Characterization of an Alginate Lyase,FlAlyA, from Flavobacterium sp. Strain UMI-01 and Its Expression in Escherichia coli

A major alginate lyase, FlAlyA, was purified from the periplasmic fraction of an alginate-assimilating bacterium, Flavobacterium sp. strain UMI-01. FlAlyA showed a single band of ~30 kDa on SDS-PAGE and exhibited the optimal temperature and pH at 55 °C and pH 7.7, respectively. Analyses for substrate preference and reaction products indicated that FlAlyA was an endolytic poly(mannuronate) lyase (EC 4.2.2.3). A gene fragment encoding the amino-acid sequence of 288 residues for FlAlyA was amplified by inverse PCR. The N-terminal region of 21 residues except for the initiation Met in the deduced sequence was predicted as the signal peptide and the following region of six residues was regarded as propeptide, while the C-terminal region of 260 residues was regarded as the polysaccharide-lyase-family-7-type catalytic domain. The entire coding region for FlAlyA was subjected to the pCold I—Escherichia coli BL21(DE3) expression system and ~eight times higher yield of recombinant FlAlyA (recFlAlyA) than that of native FlAlyA was achieved. The recFlAlyA recovered in the periplasmic fraction of E. coli had lost the signal peptide region along with the N-terminal 3 residues of propeptide region. This suggested that the signal peptide of FlAlyA could function in part in E. coli.     

DUBA: a deubiquitinase that regulates type I interferon production

Production of type I interferon (IFN-I) is a critical host defense triggered by pattern-recognition receptors (PRRs) of the innate immune system. Deubiquitinating enzyme A (DUBA), an ovarian tumor domain-containing deubiquitinating enzyme, was discovered in a small interfering RNA-based screen as a regulator of IFN-I production. Reduction of DUBA augmented the PRR-induced IFN-I response, whereas ectopic expression of DUBA had the converse effect. DUBA bound tumor necrosis factor receptor-associated factor 3 (TRAF3), an adaptor protein essential for the IFN-I response. TRAF3 is an E3 ubiquitin ligase that preferentially assembled lysine-63-linked polyubiquitin chains. DUBA selectively cleaved the lysine-63-linked polyubiquitin chains on TRAF3, resulting in its dissociation from the downstream signaling complex containing TANK-binding kinase 1. A discrete ubiquitin interaction motif within DUBA was required for efficient deubiquitination of TRAF3 and optimal suppression of IFN-I. Our data identify DUBA as a negative regulator of innate immune responses.     

Characterization of bullet tuna myoglobin with reference to the thermostability-structure relationship

Myoglobin (Mb) was isolated from bullet tuna (Auxis rochei) skeletal muscle and characterized from the viewpoint of the thermostability-structure relationship. Differential scanning calorimetry (DSC) measurement showed that the thermostability of bullet tuna Mb was the lowest among all the scombridae fish Mbs so far examined. The highest value (72.8 degrees C) of melting temperature (Tm) was obtained at pH 6.52. alpha-Helical content at 10 degrees C was 34.5%, clearly lower than that of horse Mb (55.3%). The amino acid sequence was then deduced by cloning cDNA which encodes bullet tuna Mb. Bullet tuna Mb consisted of 147 amino acids, and the sequence identity was very close to that of skipjack (Katsuwonus pelamis) Mb (91.8%). A few amino acid substitutions, which could be involved in stability difference of Mb, were recognized. By mass spectrometry of lysyl endoproteinase digest of Mb, the N-terminus was found to be acetylated like that of other fish Mbs.     

Assessment of C budget for grasslands and drylands of the world

Intergovernmental Panel on Climate Change (IPCC) estimates indicate that potential changes in seasonal rainfall and temperature patterns in central North America and the African Sahel will have a greater impact on biological response (such as plant production and biogeochemical cycling) and feedback to climate than changes in the overall amount of annual rainfall. Simulation of grassland and dryland ecosystem responses to climate and CO₂ changes demonstrates the sensitivity of plant productivity and soil C storage to projected changes in precipitation, temperature and atmospheric CO₂. Using three different land cover projections, changes in C levels in the grassland and dryland regions from 1800 to 1990 were estimated to be ?13.2, ?25.5 and ?14.7 Pg, i.e., a net source of C due to land cover removal resulting from cropland conversion. Projections into the future based on a double-CO₂ climate including climate-driven shifts in biome areas by the year 2040 resulted in a net sink of +5.6, +27.4 and +26.8 Pg, respectively, based upon sustainable grassland management. The increase in C storage resulted mainly from an increase in area for the warm grassland sub-biome, together with increased soil organic matter. Preliminary modeling estimates of soil C losses due to 50 yr of regressive land management in these grassland and dryland ecoregions result in a 11 Pg loss relative to current conditions, and a potential loss of 37 Pg during a 50 yr period relative to sustainable land-use practices, an average source of 0.7 Pg C yr^?1. Estimates of the cost of a 20 yr rehabilitation program are 5 to 8×10⁹ US$ yr^?1, for a C sequestering cost of approximately 10 US$ per tC.     

Production and characterization of monoclonal antibodies against formalin-inactivated Nipah virus isolated from the lungs of a pig

Eight clones of monoclonal antibodies (Mabs) to Nipah virus (NV) were produced against formalin-inactivated NV antigens. They reacted positive by indirect immunofluorescent antibody test, and one of them also demonstrated virus neutralizing activity. They were classified into six different types based on their biological properties. These Mabs will be useful for immunodiagnosis of NV infections in animals and further research studies involving the genomes and proteins of NV.     

Changes in allergenicity and digestibility of squid tropomyosin during the Maillard reaction with ribose

The effect of the Maillard reaction on the allergenicity of squid tropomyosin (TM) was investigated. When TM was reacted with ribose (TM-ribose), its human-specific IgE-binding ability decreased markedly and alpha-chymotryptic digestibility of TM was also altered at the early stage of the Maillard reaction. On the other hand, the modification of the lysine residues in TM using 2,4,6-trinitrobenzenesulfonic acid had no effect on the allergenicity and alpha-chymotryptic digestibility of TM. Therefore, the structural change in TM induced by the Maillard reaction would cause the reduction of the allergenicity, rather than the block of lysine residues. Although peptic digestion diminished the specific IgE-binding ability of TM, the reduction of the allergenicity by the Maillard reaction remained after peptic digestion. These results suggest that hypersensitive reaction of TM-ribose in the human body might be lower than that of native TM.     

Regulated virulence controls the ability of a pathogen to compete with the gut microbiota

The virulence mechanisms that allow pathogens to colonize the intestine remain unclear. Here, we show that germ-free animals are unable to eradicate Citrobacter rodentium, a model for human infections with attaching and effacing bacteria. Early in infection, virulence genes were expressed and required for pathogen growth in conventionally raised mice but not germ-free mice. Virulence gene expression was down-regulated during the late phase of infection, which led to relocation of the pathogen to the intestinal lumen where it was outcompeted by commensals. The ability of commensals to outcompete C. rodentium was determined, at least in part, by the capacity of the pathogen and commensals to grow on structurally similar carbohydrates. Thus, pathogen colonization is controlled by bacterial virulence and through competition with metabolically related commensals.     

Effects on flowering and seed yield of dominant alleles at maturity loci E2 and E3 in a Japanese cultivar,Enrei

‘Enrei’ is the second leading variety of soybean (Glycine max (L.) Merr.) in Japan. Its cultivation area is mainly restricted to the Hokuriku region. In order to expand the adaptability of ‘Enrei’, we developed two near-isogenic lines (NILs) of ‘Enrei’ for the dominant alleles controlling late flowering at the maturity loci, E2 and E3, by backcrossing with marker-assisted selection. The resultant NILs and the original variety were evaluated for flowering, maturity, seed productivity and other agronomic traits in five different locations. Expectedly, NILs with E2 or E3 alleles flowered later than the original variety in most locations. These NILs produced comparatively larger plants in all locations. Seed yields were improved by E2 and E3 in the southern location or in late-sowing conditions, whereas the NIL for E2 exhibited almost the same or lower productivity in the northern locations due to higher degrees of lodging. Seed quality-related traits, such as 100-seed weight and protein content, were not significantly different between the original variety and its NILs. These results suggest that the modification of genotypes at maturity loci provides new varieties that are adaptive to environments of different latitudes while retaining almost the same seed quality as that of the original.     

Alteration in the apoptosis process of rat esophageal epithelium with hyperproliferation of indigenous bacteria under a physiological condition

The apoptosis process in rat esophageal epithelium was investigated using enzyme-immunohistochemistry and transmission electron microscopy. As a result, Fas and Fas-L were expressed in the epithelial cell membrane and cytoplasm from the stratum spinosum (SS) to the stratum granulosum (SG). No TNF-R1 show immunopositivity in the cell membranes. TNF-α and caspase-8 were not observed in any layer. Caspase-10, cleaved caspase-3, XIAP and DNase-1 were found in the epithelial cytoplasm from the SS to the SG, whereas Bid, Apaf-1 and cleaved caspase-9 were detected only in the SG. Cytochrome c was observed as cytoplasmic granular positivity from the stratum basale (SB) and altered into homogeneous immunopositivity in the SG. Bcl-2 and Bcl-X immunopositivity was detected in cytoplasm from the SB to the SG. Immunoreactions of Bak in the cytoplasm and Bax beneath the cell membrane were observed from the upper portion of the SS with increasing intensity toward the SG. In the sites with the hyperproliferation of indigenous bacteria, TNF-R1, TNF-α and caspase-8 were detected in the SG and the immunopositive intensities of Bid, Apaf-1 and cleaved caspase-9 were altered to be strong. Prominently swollen cells and decreased mitochondria were ultrastructurally confirmed in the uppermost layers of stratum corneum. These findings suggest that the Fas-Fas-L-interaction initially induces apoptosis through a mitochondria-independent pathway and secondarily through a mitochondria-dependent pathway, leading to eventual epithelial cell death in the rat esophageal epithelium. The bacterial stimuli probably enhance the mitochondria-dependent pathway through the TNF-R1-TNF-α interaction.     

Pathological characteristics of thyroid glands from Japanese Black Cattle living in the restricted area of the Fukushima Daiichi Nuclear Power Plant accident

To study the effect of ionizing radiation on thyroid glands, 66 Japanese Black cattle residing in the restricted area of the Fukushima Daiichi Nuclear Power Plant in 2013–2017 were pathologically examined. There were no clinical symptoms of thyroid disease in these cattle. Three cases of goiter and seven of atrophy were found in two among the four farms examined. Cases of goiter exhibited normal morphological structure without mass or nodule formation in thyroid glands. Cellular atypia or capsular invasion of the follicular epithelium was absent. The estimated integrated dose of external radiation in goiter cases ranged from maximum 797 mSv to minimum 24 mSv. All lobules in the seven atrophic thyroid glands were affected, but pathological findings, such as inflammatory cell infiltration or stromal fibrosis, were not observed. The estimated integrated dose of external radiation in atrophic thyroids ranged from maximum 589 mSv to minimum 8 mSv. Immunohistochemical analysis of anti‐nitroguanosine and the TUNEL method in goiter and atrophic thyroid glands did not reveal any positive findings. The present study indicates that there was no significant relationship between a radiation effect and pathological findings in any thyroid glands.