The Application Of Object-oriented Techniques To Preliminary Design Problems

Preliminary structural design is an early stage in building design during which the engineer formulates and assesses a number of different structural schemes. It is conceptual in nature and involves decision making, which relies on heuristics. Whilst preliminary structural design has not been well supported by PC software, recent research has indicated the potential for knowledge-based, object-oriented systems to assist in the area. This thesis explores the issues that arise when object-oriented techniques arc used to develop knowledge-based software. lt reviews certain basic principles of structural design, methods of representing structural design knowledge and earlier approaches to the design of software to support preliminary structural design. The thesis describes how the writer created a software development methodology to apply object-oriented analysis and design techniques. It then describes the use of this methodology to develop a system for preliminary structural design, including the drafting of requirements, the creation of an object model for these requirements and their implementation in Kappa-PC software. The thesis proposes an approach to the development of Software to support preliminary design in buildings and has demonstrated this approach in a prototype design tool. It has also described some of the difficulties hindering the effective application of the object-oriented methods

Analysis of the Venoms of Four Subspecies of the Western Rattlesnake (Crotalus oreganus)

Recently, the benefits venom can have in the discovery and development of different medications to assist in treating a variety of diverse human diseases have been areas of research. In order to develop a better understanding of how to evaluate venoms for potential use as therapeutics, one needs to look at the fundamental composition of venom samples. This project aims at discovering and analyzing the basic components from the venom of four different subspecies of the Western Rattlesnake. Venom samples collected will be subjected to size exclusion chromatography to separate proteins of different sizes. After fractionation of venoms, the following assays are conducted on individual fractions to locate specific activities of enzymatic venom proteins: metalloproteinase activity, kallikrein-like and thrombin-like serine proteinase activities, phospholipase A2 activity, phosphodiesterase activity and L-amino acid oxidase activity. These tests will compare the basic biochemistry of the samples of venoms from the different subspecies to help expand knowledge on chemistry differences between closely related subspecies of rattlesnakes. Snakes use their venoms primarily to obtain food, and results will allow for further evaluation of how their differing venom compositions relate to specific aspects of their ecology, such as use of divergent habitats, potential risks of different predators, effects on various prey species utilized, as well as revealing those components that have remained static and are shared among all subspecies analyzed. Because envenomation symptoms will vary due to venom composition, these results will also help inform what medical sequelae should be expected from particular populations of rattlesnakes

The Effect of the Birth Experience on Breastfeeding Outcomes Among non-Hispanic Black Women in North Carolina

The influence of cesarean section on breastfeeding initiation and duration has been well-documented. However, few studies have looked at how the psychological impact of the birth experience may affect breastfeeding outcomes in the United States. The present study predicted that among a population of non-Hispanic Black (NHB) women in North Carolina, a mismatch between a participant’s birth intent and birth outcome (labor mismatch) would affect their breastfeeding outcome. This study used data from Mothers & Others, a two-group randomized control trial. 128 of the 265 participants (48.30%) had a mismatch between their delivery intent and delivery outcome (labor mismatch). In bivariate analysis, maternal BMI and low-income status was associated with labor mismatch. Though no association was found between labor mismatch and breastfeeding outcomes, adjusted multinomial regression analysis found that BMI, education, and low-income status were associated with breastfeeding for a shorter duration than participants intended.Master of Art

The venom gland transcriptome of the Desert Massasauga Rattlesnake (Sistrurus catenatus edwardsii): towards an understanding of venom composition among advanced snakes (Superfamily Colubroidea)

<p>Abstract</p> <p>Background</p> <p>Snake venoms are complex mixtures of pharmacologically active proteins and peptides which belong to a small number of superfamilies. Global cataloguing of the venom transcriptome facilitates the identification of new families of toxins as well as helps in understanding the evolution of venom proteomes.</p> <p>Results</p> <p>We have constructed a cDNA library of the venom gland of a threatened rattlesnake (a pitviper), <it>Sistrurus catenatus edwardsii </it>(Desert Massasauga), and sequenced 576 ESTs. Our results demonstrate a high abundance of serine proteinase and metalloproteinase transcripts, indicating that the disruption of hemostasis is a principle mechanism of action of the venom. In addition to the transcripts encoding common venom proteins, we detected two varieties of low abundance unique transcripts in the library; these encode for three-finger toxins and a novel toxin possibly generated from the fusion of two genes. We also observed polyadenylated ribosomal RNAs in the venom gland library, an interesting preliminary obsevation of this unusual phenomenon in a reptilian system.</p> <p>Conclusion</p> <p>The three-finger toxins are characteristic of most elapid venoms but are rare in viperid venoms. We detected several ESTs encoding this group of toxins in this study. We also observed the presence of a transcript encoding a fused protein of two well-characterized toxins (Kunitz/BPTI and Waprins), and this is the first report of this kind of fusion in a snake toxin transcriptome. We propose that these new venom proteins may have ancillary functions for envenomation. The presence of a fused toxin indicates that in addition to gene duplication and accelerated evolution, exon shuffling or transcriptional splicing may also contribute to generating the diversity of toxins and toxin isoforms observed among snake venoms. The detection of low abundance toxins, as observed in this and other studies, indicates a greater compositional similarity of venoms (though potency will differ) among advanced snakes than has been previously recognized.</p

Role of accelerated segment switch in exons to alter targeting (ASSET) in the molecular evolution of snake venom proteins

<p>Abstract</p> <p>Background</p> <p>Snake venom toxins evolve more rapidly than other proteins through accelerated changes in the protein coding regions. Previously we have shown that accelerated segment switch in exons to alter targeting (ASSET) might play an important role in its functional evolution of viperid three-finger toxins. In this phenomenon, short sequences in exons are radically changed to unrelated sequences and hence affect the folding and functional properties of the toxins.</p> <p>Results</p> <p>Here we analyzed other snake venom protein families to elucidate the role of ASSET in their functional evolution. ASSET appears to be involved in the functional evolution of three-finger toxins to a greater extent than in several other venom protein families. ASSET leads to replacement of some of the critical amino acid residues that affect the biological function in three-finger toxins as well as change the conformation of the loop that is involved in binding to specific target sites.</p> <p>Conclusion</p> <p>ASSET could lead to novel functions in snake venom proteins. Among snake venom serine proteases, ASSET contributes to changes in three surface segments. One of these segments near the substrate binding region is known to affect substrate specificity, and its exchange may have significant implications for differences in isoform catalytic activity on specific target protein substrates. ASSET therefore plays an important role in functional diversification of snake venom proteins, in addition to accelerated point mutations in the protein coding regions. Accelerated point mutations lead to fine-tuning of target specificity, whereas ASSET leads to large-scale replacement of multiple functionally important residues, resulting in change or gain of functions.</p

総会抄録

<p><b>Aligned Middle American Rattlesnake (<i>Crotalus simus tzabcan</i>) C-type lectins (A) and serine proteases (B).</b> A) Four unique venom-based C-type lectin transcripts (asterisks) were identified for <i>C</i>. <i>s</i>. <i>tzabcan</i> and aligned to other crotaline species. Identical nucleotide sequences are shaded and corresponding GenBank accession numbers are as follows: Crotalus_adamanteus (AEJ31974.1), Deinagkistrodon_acutus (AAM22790.1), Crotalus_d_terrificus (Q719L8.1), and Crotalus_o_helleri (AEU60004.1). B) Venom-based serine proteases cDNA sequences (asterisks) were also obtained from <i>C</i>. <i>s</i>. <i>tzabcan</i> and were aligned with toxins from several other species; identical nucleotide sequences are shaded, and the catalytic triad composed of Ser195, Asp102, and His57 associated with thrombin-like activity in snake venom serine proteases are identified (arrowheads). Isoform 3 from <i>C</i>. <i>s</i>. <i>tzabcan</i> is a partial sequence. GenBank accession numbers are as follows: Agkistrodon_p_leucostoma (HQ270466.1), Bothrops_asper (DQ247724.1), Crotalus_d_terrificus7 (EU360954.1), Crotalus_d_terrificus4 (EU360952.1), Crotalus_d_terrificus3 (EU360951.1), Crotalus_d_durissus (DQ164401.1), Sistrurus_c_edwardsi (DQ464239.1), Trimeresurus_mucrosquamatus (X83225.1), Crotalus_adamanteus (HQ414118.1), Calloselasma_rhodostoma (L07308.1), Deinagkistrodon_acutus (AY861382.1), Trimeresurus_stejnegeri (AF545575.1), and Crotalus_atrox (AF227153.1).</p

Accelerated exchange of exon segments in Viperid three-finger toxin genes (Sistrurus catenatus edwardsii; Desert Massasauga)

<p>Abstract</p> <p>Background</p> <p>Snake venoms consist primarily of proteins and peptides showing a myriad of potent biological activities which have been shaped by both adaptive and neutral selective forces. Venom proteins are encoded by multigene families that have evolved through a process of gene duplication followed by accelerated evolution in the protein coding region.</p> <p>Results</p> <p>Here we report five gene structures of three-finger toxins from a viperid snake, <it>Sistrurus catenatus edwardsii</it>. These toxin genes are structured similarly to elapid and hydrophiid three-finger toxin genes, with two introns and three exons. Both introns and exons show distinct patterns of segmentation, and the insertion/deletion of segments may define their evolutionary history. The segments in introns, when present, are highly similar to their corresponding segments in other members of the gene family. In contrast, some segments in the exons show high similarity, while others are often distinctly different among corresponding regions of the isoforms.</p> <p>Conclusion</p> <p>Ordered, conserved exon structure strongly suggests that segments in corresponding regions in exons have been exchanged with distinctly different ones during the evolution of these genes. Such a "switching" of segments in exons may result in drastically altering the molecular surface topology and charge, and hence the molecular targets of these three-finger toxins. Thus the phenomenon of accelerated segment switch in exons to alter targeting (ASSET) may play an important role in the evolution of three-finger toxins, resulting in a family of toxins with a highly conserved structural fold but widely varying biological activities.</p

Venom proteomes of South and North American opisthoglyphous (Colubridae and Dipsadidae) snake species: A preliminary approach to understanding their biological roles

Opisthoglyphous snake venoms remain under-explored despite being promising sources for ecological, evolutionary and biomedical/biotechnological research. Herein, we compared the protein composition and enzymatic properties of the venoms of Philodryas baroni (PbV), Philodryas olfersii olfersii (PooV) and Philodryas patagoniensis (PpV) from South America, and Hypsiglena torquata texana (HttV) and Trimorphodon biscutatus lambda (TblV) from North America. All venoms degraded azocasein, and this metalloproteinase activity was significantly inhibited by EDTA. PooV exhibited the highest level of catalytic activity towards synthetic substrates for serine proteinases. All venoms hydrolyzed acetylthiocholine at low levels, and only TblV showed phospholipase A2 activity. 1D and 2D SDS-PAGE profile comparisons demonstrated species-specific components as well as several shared components. Size exclusion chromatograms from the three Philodryas venoms and HttV were similar, but TblV showed a notably different pattern. MALDI-TOF MS of crude venoms revealed as many as 49 distinct protein masses, assigned to six protein families. MALDI-TOF/TOF MS analysis of tryptic peptides confirmed the presence of cysteine-rich secretory proteins in all venoms, as well as a phospholipase A2 and a three-finger toxin in TblV. Broad patterns of protein composition appear to follow phylogenetic lines, with finer scale variation likely influenced by ecological factors such as diet and habitat.Fil: Peichoto, María Elisa. Governo do Estado de Sao Paulo. Secretaria da Saude. Instituto Butantan; Brasil. Univeristy of Northern Colorado; Estados Unidos. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Instituto Nacional de Medicina Tropical; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; ArgentinaFil: Tavares, Flávio Luiz. Univeristy of Northern Colorado; Estados UnidosFil: Santoro, Marcelo Larami. Governo do Estado de Sao Paulo. Secretaria da Saude. Instituto Butantan; BrasilFil: Mackessy, Stephen. Univeristy of Northern Colorado; Estados Unido

Venom-on-a-chip: a fast and efficient method for comparative venomics

Venom research has attracted an increasing interest in disparate fields, from drug development and pharmacology, to evolutionary biology and ecology, and rational antivenom production. Advances in “-omics” technologies have allowed the characterization of an increasing number of animal venoms, but the methodology currently available is suboptimal for large-scale comparisons of venom profiles. Here, we describe a fast, reproducible and semi-automated protocol for investigating snake venom variability, especially at the intraspecific level, using the Agilent Bioanalyzer on-chip technology. Our protocol generated a phenotype matrix which can be used for robust statistical analysis and correlations of venom variation with ecological correlates, or other extrinsic factors. We also demonstrate the ease and utility of combining on-chip technology with previously fractionated venoms for detection of specific individual toxin proteins. Our study describes a novel strategy for rapid venom discrimination and analysis of compositional variation at multiple taxonomic levels, allowing researchers to tackle evolutionary questions and unveiling the drivers of the incredible biodiversity of venoms