A database of recombinant viruses and recombinant viral vectors available from the RIKEN DNA bank

BACKGROUND: Viral vectors are required as gene-delivery systems for gene therapy and basic research. Recombinant adenoviruses (rAds) expressing genes of interest are being developed as research tools and many studies in vitro and in vivo have already been performed with such rAds. METHODS: Shuttle vectors for rAds were constructed with full-length cDNAs and rAds were generated in HEK293 cells by the COS-TPC method. The rAds and shuttle vectors were developed by the Japanese research community and deposited in the RIKEN DNA Bank (RDB; http://www.brc.riken.jp/lab/dna/en/) for distribution to the scientific community. The Recombinant Virus Database (RVD; http://www.brc.riken.jp/lab/dna/rvd/) was established at the RIKEN BioResource Center (BRC) in Japan as the source of information about and distribution of the various resources. RESULTS: The RIKEN BRC is releasing more than 300 recombinant viruses (RVs) and 500 shuttle vectors, as well as all related information, which is included in a newly established database, the RVD. The RVD consists of (i) information about the RVs, the inserted cDNAs and the shuttle vectors; (ii) data about sequence-tagged sites (STSs) that are markers of viral DNAs; and (iii) experimental protocols for the use of RVs. CONCLUSIONS: The new database and available resources should be very useful to scientists who are studying human gene therapy and performing related basic research. It is a web-interfaced flat-file database that can be accessed through the internet. Moreover, all of the resources deposited in the RDB, which is a public facility in Japan, are available to researchers around the world.     

Eliminating driftnets from the North Pacific Ocean: U.S.—Japanese cooperation in the international North Pacific Fisheries Commission, 1953–1993

Japanese negotiators agreed to eliminate driftnet fishing for salmon in the North Pacific Ocean by the end of 1992. The Japanese high seas fishing fleet for salmon had been an economically valuable yet environmentally destructive operation for four decades. The Japanese government progressively phased out lucrative Japanese salmon fishing operations in the North Pacific, apparently capitulating to U.S. pressure. No U.S. enforcement with punitive sanctions proved necessary, however. Specific characteristics of the international market created the possibility of an environmentally benign international agreement. International integration of the market for fisheries products was made possible by the high market value of salmon in the United States and in Japan. In the 1970s, foreign direct investment from vertically integrated, Tokyo‐based fishing firms into canning and processing operations in Alaska and the Pacific Northwest facilitated U.S. Japanese agreement. The high existence (nonuse) value of marine mammals in the United States was also an important factor.     

Acculturation and end-of-life decision making: comparison of Japanese and Japanese-American focus groups

Variation in decision-making about end-of-life care among ethnic groups creates clinical conflicts. In order to understand changes in preferences for end-of-life care among Japanese who immigrate to the United States, we conducted 18 focus groups with 122 participants: 65 English-speaking Japanese Americans, 29 Japanese-speaking Japanese Americans and 28 Japanese living in Japan. Negative feelings toward living in adverse health states and receiving life-sustaining treatment in such states permeated all three groups. Fear of being meiwaku, a physical, psychological or financial caregiving burden on loved ones, was a prominent concern. They preferred to die pokkuri (popping off) before they become end stage or physically frail. All groups preferred group-oriented decision-making with family. Although advance directives were generally accepted, Japanese participants saw written directives as intrusive whereas Japanese Americans viewed them mainly as tools to reduce conflict created by dying person's wishes and a family's kazoku no jo--responsibility to sustain the dying patient. These findings suggest that in the United States Japanese cultural values concerning end-of-life care and decision-making process are largely preserved.     

DNA Evidence of the Origin of Varroa jacobsoni Oudemans in the Americas

Randomly amplified polymorphic DNA (RAPD) was used to examine possible origin of Varroa jacobsoni Oudemans in the Americas. Among 64 primers screened, 2 primers provided variation which was informative for this study. All V. jacobsoni collected from the United States had the same banding pattern to that of mites collected from Russia, Morocco, Germany, Italy, Spain, and Portugal (Russian pattern). This banding pattern was different from the pattern found for mites collected from Japan, Brazil, and Puerto Rico (Japanese pattern). The Japanese pattern lacked a 766-bp band found in the Russian pattern (OPE-07). With primer OPP-03, the Russian pattern had a distinct band at 442 bp not found in the Japanese pattern. Two bands located at 675 and 412 bp were specific to the Japanese pattern. These results suggest that the V. jacobsoni of the United States is probably predominantly Russian in origin (via Europe), while the V. jacobsoni of Brazil and Puerto Rico are probably predominantly Japanese in origin.     

United States patent prior art rules and the neem controversy: a case of subject-matter imperialism?

A recent United States patent covering an improvement to the naturally-occurring pesticide in neem tree seed oil might have been rejected as 'obvious' if United States patent law recognized certain forms of prior inventive activity on a par with similar activity occurring within the United States' borders. But the US only recognizes prior 'knowledge, use or invention' as blocking a claim to a patent when those activities take place within US borders, or are evidenced by publications accessible in the US, or, more commonly, by foreign patents. Neither of these last forms of tangible 'prior art' is likely to be available to block patents on biodiversity inventions – most notably because of the fact that most developing nations do not allow patents on pharmaceutical or agricultural inventions, categories subsuming most biodiversity-related advances. Although the United States patent only has direct force within the United States, it is nonetheless highly significant to this global dispute, since the United States and other developed nations stand to be the major markets for the end-products of neem. This paper argues that the border-drawing distinctions in US patent law are archaic, counter to stated policy directives and are disproportionately influencing the developing world's stance towards GATT and its intellectual property rights provisions.     

Evaluation of a rapid immunochromatographic dipstick test for detection of antibodies to Trypanosoma cruzi in dogs experimentally infected with isolates obtained from opossums (Didelphis virginiana), armadillos (Dasypus novemcinctus), and dogs (Canis familiaris) from the United States

Dogs are reservoir hosts for Trypanosoma cruzi , the causative agent of American trypanosomiasis. A rapid immunochromatographic dipstick test (ICT) is available commercially for canine serological testing. The ICT was developed with the use of sera from South American dogs, but it is not routinely used in the United States. We evaluated the utility of the ICT in detecting anti-T. cruzi antibodies in dogs from the United States. Dogs (N = 64) were experimentally infected with United States' isolates of T. cruzi from an opossum (Didelphis virginiana), an armadillo (Dasypus novemcinctus), and a domestic dog (Canis familiaris), and were tested after experimental infection. Sera from uninfected United States dogs (n = 79; hemaculture negative) were used as negative controls. In a blind study, sera were tested by the ICT and compared to the indirect immunofluorescent antibody test with the use of Brazil-strain epimastigotes as antigen. The sensitivity of the ICT was 91% and the specificity was 98% in dogs experimentally infected with United States isolates. Our study indicates that the ICT could be a useful screening tool for serological surveillance of canine T. cruzi exposure in the United States.     

Food adaptations of a transplanted Japanese macaque troop (Arashiyama West)

In 1972 Arashiyama West troop of Japanese macaques was transplanted to southcentral United States and kept in semi-free ranging conditions. The new environment provided an opportunity to assess aspects of the species' adaptive potential. About 1,500 feeding observations were made monthly over 6.5 months. Unlimited provisioned food was available, but monkeys utilized native plants immediately and use increased until it included 50+ % of the diet by weight. Shrubs provided 75% of foods in first month and 32% thereafter. Sorghum comprised 25% in May–July. Soil, arthropods, fungi, bulbs, and roots each comprised less 5%. Between 21 and 37 foods were utilized monthly. Monthly food uses corresponded to availability. Many food plants required unique handling by monkeys. Four general adaptive responses to potential foods are described. Evolution has clearly shaped the Japanese macaque into a highly omnivorous and behaviorally flexible animal.     

On the Taxonomy and Morphology of the Pine Wood Nematode, Bursaphelenchus xylophilus (Steiner &Buhrer 1934) Nickle 1970

During the past 3 yr, nematologists in the United States have found specimens of Bursaphelenchus sp. in the wood of dead and dying pine trees. This nematode-host association resembles a similar interaction reported from Japan where pine trees are being killed by the pine wood nematode. This taxonomic research was conducted to determine if the Japanese pine wood nematode and similar populations in the United States are of the same species. Based upon typical morphological characters of original specimens of Bursaphelenchus xylophilus (Steiner and Buhrer 1934) Nickle 1970 that were rediscovered in the USDA Nematode Collection and genetic crosses among the Japanese and American nematode populations, it was concluded that they are all the same species, B. xylophilus.     

美国生命科学两用性研究监管政策分析

目的:近年来高致病性禽流感H5N1病毒基因改造研究及美国国家生物安全科学咨询委员会的监管建议引起广泛争议,美国发布了生命科学两用性研究监管政策。本研究旨在通过对美国生命科学两用性研究监管政策进行分析,探讨两用性研究发展和监管趋势。方法:通过文献检索,获取生命科学两用性研究监管政策相关的情报源,对美国政府生命科学两用性研究监管的政策背景、主要内容、政策评论、政策动因进行系统梳理与分析。结果:美国政府出台的生命科学两用性研究监管政策,有助于美国对整个生命科学研究周期(从最初提交资助申请到研究结论和研究成果交流)潜在的误用风险进行管理。结论:美国生命科学两用性研究引发极大争议,两用性研究监管主要依靠生命科学团体的自我管理,政策具有指导性而非强制性。     

Genetic Variation in the Free-Living Amoeba Naegleria fowleri

In this study, 30 strains of the pathogenic free-living amoeba Naegleria fowleri were investigated by using the randomly amplified polymorphic DNA (RAPD) method. The present study confirmed our previous finding that RAPD variation is not correlated with geographical origin. In particular, Mexican strains belong to the variant previously detected in Asia, Europe, and the United States. In France, surprisingly, strains from Cattenom gave RAPD patterns identical to those of the Japanese strains. In addition, all of these strains, together with an additional French strain from Chooz, exhibited similarities to South Pacific strains. The results also confirmed the presence of numerous variants in Europe, whereas only two variants were detected in the United States. The two variants found in the United States were different from the South Pacific variants. These findings do not support the previous hypothesis concerning the origin and modes of dispersal of N. fowleri.     

Immunological similarities of proteinase inhibitors from potatoes

Proteinase inhibitors, purified independently from Japanese, United States, and German potato varieties, and having different physicochemical and inhibitory properties, are shown to be immunochemically similar. These results indicate that the heterogeneity found among proteinase inhibitors from potato tubers is apparently due both to intervarietal, as well as intravarietal, variations in isoinhibitor components.     

Age‐discrepant marriages: Cross‐national comparisons of Canadian‐American trends

Abstract

Comparisons of age‐discrepant marriages ideally involve data which are collected at the time of marriage and which are available by single years of age for the same population over time. Although such data are not available for Canadian‐American comparisons, approximations of them are derived from the United States census, from marriage statistics (including statistics for California and for British Columbia), and from selected fortuitous studies of age at marriage. Although available data are not conclusive, they suggest that Canada and the United States do not differ markedly in the incidence of age‐discrepant marriages and that both exhibit longitudinal trends which reflect a decreased incidence of marriages with large husband‐wife age differences and an increased preference for coeval marriages, but exhibit markedly little change in the incidence of wife‐older marriages. Cross‐cultural patterns of age‐discrepant marriages are suggested as an unobtrusive indicator for comparative assessments of the de facto status of women.     

Restoring species diversity: assessing capacity in the U.S. native plant industry

Large quantities of diverse and appropriately adapted native plant germplasm are required to facilitate restoration globally, yet shortages can prevent restorations from attaining desired species diversity and structure. An extensive native plant industry has developed in the United States to help meet these demands, yet very little is known about its capacity to support germplasm needs. To better understand current capacity and germplasm availability, we report results of the first comprehensive and quantitative assessment of the native plant industry in the United States, which includes at least 841 vendors nationwide and the species they make available for restoration. We synthesized lists of commercially available species from native plant vendors across the United States and identified gaps in species availability to inform germplasm research, development, and production. Of the approximately 25,000 vascular plant taxa native to the United States, 26% are sold commercially, with growth form, conservation status, distribution, and taxonomy significantly predicting availability. In contrast, only 0.07% of approximately 3,000 native nonvascular taxa are sold commercially. We also investigated how demand for germplasm to support high‐quality restoration efforts is met by vendors in the Midwestern tallgrass prairie region, which has been targeted extensively by restoration efforts for decades. In this well‐developed native plant market, 74% of more than 1,000 target species are commercially available, often from vendors that advertise genetically diverse, locally sourced germplasm. We make recommendations to build on the successes of regional markets like the tallgrass prairie region, and to fill identified gaps, including investing in research to support production, ensuring more consistent and clear demand, and fostering regional collaboration.     

Sequence comparisons for a hepatitis C virus genome RNA isolated from a patient with liver cirrhosis

The nucleotide (nt) sequence was determined for an isolate of hepatitis C virus (HCV) derived from cirrhotic tissue of a patient with hepatocellular carcinoma. The 9408-nt sequence (EMBL Acq. No. X61596) showed homology of 90.7-91.4% on the nt level, as compared to two Japanese isolates from patients with a high titer of serum transaminase, 78.4-78.8% to those obtained in the United States, and 65.0% to that from an asymptomatic Japanese carrier. The phylogenetic tree of the six isolates classified them into three groups.     

Streamlined approach for assessing embedded consumption of lithium and cobalt in the United States

In today's complex global supply chains, time and data intensive analyses are required to understand global flows of mineral commodities from mine to consumer, particularly for mineral commodities in products (electronics, automobiles, etc.) that contain multiple parts with many mineral commodities. National and regional analyses require additional time and data to incorporate international trade flows. However, data limitations and time constraints often prohibit global and national material flow analyses for minor metals. Here we present a methodological approach to circumvent these constraints by utilizing readily available industry-level global data from the United Nations Statistics Division and national industrial data to estimate total requirements for a mineral commodity. We apply this approach to lithium and cobalt use in the United States for the year 2018 and distinguish between apparent raw material consumption versus inferred embedded consumption of lithium and cobalt materials in all forms. The results show that more than half of the United States’ total requirements for both lithium and cobalt is in parts and products that were manufactured outside the United States. In large part, this is due to limited US manufacturing capability for lithium-ion battery materials and cells and the United States’ high import reliance for electronics that use those batteries.     

West Nile virus recombinant DNA vaccine protects mouse and horse from virus challenge and expresses in vitro a noninfectious recombinant antigen that can be used in enzyme-linked immunosorbent assays

Introduction of West Nile (WN) virus into the United States in 1999 created major human and animal health concerns. Currently, no human or veterinary vaccine is available to prevent WN viral infection, and mosquito control is the only practical strategy to combat the spread of disease. Starting with a previously designed eukaryotic expression vector, we constructed a recombinant plasmid (pCBWN) that expressed the WN virus prM and E proteins. A single intramuscular injection of pCBWN DNA induced protective immunity, preventing WN virus infection in mice and horses. Recombinant plasmid-transformed COS-1 cells expressed and secreted high levels of WN virus prM and E proteins into the culture medium. The medium was treated with polyethylene glycol to concentrate proteins. The resultant, containing high-titered recombinant WN virus antigen, proved to be an excellent alternative to the more traditional suckling-mouse brain WN virus antigen used in the immunoglobulin M (IgM) antibody-capture and indirect IgG enzyme-linked immunosorbent assays. This recombinant antigen has great potential to become the antigen of choice and will facilitate the standardization of reagents and implementation of WN virus surveillance in the United States and elsewhere.     

Future trends in bacterial taxonomy

The author of this paper is an employee of the US Federal Government. As the article is, under the Copyrights Act, a “work of the United States Government”, copyright protection under Title 17 of the United States code is not available; there is no copyright     

Diffusion activities in college laboratory manuals

Many have called for reform of the science curriculum to incorporate the process of inquiry: this has been shown to improve student understanding of biological concepts. Laboratory activities provide excellent opportunities to incorporate inquiry in to the curriculum. This study used a modified version of the Laboratory Task Analysis Instrument (LAI) to analyse diffusion activities in 10 manuals available to two-year and four-year colleges in the United States. The analyses revealed that most manuals did not include much inquiry, similar to previous studies of high school laboratory manuals. Furthermore, they often failed to engage students in the planning and design of the activity, and they did not encourage students to apply what they learned in a broader context — two essential components of inquiry. This study showed the need for educators to review the materials that are available and implement changes that would promote the use of inquiry.     

Compilation and comparison of averages for standing height at late childhood ages on United States boys of several ethnic groups studied between 1875 and 1980

Averages for standing height are brought together at late childhood ages on boys of different ethnic groups studied in the United States during the last 100 years. More than 80 averages are assembed at each of two ages (9 years and 11 years). Among the groups represented are boys having the following ancestries: Afro-Black, Amerind, Chinese, Japanese, Eskimo, Mexican, Spanish, Portuguese, Polish, Finnish, German, Italian, British, and Dutch. Suffice to cite examples of findings on boys age 11 years. United States Black boys studied during the period 1967–1978 were taller than those studied during 1886–1898 by 11.4 cm, or 8.6%. Average standing heights in the 1930s were near 134 cm for Pueblo boys; near 139 cm for boys whose progenitors were Navajo, Mexican, or Polish; and near 142 cm for boys of Finnish ancestry. In the 1950s, average standing heights were near 140 cm, 144 cm, and 146 cm, respectively, on United States boys of Japanese, Italian, and Dutch ancestries. Afro-Black and Amerind similarities and dissimilarities in the 1960s are illustrated by averages near 140 cm on Black and Chippewa groups in Pennsylvania and Minnesota, and near 144 cm on Black and Blackfeet groups in Ohio and Montana. In some instances, averages are compared for upper and lower socioeconomic subgroups, and for urban and rural subgroups.