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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.
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.
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.
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.
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.
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.
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).
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.
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.
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.
Intelligent systems for the molecular biologist: 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. In this paper, one objective is to identify properties of DNA sequences that determine their function, by computer-aided statistical analysis and to accurately predict its function, given a new sequence. A related problem is to predict protein structure and function from the sequence.
Doses delivered to normal brain under different treatment protocols at Brookhaven National Laboratory: As of October 31, 1996, 23 glioblastoma multiforme patients underwent BNCT under several treatment protocols at the Brookhaven Medical Research Reactor. For treatment planning and dosimetry purposes, these protocols may be divided into four groups. The first group comprises protocols that used an 8-cm collimator and allowed a peak normal brain dose of 10.5 Gy-Eq to avolume of 1 cm{sup 3} were the thermal neutron flux was maximal (even if it happened to be in the tumor volume). The second group differs from the first in that it allowed a peak normal brain dose of 12.6 Gy-Eq. The protocols of the third and fourth groups allowed the prescribed peak normal brain dose of 12.6 Gy-Eq to be outside of the tumor volume, used a 12-cm collimator and, respectively, uni- or bilateral irradiations. We describe the treatment planning procedures and report the doses delivered to various structures of the brain.
Correlation of clinical outcome to the estimated radiation dose from Boron Neutron Capture Therapy (BNCT): A phase I/II trial delivering a single fraction of BNCT using p-Boronophenylalanine-Fructose and epithermal neutrons at the the Brookhaven Medical Research Reactor was initiated in September 1994. The primary endpiont of the study was to evaluate the feasibility and safety of a given BNCT dose. The clinical outcome of the disease was a secondary endpoint of the study. The objective of this paper is to evaluate the correlation of the clinical outcome of patients to the estimated radiation dose from BNCT.
Molecular ecology of aquatic microbes: Abstracts of reports are presented from a meeting on Molecular Ecology of Aquatic Microbes. Topics included: opportunities offered to aquatic ecology by molecular biology; the role of aquatic microbes in biogeochemical cycles; characterization of the microbial community; the effect of the environment on aquatic microbes; and the targeting of specific biological processes.
Source description and sampling techniques in PEREGRINE Monte Carlo calculations of dose distributions for radiation oncology: We outline the techniques used within PEREGRINE, a 3D Monte Carlo code calculation system, to model the photon output from medical accelerators. We discuss the methods used to reduce the phase-space data to a form that is accurately and efficiently sampled.
Environmental stress-mediated changes in transcriptional and translational regulation of protein synthesis in crop plants. Final report: The research described in this final report focused on the influence of stress agents on protein synthesis in crop plants (primarily soybean). Investigations into the `heat shock` (HS) stress mediated changes in transcriptional and translocational regulation of protein synthesis coupled with studies on anaerobic water deficit and other stress mediated alterations in protein synthesis in plants provided the basis of the research. Understanding of the HS gene expression and function(s) of the HSPs may clarify regulatory mechanisms operative in development. Since the reproductive systems of plants if often very temperature sensitive, it may be that the system could be manipulated to provide greater thermotolerance.
A treatment planning comparison of BPA- or BSH-based BNCT of malignant gliomas: Accurate delivery of the prescribed dose during clinical BNCT requires knowledge (or reasonably valid assumptions) about the boron concentrations in tumor and normal tissues. For conversion of physical dose (Gy) into photon-equivalent dose (Gy-Eq), relative biological effectiveness (RBE) and/or compound-adjusted biological effectiveness (CBE) factors are required for each tissue. The BNCT treatment planning software requires input of the following values: the boron concentration in blood and tumor, RBEs in brain, tumor and skin for the high-LET beam components, the CBE factors for brain, tumor, and skin, and the RBE for the gamma component.
Computational methods for molecular docking: 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. Recently, it has been demonstrated that the knowledge of the three-dimensional structure of the protein can be used to derive new protein ligands with improved binding properties. This tutorial focuses on the following questions: What is its binding affinity toward a particular receptor? What are putative conformations of a ligand at the binding site? What are the similarities of different ligands in terms of their recognition capabilities? Where and in which orientation will a ligand bind to the active site? How is a new putative protein ligand selected? An overview is presented of the algorithms which are presently used to handle and predict protein-ligand interactions and to dock small molecule ligands into proteins.
Microbiology and physiology of anaerobic fermentation of cellulose. Annual report for 1990, 1992, 1993 and final report: This report focuses on the bioconversion of cellulose to methane by various anaerobes. The structure and enzymatic activity of cellulosome and polycellulosome was studied in Clostridium thermocellum. The extracellular enzymes involved in the degradation of plant material and the physiology of fermentation was investigated in anaerobic fungi. Enzymes dealing with CO, CO{sub 2}, H{sub 2}, CH{sub 3}OH, as well as electron transport and energy generation coupled to the acetyl-CoA autotrophic pathway was studied in acetogenic clostridia.
Protein sequence comparison and protein evolution: 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. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.
The human genome: Some assembly required. Final report: The Human Genome Project promises to be one of the most rewarding endeavors in modern biology. The cost and the ethical and social implications, however, have made this project the source of considerable debate both in the scientific community and in the public at large. The 1994 Graduate Student Symposium addresses the scientific merits of the project, the technical issues involved in accomplishing the task, as well as the medical and social issues which stem from the wealth of knowledge which the Human Genome Project will help create. To this end, speakers were brought together who represent the diverse areas of expertise characteristic of this multidisciplinary project. The keynote speaker addresses the project`s motivations and goals in the larger context of biological and medical sciences. The first two sessions address relevant technical issues, data collection with a focus on high-throughput sequencing methods and data analysis with an emphasis on identification of coding sequences. The third session explores recent advances in the understanding of genetic diseases and possible routes to treatment. Finally, the last session addresses some of the ethical, social and legal issues which will undoubtedly arise from having a detailed knowledge of the human genome.
Preliminary experience with monoenergetic photon mammography: We are using a beam port at the National Synchrotron Light Source facility at Brookhaven National Laboratory as a source of monoenergetic photons. The photon source is radiation from a bending magnet on the X-ray storage ring and provides a usable X-ray spectrum from 5 keV to over 50 keV. A tunable crystal monochromotor is used for energy selection. The beam is 79mm wide and 0.5 mm high. We imaged the ACR mammography phantom and a contrast-detail phantom using a phosphor plate as the unaging detector. Phantom images were obtained at 16, 18, 20 and 22 keV. Phantom thickness varied from 15 mm to 82 mm. These images were compared to images obtained with a conventional dedicated mammography unit. Subjective preliminary results show that image contrast of the monoenergetic images is similar to those obtained from the conventional x-ray source with somewhat sharper and cleaner images from the monoenergetic source. Quantitative analysis shows that the monoenergetic images have improved contrast compared to the polyenergetic derived images. Entrance skin dose measurements show a factor of 5 to 10 times less radiation for the monoenergetic images with equivalent or better contrast Although there remain a number of technical problems to be addressed and much more work to be done, we are encouraged to further explore the use of monoenergetic imaging.
Control of beryllium powder at a DOE facility: Beryllium is contained in a number of domestic and national defense items. Although many items might contain beryllium in some manner, few people need worry about the adverse effects caused by exposure to beryllium because it is the inhalable form of beryllium that is most toxic. Chronic beryllium disease (CBD), a granulomas and fibrotic lung disease with long latency, can be developed after inhalation exposures to beryllium. It is a progressive, debilitating lung disease. Its occurrence in those exposed to beryllium has been difficult to predict because some people seem to react to low concentration exposures whereas others do not react to high concentration exposures. Onset of the disease frequently occurs between 15 to 20 years after exposure begins. Some people develop the disease after many years of low concentration exposures but others do not develop CBD even though beryllium is shown to be present in lungs and urine. Conclusions based on these experiences are that their is some immunological dependence of developing CBD in about 3--4% of the exposed population, but the exact mechanism involved has not yet been identified. Acute beryllium disease can occur after a single exposure to a concentration of greater than 0.100 mg/m3 (inhalation exposure); it is characterized by the development of chemical pneumoconiosis, a respiratory disease. The acute effect of skin contact is a dermatitis characterized by itching and reddened, elevated, or fluid-accumulated lesions which appear particularly on the exposed surfaces of the body, especially the face, neck, arms, and hands. Small particles of beryllium that enter breaks in the skin can lead to the development of granulomas and/or open sores that do not heal until the beryllium has been removed. Our interest is only airborne beryllium, which is found in areas that machine or produce beryllium.
An editing environment for DNA sequence analysis and annotation: This paper presents a computer system for analyzing and annotating large-scale genomic sequences. The core of the system is a multiple-gene structure identification program, which predicts the most probable gene structures based on the given evidence, including pattern recognition, EST and protein homology information. A graphics-based user interface provides an environment which allows the user to interactively control the evidence to be used in the gene identification process. To overcome the computational bottleneck in the database similarity search used in the gene identification process, the authors have developed an effective way to partition a database into a set of sub-databases of related sequences, and reduced the search problem on a large database to a signature identification problem and a search problem on a much smaller sub-database. This reduces the number of sequences to be searched from N to O({radical}N) on average, and hence greatly reduces the search time, where N is the number of sequences in the original database. The system provides the user with the ability to facilitate and modify the analysis and modeling in real time.
[Studies of biologic activation associated with molecular receptor increase and tumor response in ChL6/L6 protocol patients; Studies in phantoms; Quantitative SPECT; Preclinical studies; and Clinical studies]. DOE annual report, 1994--95: The authors describe results which have not yet been published from their associated studies listed in the title. For the first, they discuss Lym-1 single chain genetically engineered molecules, analysis of molecular genetic coded messages to enhance tumor response, and human dosimetry and therapeutic human use radiopharmaceuticals. Studies in phantoms includes a discussion of planar image quantitation, counts coincidence correction, organ studies, tumor studies, and {sup 90}Y quantitation with Bremsstrahlung imaging. The study on SPECT discusses attenuation correction and scatter correction. Preclinical studies investigated uptake of {sup 90}Y-BrE-3 in mice using autoradiography. Clinical studies discuss image quantitation verses counts from biopsy samples, S factors for radiation dose calculation, {sup 67}Cu imaging studies for lymphoma cancer, and {sup 111}In MoAb imaging studies for breast cancer to predict {sup 90}Y MoAb therapy.

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