Scolicia shirahamensis isp. nov.: a triple-corded scolicia and its ichnological implications

Abstract

Peculiar meniscate burrows with three sediment cords occur in early to middle Miocene tidal-flat deposits of southwestern Japan. Two of the cords are situated at the bottom and the other is at its center. Detailed observations of the burrow structures and comparative neoichnological studies of modern spatangoid burrows in a tidal flat revealed that the former two were true drainage tubes and the latter was fecal in origin. The trace fossil was thus assigned to the ichnogenus Scolicia. Based on these findings, a new ichnospecies Scolicia shirahamensis isp. nov. has been described here. The central sediment cord is seemingly identical to the drainage tube of the ichnogenus Bichordites, another ichnogenus that has been commonly ascribed to a fossil spatangoid burrow, similar to Scolicia. Careless ichnogeneric identification of a spatangoid burrow, based only on the central sediment cord, therefore, may produce an incorrect identification.     

DNA repair after DNA fragmentation in mouse small intestinal epithelial cells

In our earlier work, we found that, in mice, i.p. injection of anti-CD3 monoclonal antibody activated intraepithelial lymphocytes (iIEL), leading to DNA fragmentation in villous epithelial cells of the duodenum and jejunum within 30 min. By 2 h after injection, nearly half of the enterocytes had detached from the villi, and DNA fragmentation could barely be detected in the remaining villous epithelium. We hypothesized that DNA had been repaired in enterocytes in which DNA fragmentation had previously been induced. In this study, enterocytes became negative for TUNEL staining at 60 min after anti-CD3 treatment, prior to detachment. The remaining villous epithelial cells, after DNA fragmentation and detachment, were found to be positive for 5-bromo-2-deoxyuridine labeling. To confirm whether fragmented DNA had been repaired in situ, we investigated the appearance and/or mobilization of DNA-repair-related proteins. Focus formation, a typical staining pattern of repair-related proteins including phosphorylated H2AX, phospo-ATM substrate, and Nbs1, was observed 30 min after anti-CD3 injection, with the kinetics virtually identical to that of DNA fragmentation. The co-localization of γ-H2AX and phospo-ATM substrate was also confirmed. The disappearance of a positive reaction for TUNEL staining in previously fragmented DNA, the appearance of representative DNA-repair-related proteins, the coincidence of the kinetics of DNA fragmentation and this appearance of DNA-repair-related proteins, and the co-localization of two of the repair-related proteins strongly indicated that enterocyte DNA could be repaired after it had been fragmented in vivo. Thus, DNA fragmentation per se may not necessarily be an immediate sign of cell death. This work was supported in part by a Grant-in-aid for Scientific Research from the Ministry of Education, Science and Culture, Japan (16590132 to T.M., 16390045 to T.I., and 20590181 to M.O.).     

Labeling of free carboxyl groups

The latest trends in the labeling of free carboxyl groups for high-performance liquid chromatography are reviewed. The labeling reagents for fluorescence detection are mainly discussed according to their reaction type (or functional group). Attention is also paid to the reagents used for ultraviolet detection and for enantiomeric separation. The reactivity and sensitivity of the reagents used for the labeling of carboxylic acids are described.     

Reverse Genetics for Fusogenic Bat-Borne Orthoreovirus Associated with Acute Respiratory Tract Infections in Humans: Role of Outer Capsid Protein σC in Viral Replication and Pathogenesis

Nelson Bay orthoreoviruses (NBVs) are members of the fusogenic orthoreoviruses and possess 10-segmented double-stranded RNA genomes. NBV was first isolated from a fruit bat in Australia more than 40 years ago, but it was not associated with any disease. However, several NBV strains have been recently identified as causative agents for respiratory tract infections in humans. Isolation of these pathogenic bat reoviruses from patients suggests that NBVs have evolved to propagate in humans in the form of zoonosis. To date, no strategy has been developed to rescue infectious viruses from cloned cDNA for any member of the fusogenic orthoreoviruses. In this study, we report the development of a plasmid-based reverse genetics system free of helper viruses and independent of any selection for NBV isolated from humans with acute respiratory infection. cDNAs corresponding to each of the 10 full-length RNA gene segments of NBV were cotransfected into culture cells expressing T7 RNA polymerase, and viable NBV was isolated using a plaque assay. The growth kinetics and cell-to-cell fusion activity of recombinant strains, rescued using the reverse genetics system, were indistinguishable from those of native strains. We used the reverse genetics system to generate viruses deficient in the cell attachment protein σC to define the biological function of this protein in the viral life cycle. Our results with σC-deficient viruses demonstrated that σC is dispensable for cell attachment in several cell lines, including murine fibroblast L929 cells but not in human lung epithelial A549 cells, and plays a critical role in viral pathogenesis. We also used the system to rescue a virus that expresses a yellow fluorescent protein. The reverse genetics system developed in this study can be applied to study the propagation and pathogenesis of pathogenic NBVs and in the generation of recombinant NBVs for future vaccines and therapeutics.     

A lesson from polybutylene succinate plastisphere to the discovery of novel plastic degrading enzyme genes in marine vibrios

Polybutylene succinate (PBS) is an eco-friendly green plastic. However, PBS was shown as being non-biodegradable in marine environments, and up until now, only a limited number of PBS-degrading marine microbes have been discovered. We first set up in vitro PBS- and PBSA (polybutylene succinate adipate)-plastispheres to characterize novel PBS-degrading marine microbes. Microbial growth and oxygen consumption were observed in both PBS- and PBSA-plastispheres enriched with natural seawater collected from Usujiri, Hokkaido, Japan, and Vibrionaceae and Pseudoalteromonadaceae were significantly enriched on these films. Further gene identification indicated that vibrios belonging to the Gazogenes clade possess genes related to a PBS degrading enzyme (PBSase). The PBS degradation assay for six Gazogenes clade vibrios identified Vibrio ruber, Vibrio rhizosphaerae, and Vibrio spartinae as being capable of degrading PBS. We further identified the gene responsible for PBSase from the type strain of V. ruber, and the purified recombinant vibrio PBSase was found to have low-temperature adaptation and was active under high NaCl concentrations. We also provided docking models between the vibrio PBSase and PBS and PBSA units to show how vibrio PBSase interacts with each substrate compared to the Acidovorax PBSase. These results could contribute to a more sustainable society through further utilization of PBS in marine environments and plastic recycling.     

Wet hibernacula promote inoculative freezing and limit the potential for cryoprotective dehydration in the Antarctic midge,Belgica antarctica

The terrestrial midge, Belgica antarctica, occupies a diverse range of microhabitats along the Antarctic Peninsula. Although overwintering larvae have the physiological potential to survive by freezing or cryoprotective dehydration, use of the latter strategy may be constrained by inoculative freezing within hibernacula. To investigate the influence of microhabitat type on larval overwintering, we selected four substrate types that differed markedly in their composition and hydric characteristics. Organic content of these substrates ranged from 14 to 89 %. High organic content was associated with higher values for saturation moisture content (up to 2.0 H₂O g^?1 dry mass) as well as elevated levels of field moisture content. Seasonal values of field moisture content remained near or above the saturation moisture value for each microhabitat type, and when larvae were cooled in substrates rehydrated to field-based levels, they were unable to avoid inoculation by environmental ice, regardless of substrate type. Consequently, our data suggest that wet hibernacula would force most larvae to overwinter in a frozen state. Yet, dehydrated larvae were collected in April during the seasonal transition to winter suggesting that spatial and temporal variations in precipitation and microhabitat conditions may expose larvae to dehydration and promote larval overwintering in a cryoprotectively dehydrated state.     

Transmembrane phospholipid translocation mediated by Atg9 is involved in autophagosome formation

The mechanism of isolation membrane formation in autophagy is receiving intensive study. We recently found that Atg9 translocates phospholipids across liposomal membranes and proposed that this functionality plays an essential role in the expansion of isolation membranes. The distribution of phosphatidylinositol 3-phosphate in both leaflets of yeast autophagosomal membranes supports this proposal, but if Atg9-mediated lipid transport is crucial, symmetrical distribution in autophagosomes should be found broadly for other phospholipids. To test this idea, we analyzed the distributions of phosphatidylcholine, phosphatidylserine, and phosphatidylinositol 4-phosphate by freeze-fracture electron microscopy. We found that all these phospholipids are distributed with comparable densities in the two leaflets of autophagosomes and autophagic bodies. Moreover, de novo–synthesized phosphatidylcholine is incorporated into autophagosomes preferentially and shows symmetrical distribution in autophagosomes within 30 min after synthesis, whereas this symmetrical distribution is compromised in yeast expressing an Atg9 mutant. These results indicate that transbilayer phospholipid movement that is mediated by Atg9 is involved in the biogenesis of autophagosomes.     

Hes1 regulates formations of the hypophyseal pars tuberalis and the hypothalamus

The hypophyseal pars tuberalis surrounds the median eminence and infundibular stalk of the hypothalamus as thin layers of cells. The pars tuberalis expresses MT1 melatonin receptor and participates in mediating the photoperiodic secretion of pituitary hormones. Both the rostral tip of Rathke’s pouch (pars tuberalis primordium) and the pars tuberalis expressed αGSU mRNA, and were immunoreactive for LH, chromogranin A, and TSHβ in mice. Hes genes control progenitor cell differentiation in many embryonic tissues and play a crucial role for neurulation in the central nervous system. We investigated the Hes1 function in outgrowth and differentiation of the pars tuberalis by using the markers for the pars tuberalis. In homozygous Hes1 null mutant embryos, the rostral tip was formed in the basal-ventral part of Rathke’s pouch at embryonic day (E)11.5 as well as in wild-type embryos. In contrast to the wild-type, the rostral tip of null mutants could not extend rostrally with age; it remained in the low extremity of Rathke’s pouch during E12.5–E13.5 and disappeared at E14.5, resulting in lack of the pars tuberalis. Development of the ventral diencephalon was impaired in the null mutants at early stages. Rathke’s pouch, therefore, could not link with the nervous tissue and failed to receive inductive signals from the diencephalon. In a very few mutant mice in which the ventral diencephalon was partially sustained, some pars tuberalis cells were distributed around the hypoplastic infundibulum. Thus, Hes1 is required for development of the pars tuberalis and its growth is dependent on the ventral diencephalon.