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PubMed2003

Glycosylation motifs that direct arabinogalactan addition to arabinogalactan-proteins.

Hydroxyproline (Hyp)-rich glycoproteins (HRGPs) participate in all aspects of plant growth and development. HRGPs are generally highly O-glycosylated through the Hyp residues, which means carbohydrates help define the interactive molecular surface and, hence, HRGP function. The Hyp contiguity hypothesis predicts that contiguous Hyp residues are sites of HRGP arabinosylation, whereas clustered noncontiguous Hyp residues are sites of galactosylation, giving rise to the arabinogalactan heteropolysaccharides that characterize the arabinogalactan-proteins. Early tests of the hypothesis using synthetic genes encoding only clustered noncontiguous Hyp in the sequence (serine [Ser]-Hyp-Ser-Hyp)(n) or contiguous Hyp in the series (Ser-Hyp-Hyp)(n) and (Ser-Hyp-Hyp-Hyp-Hyp)(n) confirmed that arabinogalactan polysaccharide was added only to noncontiguous Hyp, whereas arabinosylation occurred on contiguous Hyp. Here, we extended our tests of the codes that direct arabinogalactan polysaccharide addition to Hyp by building genes encoding the repetitive sequences (alanine [Ala]-proline [Pro]-Ala-Pro)(n), (threonine [Thr]-Pro-Thr-Pro)(n), and (valine [Val]-Pro-Val-Pro)(n), and expressing them in tobacco (Nicotiana tabacum) Bright-Yellow 2 cells as fusion proteins with green fluorescent protein. All of the Pro residues in the (Ala-Pro-Ala-Pro)(n) fusion protein were hydroxylated and consistent with the hypothesis that every Hyp residue was glycosylated with arabinogalactan polysaccharide. In contrast, 20% to 30% of Pro residues remained non-hydroxylated in the (Thr-Pro-Thr-Pro)(n), and (Val-Pro-Val-Pro)(n) fusion proteins. Furthermore, although 50% to 60% of the Hyp residues were glycosylated with arabinogalactan polysaccharide, some remained non-glycosylated or were arabinosylated. These results suggest that the amino acid side chains of flanking residues influence the extent of Pro hydroxylation and Hyp glycosylation and may explain why isolated noncontiguous Hyp in extensins do not acquire an arabinogalactan polysaccharide but are arabinosylated or remain non-glycosylated.

Amino Acid Motifs↗
PubMed2004

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.

MOTIVATION: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. RESULTS: Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. AVAILABILITY: http://www.molgenis.nl

Computational Biology↗
PubMed2005

Comparison of deterministic and Monte Carlo methods in shielding design.

In shielding calculation, deterministic methods have some advantages and also some disadvantages relative to other kind of codes, such as Monte Carlo. The main advantage is the short computer time needed to find solutions while the disadvantages are related to the often-used build-up factor that is extrapolated from high to low energies or with unknown geometrical conditions, which can lead to significant errors in shielding results. The aim of this work is to investigate how good are some deterministic methods to calculating low-energy shielding, using attenuation coefficients and build-up factor corrections. Commercial software MicroShield 5.05 has been used as the deterministic code while MCNP has been used as the Monte Carlo code. Point and cylindrical sources with slab shield have been defined allowing comparison between the capability of both Monte Carlo and deterministic methods in a day-by-day shielding calculation using sensitivity analysis of significant parameters, such as energy and geometrical conditions.

Algorithms↗
PubMed2006

Potential automata. Application to the genetic code III.

In previous notes, we have described both mathematical properties of potential (n-switches) and potential-Hamiltonian (Liénard systems) continuous differential systems, and also biological applications, especially those concerning primitive cyclic RNAs related to the genetic code. In the present note, we give a general definition of a potential automaton, and we show that a discrete Hopfield-like system already introduced by Goles et al. is a good candidate for such a potential automaton: it has a Lyapunov functional that decreases on its trajectories and whose time derivative is just its discrete velocity. Then we apply this new notion of potential automaton to the genetic code. We show in particular that the consideration of only physicochemical properties of amino-acids, like their molecular weight, hydrophobicity and ability to create hydrogen bonds suffices to build a potential decreasing on trajectories corresponding to the synonymy classes of the genetic code. Such an 'a minima' construction reinforces the classical stereochemical hypothesis about the origin of the genetic code and authorizes new views about the optimality of its synonymy classes.

Amino Acids↗
PubMed1982

Identification of the 45-base-long primordial building block of the entire class I major histocompatibility complex antigen gene.

Within the 885-base-long incomplete coding sequence for the mouse class I major histocompatibility complex (MHC) antigen H-2Kb heavy chain, we have identified 32 recurring base oligomers (1 decamer, 4 octamers, 9 heptamers, and 18 hexamers), the decamer being T-C-A-C-C-C-T-G-A-G. The compilation of these recurring base oligomers led to the identification of the 45-base-long primordial building block for this class of genes which is: C-C-T-G-C-G-G-A-C-A-A-T-G-T-C-A-C-C-C-T-G-A-G-C-T-G-C-T-G-G-G-C-T-C-T-G-G-G-C-G - T-T-G-A-C. Inasmuch as these base oligomers that recurred within the mouse H-2Kb coding sequence proper also recurred within the adjacent, transcribed noncoding sequence, we conclude that the entire approximately equal to 4,000-base-long germ-line DNA segment containing eight or nine separate exons of the coding sequence for class I MHC antigen heavy chains can be construed as having evolved from tandem repeats of this one 45-base-long primordial building block.

Amino Acid Sequence↗
PubMed1996

Man-made mineral fibre boards in buildings--health risks caused by quality deficiencies.

The Institute of Hygiene was requested to determine causes and scope of health complaints made by the employees of Haldensleben district administration after sound absorbing mineral fibre boards had been installed as suspended ceilings. The boards were coated with a lean water-carried paint; however, the edges, which were partially frayed, were not coated. The air inside the rooms was measured on all four storeys of the building, followed by scanning electron microscopy in compliance with VDI Code 3492. In addition, measurements showed fibres with diameters of > 3 microns which are not subject to the regulations for carcinogenic substances, but, in contrast to the thinner fibres, they may cause irritations of skin and mucosa. The employees were questioned about their health problems. At the beginning of 1994, a total of 79 of the 133 employees complained about itching, reddening and burning of their eyes as well as irritations of the upper respiratory tract. More than 50% had consulted a doctor. Late in 1994, another questionnaire survey was completed. The fibre content of the office air was determined to vary from 1000 to 3500 fibres/m3 and, in addition, 100-200 fibres with diameters of > 3 microns. Our investigations showed that there is an interrelationship between the degree of dust accumulation in the offices and health complaints. Independently of the current discussion of the cancer causing potential of thin man-made mineral fibres, the very long and thick mineral fibres (> 3 microns in diameter) are of topical importance to health.

Air Pollution, Indoor↗
PubMed2004

The self-organization of speech sounds.

The speech code is a vehicle of language: it defines a set of forms used by a community to carry information. Such a code is necessary to support the linguistic interactions that allow humans to communicate. How then may a speech code be formed prior to the existence of linguistic interactions? Moreover, the human speech code is discrete and compositional, shared by all the individuals of a community but different across communities, and phoneme inventories are characterized by statistical regularities. How can a speech code with these properties form? We try to approach these questions in the paper, using the "methodology of the artificial". We build a society of artificial agents, and detail a mechanism that shows the formation of a discrete speech code without pre-supposing the existence of linguistic capacities or of coordinated interactions. The mechanism is based on a low-level model of sensory-motor interactions. We show that the integration of certain very simple and non-language-specific neural devices leads to the formation of a speech code that has properties similar to the human speech code. This result relies on the self-organizing properties of a generic coupling between perception and production within agents, and on the interactions between agents. The artificial system helps us to develop better intuitions on how speech might have appeared, by showing how self-organization might have helped natural selection to find speech.

Biological Evolution↗
PubMed2003

In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon.

MOTIVATION: Motif-prediction algorithm capabilities for the analysis of bacterial regulatory networks and the prediction of new regulatory sites can be greatly enhanced by the use of comparative genomics approaches. In this study, we make use of a consensus-building algorithm and comparative genomics to conduct an in-depth analysis of the LexA-regulon of gamma proteobacteria, and we use the inferred results to study the evolution of this regulatory network and to examine the usefulness of the control sequences and gene contents of regulons in phylogenetic analysis. RESULTS: We show, for the first time, the substantial heterogeneity that the LexA-regulon of gamma proteobacteria displays in terms of gene content and we analyze possible branching points in its evolution. We also demonstrate the feasibility of using regulon-related information to derive sound phylogenetic inferences. AVAILABILITY: Complementary analysis data and both the source code and the Windows-executable files of the consensus-building software are available at http://www.cnm.es/~ivan/RCGScanner/

Algorithms↗
PubMed2006

Determination of the vertical distribution of radioelements (K, U, Th, Cs) in soils from portable HP-Ge spectrometer measurements: a tool for soil erosion studies.

Soil erosion studies, based on the 137Cs technique, require a lot of time-consuming cores to determine soil loss or gain. We show that portable HP-Ge spectrometer can be used to determine the content and the distribution in the soil of natural and artificial radionuclides. Simulations of gamma-rays transport throughout the soil profile used a Monte Carlo code. The methodology requires a unique undisturbed coring site to build the models, calibrate the spectrometer readings and derive soil denudation or accumulation thickness.

Journal Article↗
PubMed2025

NrdR in Streptococcus and Listeria spp.: DNA Helix Phase Dependence of the Bacterial Ribonucleotide Reductase Repressor.

NrdR is a universal transcriptional repressor of bacterial genes coding for ribonucleotide reductases (RNRs), essential enzymes that provide DNA building blocks in all living cells. Despite its bacterial prevalence, the NrdR mechanism has been scarcely studied. We report the biochemical, biophysical, and bioinformatical characterization of NrdR and its binding sites from two major bacterial pathogens of the phylum Bacillota Listeria monocytogenes and Streptococcus pneumoniae. NrdR consists of a Zn-ribbon domain followed by an ATP-cone domain. We show that it forms tetramers that bind to DNA when loaded with ATP and dATP, but if loaded with only ATP, NrdR forms various oligomeric complexes unable to bind DNA. The DNA-binding site in L. monocytogenes is a pair of NrdR boxes separated by 15-16 bp, whereas in S. pneumoniae, the NrdR boxes are separated by unusually long spacers of 25-26 bp. This observation triggered a comprehensive binding study of four NrdRs from L. monocytogenes, S. pneumoniae, Escherichia coli, and Streptomyces coelicolor to a series of dsDNA fragments where the NrdR boxes were separated by 12-27 bp. The in vitro results were confirmed in vivo in E. coli and revealed that NrdR binds most efficiently when there is an integer number of DNA turns between the center of the two NrdR boxes. The study facilitates the prediction of NrdR binding sites in bacterial genomes and suggests that the NrdR mechanism is conserved throughout the bacterial domain. It sheds light on RNR regulation in Listeria and Streptococcus, and since NrdR does not occur in eukaryotes, opens a way to the development of novel antibiotics.

Ribonucleotide Reductases↗
PubMed2003

Osprey: a network visualization system.

We have developed a software platform called Osprey for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale datasets can be readily combined with Osprey for comparison of different methods.

Computer Communication Networks↗
PubMed2002

Osprey: a network visualization system.

We have developed a software platform called Osprey for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale data sets can be readily combined with Osprey for comparison of different methods.

Computational Biology↗
PubMed2005

Drug-age alerting for outpatient geriatric prescriptions: a joint study using interoperable drug standards.

For more than a decade, the Beers criteria have identified specific medications that should generally be avoided in the geriatric population. Studies that have shown high prevalence rates of these potentially inappropriate medications have used disparate methodologies to identify these medications and hence are difficult to replicate and generalize. In an effort to improve prescribing behavior, we are building a drug-age alerting system utilizing standard drug coding systems for use in our Electronic Health Record (EHR) systems.

Aged↗
PubMed1995

The phylogeny of tRNAs seems to confirm the predictions of the coevolution theory of the origin of the genetic code.

An extensive analysis of the evolutionary relationships existing between transfer RNAs, performed using parsimony algorithms, is presented. After building up an estimate of the tRNA ancestral sequences, these sequences are then compared using certain methods. The results seem to suggest that the coevolution hypothesis (Wong, J.T., 1975, Proc. Natl. Acad. Sci. USA 72, 1909-1912) that sees the genetic code as a map of the biosynthetic relationships between amino acids is further supported by these results, as compared to the hypotheses that see the physicochemical properties of amino acids as the main adaptative theme that led to the structuring of the genetic code.

Amino Acid Sequence↗
PubMed2002

A novel peptide-based encoding system for "one-bead one-compound" peptidomimetic and small molecule combinatorial libraries.

The "one-bead one-compound" (OBOC) combinatorial library method is highly efficient, especially when used with well-established on-bead binding or functional assays. Literally, millions of compounds can be screened concurrently within 1 to 2 days. However, structure determination of peptidomimetic and small molecule compounds on one single bead is not trivial. A novel, highly efficient, and robust peptide-based encoding system has been developed for OBOC peptidomimetic and small molecule combinatorial libraries. In this system, topologically segregated bifunctional beads, which are made by a simple biphasic solvent strategy, are employed for the preparation and screening of an OBOC combinatorial peptidomimetic and small molecule libraries. Testing molecules are on the outer layer, and the coding tags in the interior of the bead do not interfere with screening. The coding tag is a peptide containing a large number of unnatural alpha-amino acids derived from different building blocks used for generating the peptidomimetic or small molecule. By coupling common building blocks simultaneously to the scaffold of the testing compound and to the side chains of the alpha-amino acids on the coding peptide, extra synthetic steps are eliminated and the amount of undesirable side products is minimized. Positive bead decoding is easy and straightforward as there is no need for cleavage and retrieval of the coding tag, and positive beads can be sequenced directly with Edman degradation. To demonstrate the efficiency and simplicity of our encoding system, an encoded 158 400-member model peptidomimetic library has been generated and screened for ligands that bind to streptavidin. Potent and novel ligands with clear motifs have been identified.

Amino Acids↗
PubMed2002

Multi-disciplinary working in a forensic mental health setting: ethical codes of reference.

This paper reports on a small research project on multidisciplinary team-working within a medium secure forensic unit in the United Kingdom. Although multidisciplinary team working is widely accepted as an effective strategy for the delivery of healthcare services in modern society it is also recognized that interdisciplinary problems can also occur. This study developed two questionnaires, one being delivered to a number of groups and teams in the secure unit, whilst the second one was geared to individuals. A thematic analysis was employed to develop category building and concept formation. The results highlighted a three-level ethical code referencing system that was employed by both individuals and groups. Within this, three domains, or trajectories, were identified that were polarized continuums of main tensions for multidisciplinary staff working in forensic practice.

Clinical Competence↗
PubMed1995

Injury severity and probability of survival assessment in trauma patients using a predictive hierarchical network model derived from ICD-9 codes.

UNLABELLED: Accurate assessment of injury severity is critical for decision making related to the prevention, triage, and treatment of injured patients. Presently, the standard method of controlling for variations of injury severity between groups has been based upon the Injury Severity Score (ISS) and the Trauma Score and the Trauma and Injury Severity Score (TRISS) methodology. The purpose of this study was to attempt to build upon previous work using International Classification of Diseases, ninth revision (ICD-9) coded diagnosis, and procedure information available from standard hospital discharge abstracts (UB-82 Billing format) to create a hierarchical network to provide a tool for predicting injury severity and probability of survival. METHODS: Data were obtained for this analysis from the North Carolina Medical Database. Data were available on all trauma patients admitted to hospitals in North Carolina from January 1, 1988 until June 30, 1992. The dependent variable of interest was the patient's survival after injury, coded as live or die. The independent variables used in the study included the ISS derived using the technique described by MacKenzie Abbreviated Injury Score (AIS) and body system maximum AIS scores, mortality risk ratios derived from the ICD-9-DM primary, secondary, and tertiary diagnoses, primary and secondary procedures as described in previous work, age and gender. Network generation used a commercial software package, AIM (Abtech Corp., Charlottesville, Va.), which is a numeric modeling tool that automatically "learns" knowledge from a data base of examples. RESULTS: In the test data set an ISS and a prediction of survival based upon the derived network were calculated for each and every patient. The relative predictive power of these two scores were compared by calculating the overall accuracy, sensitivity, and specificity and the false positive and false negative rates. The receiver operator characteristic curves demonstrate that the network is a more effective tool in predicting the outcome of trauma patients. All the measures of predictive power show that the network was the better predictor of outcome than the ISS. CONCLUSIONS: Given the recognized limitations of the ISS, the widespread availability of the ICD-9 coded diagnoses and procedures, and the availability of many state and regional data bases that have no ISS or Trauma Score, the purpose of this study was to assess the ability of a network derived from limited but widely available hospital discharge data to predict the outcome of injured patients. The study confirms previous work showing that the ICD-9 codes were strongly associated with outcome. The study demonstrated that the network created from these data was a better predictor of outcome than the derived ISS. When the results of the network were compared with other published series, the network, created without access to physiologic information, was almost as accurate, sensitive, and specific as reported values for TRISS and A Severity Characterization of Trauma (ASCOT). Because the present study is the first of its type, further investigations are needed to validate these findings. If other studies corroborate this study, a network model based upon ICD-9 codes could become the principal method for grading injury severity. This would provide superior predictive power of injury severity with important cost savings and universal application.

Adult↗
PubMed2002

VI. Uterine fibroid embolization: developing a clinical service.

Building a uterine fibroid embolization (UFE) practice can be a complex process. Choices must be made regarding whether to align oneself with a gynecologist or to accept direct referrals. For the interventional radiologist, the responsibilities of evaluation and patient care pose unique and time-consuming administrative and clinical challenges. Physician extenders, either nurse practitioners or physician's assistants, play key roles as clinical coordinators by guiding the patient through the medical system and making certain that she is cleared for the procedure medically and logistically. In some settings, they may also assist in many of the technical aspects of the procedure and postoperative care. Interventional radiologists must be prepared for battles with insurance companies and be willing to go through the appeals process. Business officers must also be trained to properly code for the procedures to insure optimal reimbursement. The success of building a UFE practice may also be bolstered by directly marketing to patients and by providing them with access via the Internet.

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