Chromosome-scale assembly of barley cv. 'Haruna Nijo' as a resource for barley genetics

Cultivated barley (Hordeum vulgare ssp. vulgare) is used for food, animal feed, and alcoholic beverages and is widely grown in temperate regions. Both barley and its wild progenitor (H. vulgare ssp. spontaneum) have large 5.1-Gb genomes. High-quality chromosome-scale assemblies for several representative barley genotypes, both wild and domesticated, have been constructed recently to populate the nascent barley pan-genome infrastructure. Here, we release a chromosome-scale assembly of the Japanese elite malting barley cultivar 'Haruna Nijo' using a similar methodology as in the barley pan-genome project. The 4.28-Gb assembly had a scaffold N50 size of 18.9 Mb. The assembly showed high collinearity with the barley reference genome 'Morex' cultivar, with some inversions. The pseudomolecule assembly was characterized using transcript evidence of gene projection derived from the reference genome and de novo gene annotation achieved using published full-length cDNA sequences and RNA-Seq data for 'Haruna Nijo'. We found good concordance between our whole-genome assembly and the publicly available BAC clone sequence of 'Haruna Nijo'. Interesting phenotypes have since been identified in Haruna Nijo; its genome sequence assembly will facilitate the identification of the underlying genes.

Changes in immune system and intestinal bacteria of cows during the transition period

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Transitional high-energy diets reduce peripheral blood lymphocytes in dairy cows.

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High-energy diets upregulate IL-1β and IL-2 and downregulate IL-10 expression.

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Functional lactobacillus plantarum LP1 restores normal levels of lymphocytes subset.

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Lactobacillus plantarum LP1-added diets reduce inflammatory cytokine expression.

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LP1 mitigates immune response imbalances caused by transitional high energy diets.

High-yield dairy cows need high energy feed during periods of increased milk production. The transitional feeding to high energy feed increases the risk of developing a variety of metabolic disorders. Here, five Holstein cows were fed a four-stage feeding protocol (3 weeks for each stage) ranging from 54.9 to 73.7% total digestive nutrients (TDN). The purpose of the study was to investigate the effect of lactic acid bacteria on high-energy-fed cows associated with transitional feeding, and to evaluate the effects of probiotics on intestinal bacterial changes and inflammatory responses. Three feed transition periods were established for five cows, and Lactobacillus plantarum RGU-LP1 (LP1) was fed as a probiotic during the high-energy feeding period. The number of lymphocyte subsets such as CD3-, CD4-, and CD8 positive cells decreased in response to the high energy feed. Lipopolysaccharide (LPS)-induced cytokine (IL-1β and IL-2) gene expression in peripheral blood mononuclear cells (PBMCs) was shown to increase in those animals receiving the high energy feed. However, supplementation with LP1 resulted in an increase in the number of lymphocyte subsets and the expression of IL-1β and IL-2 were returned to the level at low energy diet. These results suggest that high energy diets induce inflammatory cytokine responses following LPS stimulation, and that the addition of LP1 mitigates these results by regulating the LPS-induced inflammatory reaction. Therefore, the functional lactic acid bacteria LP1 is expected to regulate inflammation resulting from high energy feeding, and this probiotic could be applied to support inflammatory regulation in high-yield dairy cows.

MoG+: a database of genomic variations across three mouse subspecies for biomedical research

Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M. m. domesticus-derived PGN2/Ms and BFM/Ms; M. m. castaneus-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between M. m. musculus and M. m. castaneus. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.

Mouse resources at the RIKEN BioResource Research Center and the National BioResource Project core facility in Japan

The RIKEN BioResource Research Center (BRC) was established in 2001 as a comprehensive biological resource center in Japan. The Experimental Animal Division, one of the BRC infrastructure divisions, has been designated as the core facility for mouse resources within the National BioResource Project (NBRP) by the Japanese government since FY2002. Our activities regarding the collection, preservation, quality control, and distribution of mouse resources have been supported by the research community, including evaluations and guidance on advancing social and research needs, as well as the operations and future direction of the BRC. Expenditure for collection, preservation, and quality-control operations of the BRC, as a national core facility, has been funded by the government, while distribution has been separately funded by users' reimbursement fees. We have collected over 9000 strains created mainly by Japanese scientists including Nobel laureates and researchers in cutting-edge fields and distributed mice to 7000 scientists with 1500 organizations in Japan and globally. Our users have published 1000 outstanding papers and a few dozen patents. The collected mouse resources are accessible via the RIKEN BRC website, with a revised version of the searchable online catalog. In addition, to enhance the visibility of useful strains, we have launched web corners designated as the "Mouse of the Month" and "Today's Tool and Model." Only high-demand strains are maintained in live colonies, while other strains are cryopreserved as embryos or sperm to achieve cost-effective management. Since 2007, the RIKEN BRC has built up a back-up facility in the RIKEN Harima branch to protect the deposited strains from disasters. Our mice have been distributed with high quality through the application of strict microbial and genetic quality control programs that cover a globally accepted pathogens list and mutated alleles generated by various methods. Added value features, such as information about users' publications, standardized phenotyping data, and genome sequences of the collected strains, are important to facilitate the use of our resources. We have added and disseminated such information in collaboration with the NBRP Information Center and the NBRP Genome Information Upgrading Program. The RIKEN BRC has participated in international mouse resource networks such as the International Mouse Strain Resource, International Mouse Phenotyping Consortium, and Asian Mouse Mutagenesis and Resource Association to facilitate the worldwide use of high-quality mouse resources, and as a consequence it contributes to reproducible life science studies and innovation around the globe.

Collection, preservation and distribution of Oryza genetic resources by the National Bioresource Project RICE (NBRP-RICE)

Biological resources are the basic infrastructure of bioscience research. Rice (Oryza sativa L.) is a good experimental model for research in cereal crops and monocots and includes important genetic materials used in breeding. The availability of genetic materials, including mutants, is important for rice research. In addition, Oryza species are attractive to researchers for both finding useful genes for breeding and for understanding the mechanism of genome evolution that enables wild plants to adapt to their own habitats. NBRP-RICE contributes to rice research by promoting the usage of genetic materials, especially wild Oryza accessions and mutant lines. Our activity includes collection, preservation and distribution of those materials and the provision of basic information on them, such as morphological and physiological traits and genomic information. In this review paper, we introduce the activities of NBRP-RICE and our database, Oryzabase, which facilitates the access to NBRP-RICE resources and their genomic sequences as well as the current situation of wild Oryza genome sequencing efforts by NBRP-RICE and other institutes.

OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species

BACKGROUND

OryzaGenome ( http://viewer.shigen.info/oryzagenome21detail/index.xhtml ), a feature within Oryzabase ( https://shigen.nig.ac.jp/rice/oryzabase/ ), is a genomic database for wild Oryza species that provides comparative and evolutionary genomics approaches for the rice research community.

RESULTS

Here we release OryzaGenome2.1, the first major update of OryzaGenome. The main feature in this version is the inclusion of newly sequenced genotypes and their meta-information, giving a total of 217 accessions of 19 wild Oryza species (O. rufipogon, O. barthii, O. longistaminata, O. meridionalis, O. glumaepatula, O. punctata, O. minuta, O. officinalis, O. rhizomatis, O. eichingeri, O. latifolia, O. alta, O. grandiglumis, O. australiensis, O. brachyantha, O. granulata, O. meyeriana, O. ridleyi, and O. longiglumis). These 19 wild species belong to 9 genome types (AA, BB, CC, BBCC, CCDD, EE, FF, GG, and HHJJ), representing wide genomic diversity in the genus. Using the genotype information, we analyzed the genome diversity of Oryza species. Other features of OryzaGenome facilitate the use of information on single nucleotide polymorphisms (SNPs) between O. sativa and its wild progenitor O. rufipogon in rice research, including breeding as well as basic science. For example, we provide Variant Call Format (VCF) files for genome-wide SNPs of 33 O. rufipogon accessions against the O. sativa reference genome, IRGSP1.0. In addition, we provide a new SNP Effect Table function, allowing users to identify SNPs or small insertion/deletion polymorphisms in the 33 O. rufipogon accessions and to search for the effect of these polymorphisms on protein function if they reside in the coding region (e.g., are missense or nonsense mutations). Furthermore, the SNP Viewer for 446 O. rufipogon accessions was updated by implementing new tracks for possible selective sweep regions and highly mutated regions that were potentially exposed to selective pressures during the process of domestication.

CONCLUSION

OryzaGenome2.1 focuses on comparative genomic analysis of diverse wild Oryza accessions collected around the world and on the development of resources to speed up the identification of critical trait-related genes, especially from O. rufipogon. It aims to promote the use of genotype information from wild accessions in rice breeding and potential future crop improvements. Diverse genotypes will be a key resource for evolutionary studies in Oryza, including polyploid biology.

Life science database cross search: A single window system for dispersed biological databases

A comprehensive search system for the bioscience databases is in progress. We constructed a search service, Life science database cross search system (https://biosciencedbc.jp/dbsearch/index. php?lang=en) by integrating numerous biomedical databases using database crawling algorithms. The described system integrates 600 databases containing over 90 million entries indexed for biomedical research and development.

Annotated normal CT data of the abdomen for deep learning: Challenges and strategies for implementation

PURPOSE

The purpose of this study was to report procedures developed to annotate abdominal computed tomography (CT) images from subjects without pancreatic disease that will be used as the input for deep convolutional neural networks (DNN) for development of deep learning algorithms for automatic recognition of a normal pancreas.

MATERIALS AND METHODS

Dual-phase contrast-enhanced volumetric CT acquired from 2005 to 2009 from potential kidney donors were retrospectively assessed. Four trained human annotators manually and sequentially annotated 22 structures in each datasets, then expert radiologists confirmed the annotation. For efficient annotation and data management, a commercial software package that supports three-dimensional segmentation was used.

RESULTS

A total of 1150 dual-phase CT datasets from 575 subjects were annotated. There were 229 men and 346 women (mean age: 45±12years; range: 18-79years). The mean intra-observer intra-subject dual-phase CT volume difference of all annotated structures was 4.27mL (7.65%). The deep network prediction for multi-organ segmentation showed high fidelity with 89.4% and 1.29mm in terms of mean Dice similarity coefficients and mean surface distances, respectively.

CONCLUSIONS

A reliable data collection/annotation process for abdominal structures was developed. This process can be used to generate large datasets appropriate for deep learning.

Der f 35: An MD-2-like house dust mite allergen that cross-reacts with Der f 2 and Pso o 2

BACKGROUND

Dermatophagoides farinae is a source of airborne house dust mite (HDM) allergens. We elucidated IgE-reactive allergens from D. farinae by two-dimensional immunoblotting-based allergenome analysis, and identified one new allergen, named Der f 35, that possesses IgE-binding capacity comparable to that of Der f 2. The aim of this study was to clarify the allergenic capacity of new HDM allergen Der f 35.

METHODS

We cloned der f 35 from D. farinae mRNA and produced recombinant Der f 35 in Escherichia coli. The IgE-binding capacity of Der f 35 and its cross-reactivity with group 2 allergens from D. farinae and Psoroptes ovis were determined by enzyme-linked immunosorbent assay (ELISA) and ELISA inhibition assays, respectively.

RESULTS

The deduced amino acid sequence for der f 35, which possesses the MD-2-related lipid-recognition domain, showed higher identity with group 2 allergens from P. ovis (61.5%) and Blomia tropicalis (50.7%) than with Der f 2 (40.8%). Der f 35 showed IgE-binding frequencies of 77.5% (31/40) for the native form upon allergenome analysis and 51.4% (18/35) for recombinant structure by ELISA. Der f 35 showed cross-reactivity with Der f 2 and Pso o 2 in reaction with HDM-allergic patients' IgE by ELISA inhibition assay.

CONCLUSION

Der f 35 is a candidate major allergen from D. farinae, which is more similar to group 2 allergens from sheep scab mite and storage mites. Der f 35 could be responsible for the cross-reactivity among group 2 mite allergens.

Experimental evaluation of dual Multiple Aperture Devices for Fluence Field Modulated X-Ray Computed Tomography

Acquisition of CT images with comparable diagnostic power can potentially be achieved with lower radiation exposure than the current standard of care through the adoption of hardware-based fluence-field modulation (e.g. dynamic bowtie filters). While modern CT scanners employ elements such as static bowtie filters and tube-current modulation, such solutions are limited in the fluence patterns that they can achieve, and thus are limited in their ability to adapt to broad classes of patient morphology. Fluence-field modulation also enables new applications such as region-of-interest imaging, task specific imaging, reducing measurement noise or improving image quality. The work presented in this paper leverages a novel fluence modulation strategy that uses "Multiple Aperture Devices" (MADs) which are, in essence, binary filters, blocking or passing x-rays on a fine scale. Utilizing two MAD devices in series provides the capability of generating a large number of fluence patterns via small relative motions between the MAD filters. We present the first experimental evaluation of fluence-field modulation using a dual-MAD system, and demonstrate the efficacy of this technique with a characterization of achievable fluence patterns and an investigation of experimental projection data.

Left Atrial Strain at Different Stages of Myxomatous Mitral Valve Disease in Dogs

Background

Decreased function of the left atrium (LA) is a useful prognostic indicator in dogs with myxomatous mitral valve disease (MMVD). In humans, LA strain is a novel severity indicator of mitral regurgitation, but its clinical utility in dogs has not been confirmed.

Objectives

To examine whether LA strain as evaluated with speckle‐tracking echocardiography is associated with MMVD stage in dogs.

Animals

Fifty‐two client‐owned dogs with MMVD.

Methods

Cross‐sectional study. Dogs were classified as stage B1, B2, C, or D, according to the American College of Veterinary Internal Medicine consensus. Physical examination findings and echocardiographic variables were compared among the groups. To assess the comparative accuracy of echocardiographic variables in identifying dogs with the presence or history congestive heart failure (CHF), receiver operating characteristic curves and multivariate logistic analysis were used.

Results

There were no significant differences in parameters of LA strain between B1 and B2 groups. However, LA longitudinal strain during atrial contraction (ε_A) (median, 19.1%; interquartile range, 15.3–24.3% in B1, 19.6%; 14.1–21.4% in B2, 6.2%; 3.18–11.2% in C/D) and during ventricular systole (ε_S) (32.7%; 28.9–39.2% in B1, 35.6%; 31.7–41.9% in B2, 23.6%; 16.9–26.1% in C/D) were significantly lower in stages C/D than in stages B1 and B2. In multivariate logistic regression analysis, ε_A and peak early diastolic mitral inflow velocity were identified as independent indicators of stage C/D.

Conclusions and Clinical Importance

ε_A was the best predictor of the presence or history of CHF. Further studies are needed to determine the clinical implications of these findings for treatment decisions and prognosis determination.

Prospective study of dental intervention for hematopoietic malignancy

Various chemotherapeutic agents used in patients with hematopoietic malignancy cause serious side effects, including myelosuppression and immunosuppression. Immunosuppression makes patients more susceptible to infection, resulting in an increased risk of infectious complications, including the development of severe septicemia that may be life-threatening. It is necessary for dental staff to be familiar with an appropriate protocol in such cases and to share information about the chemotherapy with a hematologist. To verify the effectiveness of our dental intervention protocol, we conducted a prospective study on the incidence of complications for each myelosuppressive grade of chemotherapy in patients with hematopoietic malignancy. We compared the incidence of complications between treatment P (patients who finished all the dental treatments according to the protocol) and treatment Q (patients who did not) per grade (A, B, C, D) and incidence of systemic or oral findings. We also compared the incidence of oral complication related to the residual teeth between first chemo (patients who were undergoing chemotherapy for the first time) and prior chemo (not the first time). There were significant differences in inflammatory complications between treatment P and treatment Q. We found that both systemic and oral inflammatory complications increased with higher-grade myelosuppressive chemotherapy. Additionally, there was a significant difference between the incidence of oral complications related to the residual teeth between first chemo and prior chemo. Complete implementation of the dental intervention protocol was associated with fewer oral and systemic infectious and inflammatory complications in patients with hematopoietic malignancies undergoing chemotherapy. The incidence of oral and systemic complications also increased with grade of chemotherapy. These results support the validity of our dental intervention protocol. We should pay close attention to the oral state of de novo hematopoietic malignancy patients.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.

Effectiveness of vitamin A acetate for enhancing the production of lung cancer specific monoclonal antibodies

The antibody productivity of the human-human hybridoma cell line AE6, which produces the lung cancer specific human monoclonal antibody AE6F4, was enhanced fourfold upon stimulation with 1 mug/ml of vitamin A acetate for one day. The enhancement lasted for about two weeks, and could be repeated by another stimulation with vitamin A acetate. The enhancing effect of vitamin A acetate was influenced by the cell density. Enhancement was clearly observed when the cell density was under 10(6) cells/ml. However, when the cell density was over 10(7) cells/ml, enhancement was observed weakly or not at all. Although the enhancing effect of vitamin A acetate is not unique to AE6 cells, not all human-human hybridoma cell lines show increased productivity upon VA acetate stimulation. This study suggests that the response to vitamin A acetate may be related to the properties of a particular fusion partner which the hybridoma cell inherits. The efficacy of vitamin A acetate for production of human monoclonal antibodies using human-human hybridomas is discussed.

Antibacterial Activity of Ethanol Extract of Betel Leaf (Piper betle L.) Against Some Food Borne Pathogens

The ethanol extract of Betel leaf (Piper betle L.), an indigenous climber plant of Bangladesh was screened for its antibacterial activity against some foodborne pathogens viz. Vibrio cholerae ATCC 6395, E. coli ATCC 25922,  E. coli O157:H7 NCTC 12049, Shigella dysenteriae-1 MJ-84 and Staphylococcus aureus ATCC 25923. Experimental  findings revealed that the ethanol extract of betel leaves potentially inhibit the growth of these foodborne  pathogens. Minimum inhibitory concentration (MIC) was ranged from 0.625% (w/v) to 0.75% (w/v). The  ethanol extract of betel leaf showed the highest MIC values for E. coli ATCC 25922 (0.625 mm), Vibrio cholera ATCC 6395 (0.625 mm), and Staphylococcus aureus ATCC 25923 (0.625 mm). It was revealed that the antibacterial  activity was highest at around neutral pH and at moderate temperature. The highest temperature (100°C)  and the pH (10.0) treated ethanol extract showed a little less activity than the maximum activity at moderate  temperature and at neutral pH, suggesting that the ethanol extract of the betel leaf was to some extent high  temperature and high pH tolerant. The ethanol extract of betel leaf might have a potential application as  natural food preservative to improve the microbiological safety of the foods. DOI: http://dx.doi.org/10.3329/bjm.v28i2.11817 Bangladesh J Microbiol, Volume 28, Number 2, December 2011, pp 58-63

[Is emergency aortic root replacement combined with arch replacement safe?]

BACKGROUND

Aortic root replacement (ARR) combined with aortic arch replacement (AAR) is an invasive procedure even in elective cases. Nevertheless, such combined operations are often mandatory in acute type A aortic dissection. We examined whether emergency operation might have further incremental risks compared with elective surgery in this type of operations.

METHODS

Forty-six cases of ARR combined with AAR were divided into 2 groups, the emergency (EM) group and the elective (EL) group. The EM group consisted of 10 cases of acute type A aortic dissection, whereas the EL group of 36:23 of chronic aortic dissection and 13 of true aneurysm.

RESULTS

There were no statistical differences between the 2 groups in the durations of aortic crossclamp, selective cerebral perfusion and cardiopulmonary bypass. The incidences in the EM and EL groups were as follows:in-hospital death; 0 vs 3( 8%), respiratory failure; 4 (40%) vs 14 (39%), renal failure; 0 vs 6 (17%), IABP requirement; 1 (10%) vs 3 (8%), and cerebral infarction; 0 vs 1 (3%), respectively.

CONCLUSION

Early surgical results of emergency ARR combined with AAR were almost equal to those in elective surgery.

Twelve oxo-eicosatetraenoic acid induces fetal membrane release after delivery in cows

Fetal fibroblast cell culture from cotyledons of bovine placenta and animal experiments close to term were used to elucidate afterbirth release and factors missing in the signal transduction mechanism for retained fetal membranes (RFM) after delivery. In cell culture the addition of arachidonic acid (Ara) to the medium caused rapid release to free floating cell in the culture dish, accompanied by matrix metalloproteinase (MMP) activation, being consistent with previous in vivo observations, where a relation between MMP and fetal membrane release had been shown. Ara-induced cell floating was not inhibited by the addition of cyclooxygenase (COX) inhibitor, and not induced by the addition of PGF2α or PGE2 to replace Ara, while 12-lipoxygenase (12-LOX) metabolite of Ara, 12-oxo-eicosatetraenoic acid (12-oxoETE), strongly induced cell floating. In the animal experiments, 12-oxoETE injection to delivery-induced cows (n = 6) using prostaglandin (PG) and dexamethazone resulted in rapid release of fetal membranes. In cows with natural calf delivery, a 12-oxoETE peak (11.7-16.8 ng/ml) was observed in maternal blood plasma prior to release of fetal membranes. This investigation thus gives new indications for that the mediator for fetal membrane release is 12-oxoETE and not PG.

Quantitative evaluation of cryptococcal pathogenesis and antifungal drugs using a silkworm infection model with Cryptococcus neoformans

AIMS

To develop an in vivo system that could quantitatively evaluate the therapeutic effects of antifungal drugs using a silkworm infection model with Cryptococcus neoformans.

METHODS AND RESULTS

Silkworms reared at 37°C died after an injection of viable serotype A C. neoformans fungus into the haemolymph. The serotype A C. neoformans, which is known to have higher mammal pathogenicity than the serotype D, was also more virulent against the silkworm. Furthermore, the deletion mutants of genes gpa1, pka1 and cna1, which are genes known to be necessary for the pathogenesis in mammals, showed an increase in the number of fungal cells necessary to kill half of the silkworm population (LD(50) value). Antifungal drugs, amphotericin B, flucytosine, fluconazole and ketoconazole, showed therapeutic effects in silkworms infected with C. neoformans. However, amphotericin B was not therapeutically effective when injected into the silkworm intestine, comparable to the fact that amphotericin B is not absorbed by the intestine in mammals.

CONCLUSIONS

The silkworm-C. neoformans infection model is useful for evaluating the therapeutic effects of antifungal drugs.

SIGNIFICANCE AND IMPACT OF THE STUDY

The silkworm infection model has various advantages for screening antifungal drug candidates. We can also elucidate the cryptococcal pathogenesis and evaluate the in vivo pharmacokinetics and toxicity of each drug.

Properties of ras-amplified recombinant BHK-21 cells in protein-free culture

We compared serum and protein-free cultures ofa ras-amplified recombinant BHK-21 cell line(ras-rBHK-IgG), which hyperproduces a lungcancer specific recombinant human monoclonal antibody. Ras-rBHK-IgG cells were shown to grow well, evenin protein-free medium and to be morphologicallysimilar to cells cultured in serum containing medium. However, the growth rate of ras-rBHK-IgG cellswas considerably slower in protein-free medium, whichresults in a longer maintenance period compared with cells cultured in serum containing medium. In addition, it was found that antibody production in protein-free culture had a ten times higher maximum than cells cultured in serum containing medium. On theother hand, in high density culture, using the hollowfiber bioreactor system, ras-rBHK-IgG cellscould be maintained for a month in protein-freeculture in contrast with serum culture, which onlylasted for half a month. However, the markedincrease of antibody production was not observed. A total amount of about 15 mg of the recombinantantibody, obtained in protein-free culture, was abouttwo times of that obtained in serum culture, and wasshown to be reactive to lung cancer cells in tissue. From these properties in protein-free medium, it isconcluded that protein-free culture of ras-rBHK-IgG cells is suitable for middle scaleproduction of recombinant human monoclonal antibody.

Practical evaluation of Mung bean seed pasteurization method in Japan

The majority of the seed sprout-related outbreaks have been associated with Escherichia coli O157:H7 and Salmonella. Therefore, an effective method for inactivating these organisms on the seeds before sprouting is needed. The current pasteurization method for mung beans in Japan (hot water treatment at 85 degrees C for 10 s) was more effective for disinfecting inoculated E. coli O157:H7, Salmonella, and nonpathogenic E. coli on mung bean seeds than was the calcium hypochlorite treatment (20,000 ppm for 20 min) recommended by the U.S. Food and Drug Administration. Hot water treatment at 85 degrees C for 40 s followed by dipping in cold water for 30 s and soaking in chlorine water (2,000 ppm) for 2 h reduced the pathogens to undetectable levels, and no viable pathogens were found in a 25-g enrichment culture and during the sprouting process. Practical tests using a working pasteurization machine with nonpathogenic E. coli as a surrogate produced similar results. The harvest yield of the treated seed was within the acceptable range. These treatments could be a viable alternative to the presently recommended 20,000-ppm chlorine treatment for mung bean seeds.

Leakage of intracellular UV materials of high hydrostatic pressure-injured Escherichia coli O157:H7 strains in tomato juice

The behavior of high hydrostatic pressure-injured Escherichia coli O157:H7 cells (strain SEA13B88 and a strain from the June-July 1999 Oklahoma juice outbreak) in tomato juice (pH 4.1) and phosphate-buffered saline (PBS; pH 7.2) at final concentrations of 8.4 to 8.8 log CFU/ml, respectively, and treated at 400, 500, and 600 MPa for 40 min at 25 and 35 degrees C with storage at 5 and 23 degrees C for 1,800 min was investigated. Immediately after treatment and every 3 h for 24 h of storage, an aliquot (0.1 ml) was plated on Trypticase soy agar and sorbitol MacConkey agar to determine the percentage of injured population. Leakage of UV materials and possible recovery from injury were investigated. Pressure (600-MPa) treatment at 35 degrees C for 40 min caused a higher percentage of bacterial injury than for 10 min of treatment. A higher percentage of injured population was found among the Oklahoma strain cells than among strain SEA13B88 cells, and differences in viability loss for bacterial strains were determined. The viability loss determined in PBS was 4.8 log for SEA13B88 cells and 5.2 log for Oklahoma cells, while losses of 5.4 and 5.7 log were determined in tomato juice for SEA13B88 and Oklahoma cells, respectively. The leakage of intracellular materials of injured Oklahoma cells was higher than that observed for SEA13B88 cells, but injured Oklahoma cells recovered faster in PBS. However, injured and healthy populations for both strains were below detection in tomato juice stored at 5 degrees C for 1,440 min.

Peculiar clusters of daughter cells observed in Cryptococcus neoformans grown in sealed microtiter plates

Cryptococcus neoformans was grown in 96-well microtiter plates sealed by foil which is less than 0.01 % permeable to oxygen. On day 14 of the cultivation, we observed peculiar clusters of small droplike daughter cells arranged around < or = 4 % of mother cells. The fact that most of the other cells had died indicates that few cells had been able to survive hypoxic conditions and escape the cell-cycle arrest. However, their daughters were unable to separate from them and to continue their proliferation under such conditions.

Thermal destruction of Escherichia coli O157:H7 in sous-vide cooked ground beef as affected by tea leaf and apple skin powders

We investigated the heat resistance of a four-strain mixture of Escherichia coli O157:H7 in raw ground beef in both the absence and presence of white and green tea powders and an apple skin extract. Inoculated meat was cooked using the sous-vide technique, i.e., the meat was packaged in sterile bags and completely immersed in a circulating water bath at low temperature for a period of time. The bags were cooked for 1 h to an internal temperature of 55, 58, 60, or 62.5 degrees C, and then held from 240 min at 55 degrees C to 10 min at 62.5 degrees C. The surviving bacteria were enumerated by spiral plating onto tryptic soy agar overlaid with sorbitol-MacConkey agar. Inactivation kinetics of the pathogens deviated from first-order kinetics. D-values (time, in minutes, required for the bacteria to decrease by 90%) in the control beef ranged from 67.79 min at 55 degrees C to 2.01 min at 62.5 degrees C. D-values determined by a logistic model ranged from 36.22 (D1, the D-value of a major population of surviving cells) and 112.79 (D2, the D-value of a minor subpopulation) at 55 degrees C to 1.39 (D1) and 3.00 (D2) at 62.5 degrees C. A significant increase (P < 0.05) in the sensitivity of the bacteria to heat was observed with the addition of 3% added antimicrobials. D-value reductions of 62 to 74% were observed with apple powder and 18 to 58% with tea powders. Thermal death times from this study will assist the retail food industry to design cooking regimes that ensure the safety of beef contaminated with E. coli O157:H7.

Combination treatments for killing Escherichia coli O157:H7 on alfalfa, radish, broccoli, and mung bean seeds

In this study, the effectiveness of prolonged dry-heat treatment (50 degrees C) alone or in combination with chemical treatments (1% oxalic acid, 0.03% phytic acid, 50% ethanol, electrolyzed acidic water, and electrolyzed alkaline water) in eliminating Escherichia coli O157:H7 on laboratory-inoculated alfalfa, radish, broccoli, and mung bean seeds was compared with that of dry-heat treatment in combination with irradiation treatment. Dry-heat treatment for 17 or 24 h alone could reduce E. coli O157:H7 numbers to below detectable levels in radish, broccoli, and alfalfa seeds, but was unable to reduce the pathogen numbers to below the detectable level in mung bean seeds. In addition, dry-heat treatment for 17 h plus sanitizer treatments were effective in greatly reducing pathogen populations on radish, broccoli, and alfalfa seeds, without compromising the quality of the sprouts, but these treatments did not eliminate the pathogen from radish and alfalfa seeds. Seventeen hours of dry heat followed by a 1.0-kGy dose of irradiation completely eliminated E. coli O157:H7 from radish and mung bean seeds, whereas only a minimum radiation dose of 0.25 kGy was required to completely eliminate the pathogen from broccoli and alfalfa seeds. Dry heat in combination with radiation doses of up to 1.0 kGy did not negatively impact the seed germination rate or length of alfalfa, broccoli, and radish seeds or the length of alfalfa, broccoli, and radish sprouts, but did decrease the length of mung bean sprouts.

BodyParts3D: 3D structure database for anatomical concepts

BodyParts3D is a dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a 3D whole-body model for an adult human male. It encompasses morphological and geometrical knowledge in anatomy and complements ontological representation. Moreover, BodyParts3D introduces a universal coordinate system in human anatomy, which may facilitate management of samples and data in biomedical research and clinical practice. As of today, 382 anatomical concepts, sufficient for mapping materials in most molecular medicine experiments, have been specified. Expansion of the dictionary by adding further segments and details to the whole-body model will continue in collaboration with clinical researchers until sufficient resolution and accuracy for most clinical application are achieved. BodyParts3D is accessible at: http://lifesciencedb.jp/ag/bp3d/.

Genetic diversity of longtail macaques (Macaca fascicularis) on the island of Mauritius: an assessment of nuclear and mitochondrial DNA polymorphisms

BACKGROUND

Individuals from an introduced population of longtail macaques on Mauritius have been extensively used in recent research. This population has low MHC gene diversity, and is thus regarded as a valuable resource for research.

METHODS

We investigated the genetic diversity of this population using multiple molecular markers located in mitochondrial DNA and microsatellite DNA loci on the autosomes and the Y chromosome. We tested samples from 82 individuals taken from seven study sites.

RESULTS AND CONCLUSIONS

We found this population to be panmictic, with a low degree of genetic variability. On the basis of an mtDNA phylogeny, we inferred that these macaques' ancestors originated from Java in Asia. Weak gametic disequilibrium was observed, suggesting decay of non-random associations between genomic genes at the time of founding. The results suggest that macaques bred in Mauritius are valuable as model animals for biomedical research because of their genetic homogeneity.

Hot water treatments to inactivate Escherichia coli O157:H7 and Salmonella in mung bean seeds

The majority of the seed sprout-related outbreaks have been associated with Escherichia coli O157:H7 and Salmonella. Therefore, an effective method is needed to inactivate these organisms on the seeds before they are sprouted. This study was conducted to assess the effectiveness of various hot water treatments to inactivate E. coli O157:H7 and Salmonella populations on mung beans seeds intended for sprout production and to determine the effect of these treatments on seed germination after the seeds were dipped in chilled water for 30 s. Mung bean seed inoculated with four-strain cocktails of E. coli O157:H7 and Salmonella were soaked into hot water at 80 and 90 degrees C with shaking for various periods and then dipped in chilled water for 30 s. The treated seeds were then assessed for the efficacy of the treatment for reducing populations of the pathogens and the effects of the treatment on germination. After inoculation and air drying, 6.08 +/- 0.34 log CFU/g E. coli O157:H7 and 5.34 +/- 0.29 log CFU/g Salmonella were detected on the seeds. After hot water treatment at 90 degrees C for 90 s followed by dipping in chilled water for 30 s, no viable pathogens were found and no survivors were found in the enrichment medium and during the sprouting process. The germination yield of the seed was not affected significantly. Therefore, hot water treatment followed by dipping in chilled water for 30 s could be an effective seed decontamination method for mung bean seeds intended for sprout production.

Effect of mechanical processing of corn silage on in vitro ruminal fermentation, and in situ bacterial colonization and dry matter degradation

Rumen fermentation and bacterial colonization of mechanically processed corn silage were evaluated in a series of in vitro and in situ experiments using ruminally cannulated cows. Data from rumen-simulated continuous culture (Rusitec) showed that total VFA concentration was increased (P < 0.001) by feeding processed corn silage, while pH was reduced (P < 0.001) and ammonia nitrogen remained unchanged (P > 0.05). Mechanical processing enhanced the in situ rate and extent of dry matter disappearance for corn stems and kernels, respectively (P < 0.05). It also enhanced in situ, the initial attachment of rumen bacteria responsible for corn digestion, as monitored by real-time PCR. The16S rDNA copy numbers of amylolytic and lipolytic bacteria, such as Succinivibrio dextrinosolvens, Ruminobacter amylophilus and Anaerovibrio lipolytica, attached to corn kernels were increased for processed corn silage (P < 0.05), in particular at 2 h after the start of incubation. In addition, corn stemattached cellulolytic and hemicellulolytic bacteria, such as Fibrobacter succinogenes, ruminococci and Eubacterium ruminantium, increased in 16S rDNA copy numbers for processed corn silage (P < 0.05). This was observed for the initial incubation period from 10 min to 2 h. These results demonstrate more rapid attachment and heavier colonization of rumen bacteria to the processed compared with the unprocessed silage, which facilitates ruminal digestion and fermentation. Key words: Corn silage, mechanical processing, rumen fermentation, bacteria, attachment

Control of Clostridium perfringens spores by green tea leaf extracts during cooling of cooked ground beef, chicken, and pork

We investigated the inhibition of Clostridium perfringens spore germination and outgrowth by two green tea extracts with low (green tea leaf powder [GTL]; 141 mg of total catechins per g of green tea extract) and high (green tea leaf extract [GTE]; 697 mg of total catechins per g of extract) catechin levels during abusive chilling of retail cooked ground beef, chicken, and pork. Green tea extracts were mixed into the thawed beef, chicken, and pork at concentrations of 0.5, 1.0, and 2.0% (wt/ wt), along with a heat-activated (75 degrees C for 20 min) three-strain spore cocktail to obtain a final concentration of approximately 3 log spores per g. Samples (5 g) of the ground beef, chicken, and pork were then vacuum packaged and cooked to 71 degrees C for 1 h in a temperature-controlled water bath. Thereafter, the products were cooled from 54.4 to 7.2 degrees C in 12, 15, 18, or 21 h, resulting in significant increases (P < 0.05) in the germination and outgrowth of C. perfringens populations in the ground beef, chicken, and pork control samples without GTL or GTE. Supplementation with 0.5 to 2% levels of GTL did not inhibit C. perfringens growth from spores. In contrast, the addition of 0.5 to 2% levels of GTE to beef, chicken, and pork resulted in a concentration-and time-dependent inhibition of C. perfringens growth from spores. At a 2% level of GTE, a significant (P < 0.05) inhibition of growth occurred at all chill rates for cooked ground beef, chicken, and pork. These results suggest that widely consumed catechins from green tea can reduce the potential risk of C. perfringens spore germination and outgrowth during abusive cooling from 54.4 to 7.2 degrees C in 12, 15, 18, or 21 h of cooling for ground beef, chicken, and pork.

Histone H1 vaccine therapy for overcoming acute rejection in experimental organ transplantation

OBJECTIVE

In a rat tolerogenic orthotopic liver transplantation (OLT) model, the recipient serum (post-OLT serum) shows strong immunosuppressive activity. In our previous reports, we suggested that autoreactive antibody (Ab) against histone H1 is a major immunosuppressive factor in this serum. The present study sought to determine whether up-regulation of anti-histone H1 Ab by histone H1 vaccination led to tolerance.

MATERIALS AND METHODS

Using mixed lymphocyte reactions (MLR) and heterotopic heart transplantations (HHT), the alloreactive T-cell responses and allograft survivals of histone H1-immunized rats were compared with those of control rats. Cytokine and cellular profiles were determined by enzyme-linked immunosorbent assay (ELISA) and flow cytometry.

RESULTS

The alloreactive T-cell response of histone H1-immunized rats was significantly lower than that of control rats, although there was no difference in nonspecific T-cell activation between the 2 groups. The allograft survival of histone H1-immunized rats was significantly prolonged after HHT. The major histocompatibility complex (MHC) class II and CD25 molecules of histone H1-immunized rats were significantly down-regulated compared with those of control rats. Moreover, the serum cytokine profile was modified by the immunization with histone H1.

CONCLUSIONS

These results suggest that histone H1 vaccination of transplant recipients leads to the production of immunosuppressive factors and the modification of cytokine/cellular profiles.

Cornichon-like protein facilitates secretion of HB-EGF and regulates proper development of cranial nerves

During their migration to the periphery, cranial neural crest cells (NCCs) are repulsed by an ErbB4-dependent cue(s) in the mesenchyme adjoining rhombomeres (r) 3 and 5, which are segmented hindbrain neuromeres. ErbB4 has many ligands, but which ligand functions in the above system has not yet been clearly determined. Here we found that a cornichon-like protein/cornichon homolog 2 (CNIL/CNIH2) gene was expressed in the developing chick r3 and r5. In a cell culture system, its product facilitated the secretion of heparin-binding epidermal growth factor-like growth factor (HB-EGF), one of the ligands of ErbB4. When CNIL function was perturbed in chick embryos by forced expression of a truncated form of CNIL, the distribution of NCCs was affected, which resulted in abnormal nerve fiber connections among the cranial sensory ganglia. Also, knockdown of CNIL or HB-EGF with siRNAs yielded a similar phenotype. This phenotype closely resembled that of ErbB4 knockout mouse embryos. Because HB-EGF was uniformly expressed in the embryonic hindbrain, CNIL seems to confine the site of HB-EGF action to r3 and r5 in concert with ErbB4.

Irradiation inactivation of Listeria monocytogenes in low-fat ground pork at freezing and refrigeration temperatures

Gamma radiation effectively controls Listeria monocytogenes in uncooked and in ready-to-eat foods. This study was conducted to determine if gamma radiation could be used to control L. monocytogenes in ground pork. Ground pork was contaminated with L. monocytogenes, kept at refrigeration (4 degrees C), chilling (0 degrees C), and freezing (-18 degrees C) temperatures overnight, exposed to gamma radiation and stored at 4 degrees C for 7 days, and at 0 and -18 degrees C for 60 days. Following irradiation, the meat was assayed for L. monocytogenes viable counts and lipid oxidation. A triangle test was performed to determine if sausage made from the irradiated and nonirradiated ground pork differed in sensory quality. It was observed that a 5-log reduction of L. monocytogenes viable counts would require a 3.0-kGy radiation dose. The results of a 60-day storage study of ground pork inoculated with 10(5) to 10(6) CFU of L. monocytogenes per gram indicated that counts for nonirradiated meat remained fairly constant at refrigeration, chilling, and freezing temperatures. However, irradiation of ground pork at 3.0 kGy could inactivate L. monocytogenes totally in ground pork subsequently held at all the temperatures used in this study. Lipid oxidation measurements, as determined by the thiobarbituric acid-reactive substance assay, ranged from 0.16 nmol/g for nonirradiated ground pork and 0.20 nmol/g for meat irradiated at 3.0 kGy. Sensory panelists could distinguish between irradiated and nonirradiated sausage but were divided on whether irradiation adversely affected the sausage quality. Our results suggest that gamma radiation could be useful to control L. monocytogenes in ground pork and improve the safety of ground pork products.

Role of Antinuclear Antibodies in Experimental and Clinical Liver Transplantation

OBJECTIVE

We recently reported that autoreactive antibodies (Abs) against nuclear histone H1 was transiently induced at an early phase after orthotopic liver transplantation (OLT) in a tolerogenic rat OLT model and possessed immunosuppressive activity. It was also reported that nuclear antigen, high-mobility group box 1 (HMGB1) protein was one of the initiators of the immune reaction. The present study sought to evaluate the role of antinuclear Abs in experimental and clinical liver transplantation.

MATERIALS AND METHODS

We prepared 3 animal models: natural tolerance model (DA liver into PVG); acute rejection model (DA liver into LEW); and drug-induced tolerance model (acute rejection model + cyclosporine [CsA]). In addition, we examined clinical samples, including 1 drug-free patient, to measure the antihistone H1/HMGB1 titers at various times after OLT.

RESULTS

In a natural tolerance model, antihistone H1 and HMGB1 Ab was induced during the rejection and the tolerance induction phases, respectively. Those Ab responses were also confirmed in a drug-induced tolerance model, whereas no such responses were shown in an acute rejection model. In our clinical drug-free patient, antihistone H1/HMGB1 titer was significantly higher after cessation of CsA than that in healthy volunteers.

CONCLUSIONS

Antinuclear Ab is actively expressed in accordance with overcoming rejection episodes with subsequent tolerance induction in both a natural tolerance model and a drug-induced tolerance model. We also observed a similar tendency in our clinical drug-free patient. These results suggested that antinuclear Abs may be useful markers to determine the timing to withdraw immunosuppressants.