical analyses were performed separately for males and females. Individuals with G/G homozygosity showed significantly greater rGMV in several areas of the brain, particularly the bilateral cingulate and temporal gyrus, as well as a larger value of fractal dimension in the left lateral occipital cortex. Furthermore, of the four temperaments, the novelty seeking was significantly and positively associated with rGMV in the right superior temporal gyrus, partially overlapping with areas where differences between the rs7341475 genotypes were detected. The above findings were detected only in females, but not in males. This is the first study to demonstrate the contribution of RELN rs7341475 to differences in brain structure in Japanese females, which may indicate vulnerability to schizophrenia and variations in human personality.

Regression tree analysis of the relationship between the concentrations of antimicrobial components and the microbiota of normal milk from dairy cows.

The purpose of this study was to determine the concentrations of antimicrobial components (immunoglobulin A (IgA), lactoferrin (LF), lingual antimicrobial peptide (LAP), and S100A7) in normal milk and their relation to host factors (Age, somatic cell count (SCC), days in milk, richness, and alpha diversity of the milk microbiota) in dairy cows using multivariate regression tree analyses, and to clarify how the milk microbiota is related to the obtained results. Thirty normal milk samples were collected from a commercial dairy farm in June 2020. The thresholds that predicted the concentration of each antimicrobial component in milk were obtained by regression tree analysis, and the beta-diversity of the milk microbiota composition between groups divided according to each threshold was compared by an analysis of similarities test. The IgA and LF concentrations were mainly predicted by the SCC (177,500 and 70,000 cells/ml, respectively), and the LAP and S100A7 concentrations were predicted by Age (29.667 and 40.3 months, respectively). No relationship was observed between the concentration of IgA, LAP, or S100A7 and the milk microbiota composition between the groups divided by the threshold for prediction, but the milk microbiota composition was significantly different between the groups divided by the threshold for predicting the LF concentration. Our results indicated that the LF concentration in normal milk may be associated with the milk microbiota composition.