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Open problems of computational molecular biology: No Description Available.
Genetics and molecular biology of breast cancer: This volume contains the abstracts of oral presentations and poster sessions presented at the Cold Springs Harbor Meeting on Cancer Cells, this meeting entitled Genetics and Molecular Biology of Breast Cancer.
Recent advances in lung cancer biology: This paper provides an overview of carcinogenesis, especially as related to lung cancers. Various growth factors and their mutated forms as oncogenes are discussed with respect to gene location and their role in the oncogenic process. Finally the data is related to lung cancer induction in uranium miners and exposure to radon.
Molecular biology of signal transduction in plants. Abstracts: This volume contains abstracts of oral presentations and poster sessions of the 1991 Cold Springs Harbor Meeting entitled Molecular Biology of Signal Transduction in Plants.
Ninth International Workshop on Plant Membrane Biology: This report is a compilation of abstracts from papers which were discussed at a workshop on plant membrane biology. Topics include: plasma membrane ATP-ases; plant-environment interactions, membrane receptors; signal transduction; ion channel physiology; biophysics and molecular biology; vaculor H+ pumps; sugar carriers; membrane transport; and cellular structure and function.
Biology and Medicine Semiannual Report, Fall 1969.: This Semiannual Report reflects, but does not completely cover, the varied areas of progress in research during the past six months. The studies included, ranging from basic to clinical, re-emphasizes the increasing value of isotopes and radiation to research in Biology and Medicine.
Data Acquisition and Analysis at the Structural Biology Center: The Structural Biology Center (SBC), a national user facility for macromolecular crystallography located at Argonne National Laboratory`s Advanced Photon Source, is currently being built and commissioned. SBC facilities include a bending-magnet beamline, an insertion-device beamline, laboratory and office space adjacent to the beamlines, and associated instrumentation, experimental apparatus, and facilities. SBC technical facilities will support anomalous dispersion phasing experiments, data collection from microcrystals, data collection from crystals with large molecular structures and rapid data collection from multiple related crystal structures for protein engineering and drug design. The SBC Computing Systems and Software Engineering Group is tasked with developing the SBC Control System, which includes computing systems, network, and software. The emphasis of SBC Control System development has been to provide efficient and convenient beamline control, data acquisition, and data analysis for maximal facility and experimenter productivity. This paper describes the SBC Control System development, specifically data acquisition and analysis at the SBC, and the development methods used to meet this goal.
Plant biology research and training for the 21st century: The committee was assembled in response to a request from the National Science Foundation (NSF), the US Department of Agriculture (USDA), and the US Department of Energy (DoE). The leadership of these agencies asked the National Academy of Sciences through the National Research Council (NRC) to assess the status of plant-science research in the United States in light of the opportunities arising from advances inother areas of biology. NRC was asked to suggest ways of accelerating the application of these new biologic concepts and tools to research in plant science with the aim of enhancing the acquisition of new knowledge about plants. The charge to the committee was to examine the following: Organizations, departments, and institutions conducting plant biology research; human resources involved in plant biology research; graduate training programs in plant biology; federal, state, and private sources of support for plant-biology research; the role of industry in conducting and supporting plant-biology research; the international status of US plant-biology research; and the relationship of plant biology to leading-edge research in biology.
SUPPLEMENT TO BIOLOGY AND MEDICINE SEMIANNUAL REPORT, SPRING 1964: No Description Available.
The extracellular matrix of plants: Molecular, cellular and developmental biology: A symposium entitled ``The Extracellular Matrix of Plants: Molecular, Cellular and Developmental Biology was held in Tamarron, Colorado, March 15--21, 1996. The following topics were explored in addresses by 43 speakers: structure and biochemistry of cell walls; biochemistry, molecular biology and biosynthesis of lignin; secretory pathway and synthesis of glycoproteins; biosynthesis of matrix polysaccharides, callose and cellulose; role of the extracellular matrix in plant growth and development; plant cell walls in symbiosis and pathogenesis.
Molecular biology of Lea genes of higher plants. Progress report: Annual progress report discusses achievements on the elucidation of the function of the D-7 Lea proteins. Studies aimed at the immunoassay, fractionation, and molecular modeling are described.
Using synthetic biology to screen for functional diversity of GH1 enzymes: Advances in next-generation sequencing technologies have enabled single genomes as well as complex environmental samples (metagenomes) to be comprehensively sequenced on a routine basis. Bioinformatics analysis of the resulting sequencing data reveals a continually expanding catalogue of predicted proteins ( 14 million as of April 2011), 75 percent of which are associated with functional annotation (COG, Pfam, Enzyme, Kegg, etc). These predicted proteins cover the full spectrum of known pathways and functional activities, including many novel biocatalysts that are expected to significantly contribute to the development of clean technologies including biomass degradation, lipid transformation for biodiesel generation, intermediates for polymer production, carbon capture, and bioremediation.
59. Cold Spring Harbor symposium on quantitative biology: Molecular genetics of cancer: Investigation of the mechanistic aspects of cancer has its roots in the studies on tumor viruses and their effects on cell proliferation, function, and growth. This outstanding progress was well documented in previous Cold Spring Harbor Symposia on Quantitative Biology. In the early to mid 1980s, progress on the development of chromosome mapping strategies and the accumulation of DNA probes that identified polymorphisms, encouraged by the international Human Genome Project, enabled the identification of other genes that contributed to familial inheritance of high susceptibility to specific cancers. This approach was very successful and led to a degree of optimism that one aspect of cancer, the multistep genetic process from early neoplasia to metastatic tumors, was beginning to be understood. It therefore seemed appropriate that the 59th Symposium on Quantitative Biology focus attention on the Molecular Genetics of Cancer. The concept was to combine the exciting progress on the identification of new genetic alterations in human tumor cells with studies on the function of the cancer gene products and how they go awry in tumor cells.
Hidden Markov models and other machine learning approaches in computational molecular biology: This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Computational tools are increasingly needed to process the massive amounts of data, to organize and classify sequences, to detect weak similarities, to separate coding from non-coding regions, and reconstruct the underlying evolutionary history. The fundamental problem in machine learning is the same as in scientific reasoning in general, as well as statistical modeling: to come up with a good model for the data. In this tutorial four classes of models are reviewed. They are: Hidden Markov models; artificial Neural Networks; Belief Networks; and Stochastic Grammars. When dealing with DNA and protein primary sequences, Hidden Markov models are one of the most flexible and powerful alignments and data base searches. In this tutorial, attention is focused on the theory of Hidden Markov Models, and how to apply them to problems in molecular biology.
International symposium on cellular and molecular biology of phosphate and phosphorylated compounds in microorganisms: Proceedings: This report contains the abstracts of papers presented at the conference. Attention is focused on the following topics: regulation of phosphate metabolism in bacteria; structure-function of alkaline phosphatase; regulation of phosphate metabolism in yeast; transport of phosphate and phosphorylated compounds; and phosphate regulation in pathogenesis and secondary metabolism.
Molecular biology in marine science: Scientific questions, technological approaches, and practical implications: This report describes molecular techniques that could be invaluable in addressing process-oriented problems in the ocean sciences that have perplexed oceanographers for decades, such as understanding the basis for biogeochemical processes, recruitment processes, upper-ocean dynamics, biological impacts of global warming, and ecological impacts of human activities. The coupling of highly sophisticated methods, such as satellite remote sensing, which permits synoptic monitoring of chemical, physical, and biological parameters over large areas, with the power of modern molecular tools for ``ground truthing`` at small scales could allow scientists to address questions about marine organisms and the ocean in which they live that could not be answered previously. Clearly, the marine sciences are on the threshold of an exciting new frontier of scientific discovery and economic opportunity.
Investigation of the Influence of Thermal Discharge From a Large Electric Power Station on the Biology and Near-Shore Circulation of Lake Michigan. Part A: Biology. Technical Progress Report, August 1, 1971--April 30, 1972.: No Description Available.
Abstracts of papers presented at the LVIII Cold Spring Harbor Symposium on quantitative Biology: DNA and chromosomes: This volume contains the abstracts of oral and poster presentations made at the LVIII Cold Spring Harbor Symposium on Quantitative Biology entitles DNA & Chromosomes. The meeting was held June 2--June 9, 1993 at Cold Spring Harbor, New York.
Third international conference on intelligent systems for molecular biology (ISMB-95): Summary. Final report: The specific aims of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB-95) were to: convene a critical mass of researchers applying advanced computational techniques to problems in molecular biology; promote interchange of problems and solutions between computer scientists and molecular biologists; create education opportunities in this cross-disciplinary field for students and senior researchers wishing to either apply or benefit from these techniques; produce an archival proceedings as a forum for rapid dissemination of new results in a peer-reviewed manner; produce a set of tutorial materials for education and training of researchers interested in this field; maintain the momentum generated by the highly successful previous conferences in the series, and establish a regular event that will help to solidify the field; and foster the involvement of women and minorities in the field.
Molecular biology and genetics of the acetate-utilizing methanogenic bacteria. Progress report, [July 1, 1988--June 30, 1991]: Acetate conversion to methane and C0{sub 2} by the methanogenic archaebacteria is a primary rate limiting step in anaerobic biodegradative processes in nature. However, the genetic study of these organisms has not been experimentally tractable due to the inability to grow and plate the organisms as single cells, and to extract high molecular weight DNA and RNA without shearing. The acetate-utilizing species, Methanosarcina thermolphila TM-1, is being used for the proposed genetic and molecular studies because, unlike previously described acetotrophic methanosarcina that have a thick heteropolysaccharide cell wall, this species can be cultured in a unicellular form that has a protein cell wall lacking the heteropolysaccharide layer. These cells can be gently disrupted to obtain protoplasts or lysed to yield intact genomic DNA and RNA. Experiments are in progress to develop a gene transfer system in this bacterial species. Methods are being developed and refined for the efficient plating of M. thermophila on defined media, for chemical mutagenesis, and for the isolation of mutants defective in acetate utilization. Chromosomal DNA libraries have been constructed from M. thermophila and are being used to clone genes involved in the acetate utilization pathway (e.g. carbon monoxide dehydrogenase). Once cloned, analysis of the molecular mechanisms responsible for their regulatory control will be performed. These studies should aid our understanding of the pathway for acetate utilization in M. thermophila and serve as a model for elucidating regulatory mechanisms in the acetotrophic methanogens.
The impact of biology on risk assessment -- Workshop of the National Research Council`s board on radiation effects research. Meeting report: The linear, nonthreshold extrapolation from a dose-response relationship for ionizing radiation derived at higher doses to doses for which regulatory standards are proposed is being challenged by some scientists and defended by others. It appears that the risks associated with exposures to doses of interest are below the risks that can be measured with epidemiologic studies. Therefore, many have looked to biology to provide information relevant to risk assessment. The workshop reported here, ``The Impact of biology on Risk Assessment,`` was planned to address the need for further information by bringing together scientists who have been working in key fields of biology and others who have been contemplating the issues associated specifically with this question. The goals of the workshop were to summarize and review the status of the relevant biology, to determine how the reported biologic data might influence risk assessment, and to identify subjects on which more data is needed.
DIVISION OF BIOLOGICAL AND MEDICAL RESEARCH QUARTERLY REPORT FOR MAY, JUNE, JULY, 1952: No Description Available.
Semiannual Report to the Atomic Energy Commission, September 1964: No Description Available.
Internal Depositions of Radionuclides in Man.: No Description Available.
Main research accomplishments during the past three-year period. Annual report: During the current funding period the investigators have purified AP endonuclease to yield a peptide Mr=32000. The rat cDNA for S3 has been cloned into E. coli and has been expressed there. Enzyme activities observed appear to be the same as those of UV endonuclease III.
1993 Annual report on scientific programs: A broad research program on the sciences of complexity: This report provides a summary of many of the research projects completed by the Santa Fe Institute (SFI) during 1993. These research efforts continue to focus on two general areas: the study of, and search for, underlying scientific principles governing complex adaptive systems, and the exploration of new theories of computation that incorporate natural mechanisms of adaptation (mutation, genetics, evolution).
Studies of DNA duplexes containing damaged thymines: We prepared DNA containing two of the major forms of damaged thymidine: thymine glycol and urea.
Laboratory Studies on the Removal of Plutonium From Laundry Wastes: No Description Available.
Argonne Cancer Research Hospital Semiannual Report on Medical Research to the Atomic Energy Commission: Separate abstracts were prepared on the 12 sections of this report. Abstracts covering 4 sections have previously appeared in NSA. A list is included of staff publications during the period covered by this report. (C.H.)
Argonne Cancer Research Hospital Semiannual Report on Medical Research to the Atomic Energy Commission: Separate abstracts were prepared on 11 sections of this report. A list is included of staff publications during the period. (C.H.)
DIVISION OF BIOLOGICAL AND MEDICAL RESEARCH QUARTERLY REPORT, NOVEMBER, DECEMBER, 1951, JANUARY, 1952: No Description Available.
Construction of a genome-wide human BAC-Unigene resource. Final progress report, 1989--1996: Currently, over 30,000 mapped STSs and 27,000 mapped Unigenes (non-redundant, unigene sets of cDNA representing EST clusters) are available for human alone. A total of 44,000 Unigene cDNA clones have been supplied by Research Genetics. Unigenes, or cDNAs are excellent resource for map building for two reasons. Firstly, they exist in two alternative forms -- as both sequence information for PCR primer pairs, and cDNA clones -- thus making library screening by colony hybridization as well as pooled library PCR possible. The authors have developed an efficient and robust procedure to screen genomic libraries with large number of DNA probes. Secondly, the linkage and order of expressed sequences, or genes are highly conserved among human, mouse and other mammalian species. Therefore, mapping with cDNA markers rather than random anonymous STSs will greatly facilitate comparative, evolutionary studies as well as physical map building. They have currently deconvoluted over 10,000 Unigene probes against a 4X coverage human BAC clones from the approved library D by high density colony hybridization method. 10,000 batches of Unigenes are arrayed in an imaginary 100 X 100 matrix from which 100 row pools and 100 column pools are obtained. Library filters are hybridized with pooled probes, thus reducing the number of hybridization required for addressing the positives for each Unigene from 10,000 to 200. Details on the experimental scheme as well as daily progress report is posted on the Web site (http://www.tree.caltech.edu).
PRINCIPLES OF RADIOLOGICAL PHYSICS: No Description Available.
Molecular genetics of cancer: This volume contains abstracts of oral and poster presentations made at the LIX Cold Springs Harbor Symposium on Quantitative Biology held June 1--8, 1994.
The tomography beamline at the National Synchrotron Light Source: We compared the image contrast of a monochromatic CT, Multiple Energy Computed Tomography (MECT), and conventional CT scanner using phantoms. The experimental results indicate that monochromatic CT, with beam energy tuned just above the iodine K-edge, has about a 3 fold advantage in iodine contrast over conventional CT with a 120 kVp beam. Modeling using the same beams at a 3 rad dose and 3 mm slice height on an 18 cm diameter acrylic phantom, the simulations show a noise of 1.2 HU for MECT and 1.9 HU for CCT. Furthermore, despite the Cupping-effect corrections the bone contrast is lower in CCT and varies by 24 HU moving from the phantom`s center to the edge; this indicates an advantage for MECT in detecting and quantifying lesions differing from surrounding tissue by their mean atomic number.
On the computational complexity of sequence design problems: Inverse protein folding concerns the identification of an amino acid sequence that folds to a given structure. Sequence design problems attempt to avoid the apparent difficulty of inverse protein folding by defining an energy that can be minimized to find protein-like sequences. The authors evaluate the practical relevance of two sequence design problems by analyzing their computation complexity. They show that the canonical method of sequence design is intractable, and describe approximation algorithms for this problem. The authors also describe an efficient algorithm that exactly solves the grand canonical method. The analysis shows how sequence design problems can fail to reduce the difficulty of the inverse protein folding problem, and highlights the need to analyze these problems to evaluate their practical relevance.
SEMIANNUAL PROGRESS REPORT FOR THE PERIOD ENDING JUNE 30, 1968.: No Description Available.
NMR solution structures of adducts derived from the binding of polycyclic aromatic diol epoxides to DNA: Site-specifically modified oligonucleotides were derived from the reactions of stereoisomeric polycyclic aromatic diol epoxide metabolite model compounds with oligonucleotides of defined base composition and sequence. The NMR solution structures of ten different adducts studied so far are briefly described, and it is shown that stereochemical factors and the nature of the oligonucleotide context of the complementary strands, exert a powerful influence on the conformational features of these adducts.
Mapping site-specific endonuclease binding to DNA by direct imaging with AFM: Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1,000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 10{sup 4}, the authors demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS{sup +}) or two (pMP{sup 32}) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in the preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.
Microbiology and physiology of anaerobic fermentation of cellulose. Progress report (4/30/91--4/30/92) and outline of work for the period 9/1/92--9/1/93: The authors are continuing their efforts to partly dissociate the cellulolytic enzyme complex of C. thermocellum. This complex named cellulosome (also existing as polycellulosome) consists of perhaps as many as 26 different subunits. It is extremely resistant to dissociation and denaturation. Treatments with urea and SDS have little effect unless the latter treatment is at high temperature. Significantly, some of the subunits after SDS dissociation have CMCase (endoglucanase) activity but no activity toward crystalline cellulose. The only reported success of hydrolysis of crystalline cellulose by cellulosomal subunits is by Wu et al. who isolated two protein fractions labeled SL and SS which when combined exhibit a low (about 1% of the original cellulosome) activity toward crystalline cellulose. The long standing goal is still to determine the activities of the individual subunits, to characterize them, to find out how they are associated in the cellulosome, and to establish the minimum number of subunits needed for efficient hydrolysis of crystalline cellulose. This report also presents the results of experiments on cellulose hydrolysis in aerobic fungi, as well as other anaerobic bacteria.
The Human Genome Project: Information access, management, and regulation. Final report: The Human Genome Project is a large, internationally coordinated effort in biological research directed at creating a detailed map of human DNA. This report describes the access of information, management, and regulation of the project. The project led to the development of an instructional module titled The Human Genome Project: Biology, Computers, and Privacy, designed for use in high school biology classes. The module consists of print materials and both Macintosh and Windows versions of related computer software-Appendix A contains a copy of the print materials and discs containing the two versions of the software.
Second generation biological signal processor. Final progress report, February 15, 1993--February 14, 1995: The Biological Information Signal Processor (BISP) is a VLSI ASIC implementation of the dynamic programming methods favored for direct sequence-to-sequence comparison in order to discover local as well as global similarities. These methods, based on the local algorithm of Smith and Waterman provide the most mathematically robust solution to the problem of sequence alignment (determination of the optimal character-to-character registration between the two sequence, including relative insertions and deletions, indels). BISP provides a complete implementation of the standard Smith and Waterman algorithm in a systolic array that allows full parameterization and several novel extensions to the algorithm. BISP operates at supercomputer speeds from a VME board on a Sun workstation. Each VME array provides a complete systolic pipeline for comparison and multiple arrays can be combined linearly in order to increase the pipeline length. Overall performance is a function of the IO speed of the pipelined disk-resident data and the length of the array.
How do plants enlarge? A balancing act. Workship on plant growth: Final report: There are signals that coordinate the development of various plant parts and thus the rates of enlargement of various plant parts and these were explored during the workshop. The participants tried to systematize their knowledge and identify over-arching concepts that need more investigation. It was generally agreed that the cell wall cannot be viewed as a passive plastic material. Synthesis and deposition take place and cause changes in the molecular architecture of the wall. Questions arise from the fact that the wall is not a constant or uniform structure but undergoes highly organized changes during enlargement while bearing a considerable load. Recent advances in signaling, biochemical analysis and ultrastructure visualization are beginning to relate to the molecular load-bearing and enzymatic activities in the wall. The participants agreed that there probably is enough information to begin developing a comprehensive model that would balance wall effects with the limitation of growth by transport, especially for water, and this could help clarify events occurring at different time scales and places. Beyond that, there seems to be a need to resolve problems of solute transport and wall behavior that are poorly understood in growing regions, leaving many promising areas for future experiments. Understanding each balancing act seems to be just the beginning.
Mechanisms and determinants of RNA turnover in higher plants. Final report, 1991--1995: Studies are related on post-translation mechanisms controlling plant gene expression. It was shown that rbcS mRNA is degraded into discreet set of 5` proximal products.
Fifth Atomic Energy Commission Air Cleaning Conference Held at Harvard Air Cleaning Laboratory, Boston, June 24-27, 1957: (Separate abstracts of each of the papers presented have been prepared.)
Research in Radiobiology. Annual Report of Work in Progress on the Chronic Toxicity Program: No Description Available.
Nutritional supplements as radioprotectors -- A review and proposal: The scientific literature contains several reports that show nutritional substances, such as vitamins, minerals, and phytochemicals (plant chemicals), provide substantial radioprotective effects in animal studies. Incorporating these substances to the human diet, already voluntarily practiced by a large segment of the population, in addition to providing other favorable health effects, may also provide a radioprotective effect. This potential radioprotective effect would be very useful in mitigating the effects of occupational radiation exposure to astronauts (especially future Mars explorers), airline crews, nuclear workers, both commercial and government, and populations exposed to nuclear accidents, e.g. Chernobyl. This paper reviews the existing evidence of radioprotective effects by nutritional supplements and proposes that their efficacy be evaluated, first with animal studies, followed by human tests with astronauts and cosmonauts on long-term missions, such as to the Mir space station and the International Space Station (ISS).
[Developing a physical map of human chromosome 22 using Pace electrophoresis and large fragment cloning]. Annual report, October 1, 1990--September 30, 1991: Recent technical progress in molecular biology has made the mapping of entire mammalian chromosomes an attainable goal. However, a number of problems must still be overcome before genome mapping becomes rapid, efficient, and reliable. The limited size of cosmid inserts, as well as their tendency to rearrange, necessitates construction of very large libraries for mapping, due to the many gaps encountered in aligning cosmid contigs. Larger fragments can be cloned using the phage P1, but the maximum size of cloned inserts is fixed at only twice that of cosmids. The power of YACs has been demonstrated in isolating large regions of human DNA, recombining them to build up even larger regions and closing gaps in cosmid based maps. However, existing YAC libraries contain a high proportion of chimeric clones, and YACs are difficult to use for detailed mapping, often requiring recloning into cosmid sized pieces. The work has addressed some of these issues by creating an alternative and complementary approach to cloning and mapping large DNA.
The computational linguistics of biological sequences: This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Protein sequences are analogous in many respects, particularly their folding behavior. Proteins have a much richer variety of interactions, but in theory the same linguistic principles could come to bear in describing dependencies between distant residues that arise by virtue of three-dimensional structure. This tutorial will concentrate on nucleic acid sequences.
How do plants enlarge? A balancing act; Final report: Cells of plants are surrounded by strong walls that prevent rupture from internal pressures that can be two or three times that of an automobile tire. In this way, the walls protect the cytoplasm. However, at the same time, the cells can enlarge as they grow. How this balancing act works and how it enlarges the plant were the subject of a recent conference at the University of Delaware in Lewes. The aim was to identify areas for future research that could explain the enlargement of whole plants. There is a large practical need to predict and modify plant enlargement but the additional processes that overlie the molecular ones need to be integrated with the molecular information before a picture will emerge. How best to accomplish this involved input from cross-disciplinary areas in biomechanics, physics and engineering as well as molecular biology, biochemistry and ultrastructure.

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