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Abstract Background Codon bias is a phenomenon that refers to the differences in the frequencies of synonymous codons among different genes. In many organisms, natural selection is considered to be a cause of codon bias because codon usage in highly expressed genes is biased toward optimal codons. Methods have previously been developed to predict the expression level of genes from their nucleotide sequences, which is based on the observation that synonymous codon usage shows an overall bias toward a few codons called major codons. However, the relationship between codon bias and gene expression level, as proposed by the translation-selection model, is less evident in mammals. Findings We investigated the correlations between the expression levels of 1,182 mouse genes and amino acid composition, as well as between gene expression and codon preference. We found that a weak but significant correlation exists between gene expression levels and amino acid composition in mouse. In total, less than 10% of variation of expression levels is explained by amino acid components. We found the effect of codon preference on gene expression was weaker than the effect of amino acid composition, because no significant correlations were observed with respect to codon preference. Conclusion These results suggest that it is difficult to predict expression level from amino acid components or from codon bias in mouse.

Abstract Background Identifying protein-coding regions in genomic sequences is an essential step in genome analysis. It is well known that the proportion of false positives among genes predicted by current methods is high, especially when the exons are short. These false positives are problematic because they waste time and resources of experimental studies. Methods We developed GeneWaltz, a new filtering method that reduces the risk of false positives in gene finding. GeneWaltz utilizes a codon-to-codon substitution matrix that was constructed by comparing protein-coding regions from orthologous gene pairs between mouse and human genomes. Using this matrix, a scoring scheme was developed; it assigned higher scores to coding regions and lower scores to non-coding regions. The regions with high scores were considered candidate coding regions. One-dimensional Karlin-Altschul statistics was used to test the significance of the coding regions identified by GeneWaltz. Results The proportion of false positives among genes predicted by GENSCAN and Twinscan were high, especially when the exons were short. GeneWaltz significantly reduced the ratio of false positives to all positives predicted by GENSCAN and Twinscan, especially when the exons were short. Conclusions GeneWaltz will be helpful in experimental genomic studies. GeneWaltz binaries and the matrix are available online at http://en.sourceforge.jp/projects/genewaltz/.

Background: Strangulated intestinal obstruction is a life-threatening condition that should be considered as a differential diagnosis in children with shock. However, it has pitfalls in diagnosis and can lead to diagnostic errors., Case Presentation: A 3-month-old male patient presented with a pale complexion lasting 2 h and abnormal crying. He was in shock with lactic acidosis, altered mental status, and slight abdominal distension. He required volume resuscitation, vasoactive agents, and transfusion. On Day 2, he had marked abdominal distension and acute kidney injury, which required continuous kidney replacement therapy. Contrast-enhanced computed tomography revealed extensive intestinal ischemia. It took 33.5 h from his arrival to the computed tomography, leading to operative management. The small intestine had entered a mesenteric hiatus, leading to ischemia. He was diagnosed with strangulated mesenteric hernia., Conclusion: In this case, four pitfalls led to delayed diagnosis. Factors for diagnostic errors specific to strangulated intestinal obstruction and intensive care should be noted., Competing Interests: The authors declare no conflicts of interest., (© 2024 The Author(s). Acute Medicine & Surgery published by John Wiley & Sons Australia, Ltd on behalf of Japanese Association for Acute Medicine.)

Exact evaluation of the performance of surgical masks and biohazard protective clothing materials against pathogens is important because it can provide helpful information that healthcare workers can use to select suitable materials to reduce infection risk. Currently, to evaluate the protective performance of nonwoven fabrics used in surgical masks against viral aerosols, a non-standardized test method using phi-X174 phage aerosols is widely performed because actual respiratory viruses pose an infection risk during testing and the phage is a safe virus to humans. This method of using a phage is simply modified from a standard method for evaluation of filter performance against bacterial aerosols using Staphylococcus aureus, which is larger than virus particles. However, it is necessary to perform such evaluations based on the size of the actual pathogen particles. Thus, we developed a new method that can be performed safely using inactivated viral particles and can quantitate the influenza virus in aerosols by antigen-capture ELISA (Shimasaki et al., 2016a) . In this study, we used three different microbial aerosols of phi-X174 phage, influenza virus, and S. aureus and tested the filter efficiency by capturing microbial aerosols for two medical nonwoven fabrics. We compared the filter efficiency against each airborne microbe to analyze the dependency of filter efficiency on the microbial particle size. Our results showed that against the three types of spherical microbe particles, the filter efficiencies against influenza virus particles were the lowest and those against phi-X174 phages were the highest for both types of nonwoven fabrics. The experimental results mostly corresponded with theoretical calculations. We conclude that the filter efficiency test using the phi-X174 phage aerosol may overestimate the protective performance of nonwoven fabrics with filter structure compared to that against real pathogens such as the influenza virus.

Recent studies have investigated the efficacy of air-cleaning products against pathogens in the air. A standard method to evaluate the reduction in airborne viruses caused by an air cleaner has been established using a safe bacteriophage instead of pathogenic viruses; the reduction in airborne viruses is determined by counting the number of viable airborne phages by culture, after operating the air cleaner. The reduction in the number of viable airborne phages could be because of "physical decrease" or "inactivation". Therefore, to understand the mechanism of reduction correctly, an analysis is required to distinguish between physical decrease and inactivation. The purpose of this study was to design an analysis to distinguish between the physical decrease and inactivation of viable phi-X174 phages in aerosols. We established a suitable polymerase chain reaction (PCR) system by selecting an appropriate primer-probe set for PCR and validating the sensitivity, linearity, and specificity of the primer-probe set to robustly quantify phi-X174-specific airborne particles. Using this quantitative PCR system and culture assay, we performed a behavior analysis of the phage aerosol in a small chamber (1 m 3 ) at different levels of humidity, as humidity is known to affect the number of viable airborne phages. The results revealed that the reduction in the number of viable airborne phages was caused not only by physical decrease but also by inactivation under particular levels of humidity. Our study could provide an advanced analysis to differentiate between the physical decrease and inactivation of viable airborne phages.

To prevent nosocomial infections caused by even either Ebola virus or methicillin-resistant Staphylococcus aureus (MRSA), healthcare workers must wear the appropriate protective clothing which can inhibit contact transmission of these pathogens. Therefore, it is necessary to evaluate the performance of protective clothing for penetration resistance against infectious agents. In Japan, some standard methods were established to evaluate the penetration resistance of protective clothing fabric materials under applied pressure. However, these methods only roughly classified the penetration resistance of fabrics, and the detection sensitivity of the methods and the penetration amount with respect to the relationship between blood and the pathogen have not been studied in detail. Moreover, no standard method using bacteria for evaluation is known. Here, to evaluate penetration resistance of protective clothing materials under applied pressure, the detection sensitivity and the leak amount were investigated by using synthetic blood containing bacteriophage phi-X174 or S. aureus. And the volume of leaked synthetic blood and the amount of test microbe penetration were simultaneously quantified. Our results showed that the penetration detection sensitivity achieved using a test microbial culture was higher than that achieved using synthetic blood at invisible leak level pressures. This finding suggested that there is a potential risk of pathogen penetration even when visual leak of contaminated blood through the protective clothing was not observed. Moreover, at visible leak level pressures, it was found that the amount of test microbe penetration varied at least ten-fold among protective clothing materials classified into the same class of penetration resistance. Analysis of the penetration amount revealed a significant correlation between the volume of penetrated synthetic blood and the amount of test microbe penetration, indicating that the leaked volume of synthetic blood could be considered as a latent indicator for infection risk, that the amount of exposure to contaminated blood corresponds to the risk of infection. Our study helped us ascertain, with high sensitivity, the differences among fabric materials with respect to their protective performance, which may facilitate effective selection of protective clothing depending on the risk assessment.

To evaluate the removal of airborne microbes by air cleaners, a technique for generating airborne fungal spores in the dry state in a test chamber (dry dispersion) become necessary. The Society of Indoor Environment Japan (SIEJ) published SIEJ Standard Method No. 20110001 (SIEJ standard),in which an aerial ultrasonic oscillator was used as the device for dry dispersion. However, a more versatile apparatus is also necessary from a practical point of view. Therefore, we developed a new device using glass beads for the dispersion. Glass beads and a fungal sheet containing spores of Wallemia sebi were set in a midget impinger, which was connected to a compressor and a compact test chamber (1 m(3)). Air was blown into the impinger from the compressor. The spores on the fungal sheet were released by impingement of the glass beads when the beads were induced to float by the air blown into the impinger, and the spores were introduced to the chamber by the airflow. This newly developed technique can be used in a compact chamber system and could be applicable as an improved method for generating airborne fungal spores in the dry state in the SIEJ standard.

Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.

Despite reports of Clostridium tetani being isolated from soil in Kanazawa, Okinawa, and Tokyo, Japan, little has been studied about C. tetani distribution in other regions. We studied C. tetani in topsoil samples collected from private gardens, public road shoulders, a university campus, mountains, and fields in Sagamihara. C. tetani occurred in 8 of 35 soil samples (22.9%) and tetanus toxin in 7 of the 8 C. tetani-positive samples (87.5%). Contamination was clearly higher in soils from mountains near Tsukui-gun (Kanagawa Prefecture), Minamitsuru-gun, and Uenohara and Koshu cities (Yamanashi Prefecture) than in other regions. These findings suggest that tetanus toxin-producing strains of C. tetani tend to inhabit the topsoil of western Sagaminaha region, as a geographical feature.

We studied whether the infectivity of Cryptosporidium parvum oocysts for suckling mice could be inactivated by copper tubing or by other types of tubing used to construct water distribution systems, including stainless steel, rigid polyvinyl chloride (PVC), PVC-lined steel, polyethylene (PE), cross-linked PE, and polybutene (PB), using glass tubing as the control. Oocysts were incubated in each tubings for 24 hours. The extent of inactivation of infectious oocysts by copper tubing was -1.303 log, which significantly inactivated of infectivity. In contrast, other types of tubing had no significant effect on some oocyst infectivity, although PB did show a maximum inactivation of -0.313 log. 25% of oocysts showed degeneration morphologically after passing through copper tubing, while 0.3% to 1.8% showed degeneration after passing through other tubing. Significant inactivation of infectious oocysts was not caused by water in which copper tubing had been let stand for 24 hours, although it had a cupric ion (Cu2+) concentration of 2.4 mg/L. The direct contact of oocysts with copper surface resulted in a decrease in the recovery percentage of oocysts and generation of hydrogen peroxide (0.5 mg/L) after 24 h of incubation. The percentage of degenerating oocysts was 29%. Such cryptosporidicidal effects of the copper surface on oocysts were completely inhibited by overlaying the surface with a Millipore filter before adding oocysts and incubating oocysts in the presence of catalase, an antioxidant enzyme. These findings suggest that copper tubing inactivates infectious C. parvum oocysts cytotoxically which may be due to oxygen radicals generated by the interaction between Cu2+ and hydrogen peroxide on the tubing surface.

Killing of Legionella pneumophila by an antimicrobial ceramic was evaluated during culture in nine kinds of hot spring water at 40 degrees C. After 24 hours, the efficacy against L. pneumophila varied, depended on water quality. The strongest antibacterial effect was seen in chloride hot spring water from Wakayama and in deionized water. In four hot spring water samples (sulfur and hydrogen carbonate springs from Fukushima, simple thermals from Mie, and radioactive spring from Tottori), the decrease was < -2 log cfu after 48 hours. These results suggest that the antimicrobial ceramic is able to eradicate Legionella from hot spring waters.

CYLD was originally identified as the human familial cylindromatosis tumor suppressor. Recently, it was reported that CYLD directly interacts with NEMO/IKKgamma and TRAF2 in the NF-kappaB signaling pathway. The two proteins bind to a region of CYLD that contains a Cys-box motif and the third cytoskeleton-associated protein-glycine conserved (CAP-Gly) domain. Here we report that the third CAP-Gly domain of CYLD specifically interacts with one of the two proline-rich sequences of NEMO/IKKgamma. The tertiary structure of the CAP-Gly domain shares the five-stranded beta sheet topology with the SH3 domain, which is well known as a proline-rich sequence-recognition domain. However, chemical shift mapping revealed that the peptide binding site of the CAP-Gly domain is formed without the long peptide binding loop characteristic of the SH3 domain. Therefore, CAP-Gly is likely to be a novel proline-rich sequence binding domain with a mechanism different from that of the SH3 domain.

We examined the relationship between the distribution of Legionella bacteria and various physicochemical characteristics of hot springs in Japan. Legionella bacteria were isolated from 52 (49.5%) out of 105 water samples, particularly from outdoor hot springs (67.3%). The bacterial count in the water samples positive for Legionella (86.5%) ranged from 10(1) to < 10(3) cfu/100 mL. L. pneumophila serogroup (SG) 4 (27.8%) was predominant in the water samples, followed by SG 5 (12.2%). The pulsefield gel electrophoresis (PFGE) patterns of chromosomal DNA for L. pneumophila SG 4 isolated from different parts of a hot spring resort were identical. Isolation of Legionella species from hot spring waters did not occur at pH 1.8-3.3, SO4(2-): > 780 mg/L, and H2SiO3: > 146 mg/L. The hot water-recirculating systems were applied to 18 out of 20 (90%) hot spring facilities which were found positive for Legionella. These results indicate that Legionella species are widespread in hot springs throughout Japan, except for waters with a low pH and non-recirculating waters, and that a single strain of L. pneumophila SG 4 is predominant in a particular hot spring resort.

We have been conducting a mouse cDNA project to predict protein-coding sequences of mouse homologues of human KIAA and FLJ genes since 2001. As an extension of these projects, we herein present the entire sequences of 500 mKIAA cDNA clones and 4 novel cDNA clones that were incidentally identified during this project. We have isolated cDNA clones from the size-fractionated mouse cDNA libraries derived from 7 tissues and 3 types of cultured cells. The average size of the 504 cDNA sequences reached 4.3 kb and that of the deduced amino acid sequences from these cDNAs was 807 amino acid residues. We assigned the integrity of CDSs from the comparison with the corresponding human KIAA cDNA sequences. The comparison of mouse and human sequences revealed that two different human KIAA cDNAs are derived from single genes. Furthermore, 3 out of 4 proteins encoded in the novel cDNA clones showed moderate sequence similarity with human KIAA proteins, thus we could obtain new members of KIAA protein families through our mouse cDNA projects.

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology., Competing Interests: The authors have declared that no conflicts of interest exist.

In this study, a two-step method for systematic multiplex cloning of homologous cDNAs from related species was developed. The first step, called MUCH (multiplex cloning of homologous genes), is cloning of partial but authentic cDNA fragments of homologous cDNAs by hybridization to arrayed cRNA probes of specified genes on a nylon membrane, followed by PCR amplification of the hybridized fragments. The second step is PCR-based screening of a library that contains longer cDNA inserts based on the sequences obtained in the first step. To evaluate this method, we tried to isolate mouse counterparts of 53 human large cDNAs by MUCH and could successfully isolate 32 mouse counterpart cDNAs from a single library. Complete sequencing of two mouse cDNAs isolated by PCR-based screening further demonstrated that this method enabled us to isolate multiple homologous cDNAs in parallel. We thus expect that this method could be applied to high-throughput cloning of homologous cDNAs in related species.

We have been conducting a mouse cDNA project to predict protein-coding sequences of mouse KIAA-homologous genes since 2001. As an extension of this project, we also started to accumulate mouse cDNA clones homologous to the human FLJ cDNA clones which are another long cDNA resource produced in our institute. We have isolated the cDNA clones from size-fractionated cDNA libraries derived from five different mouse tissues and natural killer T-cells. Although the human FLJ cDNA clones were originally derived from human spleen libraries, one-third of their mouse homologues were obtained from the brain library. We designated these homologues "mFLJ" plus a 5-digit number and herein characterized 110 mFLJ cDNA clones. We assigned an integrity of the CDSs from the comparison of the 110 cDNA clones with the corresponding human FLJ cDNA clones. The average size of the 110 mouse cDNA sequences was 3.8 kb and that of the deduced amino acid sequences from their longest CDS in each cDNA was 663 amino acid residues. Homology and/or motif search against public databases revealed new domains and/or motifs in 26 mFLJ gene products which provide additional speculation regarding the function of FLJ genes.

To evaluate the efficacy of an antimicrobial ceramic for killing Legionella strains in vitro, bacteria were exposed to the ceramic soaked in PBS at 25 degrees C or 42 degrees C. The number of L. pneumophila began to decrease significantly after 4 h of exposure at 25 degrees C and reached < 10 log cfu/ml after 12 h. A similar significant decrease was also observed after exposure at 42 degrees C. Furthermore, it was found that the antimicrobial ceramic showed bactericidal activity against six strains of Legionella isolated from various water sources, including L. pneumophila (serotype 1-4), L. micdadei, and L. dumoffii, after 24 h of exposure. The antimicrobial activity against L. pneumophila of the supernatant obtained by soaking the ceramic in PBS for 24 h was also assessed. Bactericidal activity of this supernatant was also noted. Analysis of the supernatant by ICP-MS resulted in the detection of eight metals (Mg, Al, Ca, Mn, Zn, Sr, Ag, and Ba) at a maximum concentration of 2.5 mg/l. When reconstituted PBS was made with all eight metals at the same concentrations as in the supernatant, the reconstituted PBS containing Ag alone and all metals showed significantly bactericidal activity against L. pneumophila, but PBS with only one metal component except Ag or a combination of Ag with Zn and/or Ca did not. These findings suggest that the antimicrobial ceramic possesses strong bactericidal activity against Legionella species and that eight metals released from the ceramic have a synergistic bactericidal effect against Legionella. When the antimicrobial ceramic was placed in hot spring water or cooling tower water instead of PBS, the number of L. pneumophila in the water decreased to < 10 log cfu/ml after 24 h of exposure and the bactericidal activity persisted for 5 weeks. These results indicate that the antimicrobial ceramic can be used to eradicate Legionella species contaminating various water sources.

We discovered a novel small heat shock protein (sHsp) named AgsA (aggregation-suppressing protein) in the thermally aggregated fraction from a Salmonella enterica serovar Typhimurium dnaK-null strain. The -10 and -35 regions upstream of the transcriptional start site of the agsA gene are characteristic of sigma(32)- and sigma(72)-dependent promoters. AgsA was strongly induced by high temperatures. The similarity between AgsA and the other two sHsps of Salmonella serovar Typhimurium, IbpA and IbpB, is rather low (around 30% amino acid sequence identity). Phylogenetic analysis suggested that AgsA arose from an ancient gene duplication or amplification at an early evolutionary stage of gram-negative bacteria. Here we show that overproduction of AgsA partially complements the DeltadnaK52 thermosensitive phenotype and reduces the amount of heat-aggregated proteins in both DeltadnaK52 and DeltarpoH mutants of Escherichia coli. These data suggest that AgsA is an effective chaperone capable of preventing aggregation of nonnative proteins and maintaining them in a state competent for refolding in Salmonella serovar Typhimurium at high temperatures.

CLOCK is a positive component of a transcription/translation-based negative feedback loop of the central circadian oscillator in the suprachiasmatic nucleus in mammals. To examine CLOCK-regulated circadian transcription in peripheral tissues, we performed microarray analyses using liver RNA isolated from Clock mutant mice. We also compared expression profiles with those of Cryptochromes (Cry1 and Cry2) double knockout mice. We identified more than 100 genes that fluctuated from day to night and of which expression levels were decreased in Clock mutant mice. In Cry-deficient mice, the expression levels of most CLOCK-regulated genes were elevated to the upper range of normal oscillation. Most of the screened genes had a CLOCK/BMAL1 binding site (E box) in the 5'-flanking region. We found that CLOCK was absolutely concerned with the circadian transcription of one type of liver genes (such as DBP, TEF, and Usp2) and partially with another (such as mPer1, mPer2, mDec1, Nocturnin, P450 oxidoreductase, and FKBP51) because the latter were damped but remained rhythmic in the mutant mice. Our results showed that CLOCK and CRY proteins are involved in the transcriptional regulation of many circadian output genes in the mouse liver. In addition to being a core component of the negative feedback loop that drives the circadian oscillator, CLOCK also appears to be involved in various physiological functions such as cell cycle, lipid metabolism, immune functions, and proteolysis in peripheral tissues.

The Kazusa cDNA project is unique by its focus on sequencing large human cDNAs (>4 kb). We describe an overview of the human cDNA sequence data accumulated during the first phase of the project on over 2000 cDNAs and its integration with the genome sequence. In the second phase of the project, which aims at bridging the human genome and proteome using the output of the first phase, we are very carefully evaluating our cDNA clones and, when necessary, experimentally revising them.

Using a neonatal mouse model of Cryptosporidium parvum infection, we investigated whether apoptosis of epithelial cells was induced in the small intestine. At the time when the number of C. parvum oocysts in the ileum was maximal, columnar goblet cells and absorptive cells showed a decrease in the ileal epithelium that was accompanied by a significant reduction in the height of the villi. A few apoptotic epithelial cells were also observed in the vicinity of the basal crypts where C. parvum was proliferating. Morphological changes of the villous structure and apoptotic epithelial cells associated with proliferation of the parasite were scarcely detected in the duodenum, cecum, and colon of the infected mice. These findings suggest that the loss of absorptive cells and goblet cells, and the apoptosis of intestinal epithelial cells, are common events in the ileum after C. parvum infection, and that epithelial apoptosis may have a significant role in the pathogenesis of cryptosporidiosis.

We have conducted a human cDNA project to predict protein-coding sequences (CDSs) in large cDNAs (> 4 kb) since 1994, and the number of newly identified genes, known as KIAA genes, already exceeds 2000. The ultimate goal of this project is to clarify the physiological functions of the proteins encoded by KIAA genes. To this end, the project has recently been expanded to include isolation and characterization of mouse KIAA-counterpart genes. We herein present the entire sequences and the chromosome loci of 500 mKIAA cDNA clones and 13 novel cDNA clones that were incidentally identified during this project. The average size of the 513 cDNA sequences reached 4.3 kb and that of the deduced amino acid sequences from these cDNAs was 816 amino acid residues. By comparison of the predicted CDSs between mouse and human KIAAs, 12 mKIAA cDNA clones were assumed to be differently spliced isoforms of the human cDNA clones. The comparison of mouse and human sequences also revealed that four pairs of human KIAA cDNAs are derived from single genes. Notably, a homology search against the public database indicated that 4 out of 13 novel cDNA clones were homologous to the disease-related genes.

To accumulate information on the coding sequences (CDSs) of unidentified genes, we have conducted a sequencing project of human long cDNA clones. Both the end sequences of approximately 10,000 cDNA clones from two size-fractionated human spleen cDNA libraries (average sizes of 4.5 kb and 5.6 kb) were determined by single-pass sequencing to select cDNAs with unidentified sequences. We herein present the entire sequences of 81 cDNA clones, most of which were selected by two approaches based on their protein-coding potentialities in silico: Fifty-eight cDNA clones were selected as those having protein-coding potentialities at the 5'-end of single-pass sequences by applying the GeneMark analysis; and 20 cDNA clones were selected as those expected to encode proteins larger than 100 amino acid residues by analysis of the human genome sequences flanked by both the end sequences of cDNAs using the GENSCAN gene prediction program. In addition to these newly identified cDNAs, three cDNA clones were isolated by colony hybridization experiments using probes corresponding to known gene sequences since these cDNAs are likely to contain considerable amounts of new information regarding the genes already annotated. The sequence data indicated that the average sizes of the inserts and corresponding CDSs of cDNA clones analyzed here were 5.0 kb and 2.0 kb (670 amino acid residues), respectively. From the results of homology and motif searches against the public databases, functional categories of the 29 predicted gene products could be assigned; 86% of these predicted gene products (25 gene products) were classified into proteins relating to cell signaling/communication, nucleic acid management, and cell structure/motility.

We have accumulated information of the coding sequences of uncharacterized human genes, which are known as KIAA genes, and the number of these genes exceeds 2000 at present. As an extension of this sequencing project, we recently have begun to accumulate mouse KIAA-homologous cDNAs, because it would be useful to prepare a set of human and mouse homologous cDNA pairs for further functional analysis of the KIAA genes. We herein present the entire sequences of 400 mouse KIAA cDNA clones and 4 novel cDNA clones which were incidentally identified during this project. Most of clones entirely sequenced in this study were selected by computer-assisted analysis of terminal sequences of the cDNAs. The average size of the 404 cDNA sequences reached 5.3 kb and that of the deduced amino acid sequences from these cDNAs was 868 amino acid residues. The results of sequence analyses of these clones showed that single mouse KIAA cDNAs bridged two different human KIAA cDNAs in some cases, which indicated that these two human KIAA cDNAs were derived from single genes although they had been supposed to originate from different genes. Furthermore, we successfully mapped all the mouse KIAA cDNAs along the genome using a recently published mouse genome draft sequence.