The automatic detection of known beta-propeller structural motifs from protein tertiary structure

Following our previous work on the analysis of 'structural plasticity' associated with the beta-propeller structural motifs, we have now developed a simple method that can automatically detect all the known beta-propellers in protein tertiary structure, given a list of Protein Data Bank (PDB) codes as input to the computer program. Our beta-propeller detection (BPD) method identifies the location of beta-propellers in the protein structure, specifies the beta-propeller type, the beta-sheet associated beta-strand pattern and the structurally similar beta-propellers observed in other proteins. When tested on 21,566 proteins in the PDB, the BPD method was capable of correctly identifying all the known 245 beta-propellers described in the structural classification of proteins (SCOP) with the number of false positives detected being less than 0.2%. Forty-one false positives were detected that correspond to eight known protein families. When compared with some of the popular web-based programs that can automatically detect 'structural similarities' between the query and target proteins, our method has the advantage of also being capable of detecting beta-propellers associated with 'structural plasticity' and in situations where the target and query proteins differ in amino acid sequence length.     

The use of folding patterns in a multisolution approach of the all-beta protein three-dimensional structure. A beta-roll structure is predicted in the retroviral glycoprotein

An automatic macromolecular modelling package of unknown protein structures was developed using the intimate correlation which appears between the observed X-ray structures and their associated predicted folding patterns. The method can be considered as a generalization of both the combinatorial [1] and the template identification [2,3] approaches which were proposed some years ago, and provide a fast way of selecting 'structural motifs' to build new proteins. As an illustration, the tertiary fold of the all-beta-domain of the retroviral outermembrane glycoprotein is proposed.     

Fluorescent and radiolabelling of pepsin-digested human glomerular basement membrane with a newly developed hydroxy-coumarin derivative (CASE)

The labelling of pepsin-digested human glomerular basement membrane (pHGBM) with a newly developed fluorescent iodine acceptor 7-hydroxy-coumarin-3-acetic acid N-hydroxysucciniimydyl ester (CASE) is described. The binding of a monoclonal antibody to pHGBM was assessed by radiobinding assays, and when directly iodinated pHGBM was used there was no apparent binding. When CASE was conjugated to pHGBM prior to iodination 11% binding was achieved. CASE acting as an iodine acceptor may be useful for proteins containing few or inaccessible tyrosine residues or which are destroyed by introduction of 125I. Since CASE is fluorescent, small amounts of material can be detected during isolation prior to iodination.     

Specific leaf area in barley: individual leaves versus whole plants

We have explored the relationships between specific leaf area calculated for a whole plant and its individual leaves. Barley was grown in hydroponics in controlled environment cabinets. Plants were harvested on the basis of physiological age (defined as the number of days after full expansion of leaves on the main stem) and the area and weight of whole, fully expanded, leaves measured and specific leaf area (SLA) of individual leaves or whole plants calculated. Specific leaf area calculated for individual leaves (SLA_L) varied with leaf position and with leaf age after full expansion whereas SLA calculated for whole plants (SLA_P) varied with plant age. The same conclusions were reached whether the results were based on total dry weight or dry weight minus soluble carbohydrates ('structural weight'). Transferring plants to shade on the day of full expansion of the third leaf on the main stem increased the SLA_P, and also SLA_L of leaves 3 and 4 on the main stem (leaf 4 being the younger leaf of the two), because of a decrease in the 'structural weight' of these leaves. However SLA_L of leaf 2 (which was older than leaf 3) was not affected by shading; the effect was confined to leaves developing in the new conditions.     

RNA structural motifs: building blocks of a modular biomolecule

RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeatedly in RNA hairpin and internal loops, and are observed to be composed of a limited number of common 'structural elements'. In addition to secondary and tertiary structure motifs, there are functional motifs specific for certain biological roles and binding motifs that serve to complex metals or other ligands. Research is continuing into the identification and classification of RNA structural motifs and is being initiated to predict motifs from sequence, to trace their phylogenetic relationships and to use them as building blocks in RNA engineering.     

Patient autonomy, assessment of competence and surrogate decision-making: a call for reasonableness in deciding for others

In this paper, I address some of the shortcomings of established clinical ethics centring on personal autonomy and consent and what I label the Doctrine of Respecting Personal Autonomy in Healthcare. I discuss two implications of this doctrine: 1) the practice for treating patients who are considered to have borderline decision-making competence and 2) the practice of surrogate decision-making in general. I argue that none of these practices are currently aligned with respectful treatment of vulnerable individuals. Because of 'structural arbitrariness' in the whole process of how we assess decision-making competence, this area is open to disrespectful treatment of people. The practice of surrogate decision- making on the basis of a single person's judgment is arguably not consistent with ethical and political requirements derived from the doctrine itself. In response to the inadequacies of the doctrine, I suggest a framework for reasonableness in surrogate decision-making which might allow practice to avoid the problems above. I conclude by suggesting an extended concept of Patient Autonomy which integrates both personal autonomy and the regulative idea of morality that is required by reasonableness in deciding for non-competent others.     

A CASE-SAR analysis of polycyclic aromatic hydrocarbon carcinogenicity

A CASE SAR analysis was performed on a selected database of PAHs to investigate the possible use of the CASE method as an aid for preliminary assessment of carcinogenic potential of untested environmental PAHs. A data set, denoted LEARN, consisting of 78 PAHs and their experimental carcinogenicities was used to 'train' the CASE method and derive the CASE fragments. 8 activating fragments and 4 inactivating fragments were identified. These fragments predicted the activities of 94% of the LEARN set correctly. The biological significance of several of these fragments are rationalized in light of the current theories of PAH carcinogenesis. Using these fragments, the potential activities of a database of 106, mostly untested PAHs, denoted TEST, were predicted. These were compared to 'expert judgement' predictions based on mechanistic considerations in order to evaluate the extent of concordance between these two methods and their respective strengths and weaknesses. Initial poor agreement (64%) was attributed to limitations of the LEARN database involving inadequate representation of 2- and 3-ring PAH subclasses. When these subclasses were excluded from the TEST database, the concordance improved to 90%. The CASE fragments were also used to predict the activities of a database of 24 PAHs, denoted VALIDATE (not included in the LEARN set) for which carcinogenicity data were available. The total prediction accuracy of 75% (89% of the actives correctly identified), despite the structural diversity of the VALIDATE set, provided independent evidence of the utility of the present CASE results. A close examination of the CASE incorrect predictions was conducted to delineate inadequancies of these CASE results in order to provide cautionary guidance for future application of the method. Finally, the present results were compared to the results of a previous CASE analysis based on a more limited PAH data set, and were found to be of greater general utility. It is concluded that the CASE fragments derived in the current study should provide a useful tool for assisting and complementing 'expert judgement' in the preliminary screening of PAHs for carcinogenic activity.     

Structural basis of carcinogenicity in rodents of genotoxicants and non-genotoxicants

A set of 189 chemicals tested in the National Toxicology Program Cancer Bioassay was subjected to analysis by CASE, the Computer-Automated Structure Evaluation system. In the data set, 63% of the chemicals were carcinogens, approx. 40% of the carcinogens were non-genotoxic, i.e., they possessed neither "structural alerts" for DNA reactivity as defined by Ashby and Tennant, 1988, nor were they mutagenic for Salmonella. The data base can be characterized as a "combined rodent" compilation as chemicals were characterized as "carcinogenic" if they were carcinogenic in either rats or mice or both. CASE identified 23 fragments which accounted for the carcinogenicity, or lack thereof, of most of the chemicals. The sensitivity and specificity were unexpectedly high: 1.00 and 0.86, respectively. Based upon the identified biophores and biophobes, CASE performed exceedingly well in predicting the activity of chemicals not included among the 189 in the original set. CASE predicted correctly the carcinogenicity of non-genotoxic carcinogens thereby suggesting a structural commonality in the action of this group of carcinogens. As a matter of fact biophores restricted to non-genotoxic carcinogens were identified as were "non-electrophilic" biophores shared by genotoxic and non-genotoxic carcinogens. The findings suggest that the CASE program may help in the elucidation of the basis of the action of non-genotoxic carcinogens.     

Structural variation in the human genome

The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of what we term 'structural variation' in the human genome. This comprises microscopic and, more commonly, submicroscopic variants, which include deletions, duplications and large-scale copy-number variants - collectively termed copy-number variants or copy-number polymorphisms - as well as insertions, inversions and translocations. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.     

Biological function made crystal clear - annotation of hypothetical proteins via structural genomics

Many of the gene products of completely sequenced organisms are 'hypothetical' - they cannot be related to any previously characterized proteins - and so are of completely unknown function. Structural studies provide one means of obtaining functional information in these cases. A 'structural genomics' project has been initiated aimed at determining the structures of 50 hypothetical proteins from Haemophilus influenzae to gain an understanding of their function. Each stage of the project - target selection, protein production, crystallization, structure determination, and structure analysis - makes use of recent advances to streamline procedures. Early results from this and similar projects are encouraging in that some level of functional understanding can be deduced from experimentally solved structures.     

Spartina anglica C. E. Hubbard: a natural model system for analysing early evolutionary changes that affect allopolyploid genomes

Spartina anglica arose during the end of the 19th century in England by hybridization between the indigenous Spartina maritima and the introduced East American Spartina alterniflora and following genome duplication of the hybrid ( S.  ×  townsendii ). This system allows investigations of the early evolutionary changes that accompany stabilization of a new allopolyploid species in natural populations. Various molecular data indicate that S. anglica has resulted from a unique parental genotype. This young species contains two distinctly divergent homoeologous genomes that have not undergone extensive change since their reunion. No burst of retroelements has been encountered in the F₁ hybrid or in the allopolyploid, suggesting a 'structural genomic stasis' rather than 'rapid genomic changes'. However, modifications of the methylation patterns in the genomes of S.  ×  townsendii and S. anglica indicate that in this system, epigenetic changes have followed both hybridization and polyploidization.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 475–484.     

Prognostic Value and Targeted Inhibition of Survivin Expression in Esophageal Adenocarcinoma and Cancer-Adjacent Squamous Epithelium

Background

Survivin is an inhibitor of apoptosis and its over expression is associated with poor prognosis in several malignancies. While several studies have analyzed survivin expression in esophageal squamous cell carcinoma, few have focused on esophageal adenocarcinoma (EAC) and/or cancer-adjacent squamous epithelium (CASE). The purpose of this study was 1) to determine the degree of survivin up regulation in samples of EAC and CASE, 2) to evaluate if survivin expression in EAC and CASE correlates with recurrence and/or death, and 3) to examine the effect of survivin inhibition on apoptosis in EAC cells.

Methods

Fresh frozen samples of EAC and CASE from the same patient were used for qRT-PCR and Western blot analysis, and formalin-fixed, paraffin-embedded tissue was used for immunohistochemistry. EAC cell lines, OE19 and OE33, were transfected with small interfering RNAs (siRNAs) to knockdown survivin expression. This was confirmed by qRT-PCR for survivin expression and Western blot analysis of cleaved PARP, cleaved caspase 3 and survivin. Survivin expression data was correlated with clinical outcome.

Results

Survivin expression was significantly higher in EAC tumor samples compared to the CASE from the same patient. Patients with high expression of survivin in EAC tumor had an increased risk of death. Survivin expression was also noted in CASE and correlated with increased risk of distant recurrence. Cell line evaluation demonstrated that inhibition of survivin resulted in an increase in apoptosis.

Conclusion

Higher expression of survivin in tumor tissue was associated with increased risk of death; while survivin expression in CASE was a superior predictor of recurrence. Inhibition of survivin in EAC cell lines further showed increased apoptosis, supporting the potential benefits of therapeutic strategies targeted to this marker.     

The structural basis of the mutagenicity of chemicals in Salmonella typhimurium: the National Toxicology Program Data Base

A portion of the U.S. National Toxicology Program (NTP) Salmonella typhimurium mutagenicity data base was analyzed by CASE, an artificial intelligence SAR system. CASE identified 13 structural determinants which, with a high probability (p less than or equal to 0.05) predicted the likelihood of mutagenicity of the 243 chemicals in the data base (sensitivity = 0.989; specificity = 0.950) as well as of chemicals not included in the data base. CASE also identified an additional set of structures which were highly predictive of mutagenic potency (sensitivity = 0.949; specificity = 1.00). Even though there is little overlap among the chemicals included in the NTP and Gene-Tox Salmonella data bases, CASE found significant similarities between the structural determinants of the mutagenicity in the two data bases, thereby validating the analyses and indicating a commonality in the structural basis of mutagenicity.     

Neonatal juvenile xanthogranuloma. Report of a case with fine needle aspiration cytologic findings in a soft tissue mass

BACKGROUND: Juvenile xanthogranuloma is an infrequent, benign histiocytic lesion, the recognition and diagnosis of which by fine needle aspiration biopsy are important for ascertaining whether a case will have a benign course or spontaneous regression. CASE: A case of juvenile xanthogranuloma was located in the upper lip of a newborn male. CONCLUSION: Juvenile xanthogranuloma has characteristic cytologic features that may allow recognition in fine needle aspiration cytology smears.     

Diagnosis of pleomorphic adenoma in a heterotopic salivary gland: a case report

BACKGROUND: The histologic diversity encountered in pleomorphic adenoma may cause diagnostic difficulty in fine needle aspiration cytology (FNA) due to limited and selective sampling. CASE: A 40-year-old woman presented with a mass in the anterior aspect of the neck along the sternocleidomastoid muscle. FNA revealed a cellular tumor with a chondrimyxoid background and epithelial cells intermingled with a few mesenchymal cells. The diagnosis of pleomorphic adenoma was confirmed on histopathology. CONCLUSION: Primary ectopic pleomorphic adenoma can confidently be diagnosed by FNA. This technique is a useful tool in the initial assessment of the tumor.     

Use of the Computer Automated Structure Evaluation program in determining quantitative structure-activity relationships within hallucinogenic phenylalkylamines

The Computer Automated Structure Evaluation (CASE) program has been successfully used to generate automatically and identify molecular fragments relevant to the hallucinogenic activity expressed by some phenylalkylamines. Utilizing these major fragments, Quantitative Structure-Activity Relationship (QSAR) calculations were carried out to obtain an equation which was used for predictions of potencies. Correlations of these major activating/inactivating fragments with the biological activity of the compounds, as well as predictive capabilities of the CASE program, are discussed.     

Genetic defects or generative prototypes? Competing models for livestock improvement in southern Bolivia

Following neo-liberal 'structural adjustments' in Bolivia, peasant llama-herders are expected to become entrepreneurs and their animal products to compete in global markets. To facilitate the entry of llama produce into global trade, scientifically trained experts working for NGOs give herders 'capacity-building' courses in livestock management and organize livestock shows to teach them about animal conformation. This article examines negotiations and accommodations between indigenous knowledge and science, and in particular focuses upon competing claims to knowledge about herd management and animal improvement. While experts look to improve animals from without – through hybridization with animals from other areas, which also constitutes exchanges in genetic capital – herders expect improvement to come from within – placing emphasis on the unity of their herds as reproductive groups and regarding animals condemned as 'defective' by experts as generative prototypes that indicate the herds' fertility.     

Homology model building of the HMG-1 box structural domain.

Nucleoproteins belonging to the HMG-1/2 family possess homologous domains approximately 75 amino acids in length. These domains, termed HMG-1 boxes, are highly structured, compact, and mediate the interaction between HMG-1 box-containing proteins and DNA in a variety of biological contexts. Homology model building experiments on HMG-1 box sequences 'threaded' through the 1H-NMR structure of an HMG-1 box from rat indicate that the domain does not have rigid sequence requirements for its formation. Energy calculations indicate that the structure of all HMG-1 box domains is stabilized primarily through hydrophobic interactions. We have found structural relationships in the absence of statistically significant sequence similarity, identifying several candidate proteins which could possibly assume the same three-dimensional conformation as the rat HMG-1 box motif. The threading technique provides a method by which significant structural similarities in a diverse protein family can be efficiently detected, and the 'structural alignment' derived by this method provides a rational basis through which phylogenetic relationships and the precise sites of interaction between HMG-1 box proteins and DNA can be deduced.     

Fine needle aspiration of pulmonary adiaspiromycosis: a case report

BACKGROUND: Pulmonary adiaspiromycosis is a common disease of many species of wild rodents and occasionally of humans, caused by the inhalation of spores of the fungus Chrysosporium parvum var crescens (Emmonsia crescens). CASE: A 74-year-old female with pulmonary adiaspiromycosis was diagnosed by radiologically guided lung fine needle aspiration (FNA). The specimen showed intracellular and extracellular 100-300 microm conidia with a distinct thick, trilaminar wall, which was positive for Gomori-methenamine silver and periodic acid-Schiff stain. The background consisted of a granulomatous process. CONCLUSION: FNA is an effective method of diagnosing pulmonary adiaspiromycosis, and pathologists need to be aware of the characteristic features of this unusual opportunistic fungal infection.