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Abstract Visual observing muscle tissue regeneration is used to measure experimental effect size in biological research to discover the mechanism of muscle strength decline due to illness or aging. Quantitative computer imaging analysis for support evaluating the recovery phase has not been established because of the localized nature of recovery and the difficulty in selecting image features for cells in regeneration. We constructed MyoRegenTrack for segmenting cells and classifying their regeneration phase in hematoxylin–eosin (HE) stained images. A straightforward approach to classification is supervised learning. However, obtaining detailed annotations for each fiber in a whole slide image is impractical in terms of cost and accuracy. Thus, we propose to learn individual recovery phase classification utilizing the proportions of cell class depending on the days after muscle injection to induce regeneration. We extract implicit multidimensional features from the HE-stained tissue images and train a classifier using weakly supervised learning, guided by their class proportion for elapsed time on recovery. We confirmed the effectiveness of MyoRegenTrack by comparing its results with expert annotations. A comparative study of the recovery relation between two different muscle injections shows that the analysis result using MyoRegenTrack is consistent with findings from previous studies.

Abstract Background Acute liver failure (ALF) is a life-threatening disorder that progresses from self-limiting acute liver injury (ALI). Microcirculatory disturbance characterized by sinusoidal hypercoagulation and subsequent massive hypoxic hepatocyte damage have been proposed to be the mechanism by which ALI deteriorates to ALF; however, the precise molecular pathway of the sinusoidal hypercoagulation remains unknown. Here, we analyzed ALI patients and mice models to uncover the pathogenesis of ALI with microcirculatory disturbance. Methods We conducted a single-center retrospective study for ALI and blood samples and liver tissues were analyzed to evaluate the microcirculatory disturbance in ALI patients (n = 120). Single-cell RNA sequencing analysis (scRNA-seq) was applied to the liver from the concanavalin A (Con A)‑induced mouse model of ALI. Interferon-gamma (IFNγ) and tumor necrosis factor-alpha knockout mice, and primary human liver sinusoidal endothelial cells (LSECs) were used to assess the mechanism of microcirculatory disturbance. Results The serum IFNγ concentrations were significantly higher in ALI patients with microcirculatory disturbance than in patients without microcirculatory disturbance, and the IFNγ was upregulated in the Con A mouse model which presented microcirculatory disturbance. Hepatic IFNγ expression was increased as early as 1 hour after Con A treatment prior to sinusoidal hypercoagulation and hypoxic liver damage. scRNA-seq revealed that IFNγ was upregulated in innate lymphoid cells and stimulated hepatic vascular endothelial cells at the early stage of liver injury. In IFNγ knockout mice treated with Con A, the sinusoidal hypercoagulation and liver damage were remarkably attenuated, concomitant with the complete inhibition of CD40 and tissue factor (TF) upregulation in vascular endothelial cells. By ligand-receptor analysis, CD40-CD40 ligand interaction was identified in vascular endothelial cells. In human LSECs, IFNγ upregulated CD40 expression and TF was further induced by increased CD40-CD40 ligand interaction. Consistent with these findings, hepatic CD40 expression was significantly elevated in human ALI patients with microcirculatory disturbance. Conclusion We identified the critical role of the IFNγ-CD40 axis as the molecular mechanism of microcirculatory disturbance in ALI. This finding may provide novel insights into the pathogenesis of ALI and potentially contribute to the emergence of new therapeutic strategies for ALI patients.

BackgroundThis study aimed to analyze the recent prevalence of neonatal herpes simplex virus infection, maternal symptoms in the presence of neonate who has herpes simplex virus infection, and mode of delivery in Japan.MethodsWe requested 2.078 obstetrical facilities that are members of the Japan Association of Obstetricians and Gynecologists (JAOG) to provide information on neonatal herpes simplex virus infection involving deliveries at or after 22 weeks of gestation between 2020 and 2022. Of these, 1.371 (66.0%) facilities responded with information that could undergo statistical analysis.ResultsThere were 10 cases of neonatal herpes simplex virus infection, and the incidence of neonatal herpes simplex virus infection in Japan was about 1 in 1.4 × 105 live births. There were no characteristic maternal findings common to cases of neonatal herpes simplex virus infection.ConclusionThe incidence of neonatal herpes simplex virus infection in Japan was low. We could not identify any characteristic maternal findings common to cases of neonatal herpes simplex virus infection.

Background: Fusion genes are important biomarkers in cancer research because their expression can produce abnormal proteins with oncogenic properties. Long-read RNA sequencing (long-read RNA-seq), which can sequence full-length mRNA transcripts, facilitates the detection of such fusion genes. Several tools have been proposed for detecting fusion genes in long-read RNA-seq datasets derived from cancer cells. However, the high sequencing error rate in long-read RNA-seq makes fusion gene detection challenging. Methods: To address this issue, additional steps were incorporated into the fusion detection tool to improve detection accuracy. These steps include anchoring breakpoints to exon boundaries, realigning unaligned regions, and clustering breakpoints. To evaluate the accuracy of our tool in detecting fusion genes, we compared its detection accuracy with two representative existing tools, JAFFAL and FusionSeeker. Results: Our tool outperformed the two existing tools in detecting fusion genes, as demonstrated in long-read RNA-seq datasets. We also identified potentially novel fusion genes consistently detected across multiple tools or datasets. Conclusions: The application of our tool to the detection of fusion genes in long-read RNA-seq datasets from two different cancer cell lines demonstrated the detection effectiveness of this tool.

Abstract Runt-related transcription factor 2 (Runx2), a regulator of osteoblast differentiation, is pathologically involved in vascular calcification; however, the significance of Runx2 in cardiac homeostasis remains unclear. Here, we investigated the roles of Runx2 in cardiac remodeling after myocardial infarction (MI). The expression of Runx2 mRNA and protein was upregulated in murine hearts after MI. Runx2 was expressed in heart-infiltrating myeloid cells, especially in macrophages, at the border zone of post-infarct myocardium. To analyze the biological functions of Runx2 in cardiac remodeling, myeloid cell-specific Runx2 deficient (CKO) mice were exposed to MI. After MI, ventricular weight/tibia length ratio was increased in CKO mice, concomitant with severe cardiac dysfunction. Cardiac fibrosis was exacerbated in CKO mice, consistent with the upregulation of collagen 1a1 expression. Mechanistically, immunohistochemical analysis using anti-CD31 antibody showed that capillary density was decreased in CKO mice. Additionally, conditioned culture media of myeloid cells from Runx2 deficient mice exposed to MI induced the tube formation of vascular endothelial cells to a lesser extent than those from control mice. RNA-sequence showed that the expression of pro-angiogenic or anti-angiogenic factors was altered in macrophages from Runx2-deficient mice. Collectively, Runx2 + myeloid cells infiltrate into post-infarct myocardium and prevent adverse cardiac remodeling, at least partially, by regulating endothelial cell function.

The mechanism by which parathyroid hormone mediates the switch from bone resorption to bone formation is unclear. Here, the authors show that SLPI regulates the communication between osteoblasts and osteoclasts to promote the anabolic effect of parathyroid hormone.

Thrombomodulin (TM) is an integral membrane protein expressed on the surface of vascular endothelial cells that suppresses blood coagulation. Recent studies have shown that TM exhibits anti-inflammatory effects by inhibiting leukocyte recruitment. However, the actual modes of action of TM in vivo remain unclear. Here, we describe the pharmacological effects of recombinant human soluble TM (TM alfa) on leukocyte dynamics in living mice using intravital imaging techniques. Under control conditions, neutrophils exhibited three distinct types of adhesion behavior in vessels: 1) “non-adhesion”, in which cells flowed without vessel adhesion; 2) “rolling adhesion”, in which cells transiently interacted with the endothelium; and 3) “tight binding”, in which cells bound strongly to the endothelial cells. Compared to control conditions, local lipopolysaccharide stimulation resulted in an increased frequency of rolling adhesion that was not homogeneously distributed on vessel walls but occurred at specific endothelial sites. Under inflammatory conditions, TM alfa, particularly the D1 domain which is a lectin-like region of TM, significantly decreased the frequency of rolling adhesion, but did not influence the number of tight bindings. This was the first study to demonstrate that TM alfa exerts anti-inflammatory effects by inhibiting rolling adhesion of neutrophils to vascular endothelial cells in living mice. Keywords: Thrombomodulin, Rolling adhesion, Leukocyte, Endothelial cell, Intravital imaging

Pregnancy diagnosis during early gestation is important for cattle reproduction. The expression of interferon-stimulated genes (ISGs) in peripheral blood leukocytes (PBLs) was studied in embryo-transferred (ET) Japanese Black cattle. ISGs in PBLs—ISG15, MX1, MX2, and OAS1—were detected in multiple ovulation ET cattle using a real-time quantitative polymerase chain reaction, and receiver operating characteristic (ROC) curve analysis was performed. Gestational status was predicted using the average ISG levels during the normal estrous cycle (AVE) and the Youden index from the ROC curve analysis as cutoff values. The ISG15, MX1, and MX2 levels were significantly higher in pregnant cattle (n = 10) than in non-pregnant cattle (n = 23) on gestation day 21, whereas the levels of all ISGs were similar between non-pregnant and non-pregnant cattle with late embryonic death (n = 7). ISG15, MX1, and MX2 appropriately predicted the gestational status of ET cows. The statistical evaluation of the diagnostic accuracy in ET cows on day 21 of gestation presented higher values of sensitivity, specificity, accuracy, and positive predictive values of ISG15, MX1, and MX2 using the Youden index than using the AVE. Therefore, ISG15, MX1, and MX2 are excellent biomarkers of gestational status during the peri-implantation period in ET cattle.

Abstract Background The application of cryopreservation and artificial insemination technology have contributed to the advancement of animal reproduction. However, a substantial proportion of spermatozoa undergoes alterations and loses their fertility during cryopreservation, rendering the frozen-thawed semen impractical for routine use. Cryopreservation is known to reduce sperm lifespan and fertility. Variation in cryosurvival of spermatozoa from different sires and even with the individual sire is common in artificial insemination (AI) centers. Our goal is to improve post-thawed semen quality by optimization of cryopreservation technique through sperm selection prior to cryopreservation process. Results Our strategy of sperm selection based on rheotaxis and thermotaxis (SSRT) on macrosale in a rotating fluid flow demonstrated the ability to maintain the original pre-freezing structural integrity, viability and biological function related to fertilization competence. This strategy has a positive effect on the cryosurvival and fertilizing abilities of spermatozoa as supported by the improvement on pregnancy rate of Japanese Black heifers and Holstein repeat breeders. This technique protected further sublethal damage to bovine spermatozoa (higher % cryosurvival than the control) and resulted in the improvement of DNA integrity. Prefreeze selected spermatozoa demonstrated slower and controlled capacitation than unprocessed control which is thought to be related to sperm longevity and consequently to appropriate timing during in vivo fertilization. Conclusions These results provide solid evidence that improvement of post-thawed semen quality by SSRT method is beneficial in terms of cryosurvival, longevity of post-thawed sperm, and optimization of in vivo fertilization, embryo development and calving as supported by the favorable results of field fertility study.

Single-cell RNA-sequencing is a rapidly evolving technology that enables us to understand biological processes at unprecedented resolution. Single-cell expression analysis requires a complex data processing pipeline, and the pipeline is divided into two main parts: The quantification part, which converts the sequence information into gene-cell matrix data; the analysis part, which analyzes the matrix data using statistics and/or machine learning techniques. In the analysis part, unsupervised cell clustering plays an important role in identifying cell types and discovering cell diversity and subpopulations. Identified cell clusters are also used for subsequent analysis, such as finding differentially expressed genes and inferring cell trajectories. However, single-cell clustering using gene expression profiles shows different results depending on the quantification methods. Clustering results are greatly affected by the quantification method used in the upstream process. In other words, even if the original RNA-sequence data is the same, gene expression profiles processed by different quantification methods will produce different clusters. In this article, we propose a robust and highly accurate clustering method based on joint non-negative matrix factorization (joint-NMF) by utilizing the information from multiple gene expression profiles quantified using different methods from the same RNA-sequence data. Our joint-NMF can extract common factors among multiple gene expression profiles by applying each NMF under the constraint that one of the factorized matrices is shared among multiple NMFs. The joint-NMF determines more robust and accurate cell clustering results by leveraging multiple quantification methods compared to conventional clustering methods, which use only a single gene expression profile. Additionally, we showed the usefulness of discovering marker genes with the extracted features using our method.

Recent studies demonstrated that homologous repair deficiency (HRD) score is a useful marker for response to poly (ADP-ribose) polymerase inhibitors or platinum-based chemotherapy. We determined HRD scores and elucidated the clinicopathologic characteristics of HRD-high tumors and their response to non-platinum-based chemotherapy. Primary breast cancer patients (n = 120) were pre-operatively treated with paclitaxel followed by 5-fluorouracil/epirubicin/cyclophosphamide (P-FEC). Germline and somatic homologous recombination related gene mutations (gHRRm and sHRRm, respectively) and HRD scores were analyzed using whole exome sequencing (WES) in tumor tissues obtained before chemotherapy. Of 120 tumors, 30 were determined to be HRD-high tumors, significantly associated with high Ki-67 (P = 0.014), ER negativity (P = 0.007), and PR negativity (P = 0.021). Triple-negative cancers showed significantly higher HRD scores than the luminal, luminal-HER2, and HER2 subtypes (P = 0.023, 0.016, and 0.033, respectively). HRD scores were significantly higher in tumors with gHRRm than in those with sHRRm (P = 0.002) or wild-type HRR genes (P = 1.44e-4), but no significant difference was found in HRD scores between tumors with sHRRm and wild-type HRR genes (P = 0.206). HRD-high tumors had significantly (P = 0.003) higher pCR rates and higher near-pCR rates (P = 0.049) compared with those of the HRD-low tumors in all tumors and the luminal subtype, respectively. HRD-high tumors were associated with aggressive phenotypes and gHRRm, but not sHRRm. Our findings suggested that HRD scores might be useful in predicting response to P-FEC in the luminal subtype.

Background: Epithelial-mesenchymal transition (EMT) has been recognized as playing a crucial role in cancer progression. Among the studies on EMT, biomarker detection has been one of the important topics to understand the biology and mechanism of EMT related to tumor progression and treatment resistance. The existing methods often identified differentially-expressed genes as potential markers by ranking all genes by their variances. This paper proposes a novel method to detect markers for respective lineages in the EMT process. Methods and Results: Our method consists of three steps: first, perform trajectory inference to identify the lineage of transitional processes in EMT progression, and secondly, identify the lineage for EMT reversion in addition to EMT progression, and thirdly detect biomarkers for both of the EMT progression and reversion lineages with differential expression analysis. Furthermore, to elucidate the heterogeneity of the EMT process, we performed a clustering analysis of the cells in the EMT progression and reversion conditions. We then explored branching trajectories that order clusters using time information of the time-course samples. Using this method, we successfully detected two potential biomarkers related to EMT, phospholipid phosphatase 4 (PLPP4) and lymphotoxin-beta (LTB), which have not been detected by the existing method. Conclusions: In this study, we propose a method for the detection of biomarkers of EMT based on trajectory inference with single-cell RNA-seq data. The performance of the method is demonstrated by the detection of potential biomarkers related to EMT.

Abstract Background Comprehensively understanding the dynamics of biological systems is among the biggest current challenges in biology and medicine. To acquire this understanding, researchers have measured the time-series expression profiles of cell lines of various organisms. Biological technologies have also drastically improved, providing a huge amount of information with support from bioinformatics and systems biology. However, the transitions between the activation and inactivation of gene regulations, at the temporal resolution of single time points, are difficult to extract from time-course gene expression profiles. Results Our proposed method reports the activation period of each gene regulation from gene expression profiles and a gene regulatory network. The correctness and effectiveness of the method were validated by analyzing the diauxic shift from glucose to lactose in Escherichia coli. The method completely detected the three periods of the shift; 1) consumption of glucose as nutrient source, 2) the period of seeking another nutrient source and 3) consumption of lactose as nutrient source. We then applied the method to mouse adipocyte differentiation data. Cell differentiation into adipocytes is known to involve two waves of the gene regulation cascade, and sub-waves are predicted. From the gene expression profiles of the cell differentiation process from ES to adipose cells (62 time points), our method acquired four periods; three periods covering the two known waves of the cascade, and a final period of gene regulations when the differentiation to adipocytes was completed. Conclusions Our proposed method identifies the transitions of gene regulations from time-series gene expression profiles. Dynamic analyses are essential for deep understanding of biological systems and for identifying the causes of the onset of diseases such as diabetes and osteoporosis. The proposed method can greatly contribute to the progress of biology and medicine.

Abstract Bidirectional transcription has been proposed to play a role associated with enhancer activity. Transcripts called enhancer RNAs (eRNAs) play important roles in gene regulation; however, their roles in osteoclasts are unknown. To analyse eRNAs in osteoclasts comprehensively, we used cap-analysis of gene expression (CAGE) to detect adjacent transcription start sites (TSSs) that were distant from promoters for protein-coding gene expression. When comparing bidirectional TSSs between osteoclast precursors and osteoclasts, we found that bidirectional TSSs were located in the 5′-flanking regions of the Nrp2 and Dcstamp genes. We also detected bidirectional TSSs in the intron region of the Nfatc1 gene. To investigate the role of bidirectional transcription in osteoclasts, we performed loss of function analyses using the CRISPR/Cas9 system. Targeted deletion of the DNA regions between the bidirectional TSSs led to decreased expression of the bidirectional transcripts, as well as the protein-coding RNAs of Nrp2, Dcstamp, and Nfatc1, suggesting that these transcripts act as eRNAs. Furthermore, osteoclast differentiation was impaired by targeted deletion of bidirectional eRNA regions. The combined results show that eRNAs play important roles in osteoclastogenic gene regulation, and may therefore provide novel insights to elucidate the transcriptional mechanisms that control osteoclast differentiation.

Communication between osteoblasts and osteoclasts is essential for bone homeostasis, but the mode of interaction is unclear. The authors use intravital two-photon microscopy in mice to show that these cells directly interact, regulating activity of osteoclasts, and that the interaction is modulated by parathyroid hormone administration.

Abstract During antral folliculogenesis, developmental competence of prospective oocytes is regulated in large part by the follicular somatic component to prepare the oocyte for the final stage of maturation and subsequent embryo development. The underlying molecular mechanisms are poorly understood. Oocytes reaching the advanced stage of follicular growth by administration of exogenous follicle-stimulating hormone (FSH) possess higher developmental competence than oocytes in FSH-untreated smaller follicles. In this study, the transcriptomic profile of the cumulus cells from cows receiving FSH administration (FSH-priming) was compared, as a model of high oocyte competence, with that from untreated donor cows (control). Ingenuity Pathway Analysis showed that cumulus cells receiving FSH-priming were rich in down-regulated transcripts associated with cell movement and migration, including the extracellular matrix-related transcripts, probably preventing the disruption of cell-to-cell contacts. Interestingly, the transcriptomic profile of up-regulated genes in the control group was similar to that of granulosa cells from atretic follicles. Interferon regulatory factor 7 was activated as the key upstream regulator of FSH-priming. Thus, acquisition of developmental competence by oocytes can be ensured by the integrity of cumulus cells involved in cell-to-cell communication and cell survival, which may help achieve enhanced oocyte-somatic cell coupling.

Objective: Gastric cancer during pregnancy is rare, and even in Japan where a high rate of gastric cancers are reported, only 0.016% of pregnant women suffer from this disease. Generally, the cancer is already advanced at the time of detection and the prognosis for the woman is usually extremely poor. Moreover, prioritizing treatment of the woman often results in a premature birth. Case Report: We report a case of gastric cancer in a 32-year-old pregnant woman, gravida 6, para 4. The mother and the neonate had good prognoses after early diagnosis, cesarean delivery and surgery. Conclusion: Diagnosis of gastric cancer in pregnant women is often delayed even when they are symptomatic, because the symptoms are taken to be symptoms of hyperemesis or expansion of the uterus. However, since the nausea and vomiting arising from hyperemesis generally improves by the 20th week of gestation, the presence of protracted digestive symptoms in the second trimester calls for prompt investigation of digestive disorders. This case highlights the importance of early detection of gastric cancer for a positive prognosis, considering the rapidity with which gastric cancer advances in pregnancy.

Microorganisms in nature are constantly subjected to a limited availability of resources and experience repeated starvation and nutrition. Therefore, microbial life may evolve for both growth fitness and sustainability. By contrast, experimental evolution, as a powerful approach to investigate microbial evolutionary strategies, often targets the increased growth fitness in controlled, steady-state conditions. Here, we address evolutionary changes balanced between growth and maintenance while taking nutritional fluctuations into account. We performed a 290-day-long evolution experiment with a histidine-requiring Escherichia coli strain that encountered repeated histidine-rich and histidine-starved conditions. The cells that experienced seven rounds of starvation and re-feed grew more sustainably under prolonged starvation but dramatically lost growth fitness under rich conditions. The improved sustainability arose from the evolved capability to use a trace amount of histidine for cell propagation. The reduced growth rate was attributed to mutations genetically disturbing the translation machinery, that is, the ribosome, ultimately slowing protein translation. This study provides the experimental demonstration of slow growth accompanied by an enhanced affinity to resources as an evolutionary adaptation to oscillated environments and verifies that it is possible to evolve for reduced growth fitness. Growth economics favored for population increase under extreme resource limitations is most likely a common survival strategy adopted by natural microbes.

A vast amount of metagenomic data has been obtained by extracting multiple genomes simultaneously from microbial communities, including genomes from uncultivable microbes. By analyzing these metagenomic data, novel microbes are discovered and new microbial functions are elucidated. The first step in analyzing these data is sequenced-read classification into reference genomes from which each read can be derived. The Naïve Bayes Classifier is a method for this classification. To identify the derivation of the reads, this method calculates a score based on the occurrence of a DNA sequence motif in each reference genome. However, large differences in the sizes of the reference genomes can bias the scoring of the reads. This bias might cause erroneous classification and decrease the classification accuracy. To address this issue, we have updated the Naïve Bayes Classifier method using multiple sets of occurrence profiles for each reference genome by normalizing the genome sizes, dividing each genome sequence into a set of subsequences of similar length and generating profiles for each subsequence. This multiple profile strategy improves the accuracy of the results generated by the Naïve Bayes Classifier method for simulated and Sargasso Sea datasets.

Conventionally, in vitro-fertilized (IVF) bovine embryos are morphologically evaluated at the time of embryo transfer to select those that are likely to establish a pregnancy. This method is, however, subjective and results in unreliable selection. Here we describe a novel selection system for IVF bovine blastocysts for transfer that traces the development of individual embryos with time-lapse cinematography in our developed microwell culture dish and analyzes embryonic metabolism. The system can noninvasively identify prognostic factors that reflect not only blastocyst qualities detected with histological, cytogenetic, and molecular analysis but also viability after transfer. By assessing a combination of identified prognostic factors--(i) timing of the first cleavage; (ii) number of blastomeres at the end of the first cleavage; (iii) presence or absence of multiple fragments at the end of the first cleavage; (iv) number of blastomeres at the onset of lag-phase, which results in temporary developmental arrest during the fourth or fifth cell cycle; and (v) oxygen consumption at the blastocyst stage--pregnancy success could be accurately predicted (78.9%). The conventional method or individual prognostic factors could not accurately predict pregnancy. No newborn calves showed neonatal overgrowth or death. Our results demonstrate that these five predictors and our system could provide objective and reliable selection of healthy IVF bovine embryos.

Object. We present here the case of severe fetal anemia caused by anti-E antibody positive, which showed a favorable course only with fetal intraperitoneal administration of immunoglobulin. Case. The mother was 31 years old, blood type B Rh : CCDee, gravida 1, with no history of transfusion. Anti-E antibody was detected in the maternal cross-match test at the 18th gestational week. In percutaneous umbilical blood sampling, the umbilical blood hemoglobin level was 9.1 g/dL and the result of the direct Coombs' test was positive at the 26th gestational week. Immunoglobulin injection into fetal abdominal cavity (IFAC) was administered a total 7 times. During the pregnancy, the indirect Coombs' test showed a 131,072-fold increase. Conclusion. In this case, IFAC to block the reticuloendothelial system Fc receptor was successful. This procedure is promising as one of the treatment options for blood group incompatible pregnancy.

With the advancement of genome research, it is becoming clear that genes are not distributed on the genome in random order. Clusters of genes distributed at localized genome positions have been reported in several eukaryotes. Various correlations have been observed between the expressions of genes in adjacent or nearby positions along the chromosomes depending on tissue type and developmental stage. Moreover, in several cases, their transcripts, which control epigenetic transcription via processes such as transcriptional interference and genomic imprinting, occur in clusters. It is reasonable that genomic regions that have similar mechanisms show similar expression patterns and that the characteristics of expression in the same genomic regions differ depending on tissue type and developmental stage. In this study, we analyzed gene expression patterns using the cap analysis gene expression (CAGE) method for exploring systematic views of the mouse transcriptome. Counting the number of mapped CAGE tags for fixed-length regions allowed us to determine genomic expression levels. These expression levels were normalized, quantified, and converted into four types of descriptors, allowing the expression patterns along the genome to be represented by character strings. We analyzed them using dynamic programming in the same manner as for sequence analysis. We have developed a novel algorithm that provides a novel view of the genome from the perspective of genomic positional expression. In a similarity search of expression patterns across chromosomes and tissues, we found regions that had clusters of genes that showed expression patterns similar to each other depending on tissue type. Our results suggest the possibility that the regions that have sense-antisense transcription show similar expression patterns between forward and reverse strands.

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.

Lactiplantibacillus plantarum subsp. plantarum N793 (N793) is a lactic acid bacterium (LAB) isolated from corn. We previously showed that N793 increases the level of keratinocyte growth factor, which is required for hair growth, in the culture supernatant of human follicle dermal papilla cells. Additionally, an open-label, single-arm study reported that applying a lotion containing N793 to the scalp for 24 weeks improved hair density in men and women with thinning hair. The present study was a double-blind, placebo-controlled, parallel-group study aimed at verifying the efficacy of N793 for thinning hair. A lotion containing N793, and a control lotion (placebo) were applied once daily for 24 weeks to 104 healthy Japanese men and women. Analysis of all participants revealed no difference in hair density between the N793 and placebo groups. However, an additional analysis limited to participants with relatively mild progression of thinning hair showed a significantly better hair density in the N793 group than in the placebo group. These findings suggest that topical application of N793 improves thinning hair in men and women when the condition's progression is relatively mild. [ABSTRACT FROM AUTHOR]