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PubMed1999

Evidence for the unique function of docosahexaenoic acid during the evolution of the modern hominid brain.

The African savanna ecosystem of the large mammals and primates was associated with a dramatic decline in relative brain capacity associated with little docosahexaenoic acid (DHA), which is required for brain structures and growth. The biochemistry implies that the expansion of the human brain required a plentiful source of preformed DHA. The richest source of DHA is the marine food chain, while the savanna environment offers very little of it. Consequently Homo sapiens could not have evolved on the savannas. Recent fossil evidence indicates that the lacustrine and marine food chain was being extensively exploited at the time cerebral expansion took place and suggests the alternative that the transition from the archaic to modern humans took place at the land/water interface. Contemporary data on tropical lakeshore dwellers reaffirm the above view with nutritional support for the vascular system, the development of which would have been a prerequisite for cerebral expansion. Both arachidonic acid and DHA would have been freely available from such habitats providing the double stimulus of preformed acyl components for the developing blood vessels and brain. The n-3 docosapentaenoic acid precursor (n-3 DPA) was the major n-3-metabolite in the savanna mammals. Despite this abundance, neither it nor the corresponding n-6 DPA was used for the photoreceptor nor the synapse. A substantial difference between DHA and other fatty acids is required to explain this high specificity. Studies on fluidity and other mechanical features of cell membranes did not reveal a difference of such magnitude between even alpha-linolenic acid and DHA sufficient to explain the exclusive use of DHA. We suggest that the evolution of the large human brain depended on a rich source of DHA from the land/water interface. We review a number of proposals for the possible influence of DHA on physical properties of the brain that are essential for its function.

Animals↗

PubMed1983

Immediate and long-term evolution of the blood-venous graft interface. Experimental study in dogs.

Endothelial damage and repair in autogenous saphenous vein grafts was evaluated serially from 30 s to 9 months after implantation into the femoral arteries of 25 dogs. Light and scanning electron microscopy, quantitative morphometry and cytochemistry with specific rabbit antidog factor VIII-related antigen were used. These studies demonstrate: (1) early complete endothelial cell desquamation both on the venous graft and adjacent artery apparently related to dissection and suture; (2) differing early platelet activation on the venous and adjacent arterial wall, platelet aggregates were noted on the adjacent artery, whereas only adhesive platelets are noted on the exposed vein graft; (3) endothelial reconstitution being initiated after 10-15 days but not reaching completion even 9 months after implantation; (4) a mediointimal proliferation which is a constant feature. A unique cell possessing both fibroblastic and myocytic characteristics takes part in the process.

Animals↗

PubMed2001

Chemistry and chemical biology of taxane anticancer agents.

Taxol (paclitaxel) and Taxotere (docetaxel) are currently considered to be among the most important anticancer drugs in cancer chemotherapy. The anticancer activity of these drugs is ascribed to their unique mechanism of action, i.e., causing mitotic arrest in cancer cells, leading to apoptosis through inhibition of the depolymerization of microtubules. Although both paclitaxel and docetaxel possess potent antitumor activity, treatment with these drugs often results in a number of undesirable side effects, as well as multidrug resistance (MDR). Therefore, it has become essential to develop new anticancer agents with superior pharmacological properties, improved activity against various classes of tumors, and fewer side effects. This paper describes an account of our research on the chemistry of paclitaxel and taxoid anticancer agents at the biomedical interface, including: 1. The structure-activity relationship (SAR) study of taxoids leading to the development of the "second-generation" taxoids, which possess exceptional activity against drug-resistant cancer cells expressing the MDR phenotype. 2. Development of fluorinated taxoids to study the bioactive conformation of paclitaxel and photoaffinity labeling taxoids for mapping of the drug-binding domain on both microtubules and P-glycoprotein. 3. The synthesis of novel macrocyclic taxoids for the investigation into the common pharmacophore for microtubule stabilizing anticancer agents.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2004

The structure and ligand binding properties of the B. subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteins.

The crystal structure of the Bacillus subtilis YkoF gene product, a protein involved in the hydroxymethyl pyrimidine (HMP) salvage pathway, was solved by the multiwavelength anomalous dispersion (MAD) method and refined with data extending to 1.65 A resolution. The atomic model of the protein shows a homodimeric association of two polypeptide chains, each containing an internal repeat of a ferredoxin-like betaalphabetabetaalphabeta fold, as seen in the ACT and RAM-domains. Each repeat shows a remarkable similarity to two members of the COG0011 domain family, the MTH1187 and YBL001c proteins, the crystal structures of which were recently solved by the Northeast Structural Genomics Consortium. Two YkoF monomers form a tightly associated dimer, in which the amino acid residues forming the interface are conserved among family members. A putative small-ligand binding site was located within each repeat in a position analogous to the serine-binding site of the ACT-domain of the Escherichia coli phosphoglycerate dehydrogenase. Genetic data suggested that this could be a thiamin or HMP-binding site. Calorimetric data confirmed that YkoF binds two thiamin molecules with varying affinities and a thiamine-YkoF complex was obtained by co-crystallization. The atomic model of the complex was refined using data to 2.3 A resolution and revealed a unique H-bonding pattern that constitutes the molecular basis of specificity for the HMP moiety of thiamin.

Amino Acid Sequence↗

PubMed2001

Forced recombination between distinct strains of Maize streak virus.

Recombination between divergent virus genomes is believed to be a major mechanism for generation of novel virus genotypes. We have examined the recombination process in geminiviruses by forcing recombination between two distinct isolates of Maize streak virus (MSV), MSV-Kom and MSV-Set. Heterodimeric agroinfectious constructs containing tandemly cloned mixtures of complete or partial MSV-Set and MSV-Kom genomes were used to simulate a circular dimeric form similar to that which would be expected to occur following a single intermolecular crossing-over event between MSV-Set and MSV-Kom replicative form DNAs at the long intergenic region (LIR)-movement protein gene (MP) interface. We isolated, analysed and biologically characterized many of the recombinant MSV genomes that were generated from the constructs in planta. Apart from having the same simulated breakpoint at the LIR-MP interface, all the genomes examined had a second breakpoint that had been generated through either intramolecular homologous recombination or a replicational release mechanism. The pathogenicities of six predominantly MSV-Kom-like recombinants were tested in maize. While all were capable of producing a symptomatic infection in this host, none was more virulent than MSV-Kom and only two were more virulent than MSV-Set. The two most virulent recombinants were leafhopper transmitted to a range of differentially MSV-resistant maize, wheat and barley genotypes and both were found to have unique biological properties.

Base Sequence↗

PubMed2006

Cruella: developing a scalable tissue microarray data management system.

CONTEXT: Compared with DNA microarray technology, relatively little information is available concerning the special requirements, design influences, and implementation strategies of data systems for tissue microarray technology. These issues include the requirement to accommodate new and different data elements for each new project as well as the need to interact with pre-existing models for clinical, biological, and specimen-related data. OBJECTIVE: To design and implement a flexible, scalable tissue microarray data storage and management system that could accommodate information regarding different disease types and different clinical investigators, and different clinical investigation questions, all of which could potentially contribute unforeseen data types that require dynamic integration with existing data. DESIGN: The unpredictability of the data elements combined with the novelty of automated analysis algorithms and controlled vocabulary standards in this area require flexible designs and practical decisions. Our design includes a custom Java-based persistence layer to mediate and facilitate interaction with an object-relational database model and a novel database schema. User interaction is provided through a Java Servlet-based Web interface. RESULTS: Cruella has become an indispensable resource and is used by dozens of researchers every day. The system stores millions of experimental values covering more than 300 biological markers and more than 30 disease types. The experimental data are merged with clinical data that has been aggregated from multiple sources and is available to the researchers for management, analysis, and export. CONCLUSION: Cruella addresses many of the special considerations for managing tissue microarray experimental data and the associated clinical information. A metadata-driven approach provides a practical solution to many of the unique issues inherent in tissue microarray research, and allows relatively straightforward interoperability with and accommodation of new data models.

Database Management Systems↗

PubMed2004

Effects of keyswitch design and finger posture on finger joint kinematics and dynamics during tapping on computer keyswitches.

OBJECTIVE: To examine the effects of postural and keyswitch characteristics on musculoskeletal tissue loading during tapping on computer keyswitches. DESIGN: We hypothesized that joint torques, stiffness and work parameters differ across keyswitch designs and finger postures typical of those observed during computer keyboard typing. We experimentally measured joint kinematics and calculated joint torques while tapping on different keyswitches in different postures, and analyzed the data using mechanical impedance models. METHODS: Sixteen human subjects tapped with the index finger on computer keyswitches mounted on a sensor which measured vertical and horizontal forces. Miniature electro-optical goniometers mounted dorsally across each finger joint measured joint kinematics. Joint torques were calculated from endpoint forces and joint kinematics using an inverse dynamics algorithm. A linear spring-damper impedance model was fitted to joint torque, position, and velocity during the contact period of each tap. Subjects tapped in three postures approximating those employed during tapping on three rows of a computer keyboard, on four different keyswitches, resulting in 12 conditions. RESULTS: More extended finger posture was associated with greater joint torques, energies, and stiffnesses, despite minimal differences in endpoint forces across posture. Greater keyswitch make forces were associated with increased forces, joint torques and joint stiffnesses, however this relationship was not monotonic. CONCLUSIONS: Joint torques and stiffness parameters differed across keyswitch designs and finger postures. Estimates of joint impedance and work provided a unique perspective into finger dynamics. RELEVANCE: Determining the causes of work-related musculoskeletal disorders is facilitated by characterizing workplace task biomechanics, which can be linked to specific injury mechanisms.

Adult↗

PubMed2005

MuPlex: multi-objective multiplex PCR assay design.

We have developed a web-enabled system called MuPlex that aids researchers in the design of multiplex PCR assays. Multiplex PCR is a key technology for an endless list of applications, including detecting infectious microorganisms, whole-genome sequencing and closure, forensic analysis and for enabling flexible yet low-cost genotyping. However, the design of a multiplex PCR assays is computationally challenging because it involves tradeoffs among competing objectives, and extensive computational analysis is required in order to screen out primer-pair cross interactions. With MuPlex, users specify a set of DNA sequences along with primer selection criteria, interaction parameters and the target multiplexing level. MuPlex designs a set of multiplex PCR assays designed to cover as many of the input sequences as possible. MuPlex provides multiple solution alternatives that reveal tradeoffs among competing objectives. MuPlex is uniquely designed for large-scale multiplex PCR assay design in an automated high-throughput environment, where high coverage of potentially thousands of single nucleotide polymorphisms is required. The server is available at http://genomics14.bu.edu:8080/MuPlex/MuPlex.html.

Algorithms↗

PubMed1997

Using World Wide Web technology for educating students in the health care sector.

The Internet was born in December of 1969 and has grown phenomenally since. Its graphically interactive, user-friendly modality, the World Wide Web (WWW), is younger and growing even more explosively. By its nature, the WWW is a tool ideally and uniquely suited for the advancement education. This paper describes the design, development and the implementation of a Web Site for supporting the education of the students in the Faculty of Nursing at the University of Athens.

Computer Communication Networks↗

PubMed2002

Volumetric virtual body structures.

Understanding the visuospatial aspects of anatomic structures is one of the most important goals of gross anatomy. Creation of realistic three-dimensional structures of human anatomy has thus been a goal of medical doctors and computer scientists. In this paper, we describe a PC/NT based system in which a user can easily select anatomical structures to be created, along with the chosen connected structures. The system then constructs a three-dimensional volumetric model, a virtual body structure, slice-by-slide. Once the virtual structure is assembled it is possible to "walk" through the volume with coronal, sagittal, and transverse views, or at any angle. The dynamic nature of the system is unique in that it allows for real time choice of volumetric body structures to be created, their rapid generation, and the ability to manipulate the resulting visualization.

Anatomy, Regional↗

PubMed1996

Computer-aided discrimination between active and inactive mutants of the N-terminal domain of the bacteriophage lambda repressor.

Binding of the N-terminal domain of the lambda repressor to DNA is coupled to dimerization. Hydrophobic interactions between helix-5 and helix-5' drive the packing at the dimer interface. We have carried out computations of the conformational energy of packing of the fifth helices (and of the helix-4-loop-helix-5 portions) of variants of the lambda repressor operator binding domain, using an ECEPP/3-based packing algorithm. Here, we report the results for 26 mutants chosen among those that hve been characterized experimentally. We find that the relative orientation of the fifth helices for active mutants is very similar to the wild-type. The fifth helices of the inactive mutants have a significantly different relative orientation. This result illustrates that a unique specific orientation pattern of helix-5 relative to helix-5' is required for dimerization-coupled DNA binding activity. This finding is further supported by computational studies of the whole N-terminal domain of ten variants that showed that the active mutants, including the wild-type protein, have similar values of the number of contacts between the two monomers in the dimer, involving two amino acid residues of the fifth helices (positions 84 and 87 in each monomer). A decrease in the number of such contacts abolishes DNA-binding activity. Furthermore, all active mutants have their "DNA-recognition helices", numbers 3 and 3' positioned so that they can fit in the DNA operator like those of the wild-type protein, while some inactive mutants exhibit a substantial change in the relative orientation of their recognition helices.

Algorithms↗

PubMed2000

Innate immunity and the gut.

The intestinal epithelium encounters a unique environment consisting of microbes, both commensals and pathogens, as well as dietary nutrients and antigens. This complex composition necessitates the presence of a dynamic system of defense to contain both pathogenic and commensal bacteria within the lumen yet allow for nutrient absorption. Tight junctions provide protection of the intercellular spaces while other surface molecules, such as intestinal trefoil factor, help to maintain the structural integrity of the epithelium. Other more active processes, including upregulated expression and activation of antimicrobial peptides and enhanced fluid secretion, provide a second level of innate defense. Despite providing the interface between an exuberant immune system and a highly antigenic lumenal environment, the intestinal epithelium must remain quiescent. As such, several novel antiinflammatory mechanisms were recently identified. Studies that elaborate the various aspects of these pathways are discussed in this review.

Journal Article↗

PubMed2004

Mechanisms of failure of total hip replacements: lessons learned from retrieval studies.

The value of implant retrieval analysis in orthopaedic surgery has been well recognized. Prosthetic devices retrieved for cause at revision surgery (for implant failure) or devices retrieved postmortem from patients with clinically successful reconstructions provide a unique set of specimens that can be studied to evaluate the effect of the implant on the host environment and the effect of the host environment on the implant. A systematic analysis of retrieved components, in combination with histologic, radiographic, and clinical data can provide valuable insights into the mechanisms of failure of the biomaterials used in joint replacement applications. From the hip implant retrieval studies reported to date, it has been established that the local reaction to particulate wear debris initiates the formation of a granulomatous tissue that ultimately invades the bone-implant interface and results in aseptic loosening. Cement mantle defects, noncircumferential porous coatings, and screw holes can serve as preferential access pathways for the progression of this granulomatous process yielding distinctive patterns of implant loosening and osteolysis. Continued surveillance of retrieved devices is strongly recommended to deepen our understanding of implant failure mechanisms and to evaluate the impact of newer designs and materials on the performance of joint replacement devices.

Animals↗

PubMed2001

Acoustic waveform inversion with application to seasonal snow covers.

The amplitude and waveform shape of atmospheric acoustic pulses propagating horizontally over a seasonal snow cover are profoundly changed by the air forced into the snow pores as the pulses move over the surface. This interaction greatly reduces the pulse amplitude and elongates the waveform compared to propagation above other ground surfaces. To investigate variations in snow-cover effects, acoustic pulses were recorded while propagating horizontally over 11 different naturally occurring snow covers during two winters. Two inversion procedures were developed to automatically match the observed waveforms by varying the snow-cover parameters in theoretical calculations. A simple frequency-domain technique to match the dominant frequency of the measured waveform suffered from multiple solutions and poor waveform matching, while a time-domain minimization method gave unique solutions and excellent waveform agreement. Results show that the effective flow resistivity and depth of the snow are the parameters controlling waveform shape, with the pore shape factor ratio of secondary importance. Inversion estimates gave flow resistivities ranging from 11 to 29 kN s m(-4), except for two late-season cases where values of 60 and 140 were determined (compared to 345 for the vegetation-covered site in the summer). Acoustically determined snow depths agreed with the measured values in all but one case, when the depth to a snow layer interface instead of the total snow depth was determined. Except for newly fallen snow, the pore shape factor ratio values clustered near two values that appear to correspond to wet (1.0) or dry (0.8) snow.

Acoustics↗

PubMed2002

Evidence based medicine in clinical practice: how to advise patients on the influence of age on the outcome of surgical anterior cruciate ligament reconstruction: a review of the literature.

OBJECTIVE: To determine, using a literature search, whether patient age influences the outcome of surgical reconstruction of a torn anterior cruciate ligament. METHODS: Medline (1966 to present) was searched using the PubMed interface, Embase (1974 to present) using the Datastar system, and the Cochrane Library at the Update Software web site. Papers retrieved from the three databases were independently assessed by two reviewers using preliminary inclusion criteria. Reference lists of papers satisfying the preliminary criteria were then scanned and appropriate papers reviewed. Any new papers in turn had their reference lists scanned, this process continuing until no new papers were identified. Final inclusion criteria were then applied to all papers satisfying the preliminary inclusion criteria. RESULTS: The initial search identified 661 papers. Exclusion of duplicates produced 536 unique papers. Medline contained 445, Embase 185, and the Cochrane Library 31. Of the 536, 523 were assessed by abstract and 12 by full text; one paper was not retrieved. Application of the preliminary inclusion criteria produced 33 papers. Their reference lists contained 950 references. Scanning of these added six new papers to the dataset. These six had their reference lists assessed; no new papers were identified. Four of the 39 papers in the completed dataset satisfied the final inclusion criteria. There was wide variation in the total number of subjects in the four studies, ranging from 22 to 203 patients. The total number of different outcome measures was 17; only one measure was used by all four studies. None of the objective outcome measures showed any significant difference between age groups, and the subjective measures, which did show differences, were contradictory. A total of 108 interlibrary loans were requested, by a full time researcher, at a total cost of 432.00 Irish pounds over a 10 week period. CONCLUSIONS: When advising patients on the outcome of anterior cruciate ligament reconstruction, age should not be considered in isolation. In the absence of relevant guidelines, meta-analyses, or systematic reviews, the application of evidence based medicine to clinical practice has significant resource implications.

Adult↗

PubMed2006

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools.

BACKGROUND: Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects in widely differing species. To meet this challenge, we have developed the flexible, scalable, and automated sequence processing package described here. RESULTS: MAGIC-SPP is a DNA sequence processing package consisting of an Oracle 9i relational database, a Perl pipeline, and user interfaces implemented either as JavaServer Pages (JSP) or as a Java graphical user interface (GUI). The database not only serves as a data repository, but also controls processing of trace files. MAGIC-SPP includes an administrative interface, a laboratory information management system, and interfaces for exploring sequences, monitoring quality control, and troubleshooting problems related to sequencing activities. In the sequence trimming algorithm it employs new features designed to improve performance with respect to concerns such as concatenated linkers, identification of the expected start position of a vector insert, and extending the useful length of trimmed sequences by bridging short regions of low quality when the following high quality segment is sufficiently long to justify doing so. CONCLUSION: MAGIC-SPP has been designed to minimize human error, while simultaneously being robust, versatile, flexible and automated. It offers a unique combination of features that permit administration by a biologist with little or no informatics background. It is well suited to both individual research programs and core facilities.

Algorithms↗

PubMed2001

Differentiation of rat neural tissue in a serum-free embryo culture model followed by in vivo transplantation.

AIM: To analyze neural tissue differentiation in a unique, chemically-defined in vitro culture model of gastrulating rat embryo proper by use of transmission electron microscopy (TEM), proliferating cell nuclear antigen (PCNA) expression, and in vivo transplantation after a 2-week culture in serum-free or serum-supplemented media. Influence of protein-free medium unfavorable for differentiation of neural tissue in vitro was compared with favorable serum-free media enriched with transferrin or albumin. Differentiation of mesodermal derivatives in transplants was also investigated. METHODS: We cultivated 9.5-day-old Fischer rat embryos on the gas-liquid interface in the protein-free Eagle's Minimum Essential Medium (MEM), in MEM with either iron-saturated holotransferrin (50 microg/mL) or iron-free apotransferrin (50 microg/mL), and in medium saturated with either bovine serum albumin (BSA) (4 mg/mL or 400 microg/mL) or rat serum (50%). After the two-week culture period, light microscopy, TEM, and immunohistochemical method for detection of PCNA were done. Some explants were transplanted under the kidney capsule of adult male rats to be cultured in vivo for additional two weeks. Chi-square test or Fisher exact test were used to compare the proportion of tissues developed. RESULTS: Proportion of differentiated neural tissue was similar in explants cultivated in apotransferrin- and holotransferrin-supplemented media (13/33 and 9/20, respectively), but higher than in explants cultivated in protein-free medium (1/13). Neurons and glia cells produced a neuropil structure. Myelinization occurred only in serum-supplemented medium. PCNA expression was detected in a small number of neural tissue cells, even in serum-free cultivated embryos. Differentiation of brain-like tissue, cerebrospinal, and vegetative ganglionic cells occurred in all groups of transplants. However, in the transplants derived from protein-free medium, the proportion of neural tissue, cartilage, bone, skeletal and smooth muscle was significantly lower than in transferrin-supplemented media (p<0.01). Albumin seemed to promote differentiation of all tissues except vegetative ganglionic cells. CONCLUSION: Nerve tissue differentiated to a rather high degree in a two-week in vitro postimplantation embryo culture. Transferrin or albumin, as the only proteins used for serum-free precultivation, significantly improved subsequent differentiation of nerve tissue and mesodermal derivatives in transplants in vivo.

Animals↗

PubMed1999

Nucleotide analog interference mapping of the hairpin ribozyme: implications for secondary and tertiary structure formation.

The hairpin ribozyme is a small, naturally occurring RNA capable of folding into a distinct three-dimensional structure and catalyzing a specific phosphodiester transfer reaction. We have adapted a high throughput screening procedure entitled nucleotide analog interference mapping (NAIM) to identify functional groups important for proper folding and catalysis of this ribozyme. A total of 18 phosphorothioate-tagged nucleotide analogs were used to determine the contribution made by individual ribose 2'-OH and purine functional groups to the hairpin ribozyme ligation reaction. Substitution with 2'-deoxy-nucleotide analogs disrupted activity at six sites within the ribozyme, and a unique interference pattern was observed at each of the 11 conserved purine nucleotides. In most cases where such information is available, the NAIM data agree with the previously reported single-site substitution results. The interference patterns are interpreted in comparison to the isolated loop A and loop B NMR structures and a model of the intact ribozyme. These data provide biochemical evidence in support of many, but not all, of the non-canonical base-pairs observed by NMR in each loop, and identify the functional groups most likely to participate in the tertiary interface between loop A and loop B. These groups include the 2'-OH groups of A10, G11, U12, C25, and A38, the exocyclic amine of G11, and the minor groove edge of A9 and A24. The data also predict non-A form sugar pucker geometry at U39 and U41. Based upon these results, a revised model for the loop A tertiary interaction with loop B is proposed. This work defines the chemical basis of purine nucleotide conservation in the hairpin ribozyme, and provides a basis for the design and interpretation of interference suppression experiments.

Base Sequence↗