Fish assemblages associated with three types of artificial reefs: density of assemblages and possible impacts on adjacent fish abundance

We evaluated the effectiveness of wooden artificial reefs (ARs) as fish habitat. Three types of ARs, made of cedar logs, broadleaf tree logs, and PVC pipes, respectively, were deployed in triplicate at 8-m depth off Maizuru, Kyoto Prefecture, Sea of Japan, in May 2004. Fish assemblages associated with each of the nine ARs were observed by using SCUBA twice a month for four years. Fish assemblages in the adjacent habitat were also monitored for two years before and four years after reef deployment. In the surveyed areas (ca. 10 m2) associated with each of the cedar, broadleaf, and PVC ARs, the average number of fish species was 4.14, 3.49, and 3.00, and the average number of individuals was 40.7, 27.9, and 20.3, respectively. The estimated biomass was also more greater when associated with the cedar ARs than with other ARs. Visual censuses of the habitat adjacent to the ARs revealed that the number of fish species and the density of individuals were not affected by the deployment of the ARs. Our results support the superiority of cedar as an AR material and indicate that deployment of wooden ARs causes no reduction of fish abundance in adjacent natural reefs

Long-term Performance of Repairs to Reinforced Concrete Exposed to Coastal Conditions

Reinforced concrete (RC) specimens were treated using different combinations of surface coating and/or patch repair methods and materials, left in a coastal region with frost damage risk, and their properties characterized after 25 years of exposure. Specimens were prepared by chipping away concrete from one section of concrete block with embedded reinforcement bars to expose the bars, followed by patch repair and then surface coating. Four types of material were used for patch repair: cement mortar, styrene-butadiene rubber (SBR) polymer cement mortar, rust-resistant SBR polymer cement mortar, and lightweight epoxy mortar. Two types of material were used for surface coating: multi-layer textured and thin textured coating. Following exposure, cracks were visible only on the surfaces of untreated specimens, apparently due to rebar corrosion; they were absent from all specimens that had undergone surface coating and/or patch repair. In addition, the corrosion resistance of these methods and materials was investigated by measuring and comparing the surface areas of corroded rebar between three segments: the repaired part, the unrepaired part, and the boundary between them. Concrete carbonation and rebar corrosion were greatly dependent on surface coating material, with the multilayer-textured coating especially effective at blocking chloride penetration. In addition, rebar corrosion was more effectively prevented by patch repair with the SBR polymer cement mortar than with the lightweight epoxy mortar

HybGFS: a hybrid method for genome-fingerprint scanning

BACKGROUND: Protein identification based on mass spectrometry (MS) has previously been performed using peptide mass fingerprinting (PMF) or tandem MS (MS/MS) database searching. However, these methods cannot identify proteins that are not already listed in existing databases. Moreover, the alternative approach of de novo sequencing requires costly equipment and the interpretation of complex MS/MS spectra. Thus, there is a need for novel high-throughput protein-identification methods that are independent of existing predefined protein databases. RESULTS: Here, we present a hybrid method for genome-fingerprint scanning, known as HybGFS. This technique combines genome sequence-based peptide MS/MS ion searching with liquid-chromatography elution-time (LC-ET) prediction, to improve the reliability of identification. The hybrid method allows the simultaneous identification and mapping of proteins without a priori information about their coding sequences. The current study used standard LC-MS/MS data to query an in silico-generated six-reading-frame translation and the enzymatic digest of an entire genome. Used in conjunction with precursor/product ion-mass searching, the LC-ETs increased confidence in the peptide-identification process and reduced the number of false-positive matches. The power of this method was demonstrated using recombinant proteins from the Escherichia coli K12 strain. CONCLUSION: The novel hybrid method described in this study will be useful for the large-scale experimental confirmation of genome coding sequences, without the need for transcriptome-level expression analysis or costly MS database searching

Bronchiolitis Obliterans Organizing Pneumonia: Case Report and Review of Literature

A 69-year-old female complaining of fever, cough and dyspnea was admitted to our hospital. Chest X-ray examination showed bilateral infiltration shadows that increased in spite of antibiotics therapy. Broncho-alveolar lavage fluid analysis demonstrated an increased lymphocytes with an inverted CD4/CD8 ratio. Histopathology of lung biopsy specimens showed organizing granulation tissue in the lumens of bronchioles, alveolar ducts, and alveoli, along with mononuclear cell infiltration in the interstitium. A diagnosis of bronchiolitis obliterans organizing pneumonia (BOOP) was thus made. The patient completely recovered by cortico steroid therapy, and is now without any indication of disease

Tomato root-associated Sphingobium harbors genes for catabolizing toxic steroidal glycoalkaloids

トマト根に定着する細菌からトマトの毒を分解する酵素を発見 --土壌微生物が植物の分泌する有害成分を解毒するメカニズムの理解に貢献--. 京都大学プレスリリース. 2023-10-02.Roots of Bloody Mary. Tomato root-associated Sphingobium harbors genes for neutralizing toxic compound. 京都大学プレスリリース. 2023-10-06.Plant roots exude various organic compounds, including plant specialized metabolites (PSMs), into the rhizosphere. The secreted PSMs enrich specific microbial taxa to shape the rhizosphere microbiome, which is crucial for the healthy growth of the host plants. PSMs often exhibit biological activities; in turn, some microorganisms possess the capability to either resist or detoxify them. Saponins are structurally diverse triterpene-type PSMs that are mainly produced by angiosperms. They are generally considered as plant defense compounds. We have revealed that α-tomatine, a steroid-type saponin secreted from tomato (Solanum lycopersicum) roots, increases the abundance of Sphingobium bacteria. To elucidate the mechanisms underlying the α-tomatine-mediated enrichment of Sphingobium, we isolated Sphingobium spp. from tomato roots and characterized their saponin-catabolizing abilities. We obtained the whole-genome sequence of Sphingobium sp. RC1, which degrades steroid-type saponins but not oleanane-type ones, and performed a gene cluster analysis together with a transcriptome analysis of α-tomatine degradation. The in vitro characterization of candidate genes identified six enzymes that hydrolyzed the different sugar moieties of steroid-type saponins at different positions. In addition, the enzymes involved in the early steps of the degradation of sapogenins (i.e., aglycones of saponins) were identified, suggesting that orthologs of the known bacterial steroid catabolic enzymes can metabolize sapogenins. Furthermore, a comparative genomic analysis revealed that the saponin-degrading enzymes were present exclusively in certain strains of Sphingobium spp., most of which were isolated from tomato roots or α-tomatine-treated soil. Taken together, these results suggest a catabolic pathway for highly bioactive steroid-type saponins in the rhizosphere

Leukocytapheresis Therapy Improved Cholestasis in a Patient Suffering from Primary Sclerosing Cholangitis with Ulcerative Colitis

Primary sclerosing cholangitis (PSC) is an autoimmune disease of the hepatobiliary system for which effective therapy has not been established. Leukocytapheresis (LCAP) therapy is known to effective in patients with ulcerative colitis (UC). In addition, effects of LCAP therapy were reported on some autoimmune diseases such as Crohn's disease, rheumatoid arthritis and rapidly progressive glomerulonephritis. Here we report the case of a 29-year-old man with PSC associated with UC who was treated with LCAP therapy. He had a 16-year history of UC and a 12-year history of PSC. Although he was under treatment with prednisolone and ursodeoxycholic acid, exacerbation of UC and PSC-associated cholestasis were seen. Since he showed side effects of prednisolone, he was treated with LCAP. Not only improvement of UC, but also decreased serum alkaline phosphatase, γ-guanosine triphosphate and total bile acids, suggesting improvement of PSC-associated cholestaisis, were seen after treatment with LCAP. Our experience with this case suggests that LCAP therapy could be a new effective therapeutic strategy for patients with PSC associated with UC

Nematode-specific tRNAs that decode an alternative genetic code for leucine

Class II transfer RNAs (tRNAs), including tRNALeu and tRNASer, have an additional stem and loop structure, the long variable arm (V-arm). Here, we describe Class II tRNAs with a unique anticodon corresponding to neither leucine nor serine. Because these tRNAs are specifically conserved among the nematodes, we have called them ‘nematode-specific V-arm-containing tRNAs’ (nev-tRNAs). The expression of nev-tRNA genes in Caenorhabditis elegans was confirmed experimentally. A comparative sequence analysis suggested that the nev-tRNAs derived phylogenetically from tRNALeu. In vitro aminoacylation assays showed that nev-tRNAGly and nev-tRNAIle are only charged with leucine, which is inconsistent with their anticodons. Furthermore, the deletion and mutation of crucial determinants for leucylation in nev-tRNA led to a marked loss of activity. An in vitro translation analysis showed that nev-tRNAGly decodes GGG as leucine instead of the universal glycine code, indicating that nev-tRNAs can be incorporated into ribosomes and participate in protein biosynthesis. Our findings provide the first example of unexpected tRNAs that do not consistently obey the general translation rules for higher eukaryotes