The importance of scientific collecting and natural history museums for comparative neuroanatomy

The comparative study of vertebrate brains is inherently dependent upon access to a sufficient number of species and specimens to perform meaningful comparisons. Although many studies rely on compiling published information, continued specimen collection, in addition to more extensive use of existing brain collections and natural history museums, are crucial for detailed neuroanatomical comparisons across species. This review highlights the importance of collecting species through a variety of means, details a marsupial brain collection, and stresses the potential of natural history museums as a resource for comparative neuroanatomy. By taking advantage of as many of these resources as possible, researchers can rapidly increase species coverage and generate a better understanding of how the brain evolves.     

156 Effects of Light and Nutrients on Periphyton Community Composition in a Hawaiian Stream

The commercial harvest of floating kelps has promise as a business opportunity that could be especially valuable for small communities in southeast Alaska. The giant kelp, Macrocystis , is harvested mainly for the commercial herring roe-on-kelp harvest in Alaska. In addition, in southeast Alaska the two other species of floating kelps, Nereocystis luetkeana and Alaria fistulosa , have been commercially harvested since 1992 for use as agrochemicals by the Alaska KelpCo. The continued existence of this company and others that may wish to harvest seaweeds on a commercial basis is threatened by the lack of a kelp harvest management system in Alaska. The objective of this research is to develop a reliable and cost effective method for estimating the aerial extent and the standing crop biomass of the floating kelps in SE Alaska. We are employing an aerial multispectral imaging system that can be flown at varying altitudes to achieve spatial resolutions ranging from 0.5 to 2 meters. We are investigating whether the three species have unique spectral or textural characteristics in the multispectral imagery that can be used to differentiate the populations. The end products for this project will be kelp resource maps that delineate the spatial extent and biomass of kelp populations within the beds and a methodology for assessing kelp beds with mixed species composition. These products will find use by resource managers such as the Alaska Department of Fish and Game and the Department of Natural Resources.     

Studies on the expression of the microtubule-associated protein, tau, during mouse brain development, with newly isolated complementary DNA probes

Tau protein is a collection of closely related polypeptides that associate with microtubules in vivo and stimulate their assembly in vitro. Using an affinity-purified antiserum against bovine brain tau protein, we found that the number and amount of tau polypeptides changes dramatically during mouse brain development. The different forms appear to result from changes in tau mRNA since in vitro translation products reflect the qualitative and quantitative changes found in vivo. To study the mRNA and genomic complexity of tau protein, we used tau mRNA, purified from polysomes with tau antiserum, to isolate embryonic mouse tau complementary DNA clones. With these probes we have determined that embryonic tau protein is translated from a 6-kb mRNA that persists throughout brain development.     

中国高等植物数字化标本分析

传统上馆藏标本,主要用于植物分类学、植物资源学的研究。数字标本的出现将标本的使用拓展到从研究生物多样性时间空间分布到生态学和进化学理论、生物多样性保护、农业和人类健康等广泛领域。截至目前,从互联网上获取的采自中国的植物标本数量已有1 200多万份。该文通过整理和分析这些数据以了解中国植物标本的数字化精度、采集时间和采集地区规律以及采集空缺等状况。结果表明:中国标本采集形成了4个高峰,即20世纪30年代、60年代、80年代和21世纪初,中国植物标本采集和研究工作主要在20世纪50年代后由中国学者完成。标本采集地区覆盖度在省级较好,县级标本采集则很不平衡; 标本采集类群在科属层面覆盖率高,但近五分之一的物种采集不足; 标本的采集量既与植物分布幅度相关,也与采集地区的知名度、所获科研项目及采集者偏好有关。未来中国植物标本数字化方向应该在继续挖掘馆藏标本的同时,一方面开展对现有数字化标本信息再审核及补充,并加强与欧美大馆的信息共享以获取早期历史标本信息; 另一方面应用数字化标本信息分析结果,指导境内标本的精准采集,包括采集薄弱/空白地区、采集薄弱/空白属种的采集,以进一步增强实体标本馆能力,提高数字化标本质量,为进一步完善植物标本数字化和精准化采集提供依据,更好地服务科学和社会的发展。     

The Sun Health Research Institute Brain Donation Program: Description and Eexperience, 1987–2007

The Brain Donation Program at Sun Health Research Institute has been in continual operation since 1987, with over 1000 brains banked. The population studied primarily resides in the retirement communities of northwest metropolitan Phoenix, Arizona. The Institute is affiliated with Sun Health, a nonprofit community-owned and operated health care provider. Subjects are enrolled prospectively to allow standardized clinical assessments during life. Funding comes primarily from competitive grants. The Program has made short postmortem brain retrieval a priority, with a 2.75-h median postmortem interval for the entire collection. This maximizes the utility of the resource for molecular studies; frozen tissue from approximately 82% of all cases is suitable for RNA studies. Studies performed in-house have shown that, even with very short postmortem intervals, increasing delays in brain retrieval adversely affect RNA integrity and that cerebrospinal fluid pH increases with postmortem interval but does not predict tissue viability.     

Qualitative and quantitative methodologies for determination of airborne microorganisms at concentrated animal-feeding operations

The generation of airborne microorganisms from concentrated animal-feeding operations (CAFOs) is a concern from a human and animal health perspective. To better understand the airborne microorganisms found in these environments, a number of collection and analytical techniques have been utilized and will be discussed in this review. The most commonly used bioaerosol collection method is the liquid impingement format, which is suitable with a number of culture-based and non-culture molecular-based approaches, such as polymerase chain reaction. However, the vast majority of airborne microorganism studies conducted at CAFOs utilize culture-based analyses. Because of the limitations often associated with culture-based analyses, we focused our discussion on the application of molecular-based techniques to identify and/or quantify microorganisms, as they have promising application in bioaerosol research. The ability to rapidly characterize airborne microorganisms will help to ensure protection of public and environmental health. The use or mention of any commercial products does not imply any endorsement of that product by either the authors or the US Department of Agriculture.     

155 Mapping Floating Kelp Beds in Alaska With Remote Sensing

The commercial harvest of floating kelps has promise as a business opportunity that could be especially valuable for small communities in southeast Alaska. The giant kelp, Macrocystis, is harvested mainly for the commercial herring roe‐on‐kelp harvest in Alaska. In addition, in southeast Alaska the two other species of floating kelps, Nereocystis luetkeana and Alaria fistulosa, have been commercially harvested since 1992 for use as agrochemicals by the Alaska KelpCo. The continued existence of this company and others that may wish to harvest seaweeds on a commercial basis is threatened by the lack of a kelp harvest management system in Alaska. The objective of this research is to develop a reliable and cost effective method for estimating the aerial extent and the standing crop biomass of the floating kelps in SE Alaska. We are employing an aerial multispectral imaging system that can be flown at varying altitudes to achieve spatial resolutions ranging from 0.5 to 2 meters. We are investigating whether the three species have unique spectral or textural characteristics in the multispectral imagery that can be used to differentiate the populations. The end products for this project will be kelp resource maps that delineate the spatial extent and biomass of kelp populations within the beds and a methodology for assessing kelp beds with mixed species composition. These products will find use by resource managers such as the Alaska Department of Fish and Game and the Department of Natural Resources.     

The rediscovery of Tetrataxis Hooker fil. (Lythraceae)

Tetrataxis, a monotypic endemic of Mauritius, has been known since the 1790s only by the type collection in the Paris Herbarium. Now a colony of seven individuals has been discovered in a valley south-east of the type area. The small trees grow in saturated soil in a low open wet forest. Vegetatively, they resemble the more common Syzygium or Eugenia. Characteristics of the pollen and seed, anatomy of stems and leaves, and an approximate chromosome number are reported for the first time. A lectotype is selected from material of the original collection. Tetrataxis displays a number of advanced characters. It appears to have no close affinity to any single member of the family.     

Relevance of aquatic environments for hominins: a case study from Trinil (Java, Indonesia)

Knowledge about dietary niche is key to understanding hominin evolution, since diet influences body proportions, brain size, cognition, and habitat preference. In this study we provide ecological context for the current debate on modernity (or not) of aquatic resource exploitation by hominins. We use the Homo erectus site of Trinil as a case study to investigate how research questions on possible dietary relevance of aquatic environments can be addressed. Faunal and geochemical analysis of aquatic fossils from Trinil Hauptknochenschicht (HK) fauna demonstrate that Trinil at ∼1.5 Ma contained near-coastal rivers, lakes, swamp forests, lagoons, and marshes with minor marine influence, laterally grading into grasslands. Trinil HK environments yielded at least eleven edible mollusc species and four edible fish species that could be procured with no or minimal technology. We demonstrate that, from an ecological point of view, the default assumption should be that omnivorous hominins in coastal habitats with catchable aquatic fauna could have consumed aquatic resources. The hypothesis of aquatic exploitation can be tested with taphonomic analysis of aquatic fossils associated with hominin fossils. We show that midden-like characteristics of large bivalve shell assemblages containing Pseudodon and Elongaria from Trinil HK indicate deliberate collection by a selective agent, possibly hominin.     

The Pretoria Bone Collection: a modern South African skeletal sample.

The Pretoria Bone Collection began with the inception of the Department of Anatomy and the Medical School at the University of Pretoria in August 1942. Since then the collection has grown from a student aid to a resource for research. In the year 2000, the Pretoria Bone Collection was reorganised. The research material was divided into skulls, complete postcranial and incomplete postcranial remains. The collection presently contains 290 complete skeletons, 704 complete skulls and 541 complete postcranial remains. This paper presents information on the composition of this collection and hopes to heighten both national and international awareness of the collection and research opportunities in South Africa.     

The Clinical Breast Care Project: an important resource in investigating environmental and genetic contributions to breast cancer in African American women

Age at diagnosis, pathological characteristics, and tumor behavior differ between African American (AAW) and Caucasian women (CW) with breast cancer, with AAW having more aggressive tumors and higher mortality rates. Although both societal and molecular contributions to these disparities have been suggested, the African American population has traditionally been under-represented in research and clinical protocols, limiting the power of epidemiologic and molecular studies to provide better understanding of disease pathogenesis in this minority population. The Clinical Breast Care Project (CBCP) has developed a large tissue and blood repository from patients undergoing treatment for breast cancer, with previous history of breast cancer, counseled in the Risk Reduction Clinic, screened by routine mammography, or undergoing elective reductive mammoplasty. Recruitment of AAW into the CBCP was successful; 25% of the 2,454 female patients were African American, including 35% disease-free, 3% high-risk, 40% benign, 8% preinvasive and 14% with invasive breast disease. More than 500 data fields regarding lifestyle choices, socioeconomic status, health history and geography were collected from all participants, and all consenting individuals provided blood specimens for genomic and proteomic studies. Tissues were collected from all patients undergoing surgical procedures using protocols that preserve the macromolecules for downstream research applications. In addition, patients were followed after diagnosis, with >85% of patients providing ongoing and updated demographic and clinical information. Thus, recruitment efforts in the CBCP have resulted in collection of well-annotated information and research-quality specimens from a large number of AAW. This unique resource will allow for the identification of biological and environmental factors associated with the identification of genetic and non-genetic factors associated with the occurrence, detection, prognosis, or survival of breast cancer in AAW. The opinion and assertions contained herein are the private views of the authors and are not to be construed as official or as representing the views of the Department of the Army or the Department of Defense.     

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from multiple organisms. In addition, each bacterial PGDB includes predicted operons for the corresponding species. The BioCyc collection provides a unique resource for computational systems biology, namely global and comparative analyses of genomes and metabolic networks, and a supplement to the BioCyc resource of curated PGDBs. The Omics viewer available through the BioCyc website allows scientists to visualize combinations of gene expression, proteomics and metabolomics data on the metabolic maps of these organisms. This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways present in these organisms, and the most frequently observed pathways. We seek scientists to adopt and curate individual PGDBs within the BioCyc collection. Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing.     

园艺作物核心种质构建的研究进展

构建核心种质是植物遗传资源的研究热点和重点之一,对种质资源的鉴定、保存、利用与交流具有重要意义。本文简要介绍了植物遗传资源核心种质的概念及其构建方法,综述了园艺作物核心种质构建的研究新进展,并对今后该领域的研究趋势进行了展望。提出了种质分组及取样策略是园艺作物核心种质构建方法研究的重点;应及时构建一批大宗园艺作物以及我国原产和特产园艺作物的核心种质;高度重视基于重测序技术快速、精准、高通量地挖掘园艺作物核心种质优异基因的研究以及要加强科研管理与协作,切实提高我国园艺作物核心种质研究成果的共享性等观点,为园艺作物种质资源的深入研究与高效利用提供理论依据和技术参考。     

Prediction of the coding sequences of mouse homologues of FLJ genes: the complete nucleotide sequences of 110 mouse FLJ-homologous cDnas identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.

We have been conducting a mouse cDNA project to predict protein-coding sequences of mouse KIAA-homologous genes since 2001. As an extension of this project, we also started to accumulate mouse cDNA clones homologous to the human FLJ cDNA clones which are another long cDNA resource produced in our institute. We have isolated the cDNA clones from size-fractionated cDNA libraries derived from five different mouse tissues and natural killer T-cells. Although the human FLJ cDNA clones were originally derived from human spleen libraries, one-third of their mouse homologues were obtained from the brain library. We designated these homologues "mFLJ" plus a 5-digit number and herein characterized 110 mFLJ cDNA clones. We assigned an integrity of the CDSs from the comparison of the 110 cDNA clones with the corresponding human FLJ cDNA clones. The average size of the 110 mouse cDNA sequences was 3.8 kb and that of the deduced amino acid sequences from their longest CDS in each cDNA was 663 amino acid residues. Homology and/or motif search against public databases revealed new domains and/or motifs in 26 mFLJ gene products which provide additional speculation regarding the function of FLJ genes.     

The Vietnam Era Twin Registry.

The Vietnam Era Twin (VET) Registry is composed of 7369 middle-aged male-male twin pairs both of whom served in the military during the time of the Vietnam conflict (1965-1975). The Registry is a United States Department of Veterans Affairs resource that was originally constructed from military records; the Registry has been in existence for more than 15 years. It is one of the largest national twin registries in the US and currently has subjects living in all 50 states. Initially formed to address questions about the long-term health effects of service in Vietnam the Registry has evolved into a resource for genetic epidemiologic studies of mental and physical health conditions. The management and administration of the VET Registry is described with particular attention given to the processes involved with database maintenance and study coordination. Several waves of mail and telephone surveys have collected a wealth of health-related information on Registry twins. More recent data collection efforts have focused on specific sets of twin pairs and conducted detailed clinical or laboratory testing. New Registry initiatives for the future include the construction of a web site and the development of a DNA repository.     

A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins II: public release of inaugural version of InGaP database containing gene/protein expression profiles for 127 mouse KIAA genes/proteins.

The inaugural version of the InGaP database (Integrative Gene and Protein expression database; http://www.kazusa.or.jp/ingap/index.html) is a comprehensive database of gene/protein expression profiles of 127 mKIAA genes/proteins related to hypothetical ones obtained in our ongoing cDNA project. Information about each gene/protein consists of cDNA microarray analysis, subcellular localization of the ectopically expressed gene, and experimental data using anti-mKIAA antibody such as Western blotting and immunohistochemical analyses. KIAA cDNAs and their mouse counterparts, mKIAA cDNAs, were mainly isolated from cDNA libraries derived from brain tissues, thus we expect our database to contribute to the field of neuroscience. In fact, cDNA microarray analysis revealed that nearly half of our gene collection is predominantly expressed in brain tissues. Immunohistochemical analysis of the mouse brain provides functional insight into the specific area and/or cell type of the brain. This database will be a resource for the neuroscience community by seamlessly integrating the genomic and proteomic information about the mouse KIAA genes/proteins.     

Best practices for fungal germplasm repositories and perspectives on their implementation

In over 50 years, the Fungal Genetics Stock Center has grown to become a world-recognized biological resource center. Along with this growth comes the development and implementation of myriad practices for the management and curation of a diverse collection of filamentous fungi, yeast, and molecular genetic tools for working with the fungi. These practices include techniques for the testing, manipulation, and preservation of individual fungal isolates as well as for processing of thousands of isolates in parallel. In addition to providing accurate record keeping, an electronic managements system allows the observation of trends in strain distribution and in sample characteristics. Because many ex situ fungal germplasm repositories around the world share similar objectives, best-practice guidelines have been developed by a number of organizations such as the Organization for Economic Cooperation and Development or the International Society for Biological and Environmental Repositories. These best-practice guidelines provide a framework for the successful operation of collections and promote the development and interactions of biological resource centers around the world.     

Characterization of a genetic resource collection for Miscanthus (Saccharinae,Andropogoneae, Poaceae) using AFLP and ISSR PCR

Amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat markers were employed to characterize a genetic resource collection of Miscanthus, a grass under trial in Europe as a biomass crop. The 26 polymorphic markers produced by two ISSR fingerprinting primers were able to discriminate taxa and identify putative clones. AFLP fingerprints were fully reproducible and produced a larger number of markers for the three primer pairs tested, of which 998 were polymorphic (representing 79.3% of all bands). AFLP markers distinguished species, infra-specific taxa (varieties and cultivars) and putatively clonal material. They were also used to assess the inter-relationships of the taxa, to investigate the origin of important hybrid plants and to estimate the overall level of genetic variation in the collection. They were useful for assessing the species status of certain taxa such as M. transmorrisonensis, an endemic from Taiwan that was clearly distinct from M. sinensis; whereas other taxa of disputed species status, such as M. condensatus and M. yakushimanum were not genetically distinct from M. sinensis. The AFLP markers detected a high degree of infra-specific variation and allowed subdivisions of the genetic resource collection to be made, particularly within M. sinensis.     

Duke University Primate Center

The Duke University Primate Center houses the world's largest collection of prosimian primates. The Center is a research resource for undergraduate and graduate students, as well as faculty from Duke University and other U.S. and international universities. Researchers have access to the animals for noninvasive studies, to a large collection of preserved tissues and cadavers, and to an extensive collection of Eocene and Oligocene fossils. The Center is also involved in conservation programs in Madagascar which provide opportunities for field research in primatology and conservation.     

The first fifty years of the Connecticut Tumor Registry: reminiscences and prospects

The first fifty years of the Connecticut Tumor Registry (1935-1985) have seen unprecedented progress in the collection of standardized data on cancer patients and in the processing of these data, from paper documents to punch cards and magnetic tapes. The need for collecting such information was first recognized, in the early 1930s, by a group of physicians, health professionals, and laymen in New Haven who observed alarming increases in cancer rates and poor survival of cancer patients in this city. This paper recalls the growth and development of the registry and the role played by the Connecticut legislature, the State Medical Society, the Connecticut Department of Health, and the National Cancer Institute in this process. For half a century, the registry has provided assistance to practitioners, hospitals, and research scientists, not only in Connecticut but across the country and around the world. By making available reliable data on incidence and survival, the registry has played a key role in patient management, clinical trials, and etiologic studies. It has also demonstrated the value and served as an exemplary model of a population-based registry. At this juncture in its history, prospects for the future of the Connecticut Tumor Registry appear bright. Its data base will be an essential resource for the recently established Cancer Control Research Unit (CCRU) in the state and for new intervention studies by investigators at Yale, the University of Connecticut, and the State Health Department.