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This study investigated six-month outcomes of first models of ascending aortic replacement. The molds used to produce the Biotube were implanted subcutaneously in goats. After 2–3 months, the molds were explanted to obtain the Biotubes (inner diameter, 12 mm; wall thickness, 1.5 mm). Next, we performed ascending aortic replacement using the Biotube in five allogenic goats. At 6 months, the animals underwent computed tomography (CT) and histologic evaluation. As a comparison, we performed similar surgeries using glutaraldehyde-fixed autologous pericardial rolls or pig-derived heterogenous Biotubes. At 6 months, CT revealed no aneurysmalization of the Biotube or pseudoaneurysm formation. The histologic evaluation showed development of endothelial cells, smooth muscle cells, and elastic fibers along the Biotube. In the autologous pericardium group, there was no evidence of new cell development, but there was calcification. The histologic changes observed in the heterologous Biotube group were similar to those in the allogenic Biotube group. However, there was inflammatory cell infiltration in some heterologous Biotubes. Based on the above, we could successfully create the world's first Biotube-based ascending aortic replacement models. The present results indicate that the Biotube may serve as a scaffold for aortic tissue regeneration. [ABSTRACT FROM AUTHOR]

Biotubes are autologous tubular tissues developed within a patient's body through in-body tissue architecture, and they demonstrate high potential for early clinical application as a vascular replacement. In this pilot study, we used large animals to perform implantation experiments in preparation for preclinical testing of Biotube. The biological response after Biotube implantation was histologically evaluated. The designed Biotubes (length: 50 cm, internal diameter: 4 mm, and wall thickness: 0.85 mm) were obtained by embedding molds on the backs of six goats for a predetermined period (1–5 months). The same goats underwent bypass surgery on the carotid arteries using Biotubes (average length: 12 cm). After implantation, echocardiography was used to periodically monitor patency and blood flow velocity. The maximum observation period was 6 months, and tissue analysis was conducted after graft removal, including the anastomosis. All molds generated Biotubes that exceeded the tensile strength of normal goat carotid arteries, and eight randomly selected Biotubes were implanted. Thrombotic occlusion occurred immediately postoperatively (1 tube) if anticoagulation was insufficient, and two tubes, with insufficient Biotube strength (<5 N), were ruptured within a week. Five tubes maintained patency for >2 months without aneurysm formation. The spots far from the anastomosis became stenosed within 3 months (3 tubes) when Biotubes had a wide intensity distribution, but the shape of the remaining two tubes remained unchanged for 6 months. The entire length of the bypass region was walled with an αSMA-positive cell layer, and an endothelial cell layer covered most of the lumen at 2 months. Complete endothelial laying of the luminal surface was obtained at 3 months after implantation, and a vascular wall structure similar to that of native blood vessels was formed, which was maintained even at 6 months. The stenosis was indicated to be caused by fibrin adhesion on the luminal surface, migration of repair macrophages, and granulation formation due to the overproliferation of αSMA-positive fibroblasts. We revealed the importance of Biotubes that are homogeneous, demonstrate a tensile strength > 5 N, and are implanted under appropriate antithrombotic conditions to achieve long-term patency of Biotube. Further, we clarified the Biotube regeneration process and the mechanism of stenosis. Finally, we obtained the necessary conditions for a confirmatory implant study planned shortly. [ABSTRACT FROM AUTHOR]

Simple Summary: Clinically, early-stage oral cancers are difficult to distinguish from oral potentially malignant disorders (OPMDs) because they show a variety of mucosal pathologies. Therefore, invasive tissue biopsies should be performed to determine the treatment strategy. Previously, we focused on gargle fluid as a noninvasive testing method and reported aberrant methylation in gargle fluid in patients with oral cancer. In this study, we successfully identified aberrantly methylated genes in early-stage oral cancer and reported that a combination of methylation of six genes could distinguish early-stage oral cancer from OPMDs, with high diagnostic performance. In addition, the methylation panel more accurately reflected the presence of early-stage oral cancer than cytology testing. Our results suggest that the methylation panel using gargle fluid has the potential to be used as a noninvasive screening tool to diagnose early-stage cancer. Clinically, early-stage oral cancers are difficult to distinguish from oral potentially malignant disorders (OPMDs), and invasive tissue biopsy should be performed to determine a treatment strategy. Previously, we focused on gargle fluid as a noninvasive testing method and reported aberrant methylation in gargle fluid in patients with oral cancer. This study aimed to distinguish early-stage oral cancer from clinically diagnosed OPMDs using gargle fluid samples. We collected gargle fluid samples from 40 patients who were clinically diagnosed with OPMDs in the training set; among them, 9 patients were pathologically diagnosed with oral cancer. Methylation levels of 25 tumor suppressor genes were analyzed using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) method. We found that a combination of six genes (TP73, CASP8, RARB, KLLN, GSTP1, and CHFR) could distinguish oral cancer from clinically diagnosed OPMDs with high diagnostic performance (area under the curve [AUC], 0.885; sensitivity, 77.8%; and specificity, 87.1%). Additionally, the panel comprised of the six methylated genes was validated in the test set. Furthermore, when compared with cytology testing, the panel could accurately detect oral cancer. The present methylated gene panel may serve as a novel biomarker for oral cancer. [ABSTRACT FROM AUTHOR]

Autologous-engineered artificial tissues constitute an ideal alternative for radical surgery in terms of natural anticoagulation, self-repair, tissue regeneration, and the possibility of growth. Previously, we focused on the development and practical application of artificial tissues using "in-body tissue architecture (iBTA)", a technique that uses living bodies as bioreactors. This study aimed to further develop iBTA by fabricating tissues with diverse shapes and evaluating their physical properties. Although the breaking strength increased with tissue thickness, the nominal breaking stress increased with thinner tissues. By carving narrow grooves on the outer periphery of an inner core with narrow grooves, we fabricated approximately 2.2 m long cord-shaped tissues and net-shaped tissues with various designs. By assembling the two inner cores inside the branched stainless-steel pipes, a large graft with branching was successfully fabricated, and its aortic arch replacement was conducted in a donor goat without causing damage. In conclusion, by applying iBTA technology, we have made it possible, for the first time, to create tissues of various shapes and designs that are difficult using existing tissue-engineering techniques. Thicker iBTA-induced tissues exhibited higher rupture strength; however, rupture stress was inversely proportional to thickness. These findings broaden the range of iBTA-induced tissue applications. [ABSTRACT FROM AUTHOR]

The behavior of microparticle assemblage moving through the saturated pores in a fibrous layer has been investigated numerically. We adopted a particle model to express the straight and tortuous fibrous layers and calculated the velocities of individual microparticles using the Stokesian dynamics approach assuming the Stokes flow. The simulation results showed that the particles spread as they moved through the layer. This is interpreted as hydrodynamic diffusion caused by the hydrodynamic interaction dominant in the Stokes flow. More pronounced diffusion was observed in the tortuous fibrous layer than in the straight one. It was found that the velocity of each particle deviated more from the ensemble average velocity of the assemblage in the tortuous fibrous layer. It was also observed that the tortuous fibrous layers exhibited greater variation in the size of the pores where particles passed. Our results quantitatively indicated that the tortuous fibrous layer consisted of a wide variety of pore sizes, which affects the velocity of the particles passing through it. Consequently, the difference in each particle velocity causes the hydrodynamic diffusion. It was also revealed that the subtle difference in the fiber shape substantially influences the hydrodynamic behavior of the particles moving inside. [ABSTRACT FROM AUTHOR]

In this study, the authors investigate the tensile strength at a carbon fiber/epoxy resin interface using molecular dynamics (MD) simulations. The simulated tension speed and strength were initially estimated, and a realistic tension speed was subsequently selected. The tensile strength calculated using the simulations was in good agreement with the experimental data. Based on the present study and our previous work, the factors contributing to the tensile strength of composite materials were investigated and analyzed. The surface energy between the graphene sheet and resin as well as the molecular structure of the resin in the vicinity of graphene was shown to significantly affect the tensile strength. In addition, the applicability of MD simulation as a useful tool for the prediction and analysis of composite materials was demonstrated. This work used graphene sheets as carbon fiber because it is difficult to express the real carbon fiber for simulation model. [ABSTRACT FROM AUTHOR]

The effect of fiber tortuosity on fluid permeability in fibrous beds has been investigated. A particle model is employed in which a fiber is replaced by spherical particles and fiber tortuosity is represented by a bending angle. Assuming a low Reynolds number, the fluid permeability is calculated based on the Stokesian dynamics approach. The results show that the permeability of a tortuous fibrous bed is lower than that of a straight fibrous bed. To examine the permeability dependence on the fiber tortuosity in detail, the pore distribution and pore connectivity are evaluated quantitatively by defining the pore radius. It is found that the tortuous fibers prevent the formation of large pores and their connection in the flow direction, thereby decreasing the permeability. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulation has been performed on five native proteins in water to evaluate their intrinsic isothermal compressibilities βT,int. To identify physical factors contributing to protein compressibility, a general method is presented for analyzing the compressibility of mechanically inhomogeneous systems. The value of βT,int varies with protein species considerably: β-lactoglobulin 14.1510-2 GPa-1 is more than twice as compressible as ribonuclease A 6.77 × 10-2 GPa-1. β-lactoglobulin and myoglobin 13.95 ×10-2 GPa-1 have similar values of βT,int, but the mechanisms responsible for them are significantly different. The volume fluctuations of internal cavities and the magnitudes of the crosscorrelation between them are the key factors determining βT,int of proteins. Though the volume fractions of internal cavity for the five studied proteins are nearly equal to one another, the mean cavity compressibilities βT,int vary considerably with protein species and range from 0.35 to 0.69 GPa-1, which are much smaller than those of normal organic liquids such as methanol, ethanol, and benzene and close to that of glycerol 0.55 GPa-1, a strongly associated liquid. [ABSTRACT FROM AUTHOR]

Classical molecular dynamics (MD) calculations were performed to reveal the effect of high pressure on the crystal structure of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), an insensitive energetic material. The primary simulation cell consisted of 54 molecules in a triclinic cell, corresponding to 27 unit cells obtained by replicating the experimentally determined unit cell. Inter- and intra-molecular hydrogen bonds were maintained in the range of 1.0 atm to 20.0 GPa as pressure was incremented by 0.5 GPa. The pressure dependence of the interlayer distances ( h 1 ) and farthest intermolecular distance ( d 1 ) between nitro groups in the TATB crystal’s unit cell was investigated in the same range. h 1 decreased monotonously from 3.50 to 2.90 Å as pressure increased to 20.0 GPa. However, d 1 increased considerably with pressure up to 4.0 GPa, most remarkably between 2.0 and 4.0 GPa. Thus, a unique structural change occurred in TATB crystal in this range. On the other hand, 1,3-diamino-2,4,6-trinitrobenzene (DATB) crystal showed a unique structural change between 7.0 and 8.0 GPa. These discrepancies are attributed to the different network systems of hydrogen bonding of these two molecules. To validate the MD calculation results, we conducted first-principles calculations. MD and first-principles calculations showed good agreement with previous experimental results. [ABSTRACT FROM AUTHOR]

[Display omitted] • This study developed a method to create interatomic potentials using a neural network (NN). • Ab initio molecular dynamics (AIMD) simulations were conducted to produce training data for the NN. • The developed NN potential (NNP) was verified using MD simulation with MEAM potential and its experiment. • MD simulation using the developed NNP revealed higher strength and brittleness for Ti 2 N. Titanium nitride (TiN) is used in various applications because of its excellent wear and corrosion resistance. TiN with a rock-salt-type crystal structure has been investigated extensively, but the existence of non-rock-salt-type phases (e.g., Ti 2 N) has only been reported recently from first-principles calculations. Molecular dynamics (MD) simulation is a powerful tool to predict mechanical properties, but it generally requires interatomic potentials. The conventional many-body interatomic potentials (e.g., modified embedded-atom method (MEAM) potential) for rock-salt TiN are not applicable to these other phases. Hence, in this study, a neural network (NN)-based method to create interatomic potentials is developed, which are referred to as neural network potentials (NNPs); hence, MD simulations can be conducted for TiN and other phases. First, ab initio molecular dynamics (AIMD) simulations are conducted to obtain the relationships between atomic configurations and the corresponding total potential energies and forces on each atom. Subsequently, these relationships are used for the NN to generate NNP. NNP can accurately reproduce the energies and forces calculated by AIMD simulations. The mechanical properties of TiN are computed using the NNP and MD simulation and verified with the MEAM potential and its experiment. Finally, MD simulation using the developed NNP is conducted for the other phase (Ti 2 N) to investigate its mechanical properties. [ABSTRACT FROM AUTHOR]

Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (5W52), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management. [ABSTRACT FROM AUTHOR]

Abstract: The end-to-end distance, R, of individual poly(methyl methacrylate) (PMMA) chains was evaluated for the individual chains by the super-resolution fluorescence microscopy, which determines the positions of the dye molecules introduced at both ends of a PMMA chain. The observed value of R was in good agreement with that reported by SANS experiments, and the distribution function was well fitted to the theoretical model of the random walk chain. The accuracy to determine the root of mean-square end-to-end distance is on the order of 1nm. The distribution function of R obtained for the single PMMA chain in an ultra-thin film was almost the same as that in a bulk state. This indicates that the chain dimension in the ultra-thin was not significantly altered in the direction normal to the spatial confinement. [Copyright &y& Elsevier]

Abstract: We investigated the possibility of proton exchange reaction between protic ionic liquid of diethylmethylammonium trifluoromethanesulfonate ([dema][TfOH]) and H2O by using NMR spectroscopy and theoretical calculation. NMR spectroscopy experiment showed that the proton exchange between [dema][TfOH] and H2O in a 1:1M ratio occurred at room temperature. From the theoretical calculation, we found two reaction pathways for proton exchange between [dema][TfOH] and H2O. Both pathways have stepwise reaction with two transition states. After finishing the reaction along these pathways, the same complex structures of [dema][TfOH] and H2O are again formed, respectively. But the proton is exchanged between [dema][TfOH] and H2O. [Copyright &y& Elsevier]

In the present works effective application of partial preheating by high frequency induction to enlarge the partial diameter of middle carbon steel was experimentally investigated. The partial reheating was carried out by varying preheating times under the same electric power conditions. As all other conditions other than temperature remained constant during the diameter enlargement experiments, the partial preheating effects were clarified to be estimative using a parameter of the σ/σy, which was found to be dependent on temperature regardless of constant compressive axial stress. For heating times of less than 50 sec, the preheating effect for promoting partial diameter-enlargement did not appear. In fact the reverse effect appeared in times ranging from 30 sec to 50 sec due to blue brittleness generated at temperatures from about 523K to about 623K. Also, low cycle fatigue cracks must be avoided when initiating at the filet end of an enlarged shaft while passing through the temperature range of blue brittleness during the cooling process. Therefore, the preheating temperature found to be most effective for promoting the diameter enlargement was greater than about 856K so as to increase easily the Df/D0 to above 2 times without generating damage cracks from fatigue. [ABSTRACT FROM AUTHOR]

Abstract: Electrochemical bromination of germacrene D 1 and geraniol 2 carrying plural olefinic bonds provided the corresponding brominated products 3–10. The bicyclic derivative 6 was preferentially produced from 1, while chemical brominations provided no clear selectivity of its product distribution. Influence of the parameters of the electrochemical reaction conditions was evaluated, aiming at improvement of regioselectivity and yields of the brominated products. [Copyright &y& Elsevier]

Sjögren syndrome (SS) is diagnosed based on invasive tissue biopsies and blood sampling. Therefore, a novel non-invasive and simple inspection diagnostic marker of SS is required. Here, we identified exosome-derived microRNAs (miRNAs) as biomarkers for SS using non-invasive mouthrinse samples collected from patients with SS and healthy volunteers. We compared miRNAs derived from exosomes in mouthrinse samples from the two groups using microarrays and real-time polymerase chain reaction (PCR) and identified 12 miRNAs as biomarker candidates. The expression ratios of four miRNAs were significantly increased in the SS group compared to the control group. Logistic regression analysis revealed a more significant influence of miR-1290 and let-7b-5p in the SS group than that in the control group. We combined these miRNAs to create a diagnostic prediction formula using logistic regression analysis. The combination of miR-1290 and let-7b-5p distinguished SS from the control samples with an AUC, sensitivity, specificity, positive predictive value, and negative predictive value of 0.856, 91.7%, 83.3%, 84.6%, and 90.9%, respectively. These results indicated that an increased ratio of these miRNAs could serve as a novel and non-invasive diagnostic marker for SS. This is the first report of diagnosis and screening of SS by adopting a non-invasive method using mouthrinse. [ABSTRACT FROM AUTHOR]

In this study, we investigated a deleterious mutation in the β-xylosidase gene, xylA (AkxylA), in Aspergillus luchuensis mut. kawachii IFO 4308 by constructing an AkxylA disruptant and complementation strains of AkxylA and xylA derived from A. luchuensis RIB2604 (AlxylA), which does not harbor the mutation in xylA. Only the AlxylA complementation strain exhibited significantly higher growth and substantial β-xylosidase activity in medium containing xylan, accompanied by an increase in XylA expression. This resulted in lower xylobiose and higher xylose concentrations in the mash of barley shochu. These findings suggest that the mutation in xylA affects xylose levels during the fermentation process. Because the mutation in xylA was identified not only in the genome of strain IFO 4308 but also the genomes of other industrial strains of A. luchuensis and A. luchuensis mut. kawachii , these findings enhance our understanding of the genetic factors that affect the fermentation characteristics. [ABSTRACT FROM AUTHOR]

Introduction: Some previous studies have reported that a first‐step ethanol infusion into the vein of Marshall (EIVOM) with touch‐up radiofrequency (RF) ablation can facilitate mitral isthmus (MI) block and improves the ablation outcomes in persistent atrial fibrillation (PeAF) patients. However, the effect of an initial RF ablation with an adjunctive EIVOM has not been fully investigated. Methods: This study enrolled 233 PeAF patients undergoing pulmonary vein isolation and linear ablation including an MI, roof line, and cavotricuspid isthmus ablation. An EIVOM was performed when endocardial ablation with or without coronary sinus ablation failed to create MI block. Results: Bidirectional MI block was achieved in 224 patients (96.1%). Among them, MI block was obtained by only RF ablation in 174/224 patients (77.7%) (RF group) and an adjunctive EIVOM was needed in 50/224 (22.3%) (EIVOM group). During the follow‐up, 113 (64.9%) RF group patients were free from AF/atrial tachycardia compared to 41 (82.0%) EIVOM group patients (log‐rank p =.045). In a multivariate Cox regression analysis, an adjunctive EIVOM was associated with a lower recurrence rate (hazard ratio = 0.39, 95% confidence interval = 0.17–0.78, p =.006). Conclusion: An initial RF ablation with an adjunctive EIVOM strategy improved MI ablation's acute success rate and was associated with better clinical outcomes. [ABSTRACT FROM AUTHOR]

Background: Anomalous left coronary artery from the pulmonary artery is a congenital heart disease in which myocardial ischemia occurs within 1 year of birth. Adults have been reported to survive owing to the development of collateral perfusion from right coronary artery. In these cases, however, revascularization is necessary to prevent sudden cardiac death.Case Presentation: A 62-year-old female gradually started experiencing dyspnea during exercise. Coronary computed tomography revealed that the left coronary artery arose from the main pulmonary artery. The patient was subsequently diagnosed with adult-type, anomalous left coronary artery from the pulmonary artery. She underwent a surgery, in which a 6-mm vascular prosthesis was passed through the main pulmonary artery to anastomose the left coronary artery and ascending aorta.Conclusion: Our reconstructive technique using vascular prosthesis is effective for anomalous left coronary artery from pulmonary artery in adults. [ABSTRACT FROM AUTHOR]

Evaluation of interface strength is important in composite material design such as carbon fiber reinforced plastic. Molecular simulation, which considers aspects such as chemical structure, can be used to evaluate the composite interface strength. Therefore, in this study, the interface energies between graphene, considering the electric charge state, and resin (TriA-X polyimide, DGEBA, triethylenetetramine, vinyl ester, and PA6) were evaluated via molecular dynamics simulation. First, the interface energy and experimentally obtained interface strength were compared. Subsequently, the coefficient of determination R2 was calculated using linear approximations from the interface energy and interface strength. In addition, the correlation coefficient was calculated and showed a high correlation. Based on this data, it was conjectured that a relationship exists between the interface strength and interface energy. Furthermore, the validity of the relationship magnitude between the experimentally obtained interface strength and the interface energy obtained via simulation was evaluated. Moreover, considering graphene oxidation, the interface energies between the resin and three forms of graphene (functionalized with OH, COOH, and O groups) were obtained, and the effect of various oxidation surface treatments of graphene on their corresponding interface strengths was investigated. [ABSTRACT FROM AUTHOR]

A putative methyltransferase, LaeA, controls citric acid production through epigenetic regulation of the citrate exporter gene, cexA , in the white koji fungus Aspergillus luchuensis mut. kawachii. In this study, we investigated the role of another epigenetic regulator, heterochromatin protein 1, HepA, in citric acid production. The Δ hepA strain exhibited reduced citric acid production in liquid culture, although to a lesser extent compared to the Δ laeA strain. In addition, the Δ laeA Δ hepA strain showed citric acid production similar to the Δ laeA strain, indicating that HepA plays a role in citric acid production, albeit with a less-significant regulatory effect than LaeA. RNA-seq analysis revealed that the transcriptomic profiles of the Δ hepA and Δ laeA strains were similar, and the expression level of cexA was reduced in both strains. These findings suggest that the genes regulated by HepA are similar to those regulated by LaeA in A. luchuensis mut. kawachii. However, the reductions in citric acid production and cexA expression observed in the disruptants were mitigated in rice koji, a solid-state culture. Thus, the mechanism by which citric acid production is regulated differs between liquid and solid cultivation. Further investigation is thus needed to understand the regulatory mechanism in koji. [ABSTRACT FROM AUTHOR]

Sirtuins are understood to play a significant role in growth phase-dependent gene expression. In the study presented here, we examined the sirtuins in the white koji fungus, Aspergillus luchuensis mut. kawachii (Aspergillus kawachii), to examine their role in the regulation of amylolytic enzymes and citric acid production during solid-state culture (koji). Characterization of rice koji made using five sirtuin gene disruptants indicated that these genes are involved in the amylolytic activity and acidity of rice koji; the sirD disruptant in particular showed lower levels of acid-stable α-amylase activity and citric acid production per mycelial weight in koji compared to the control strain. The sirD disruptant also showed a change in mycelial pigmentation, and had higher sensitivity to cell wall biogenesis inhibitors such as calcofluor white and Congo red and reduced conidia formation. These results indicate that SirD is required for secondary metabolism, cell wall integrity, and conidial development. Cap analysis gene expression (CAGE) and quantitative RT-PCR analysis indicated that transcriptional changes were related to the characteristic phenotype of the sirD disruptant, including a reduced transcript level of the acid-stable α-amylase gene and a citric acid exporter in rice koji. These results indicate that SirD has a significant role in global transcriptional regulation, including the production of acid-stable α-amylase and citric acid, in A. kawachii during the solid-state fermentation process. [ABSTRACT FROM AUTHOR]

The ascomycete Trichoderma reesei is known to produce a variety of cellulases and hemicellulases and the hyper-cellulolytic mutants of this fungus are useful as industrial cellulase producers. In Japan, PC-3-7, derived from the early mutant QM9414, is well-known as a cellulase hyperproducing mutant. In addition to the productivity of enzymes, the composition of secreted enzymes greatly influences biomass saccharification. Therefore, we evaluated the cellulase productivity of T. reesei mutants in Japan at different pH as a factor influencing enzyme production. At higher pH values, QM9414 exhibited reduced cellulase productivity whereas PC-3-7 maintained high cellulase productivity and gene expression at the transcriptional level. The gene encoding the pH-responsive transcription factor PACI did not mutate in PC-3-7, and its expression pattern against different pH conditions was similar between QM9414 and PC-3-7. Furthermore, the deletion of pac1 encoding PACI caused different expression patterns of cellulase genes between QM9414 and PC-3-7. Therefore, we suggest that T. reesei possesses a pH-responsive cellulase production mechanism that is different from the PACI-related mechanism. Finally, we identified that N-25, a strain developed at an early stage of mutant development acquired cellulase productivity at a higher pH. In this investigation, we also found and tested candidate genes possibly affecting pH response using comparative genome analysis. [ABSTRACT FROM AUTHOR]

Simple Summary: There are no established biomarkers for oral squamous cell carcinoma (OSCC), and detection of neck lymph node metastases relies on imaging studies. Diagnosis and prediction using biomarkers, which are less invasive and simpler than imaging tests, could improve prognosis if lymph node metastases could be treated earlier. In this study, serum microRNAs were successfully used to diagnose primary neck lymph node metastases and predict late neck lymph node metastases. They reflected the presence of lymph node metastasis more accurately than serum squamous cell carcinoma antigens or pathological factors. MicroRNAs (miRNAs) have attracted attention as non-invasive cancer biomarkers in various cancers; however, they have not been adequately investigated in oral squamous cell carcinoma (OSCC). This study investigated the diagnostic performance of serum-derived miRNAs at initial diagnosis for primary neck lymph node metastasis and the predictive performance for late neck lymph node metastasis based on long-term (up to approximately 8 years) follow-up of patients with OSCC. The expression of miRNAs in 40 patients with OSCC was quantified using real-time PCR (qPCR), and a comprehensive statistical analysis of the correlation of miRNA expression for primary and late neck lymph node metastases was performed. For the diagnosis of primary neck lymph node metastases, miR-423 and miR-125 were accurate. The miRNA index for primary metastasis diagnosis (miR-PM) calculated by regression analysis showed high diagnostic accuracy. The miR-5100 was useful for predicting late neck lymph node metastases. The miRNA index for late metastasis prediction (miR-LM) calculated using regression analysis showed high prediction accuracy. MiRNAs were useful for diagnosing primary neck lymph node metastases in OSCC and predicting late neck lymph node metastases. It may help to consider individualized treatment, including follow-up, surgical methods, and postoperative management. [ABSTRACT FROM AUTHOR]

With the aim of identifying sex determinants of fig, we generated the first draft genome sequence of fig and conducted the subsequent analyses. Linkage analysis with a high-density genetic map established by a restriction-site associated sequencing technique, and genome-wide association study followed by whole-genome resequencing analysis identified two missense mutations in RESPONSIVE-TO-ANTAGONIST1 (RAN1) orthologue encoding copper-transporting ATPase completely associated with sex phenotypes of investigated figs. This result suggests that RAN1 is a possible sex determinant candidate in the fig genome. The genomic resources and genetic findings obtained in this study can contribute to general understanding of Ficus species and provide an insight into fig's and plant's sex determination system. [ABSTRACT FROM AUTHOR]

Pantoea agglomerans is a Gram-negative bacterium that grows symbiotically with various plants. Here we report the 4.8-Mb genome sequence of P. agglomerans strain IG1. The lipopolysaccharides derived from P. agglomerans IG1 have been shown to be effective in the prevention of various diseases, such as bacterial or viral infection, lifestyle-related diseases. This genome sequence represents a substantial step toward the elucidation of pathways for production of lipopolysaccharides. [ABSTRACT FROM AUTHOR]

Proanthocyanidins, also known as condensed tannins or oligomeric flavonoids, are found in many edible plants and exhibit interesting biological activities. Herein, we report a new, simple method for the stereoselective synthesis of procyanidin B6, a (+)-catechin-(4-6)-(+)-catechin dimer, by Lewis acid-catalyzed intramolecular condensation. The 5-O-t-butyldimethylsilyl (TBDMS) group of 5,7,3' 4' -tetra-O-TBDMS-(+)-catechin was regioselectively removed using trifluoroacetic acid, leading to the "regio-controlled" synthesis of procyanidin B6. The 5-hydroxyl group of the 7,3',4' -tri-O-TBDMS-(+)-catechin nucleophile and the 3-hydroxyl group of 5,7,3',4' -tetra-O-benzylated-(+)-catechin electrophile were connected with an azelaic acid. The subsequent SnCl4-catalyzed intramolecular condensation proceeded smoothly to give the 4-6-condensed catechin dimer. This is the first report on the complete regioselective synthesis of a 4-6-connected oligomer without modifying the 8-position. [ABSTRACT FROM AUTHOR]

A novel algorithm for covalent bond dissociation is developed to accurately predict fracture behavior of thermosetting polymers via molecular dynamics simulation. This algorithm is based on the Monte Carlo method that considers the difference in local strain and bond-dissociation energies to reproduce a thermally activated process in a covalent bond dissociation. This study demonstrates the effectiveness of this algorithm in predicting the stress–strain relationship of fully crosslinked thermosetting polymers under uniaxial tensile conditions. Our results indicate that the bond-dissociation energy plays an important role in reproducing the brittle fracture behavior of a thermosetting polymer by affecting the number of covalent bonds that are dissociated simultaneously. [ABSTRACT FROM AUTHOR]

The oleaginous yeast Lipomyces starkeyi has considerable potential in industrial application, since it can accumulate a large amount of triacylglycerol (TAG), which is produced from sugars under nitrogen limitation condition. However, the regulation of lipogenesis in L. starkeyi has not been investigated in depth. In this study, we compared the genome sequences of wild-type and mutants with increased TAG productivity, and identified a regulatory protein, LsSpt23p, which contributes to the regulation of TAG synthesis in L. starkeyi. L. starkeyi mutants overexpressing LsSPT23 had increased TAG productivity compared with the wild-type strain. Quantitative real-time PCR analysis showed that LsSpt23p upregulated the expression of GPD1, which encodes glycerol 3-phosphate dehydrogenase; the Kennedy pathway genes SCT1, SLC1, PAH1, DGA1, and DGA2; the citrate-mediated acyl-CoA synthesis pathway-related genes ACL1, ACL2, ACC1, FAS1, and FAS2; and OLE1, which encodes ∆9 fatty acid desaturase. Chromatin immunoprecipitation-quantitative PCR assays indicated that LsSpt23p acts as a direct regulator of SLC1 and PAH1, all the citrate-mediated acyl-CoA synthesis pathway–related genes, and OLE1. These results indicate that LsSpt23p regulates TAG synthesis. Phosphatidic acid is a common substrate of phosphatidic acid phosphohydrolase, which is used for TAG synthesis, and phosphatidate cytidylyltransferase 1 for phospholipid synthesis in the Kennedy pathway. LsSpt23p directly regulated PAH1 but did not affect the expression of CDS1, suggesting that the preferred route of carbon is the Pah1p-mediated TAG synthesis pathway under nitrogen limitation condition. The present study contributes to understanding the regulation of TAG synthesis, and will be valuable in future improvement of TAG productivity in oleaginous yeasts. Key points: LsSpt23p was identified as a positive regulator of TAG biosynthesis LsSPT23 overexpression enhanced TAG biosynthesis gene expression and TAG production LsSPT23M1108Toverexpression mutant showed fivefold higher TAG production than control [ABSTRACT FROM AUTHOR]

As a constituent of polysaccharides and glycoconjugates, β-d-galactofuranose (Galf) exists in several pathogenic microorganisms. Although we recently identified a β-d-galactofuranosidase (Galf-ase) gene, ORF1110, in theStreptomycesstrain JHA19, very little is known about the Galf-ase gene. Here, we characterized a strain, named JHA26, in the culture supernatant of which exhibited Galf-ase activity for 4-nitrophenyl β-d-galactofuranoside (pNP-β-d-Galf) as a substrate. Draft genome sequencing of the JHA26 strain revealed a putative gene, termed ORF0643, that encodes Galf-ase containing a PA14 domain, which is thought to function in substrate recognition. The recombinant protein expressed inEscherichia colishowed the Galf-specific Galf-ase activity and also released galactose residue of the polysaccharide galactomannan prepared fromAspergillus fumigatus, suggesting that this enzyme is an exo-type Galf-ase. BLAST searches using the amino acid sequences of ORF0643 and ORF1110 Galf-ases revealed two types of Galf-ases in Actinobacteria, suggesting that Galf-specific Galf-ases may exhibit discrete substrate specificities. Galf-specific Galf-ases with discrete substrate recognition domains in Actinobacteria [ABSTRACT FROM PUBLISHER]

β-D-galactofuranose (Galf) is a component of polysaccharides and glycoconjugates and its transferase has been well analyzed. However, no β-D-galactofuranosidase (Galf-ase) gene has been identified in any organism. To search for a Galf-ase gene we screened soil samples and discovered a strain, identified as a Streptomyces species by the 16S ribosomal RNA gene analysis, that exhibits Galf-ase activity for 4-nitrophenyl β-D-galactofuranoside (pNP-β-D-Galf) in culture supernatants. By draft genome sequencing of the strain, named JHA19, we found four candidate genes encoding Galf-ases. Using recombinant proteins expressed in Escherichia coli, we found that three out of four candidates displayed the activity of not only Galf-ase but also α-L-arabinofuranosidase (Araf-ase), whereas the other one showed only the Galf-ase activity. This novel Galf-specific hydrolase is encoded by ORF1110 and has an optimum pH of 5.5 and a Km of 4.4 mM for the substrate pNP-β-D-Galf. In addition, this enzyme was able to release galactose residue from galactomannan prepared from the filamentous fungus Aspergillus fumigatus, suggesting that natural polysaccharides could be also substrates. By the BLAST search using the amino acid sequence of ORF1110 Galf-ase, we found that there are homolog genes in both prokaryotes and eukaryotes, indicating that Galf-specific Galf-ases widely exist in microorganisms. [ABSTRACT FROM AUTHOR]

In this study, the atomistic-scale mechanisms affecting the interfacial stability of a thermoplastic polymer/graphene oxide interface are investigated using molecular dynamics simulations. Different combinations of thermoplastic polymers (polyethersulfone (PES) and polyetherimide (PEI)) and graphene oxides modified with –O–, –OH, and –COOH are prepared. PES is found to be more strongly stabilized with modified/functionalized graphene oxide in the order of –COOH, –OH, –O–, which is opposite to the stability order of PEI. Our results suggest that these orders of stability are governed by a balance between the following two factors resulting from electrostatic interactions: (1) atoms with a strong charge bias attract each other, thereby stabilizing the interface; (2) the excluded-volume effect of the functional groups on graphene oxide destabilizes the interface by preventing π - π stacking of aromatic rings. [ABSTRACT FROM AUTHOR]

The article studies the phylogenetic relationship of Paenibacillus (P.) species and analysis of an yheCD-like sequence found in replication origin region. The study found that in the rsmG-gyrA region, gene arrangements in Paenibacillus species were identical to those of Bacillus species except an open reading frame (orfl4) positioned between gyrB and gyrA. The phylogenetic tree suggested that P. popilliae, P. thiaminolyticus, and P. dendritiformis were closely related species.

The demand for n-3 long-chain polyunsaturated fatty acids (n-3LC-PUFAs), such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), will exceed their supply in the near future, and a sustainable source of n-3LC-PUFAs is needed. Thraustochytrids are marine protists characterized by anaerobic biosynthesis of DHA via polyunsaturated fatty acid synthase (PUFA-S). Analysis of a homemade draft genome database suggested that Parietichytrium sp. lacks PUFA-S but possesses all fatty acid elongase (ELO) and desaturase (DES) genes required for DHA synthesis. The reverse genetic approach and a tracing experiment using stable isotope-labeled fatty acids revealed that the ELO/DES pathway is the only DHA synthesis pathway in Parietichytrium sp. Disruption of the C20 fatty acid ELO (C20ELO) and ∆4 fatty acid DES (∆4DES) genes with expression of ω3 fatty acid DES in this thraustochytrid allowed the production of EPA and n-3docosapentaenoic acid (n-3DPA), respectively, at the highest level among known microbial sources using fed-batch culture. Yohei Ishibashi and co-workers report that Parietichytrium sp. synthesizes DHA only via the elongase/desaturase pathway. They then engineered this thraustochytrid to produce EPA and n-3DPA by disrupting C20ELO and delta4 DES genes, respectively, in this biosynthetic pathway, suggesting that this may be a suitable system for the large scale production of these omega-3 fatty acids. [ABSTRACT FROM AUTHOR]

The article focuses on the single-nucleotide polymorphisms (SNPs) analysis of the hyper-cellulolytic mutant of the ascomycete Trichoderma reesei that has been developed in Japan. It mentions that the carbon catabolite repressor gene cre1 detected are responsible for increased cellulase production. It also presents several tables related to the SNP analysis of several mutants.

A novel processing method to enlarge a partial diameter in the middle of shaft by means of combining a rotational-bending stress and an axial-compressive stress, can work various kinds of structural carbon steel without temperature-rise above 20K at room temperature. However, it was found that the maximum diameter-enlargement rate Df/D0 without initiating a fatigue damage crack decreased with increase in carbon contents of steel with mixed microstructure of ferrite and pearlite. It is thought that the mixed microstructure causes initiating the fatigue damage crack. In the present research, six kinds of heat-treatments of 823K-948K×5.4ks-tempering after 1153K×7.2ks-quenching were conducted for carbon steel shafts. The heat-treatments with change from mixed microstructure to uniform minute microstructures, are useful in increasing the diameter-enlargement rate $D^*_{\rm f}/D_0$. [ABSTRACT FROM AUTHOR]

Light stimulates carotenoid production in an oleaginous yeast Rhodosporidium toruloides NBRC 10032 by promoting carotenoid biosynthesis genes. These genes undergo two-step transcriptional activation. The potential light regulator, Cryptochrome DASH (CRY1), has been suggested to contribute to this mechanism. In this study, based on KU70 (a component of nonhomologous end joining (NHEJ)) disrupting background, CRY1 disruptant was constructed to clarify CRY1 function. From analysis of CRY1 disruptant, it was suggested that CRY1 has the activation role of the carotenogenic gene expression. To obtain further insights into the light response, mutants varying carotenoid production were generated. Through analysis of mutants, the existence of the control two-step gene activation was proposed. In addition, our data analysis showed the strong possibility that R. toruloides NBRC 10032 is a homo-diploid strain. [ABSTRACT FROM AUTHOR]

Herein, the stress-state dependence of fracture entropy for a polyamide 6 material is investigated through molecular dynamics simulations. Although previous research suggests that a constant entropy increase can be universally applied for the definition of material fracture, the dependence of stress triaxiality has not yet been discussed. In this study, entropy values are evaluated by molecular dynamics simulations with varied combined stress states. The calculation is implemented using the 570,000 all-atom model. Similar entropy values are obtained independently of stress triaxiality. This study also reveals the relationship between material damage, which is correlated with void size, and the entropy value. [ABSTRACT FROM AUTHOR]

Augmenting T-cell activity is a promising approach to enhance the efficacy of cancer immunotherapy treatment. Hematopoietic progenitor kinase 1 (HPK1) is predominantly expressed in immune cells and negatively regulates T-cell receptor signaling. It is reported that inhibition of the kinase function of HPK1 results in tumor growth suppression by enhancing cancer immunity. Thus, developing HPK1 inhibitors has attracted considerable attention as a future cancer immunotherapy approach. However, despite recent progress in HPK1 biology and pharmacology, various challenges still remain, such as developing HPK1 inhibitors with favorable pharmacological profiles and identifying tumor characteristics that can be applied to define susceptibility to HPK1 inhibition. Here, we present the identification and pharmacological evaluation of DS21150768, a potent small-molecule HPK1 inhibitor with a novel chemical scaffold. DS21150768 shows remarkable inhibition of HPK1 kinase activity, and in vitro studies demonstrated its potent activity to enhance T-cell function. DS21150768 is orally bioavailable and shows sustained plasma exposure, which leads to enhanced cytokine responses in vivo. We conducted a comparison of the anti-tumor efficacy of DS21150768 alone or in combination with anti-PD-1 antibody in 12 different mouse cancer cell models, and observed that the treatments suppressed tumor growth in multiple models. Furthermore, Gene Set Enrichment Analysis demonstrated significant enrichment of immune-related gene signatures in the tumor models responsive to DS21150768 treatment. Our results provide a path forward for the future development of HPK1 inhibitors and fundamental insights into biomarkers of HPK1-targeted therapy. • DS21150768 is a potent, selective, small-molecule HPK1 inhibitor. • DS21150768 has a novel chemical scaffold that confers oral absorption. • DS21150768 showed anti-tumor effects in multiple syngeneic tumor models. • DS21150768 exerted its effects as monotherapy and combined with anti-PD-1 antibody. • Immune-related gene signatures are enriched in DS21150768-sensitive tumor models. [ABSTRACT FROM AUTHOR]

The oleaginous yeast Rhodosporodium toruloides is receiving widespread attention as an alternative energy source for biofuels due to its unicellular nature, high growth rate and because it can be fermented on a large-scale. In this study, R. toruloides was cultured under both light and dark conditions in order to understand the light response involved in lipid and carotenoid biosynthesis. Our results from phenotype and gene expression analysis showed that R. toruloides responded to light by producing darker pigmentation with an associated increase in carotenoid production. Whilst there was no observable difference in lipid production, slight changes in the fatty acid composition were recorded. Furthermore, a two-step response was found in three genes (GGPSI, CAR1, and CAR2) under light conditions and the expression of the gene encoding the photoreceptor CRY1 was similarly affected. Light effect on carotenoid production in Rhodosporidium toruloides [ABSTRACT FROM AUTHOR]

Herein, we evaluate the mechanical properties of carbon fiber/polymer interfaces using three types of specimens: carbon fiber/vinyl ester resin, carbon fiber/epoxy resin, and carbon fiber/polyimide resin. Microbonding tests were performed and the fiber load at interfacial debonding was obtained. By performing finite element analysis, the true interfacial strengths were determined. The strength values followed the order: polyimide > epoxy > vinyl ester for the specimens tested. Molecular modeling was also performed for these specimens. Three stacked graphene layers were used to represent the carbon fiber surface and the interfacial energy was determined. The interfacial energy of the three systems followed the same order as the strength values. The molecular simulations allowed for a qualitative discussion of the material properties. In addition, an interfacial debonding simulation was performed, however the resin part failed instead of the interface, indicating that we evaluated the resin strength but not the interfacial strength. For the quantitative evaluation of interfacial debonding strength, further studies are necessary. [ABSTRACT FROM AUTHOR]

A cavity-resonator-integrated guided-mode resonance mirror (CRIGM) consists of a grating coupler integrated in a waveguide cavity formed by a pair of distributed Bragg reflectors (DBRs) on a high-reflectance substrate. It is theoretically predicted that a CRIGM can give interesting characteristics of not only a narrow band-stop reflection spectrum but also flat high reflectance with steep reflection-phase spectrum according to its structure, whereas only a CRIGM with a band-stop reflection spectrum has been confirmed experimentally so far. This time, the cause of undesirable reflectance drop in a CRIGM for flat high reflectance spectrum is investigated theoretically and experimentally. It is theoretically shown that the CRIGM reflectance at the resonance wavelength is affected considerably by a slight reduction of the DBR reflectance. A CRIGM with a rib-structured channel for high lateral confinement is designed and fabricated to keep the DBR reflectance high by suppressing a propagation loss of a guided wave. The improvement of the CRIGM reflection spectrum is confirmed experimentally by measurement of the reflection spectra of the fabricated devices. [ABSTRACT FROM AUTHOR]

The Co(III)TPPCl complex dimerizes and forms paramagnetic Co(III)TPPCl 2 and Co(II)TPP. • Theoretical study of the cobalt(III) cluster complex Co(III)TPPCl using DFT. • The complex dimerizes and forms, the so-called cation radicals, Co(III)TPPCl 2 and Co(II)TPP. • Existence of the paramagnetic species is consistent with experimental results. Chloro-α,β,γ,δ-tetraphenylporphyrinato-cobalt(III) (Co(III)TPPCl) is a five-coordinate Co complex ([Co(III)(N) 4 Cl]) having square-pyramidal structure with chlorine atom at the apex. The compound is diamagnetic. Its 1H NMR spectra in inert solvents show unusual signal broadening at higher temperatures. This was attributed to the partial transformation of the complex to paramagnetic species. To elucidate this specific phenomenon, we proposed a dimer reaction mechanism based on density functional theory calculations with M06-2X/segmented all-electron Gaussian (for Co atom) and 6-31G(d, p) (for C, H, N, Cl atoms) basis sets. The porphyrin dimer, [Co(III)TPPCl] 2 (S = 0), is assumed as the important reaction intermediate. The optimized geometry of the dimer is stable compared to two optimized monomers (S = 0) by 22.27 kcal mol−1, but is unstable compared to one Co(III)TPPCl 2 (S = 1/2) and one Co(II)TPP (S = 1/2) by 0.95 kcal mol−1. Using the vibrational frequencies from the geometry optimization, the sum of Co(III)TPPCl 2 and Co(II)TPP species, the so-called π cation radicals, is the overwhelming majority in the theoretical product distribution at 298.15 K and 1 atm. The dimer reaction can produce the paramagnetic species with a potential energy barrier of 1.65 kcal mol−1. [ABSTRACT FROM AUTHOR]

Fruit set involves the developmental transition of an unfertilized quiescent ovary in the pistil into a fruit. While fruit set is known to involve the activation of signals (including various plant hormones) in the ovary, many biological aspects of this process remain elusive. To further expand our understanding of this process, we identified genes that are specifically expressed in tomato (Solanum lycopersicum L.) pistils during fruit set through comprehensive RNA-seq-based transcriptome analysis using 17 different tissues including pistils at six different developmental stages. First, we identified 532 candidate genes that are preferentially expressed in the pistil based on their tissue-specific expression profiles. Next, we compared our RNA-seq data with publically available transcriptome data, further refining the candidate genes that are specifically expressed within the pistil. As a result, 108 pistil-specific genes were identified, including several transcription factor genes that function in reproductive development. We also identified genes encoding hormone-like peptides with a secretion signal and cysteine-rich residues that are conserved among some Solanaceae species, suggesting that peptide hormones may function as signaling molecules during fruit set initiation. This study provides important information about pistil-specific genes, which may play specific roles in regulating pistil development in relation to fruit set. [ABSTRACT FROM AUTHOR]

• Ischemic mitral regurgitation is a ventricular disease that affects the mitral valve. • 3D transesophageal echocardiography (TEE) is used for pre-surgical evaluation. • Medial preserving flows of diffeomorphisms prevent model self-intersection. • First left ventricle mitral valve segmentation and modeling from 3D TEE algorithm. • This allows for more comprehensive and fully automated pre-surgical assessment. [Display omitted] There is an urgent unmet need to develop a fully-automated image-based left ventricle mitral valve analysis tool to support surgical decision making for ischemic mitral regurgitation patients. This requires an automated tool for segmentation and modeling of the left ventricle and mitral valve from immediate pre-operative 3D transesophageal echocardiography. Previous works have presented methods for semi-automatically segmenting and modeling the mitral valve, but do not include the left ventricle and do not avoid self-intersection of the mitral valve leaflets during shape modeling. In this study, we develop and validate a fully automated algorithm for segmentation and shape modeling of the left ventricular mitral valve complex from pre-operative 3D transesophageal echocardiography. We performed a 3-fold nested cross validation study on two datasets from separate institutions to evaluate automated segmentations generated by nnU-net with the expert manual segmentation which yielded average overall Dice scores of 0.82 ± 0.03 (set A), 0.87 ± 0.08 (set B) respectively. A deformable medial template was subsequently fitted to the segmentation to generate shape models. Comparison of shape models to the manual and automatically generated segmentations resulted in an average Dice score of 0.93-0.94 and 0.75-0.81 for the left ventricle and mitral valve, respectively. This is a substantial step towards automatically analyzing the left ventricle mitral valve complex in the operating room. [ABSTRACT FROM AUTHOR]

In mammalian reproduction, embryo implantation into the uterus is spatiotemporally regulated by a complex process triggered by a number of factors. Although previous studies have suggested that uterine receptivity is mediated by blastocyst-derived factors, specific functions of embryos remain to be defined during preimplantation. Therefore, the present study was conducted to identify the maternal genes regulated by embryo-secreted factors in the rat uterus. RNA-sequencing (RNA-seq) data revealed that 10 genes are up-regulated in the delayed implantation uterus compared with the pseudopregnancy uterus. The RNA-seq results were further verified by real-time quantitative polymerase chain reaction. Sulf1 expression is significantly ( P < 0.05) induced in the delayed implantation uterus, although Areg, Calca, Fxyd4 and Lamc3 show a definite but non-statistically significant increase in their expression levels. During early pregnancy, the levels of Areg, Calca, Fxyd4, Lamc3 and Sulf1 expression at 3.5 days post coitus (dpc) are significantly ( P < 0.05) higher than those at 1.5 dpc. Treatment with embryo-conditioned media revealed that Lamc3 and Sulf1 are up-regulated compared with the other genes studied. Thus, embryo-derived factors regulate maternal gene expression, with Lamc3 and Sulf1 possibly being suitable markers for a response study of embryo-secreted factors to improve our understanding of embryo-maternal communication. [ABSTRACT FROM AUTHOR]

Summary A confined aquifer system, isolated from modern seawater, is developed in argillaceous marine and freshwater sediments of Pliocene–Holocene age in southwestern Nobi Plain (SWNP), central Japan. A tongue of brackish confined groundwater (Cl − >1000 mg/L), which extends from the shoreline of Ise Bay inland, mostly has negative δ 37 Cl values with −0.90‰ to 0.21‰. The Cl isotopic compositions are negatively correlated with paleo seawater Cl − concentrations discriminated by a Rayleigh distillation model with δ 34 S values, while they are not correlated with either total Cl − concentrations or δ 34 S values. Furthermore, Cl − concentrations from modern seawater are positively correlated with δ 37 Cl values. In addition to these observations, diffusion model calculations suggest that paleo seawater Cl − has diffused out from argillaceous marine sediments whereas modern seawater Cl − has not been affected by preferential diffusion of Cl isotopes because it has migrated by advection via both an unconfined aquifer and non-pumping wells. Moreover, the brackish groundwater is characterized by an excess of Na/Cl ratio and deficits of Mg/Cl and Ca/Cl ratios compared to those predicted from simple mixing of freshwater with seawater. This would be caused by cation exchange reactions in the confined aquifer system in which groundwater is freshening after salinization by both paleo seawater and/or modern seawater. [ABSTRACT FROM AUTHOR]

Abstract: BglR (PI: 52368, beta-glucosidase regulator) was identified as a new transcription factor that up-regulates expression of specific genes encoding β-glucosidases. Based on a comparative genomic analysis to verify SNPs between Trichoderma reesei mutant PC-3-7 and its parent KDG-12, 19 were confirmed. One of the SNPs was found to cause a missense mutation close to the end of the DNA-binding region of BglR that turned out to be a Zn(II)2Cys6-type fungal-specific transcription factor. BglR was found to share little homologous to amyR of Aspergillus oryzae that is commonly considered a key regulator of starch degradation. A mutant lacking the bglr gene as well as the PC-3-7 mutant exhibited elevated cellulase production during growth on cellobiose. Reversion of the SNP missence mutation within bglr to the wild-type allele resulted in reduced cellulase production. Expression of specific β-glucosidase genes in a bglr gene disruptant was repressed with the mutant exhibiting little ability to hydrolyze cellobiose during early log phase even when induced. Thus, one of the functions of BglR is to up-regulate specific β-glucosidase genes (with the exception of bgl1, which is seemingly under the direct control of Xyr1). The glucose produced then triggers carbon catabolite repression in cellobiose culture. [Copyright &y& Elsevier]

Abstract: The transcriptional activator XYR1 is the central regulator that governs cellulolytic and xylanolytic gene expression in Trichoderma reesei. However, despite its biological importance, relatively little is known about its functional binding sequences. In the present study, we investigated the binding characteristics and specific target for XYR1 by using DNase I footprinting analysis and electrophoretic mobility shift assays. We demonstrate that XYR1 can interact not only with the 5′-GGCTAA-3′ motif but also with several 5′-GGC(A/T)3-3′ motifs. In silico analysis revealed that the 5′-GGC(A/T)3-3′ motifs are widespread as single site in 5′-upstream region of all the XYR1-regulated genes. Furthermore, we defined the important nucleotides within the binding site that contribute to specific interaction with XYR1. Our results suggest that, together with the inverted repeat motifs, the single 5′-GGC(A/T)4-3′ motifs play important roles as functional XYR1-binding sites in the regulation of cellulase and xylanase gene expression in T. reesei. [Copyright &y& Elsevier]