Edaravone is a free-radical scavenger drug that was recently approved for the treatment of amyotrophic lateral sclerosis (ALS), a neurodegenerative disease. A pathological hallmark of ALS is the accumulation of ubiquitinated or phosphorylated aggregates of the 43-kDa transactive response DNA binding protein (TDP-43) within the cytoplasm of motor neurons. This study revealed the efficacy of edaravone in preventing neuronal cell death in a TDP-43 proteinopathy model and analyzed the molecular changes associated with the neuroprotection. The viability of the neuronal cells expressing TDP-43 was reduced by oxidative stress, and edaravone (≥10 μmol/L) protected in a concentration-dependent manner against the neurotoxic insult. Differential gene expression analysis revealed changes among pathways related to nuclear erythroid 2-related-factor (Nrf2)-mediated oxidative stress response in cells expressing TDP-43. In edaravone-treated cells expressing TDP-43, significant changes in gene expression were also identified among Nrf2-oxidative response, unfolded protein response, and autophagy pathways. In addition, the expression of genes belonging to phosphatidylinositol metabolism pathways was modified. These findings suggest that the neuroprotective effect of edaravone involves the prevention of TDP-43 misfolding and enhanced clearance of pathological TDP-43 in TDP-43 proteinopathy.

Background Entry into a new therapeutic area, that is, one in which a pharmaceutical firm lacks experience, is a considerable challenge for firms that need to overcome scientific and technological barriers. To address this issue, the present study aims to explore the potentiality of alliances in an empirical manner. Methods From the clinical trials sponsored by 20 major pharmaceutical firms during 2008–2016 listed at ClinicalTrials.gov (n = 14,941 clinical trials), cases of entering a new therapeutic area for a pharmaceutical firm were extracted (n = 73), followed by statistical analyses to evaluate the effect of alliances in this regard. Results We found that the average number of participating organizations in the cases of entering a new therapeutic area was significantly larger than that in the cases of entering an area in which firms had experience ( P < .01), suggesting that alliance has a positive effect on new therapeutic entry for these pharmaceutical firms. Second, we found that the cases of partnering with nonindustrial or nongovernmental organizations (ie, universities, research institutes, hospitals, funding agencies, and others; n = 32 of the 73) were significantly associated with these new entry trials (adjusted odds ratio = 1.1, P < .05). Furthermore, we identified that 10 of the 32 clinical trials were associated with rare diseases, which is an overrepresentation compared to the occurrence in the universe (1015 of the 14,941; P < 10–5). Conclusions These findings strongly suggest the importance of alliances with diversified partners in new therapeutic entry and also provide a basis for further detailed investigation of key success factors for pharmaceutical firms.

The molecular basis of vulnerability to stress during the adolescent period is largely unknown. To identify potential molecular mediators that may play a role in stress-induced behavioral deficits, we imposed social isolation on a genetically vulnerable mouse model. We report that 3-week (5-8weeks of age) adolescent stress in combination with disrupted-in-schizophrenia 1 (Disc1) genetic risk elicits alterations in DNA methylation of a specific set of genes, tyrosine hydroxylase, brain-derived neurotrophic factor and FK506 binding protein 5. The epigenetic changes in the mesocortical dopaminergic neurons were prevented when animals were treated with a glucocorticoid receptor (GR) antagonist RU486 during social isolation, which implicates the role for glucocorticoid signaling in this pathological event. We define the critical period of GR intervention as the first 1-week period during the stress regimen, suggesting that this particular week in adolescence may be a specific period of maturation and function of mesocortical dopaminergic neurons and their sensitivity to glucocorticoids. Our study may also imply the clinical significance of early detection and prophylactic intervention against conditions associated with adolescent social stress in individuals with genetic risk.

Cognitive impairment is a key feature of schizophrenia (SZ) and determines functional outcome. Nonetheless, molecular signatures in neuronal tissues that associate with deficits are not well understood. We conducted nasal biopsy to obtain olfactory epithelium from patients with SZ and control subjects. The neural layers from the biopsied epithelium were enriched by laser-captured microdissection. We then performed an unbiased microarray expression study and implemented a systematic neuropsychological assessment on the same participants. The differentially regulated genes in SZ were further filtered based on correlation with neuropsychological traits. This strategy identified the SMAD 5 gene, and real-time quantitative PCR analysis also supports downregulation of the SMAD pathway in SZ. The SMAD pathway has been important in multiple tissues, including the role for neurodevelopment and bone formation. Here the involvement of the pathway in adult brain function is suggested. This exploratory study establishes a strategy to better identify neuronal molecular signatures that are potentially associated with mental illness and cognitive deficits. We propose that the SMAD pathway may be a novel target in addressing cognitive deficit of SZ in future studies.

The corticostriatothalamic circuit regulates learning behaviors via dopamine neurotransmission. D2 long (D2L) receptors are an isoform of dopamine D2 receptors (D2Rs) and may act mainly at postsynaptic sites. It is well known that D2Rs influence high brain functions, but the roles of individual D2R isoforms are still unclear. To assess the influence of D2L receptors in visual discrimination learning, we performed visual discrimination and reversal tasks with D2L knockout mice using a touchscreen operant system. There were no significant differences in an operant conditioning task between genotypes. However, D2L knockout mice were impaired in both visual discrimination and reversal learning tasks. D2L knockout mice were also significantly slower than wild-type mice in collecting the reward in the visual discrimination task. These results indicate that D2L receptors play an important role in visual discrimination and reversal learning.

Japan Pharmacogenomics Data Science Consortium (JPDSC) has assembled a database for conducting pharmacogenomics (PGx) studies in Japanese subjects. The database contains the genotypes of 2.5 million single-nucleotide polymorphisms (SNPs) and 5 human leukocyte antigen loci from 2994 Japanese healthy volunteers, as well as 121 kinds of clinical information, including self-reports, physiological data, hematological data and biochemical data. In this article, the reliability of our data was evaluated by principal component analysis (PCA) and association analysis for hematological and biochemical traits by using genome-wide SNP data. PCA of the SNPs showed that all the samples were collected from the Japanese population and that the samples were separated into two major clusters by birthplace, Okinawa and other than Okinawa, as had been previously reported. Among 87 SNPs that have been reported to be associated with 18 hematological and biochemical traits in genome-wide association studies (GWAS), the associations of 56 SNPs were replicated using our data base. Statistical power simulations showed that the sample size of the JPDSC control database is large enough to detect genetic markers having a relatively strong association even when the case sample size is small. The JPDSC database will be useful as control data for conducting PGx studies to explore genetic markers to improve the safety and efficacy of drugs either during clinical development or in post-marketing.

BACKGROUND:The detection of the glomeruli is a key step in the histopathological evaluation of microscopic images of the kidneys. However, the task of automatic detection of the glomeruli poses challenges owing to the differences in their sizes and shapes in renal sections as well as the extensive variations in their intensities due to heterogeneity in immunohistochemistry staining. Although the rectangular histogram of oriented gradients (Rectangular HOG) is a widely recognized powerful descriptor for general object detection, it shows many false positives owing to the aforementioned difficulties in the context of glomeruli detection.RESULTS:A new descriptor referred to as Segmental HOG was developed to perform a comprehensive detection of hundreds of glomeruli in images of whole kidney sections. The new descriptor possesses flexible blocks that can be adaptively fitted to input images in order to acquire robustness for the detection of the glomeruli. Moreover, the novel segmentation technique employed herewith generates high-quality segmentation outputs, and the algorithm is assured to converge to an optimal solution. Consequently, experiments using real-world image data revealed that Segmental HOG achieved significant improvements in detection performance compared to Rectangular HOG.CONCLUSION:The proposed descriptor for glomeruli detection presents promising results, and it is expected to be useful in pathological evaluation.

Podocytes are an essential component of the renal glomerular filtration barrier, their injury playing an early and important role in progressive renal dysfunction. This makes quantification of podocyte marker immunoreactivity important for early detection of glomerular histopathological changes. Here we have specifically applied a state-of-the-art automated computational method of glomerulus recognition, which we have recently developed, to study quantitatively podocyte markers in a model with selective podocyte injury, namely the rat puromycin aminonucleoside (PAN) nephropathy model. We also retrospectively investigated mRNA expression levels of these markers in glomeruli which were isolated from the same formalin-fixed, paraffin-embedded kidney samples by laser microdissection. Among the examined podocyte markers, the immunopositive area and mRNA expression level of both podoplanin and synaptopodin were decreased in PAN glomeruli. The immunopositive area of podocin showed a slight decrease in PAN glomeruli, while its mRNA level showed no change. We have also identified a novel podocyte injury marker β-enolase, which was increased exclusively by podocytes in PAN glomeruli, similarly to another widely used marker, desmin. Thus, we have shown the specific application of a state-of-the-art computational method and retrospective mRNA expression analysis to quantitatively study the changes of various podocyte markers. The proposed methods will open new avenues for quantitative elucidation of renal glomerular histopathology.

Diabetic nephropathy is a major complication in diabetes and a leading cause of end-stage renal failure. Glomerular podocytes are functionally and structurally injured early in diabetic nephropathy. A non-obese type 2 diabetes model, the spontaneously diabetic Torii (SDT) rat, is of increasing preclinical interest because of its pathophysiological similarities to human type 2 diabetic complications including diabetic nephropathy. However, podocyte injury in SDT rat glomeruli and the effect of angiotensin II receptor blocker treatment in the early stage have not been reported in detail. Therefore, we have evaluated early stages of glomerular podocyte damage and the beneficial effect of early treatment with losartan in SDT rats using desmin as a sensitive podocyte injury marker. Moreover, we have developed an automated, computational glomerulus recognition method and illustrated its specific application for quantitatively studying glomerular desmin immunoreactivity. This state-of-the-art method enabled automatic recognition and quantification of glomerular desmin-positive areas, eliminating the need to laboriously trace glomerulus borders by hand. The image analysis method not only enabled assessment of a large number of glomeruli, but also clearly demonstrated that glomerular injury was more severe in the juxtamedullary region than in the superficial cortex region. This applied not only in SDT rat diabetic nephropathy but also in puromycin aminonucleoside-induced nephropathy, which was also studied. The proposed glomerulus image analysis method combined with desmin immunohistochemistry should facilitate evaluations in preclinical drug efficacy studies as well as elucidation of the pathophysiology of diabetic nephropathy.

A growing body of evidence suggests the involvement of inflammatory processes in the pathophysiology of schizophrenia. Four- to 8-week exposure to cuprizone, a copper chelator, causes robust demyelination and has been used to build a model for multiple sclerosis. In contrast, we report here the effects of 1-week cuprizone exposure in mice. This short-term cuprizone exposure elicits behavioral changes that include augmented responsiveness to methamphetamine and phencyclidine, as well as impaired working memory. The cellular effects of 1-week cuprizone exposure differ substantially from the longer-term exposure; perturbation of astrocytes and microglia is induced without any sign of demyelination. Furthermore, the proinflammatory cytokine interleukin-6 was significantly up-regulated in glial fibrillary acidic protein (GFAP)-positive cells. We propose that this cuprizone short-term exposure may offer a model to study some aspects of biology relevant to schizophrenia and related conditions.

The authors’ algorithm was favorably examined on two kinds of biological networks: a metabolic network and a protein interaction network. A statistical test confirmed that the weight that our algorithm assigned to each assay was meaningful.

BACKGROUND:The adaptive immune system (AIS) of jawed vertebrates is a sophisticated system mediated by numerous genes in specialized cells. Phylogenetic analysis indicates that emergence of the AIS followed the occurrence of two rounds of whole-genome duplication (2R-WGD) in early vertebrates, but little direct evidence linking these two events is available.RESULTS:We examined the relationship between 2R-WGD and the gain of AIS-related functions by numerous genes. To analyze the evolution of the many genes related to signal transduction in the AIS (defined as AIS genes), we identified groups of genes (defined as AIS subfamilies) that included at least one human AIS gene, its paralogs (if any), and its Drosophila ortholog(s). Genomic mapping revealed that numerous pairs of AIS genes and their paralogs were part of paralogons - series of paralogous regions that derive from a common ancestor - throughout the human genome, indicating that the genes were retained as duplicates after 2R-WGD. Outgroup comparison analysis revealed that subfamilies in which human and fly genes shared a nervous system-related function were significantly enriched among AIS subfamilies, as compared with the overall incidence of shared nervous system-related functions among all subfamilies in bilaterians. This finding statistically supports the hypothesis that AIS-related signaling genes were ancestrally involved in the nervous system of urbilaterians.CONCLUSION:The current results suggest that 2R-WGD played a major role in the duplication of many signaling genes, ancestrally used in nervous system development and function, that were later co-opted for new functions during evolution of the AIS.

The adenohypophysis of vertebrates receives peptide hormones from the hypothalamus and secretes hormones that regulate diverse physiologic processes in peripheral organs. The adenohypophysis-mediated endocrine system is widely conserved across vertebrates but not invertebrates. Phylogenetic analysis indicates that the emergence of this system coincided with two rounds of whole-genome duplication (2R-WGD) in early vertebrates, but direct evidence linking these events has been unavailable. We detected all human paralogons (series of paralogous regions) formed in early vertebrates as traces of 2R-WGD, and examined the relationship between 2R-WGD and the evolution of genes essential to the adenohypophysis-mediated endocrine system. Regarding genes encoding transcription factors (TFs) involved in the terminal differentiation into hormone-secreting cells in adenohypophyseal development, we showed that most pairs of these genes and their paralogs were part of paralogons. In addition, our analysis also indicated that most of the paralog pairs in families of adenohypophyseal hormones and their receptors were part of paralogons. These results suggest that 2R-WGD played an important role in generating genes encoding adenohypophyseal TFs, hormones, and their receptors for increasing the diversification of hormone repertoire in the adenohypophysis-mediated endocrine system of vertebrates.

Large-scale protein-protein interactions (PPIs) detected by yeast-two-hybrid (Y2H) systems are known to contain many false positives. The separation of credible interactions from background noise is still an unavoidable task. In the present study, we propose the relative reliability score for PPI as an intrinsic characteristic of global topology in the PPI networks. Our score is calculated as the dominant eigenvector of an adjacency matrix and represents the steady state of the network flow. By using this reliability score as a cut-off threshold from noisy Y2H PPI data, the credible interactions were extracted with better or comparable performance of previously proposed methods which were also based on the network topology. The result suggests that the application of the network-flow model to PPI data is useful for extracting credible interactions from noisy experimental data.

MOTIVATION Genomic and proteomic approaches have accumulated a huge amount of data which provide clues to protein function. However, interpreting single omic data for predicting uncharacterized protein functions has been a challenging task, because the data contain a lot of false positives. To overcome this problem, methods for integrating data from various omic approaches are needed for more accurate function prediction. RESULT In this paper, we have developed a method which extracts functionally similar proteins with high confidence by integrating protein-protein interaction data and domain information. We used this method to analyze publicly available data from Saccharomyces cerevisiae. We identified 1042 functional associations, involving 765 proteins of which 98 (12.8%) had no previously ascribed function. Our method extracts functionally similar protein pairs more accurately than conventional methods, and predicting function for previously uncharacterized proteins can be achieved. Our method can of course be applied to protein-protein interaction data for any species.

The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.

The alteration mineralogy of a porphyry-skarn system near Yerington, Nevada, was mapped using combined airborne hyperspectral HyMap and SEBASS data. The VNIR-SWIR HyMap data provided information about the abundance and levels of Tschermak substitution in white micas, as well as mapping the Mg-Fe chemistry of chlorite. The TIR SEBASS data provided unique information about the abundance and Fe-Al chemistry of garnet and Na-Ca chemistry of plagioclase feldspar. Both wavelength regions mapped calcite, dolomite, amphibole and epidote. The derived mineral maps were validated through spectral, mineralogical and chemical analyses of associated field samples. From these mineral maps, the geometry and physicochemistry of porphyry-skarn hydrothermal system becomes apparent, including the sites for Cu mineralization.

The Na-Ca chemistry of plagioclase felspar was measured and mapped remotely using airborne hyperspectral thermal infrared (TIR) SEBASS image data collected from a well-exposed porphyry system near Yerington, Nevada. This followed correction of the airborne SEBASS data for instrument and atmospheric effects and temperature-emissivity separation and was validated through associated field and laboratory studies. The later found a linear correlation between the relative intensities of the plagioclase /spl mu/FTIR emissivity spectral features at 9.6 and 10.0 /spl mu/m and the XRD dspacing of the felspar 111/130 hkl reflection, both of which are sensitive to the Na-Ca chemistry of plagioclase. The SEBASS derived felspar mineralogy maps clearly show variations in Na-Ca plagioclase felspar chemistry related to the nature of the host rock and any superimposed hydrothermal alteration.