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BlastKOALA and GhostKOALA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct KEGG pathways, BRITE hierarchies and KEGG modules to infer high-level functions of the organism or the ecosystem. Both servers are made freely available at the KEGG Web site ( http://www.kegg.jp/blastkoala/ ). In BlastKOALA, the KO assignment is performed by a modified version of the internally used KOALA algorithm after the BLAST search against a non-redundant dataset of pangenome sequences at the species, genus or family level, which is generated from the KEGG GENES database by retaining the KO content of each taxonomic category. In GhostKOALA, which utilizes more rapid GHOSTX for database search and is suitable for metagenome annotation, the pangenome dataset is supplemented with Cd-hit clusters including those for viral genes. The result files may be downloaded and manipulated for further KEGG Mapper analysis, such as comparative pathway analysis using multiple BlastKOALA results. [ABSTRACT FROM AUTHOR]

Abstract: Shell of the adult hermit crab has some important roles for its fitness. In the same time, the shell size often limits the body growth of its owner. To grow the body size larger, the individual must change the shell to another larger shell. If the individual cannot get another larger one, the individual has to suppress the body size growth as the occupied shell size allows. Growth suppression would result in the lower fitness. With a simple mathematical model, we consider the criterion about whether the individual should try to change the shell or not in order to get the higher fitness. We show that the optimality of a shell change behavior has a relation with the body size and the season length for the shell change. They also affect the optimal timing for the shell change. It is implied that the probability of the success in a shell change and the cost for the shell change behavior do not affect the optimal timing for the shell change at all but significantly do the optimality of the behavioral choice. [Copyright &y& Elsevier]

Multispanning membrane proteins are synthesized by membrane-bound ribosomes and integrated into the endoplasmic reticulum membrane cotranslationally. To uncover the topogenic process of membrane loop, of which both ends are in the same side of the membrane, we examined topogenesis of a relatively hydrophobic lumenal loop segment (H10 segment) between TM9 and TM10 of human Na+/H+ exchanger isoform 1 using an in vitro expression system. The H10 segment was translocated through the membrane. Any potential sites created within the H10 segment were not glycosylated. Just after TM9, there are potential glycosylation and signal peptidase processing sites. When the reporter domain of prolactin was fused at the position preceding the H10 segment, these sites were modified by the enzymes, while they were not modified in the original molecule. Thus, we concluded that the H10 segment was translocated through the membrane and directly inserted into the membrane and that its membrane insertion caused sequestration of the preceding processing and glycosylation sites from the lumenal modifying enzymes. This topogenic process shows clear contrast to that of pore loops of K+ channels, which are once exposed in the lumen and accessible to glycosylation enzyme. [Copyright &y& Elsevier]

Abstract: We examined the feasibility of voltage-sensitive dye imaging for detecting the neuronal activity in the neonatal rat corticostriatal projection and analyzed postnatal development of synaptic function in this projection. Coronal slice preparations were dissected from postnatal 3 to 14day (P3–14) rats and were then stained with the voltage-sensitive absorption dye, NK2761. The transmembrane voltage-related optical changes evoked by cortical stimulation using a bipolar electrode could be recorded simultaneously from many loci in the preparation, using a 464ch hexagonal diode array system. In the striatum, the optical signal was composed of a fast spike-like signal and a slow signal. The slow signal was blocked by dl-2-amino-5-phosphonovaleric acid (APV) and 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) and enhanced by bicuculline, suggesting that (1) the slow signal includes glutamatergic excitatory postsynaptic potentials (EPSPs) and that (2) inhibitory γ-aminobutyric acid A (GABAA) receptor function is expressed in the corticostriatal pathway from the early postnatal stage. We compared the excitatory and inhibitory synaptic responses between the first and second postnatal week preparations, and we showed that (1) in the first postnatal week, excitatory transmission in the corticostriatal pathway is mostly mediated by glutamate, (2) in addition to glutamatergic transmission, other excitatory transmission mechanisms emerge in this pathway until the second postnatal week, and (3) the inhibitory transmission mediated by GABA rapidly develops during the postnatal 2weeks. [ABSTRACT FROM AUTHOR]

Natto, a traditional Japanese fermented soybean food, is well known to be nutritious and beneficial for health. In this study, we examined whether natto impairs infection by viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as well as bovine herpesvirus 1 (BHV-1). Interestingly, our results show that both SARS-CoV-2 and BHV-1 treated with a natto extract were fully inhibited infection to the cells. We also found that the glycoprotein D of BHV-1 was shown to be degraded by Western blot analysis and that a recombinant SARS-CoV-2 receptor-binding domain (RBD) was proteolytically degraded when incubated with the natto extract. In addition, RBD protein carrying a point mutation (UK variant N501Y) was also degraded by the natto extract. When the natto extract was heated at 100 °C for 10 min, the ability of both SARS-CoV-2 and BHV-1 to infect to the cells was restored. Consistent with the results of the heat inactivation, a serine protease inhibitor inhibited anti-BHV-1 activity caused by the natto extract. Thus, our findings provide the first evidence that the natto extract contains a protease(s) that inhibits viral infection through the proteolysis of the viral proteins. • Natto extract, which is a traditional Japanese fermented soybean food, fully inhibited infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and bovine herpesvirus 1 (BHV-1) to the cells. • The UK variant of spike protein (receptor binding domain; RBD) of SARS-CoV-2 and Glycoprotein D of BHV-1 were proteolytically degraded by the natto extract. •A serine-protease(s) in the natto extract is worth to be further investigated as antiviral drug(s). [ABSTRACT FROM AUTHOR]

Highlights: [•] Effects of silk protein sericin (SPS) for serum-free freezing of bovine embryos were studied. [•] We assessed SPS effects on the survival of frozen-thawed embryos after in vitro culture and direct transfer to recipients. [•] Survival of SPS embryos and conventionally processed embryos were equal. [•] Embryos frozen with 0.5% SPS showed normal pregnancy and calving in recipients. [ABSTRACT FROM AUTHOR]

Abstract: The objectives of this study were to examine the effects of the presence or absence of serum during the in vitro culturing period of domestic cat embryos on their developmental potential into blastocysts as well as their tolerance to cryopreservation using a slow-freezing method. In vitro-fertilized cat oocytes were incubated in a modified synthetic oviduct fluid (mSOF) containing 4mg/mL bovine serum albumin (BSA) throughout culturing (BSA group) or in mSOF containing 4mg/mL BSA for the first 3days followed by mSOF containing 5% fetal bovine serum (FBS group). The developmental potential of the embryos to the blastocyst and expanded blastocyst stages was evaluated 7days after in vitro fertilization. The blastocysts were frozen-thawed by the slow-freezing method and cultured for 3days to examine their viability in vitro. There were no differences in the formation rates of blastocysts or expanded blastocysts, or number of cells in the embryos between the two groups. After cryopreservation, the hatching rates of the expanded blastocysts in the BSA group were significantly higher (P< 0.05) than those of the FBS group. The postthaw viability of blastocysts was lower than that of expanded blastocysts irrespective of culture medium. These results indicate that the developmental potential of cat embryos cultured in serum-free medium is comparable to those cultured in serum-containing medium. Furthermore, expanded blastocysts produced without serum exhibit better postthaw viability than those produced with serum. [Copyright &y& Elsevier]

Abstract: We applied the intrinsic optical imaging technique to the human primary somatosensory cortex during brain tumor/epilepsy surgery for nine patients. The cortical surface was illuminated with a Xenon light through an operating microscope, and the reflected light, which passed through a 605 nm bandpass filter, was detected by a CCD camera-based optical imaging system. Individual electrical stimulation of five digits induced changes in the reflected light intensities. Visualizing the intrinsic optical responses, we constructed maps of finger representation in Brodmann''s area 1. In the maps, response areas of Digits I to V were sequentially aligned along the central sulcus in the crown of the postcentral gyrus from the latero-inferior region (Digit I) to the medio-superior region (Digit V). The neighboring response areas partially overlapped each other, as previously described in the monkey somatosensory cortex. Similar results were obtained in the face region with stimulation of the three branches of the trigeminal nerve. These results suggest that the overlap of the response areas is a common feature in the somatosensory cortex not only in monkeys, but also in humans. [Copyright &y& Elsevier]

We examined the spatiotemporal patterns of spontaneous epileptiform activity observed in the in vivo rat cerebral cortex using an optical recording technique of detecting transmembrane voltage changes. The surface of the cerebral cortex was exposed under anesthesia and stained with a fluorescent voltage-sensitive dye, RH414. Acute spontaneous epileptiform discharges were induced by application of a GABAA receptor antagonist, bicuculline. Changes in the intensity of fluorescence were recorded from the cerebral cortex using a 464-channel optic fiber photodiode system. We succeeded in recording spontaneous epileptiform discharges, and constructed their initiation-site maps. We found that the initiation site was neither unique nor randomly located, but exhibited a multimodal distribution pattern. The incidence of epileptiform discharges was different between the initiation sites, and some sites showed dominance in the induction of spontaneous epileptiform discharges. [Copyright &y& Elsevier]

We examined neural response patterns evoked by peripheral nerve stimulation in in vivo rat spinal cords using an intrinsic optical imaging technique to monitor neural activity. Adult rats were anesthetized by urethane, and laminectomy was performed between C5 and Th1 to expose the dorsal surface of the cervical spinal cord. The median, ulnar, and radial nerves were dissected, and bipolar electrodes were implanted in the forelimb. Changes in optical reflectance were recorded from the dorsal cervical spinal cord in response to simultaneous stimulation of the median and ulnar nerves using a differential video acquisition system. In the region of the cervical spinal cord, intrinsic optical signals were detected between C5 and Th1 at wavelengths of 605, 630, 730, 750, and 850 nm: the image with the largest signal intensity and highest contrast was obtained at 605 nm. The signal intensity and response area expanded with an increase in the stimulation intensity and varied with the depth of the focal plane of the macroscope. The intrinsic optical response was mostly eliminated by Cd2+, suggesting that the detected signals were mainly mediated by postsynaptic mechanisms activated by sensory nerve fibers. Furthermore, we succeeded in imaging neural activity evoked by individual peripheral nerve stimulation. We found that the response areas related to each peripheral nerve exhibited different spatial distribution patterns and that there were animal-to-animal variations in the evoked neural responses in the spinal cord. The results obtained in this study confirmed that intrinsic optical imaging is a very useful technique for acquiring fine functional maps of the in vivo spinal cord. [Copyright &y& Elsevier]