Leishmania (sauroleishmania): a comment on classification.
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Journal Article↗
Biomedical subjects
J T Ellis
Publications and source records attributed to J T Ellis.
The development of random DNA probes specific for Aeromonas salmonicida.
RAPD-PCR has been used to produce DNA probes for Aeromonas salmonicida. DNA hybridization studies showed that RAPD-PCR fragments of the same size did not necessarily hybridize to each other and therefore these sequences were not always homologous. However, a single RAPD-PCR fragment (designated 15e) was identified as being common to Aer. salmonicida. Subsequently, 15e was found to comprise five DNA fragments of similar size which differed in their nucleotide sequences. All five fragments were evaluated as DNA probes for the specific detection of Aer. salmonicida DNA: two hybridized specifically to DNA of all Aer. salmonicida isolates tested, including the four current subspecies and atypical isolates; one hybridized to subspecies salmonicida, achromogenes and masoucida, but not subspecies smithia; one hybridized to subspecies salmonicida and achromogenes, but not subspecies masoucida or smithia; and one hybridized to subspecies salmonicida, achromogenes and smithia, but not subspecies masoucida. It is believed that these fragments could be useful as non-radioactive probes for the safe and rapid diagnosis of these fish pathogens.
Aeromonas↗
Fluid dynamic studies for the year 2000.
The authors recommend changes to the paradigm employed in the current ISO Heart Valve Standard (ISO 5840) so that future patients who receive a heart valve prosthesis are assured of a device that will function with minimal complications for at least 25 years. Based on valve failures of the past decade, it is clear that current standards are inadequate because present-day Standards and Regulatory Agencies operate in a manner which inhibits innovation and creativity. Thus, engineers and scientists in this field react to problems, rather than proact. As we approach the new millennium, the authors consider it time to rethink the ground rules.
Animals↗
Prosthesis-induced hemolysis: mechanisms and quantification of shear stress.
Over the past four decades, nearly three million prosthetic heart valves have been implanted worldwide. Despite improvements in valve designs and clinical management, the ideal mechanical heart valve has yet to be realized; hemolytic and thromboembolic complications remain the major obstacles. Towards this goal, a number of clinical and basic engineering studies have improved our understanding of how red blood cells can be damaged by the turbulent flow fields associated with current prosthetic mechanical heart valve designs. However, continued advances in understanding the hemolytic complications associated with different valve designs, and progress in making improvements to existing designs, will depend on the development of more sophisticated in vitro quantitative engineering techniques such as those described in this paper.
Blood Flow Velocity↗
Evolution of the genus Leishmania revealed by comparison of DNA and RNA polymerase gene sequences.
Previous hypotheses of Leishmania evolution are undermined by limitations in the phylogenetic reconstruction method employed or due to the omission of key parasites. In this experiment, sequences of the gene encoding the DNA polymerase alpha catalytic polypeptide (POLA) were analysed phylogenetically in combination with those encoding the RNA polymerase II largest subunit gene (RPOIILS) to infer a comprehensive phylogeny of Leishmania. Nineteen species of parasites were studied, comprising representatives of each Leishmania species-complex (Leishmania Leishmania tropica, Leishmania Leishmania donovani, Leishmania Leishmania mexicana, Leishmania Leishmania hertigi and Leishmania Viannia braziliensis), as well as parasites of questionable taxonomy (Leishmania herreri, Sauroleishmania adleri, Sauroleishmania deanei, Sauroleishmania gymnodactyli and Sauroleishmania tarentolae). The analyses presented here provide strong support for the hypothesis that the Leishmania that infect reptiles (also known as Sauroleishmania) evolved from mammalian Leishmania. One implication of this finding is that the taxonomic definition of Leishmania should be broadened to encompass characteristics of the reptilian parasites. However, this taxonomic revision is complicated in that Leishmania (L.) hertigi, Leishmania (L.) deanei and Leishmania herreri, which exhibit some biological properties of Leishmania, are more closely related to Endotrypanum on the basis of these sequence comparisons. Consequently, the taxonomic discrimination between Leishmania that infect mammals, Leishmania that infect reptiles and Endotrypanum may be more problematic than has been previously thought. Since our resulting phylogenetic hypothesis is supported by the analyses of two different genes, we speculate on the origin and evolutionary expansion of this lineage of kinetoplastid protozoa.
Animals↗
Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa.
The reconstruction of phylogenetic history is predicated on being able to accurately establish hypotheses of character homology, which involves sequence alignment for studies based on molecular sequence data. In an empirical study investigating nucleotide sequence alignment, we inferred phylogenetic trees for 43 species of the Apicomplexa and 3 of Dinozoa based on complete small-subunit rDNA sequences, using six different multiple-alignment procedures: manual alignment based on the secondary structure of the 18S rRNA molecule, and automated similarity-based alignment algorithms using the PileUp, ClustalW, TreeAlign, MALIGN, and SAM computer programs. Trees were constructed using neighboring-joining, weighted-parsimony, and maximum-likelihood methods. All of the multiple sequence alignment procedures yielded the same basic structure for the estimate of the phylogenetic relationship among the taxa, which presumably represents the underlying phylogenetic signal. However, the placement of many of the taxa was sensitive to the alignment procedure used; and the different alignments produced trees that were on average more dissimilar from each other than did the different tree-building methods used. The multiple alignments from the different procedures varied greatly in length, but aligned sequence length was not a good predictor of the similarity of the resulting phylogenetic trees. We also systematically varied the gap weights (the relative cost of inserting a new gap into a sequence or extending an already-existing gap) for the ClustalW program, and this produced alignments that were at least as different from each other as those produced by the different alignment algorithms. Furthermore, there was no combination of gap weights that produced the same tree as that from the structure alignment, in spite of the fact that many of the alignments were similar in length to the structure alignment. We also investigated the phylogenetic information content of the helical and nonhelical regions of the rDNA, and conclude that the helical regions are the most informative. We therefore conclude that many of the literature disagreements concerning the phylogeny of the Apicomplexa are probably based on differences in sequence alignment strategies rather than differences in data or tree-building methods.
Algorithms↗
Production of a recombinant fusion protein of Sarcocystis tenella and evaluation of its diagnostic potential in an ELISA.
We have isolated a cDNA clone encoding an antigenic polypeptide of Sarcocystis tenella by screening a cystozoite-derived cDNA library in lambda gt11 with antibodies from sheep infected experimentally with S. tenella. This clone, termed STC29, was subcloned and expressed in the vector pGEX-3X as a soluble fusion protein with glutathione S-transferase having an apparent molecular mass of 46 kDa. Antibody raised against the recombinant fusion protein recognized a native polypeptide of 25 kDa in cystozoites of S. tenella. In an ELISA with sera from experimentally infected sheep, the recombinant STC29 antigen could differentiate infections with S. tenella from those with Sarcocystis arieticanis or Toxoplasma gondii. Hence, the research described here reports the identification of the first recombinant S. tenella antigen that may be useful for standardization of a serological test for the diagnosis of S.tenella infections in sheep.
Amino Acid Sequence↗
A biochemical protocol for the differentiation of current genomospecies of Aeromonas.
A data file consisting of 40 biochemical and physiological tests for the differentiation of aeromonads was constructed based upon existing published data from various geographical locations and laboratories. The data file covers all the current genomospecies (or hybridisation groups) of Aeromonas and is therefore applicable to bacteriologists from a wide variety of fields. The protocol derived from the data file was adapted for use with a semi-interactive computer identification program. This program was challenged with the type strains of all the currently recognised genomospecies and each genomospecies was correctly identified, with only one strain (ATCC 7966, HG1) having an identification probability of less than 90%. The program was also tested with environmental and clinical isolates and again identifications were achieved with high probabilities. This protocol is designed for use on presumptive isolates of Aeromonas spp. and can be carried out in routine laboratories not equipped to perform the complex DNA hybridisation techniques which are currently used for the differentiation of genomospecies of Aeromonas.
Aeromonas↗
Differentiation of Aeromonas genomospecies using random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR).
Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) was used to investigate the differentiation of the genus Aeromonas at the genomospecies level. Of 20 primers evaluated, six produced profiles which contained multiple bands capable of differentiating the genomospecies. These six primers were also used in RAPD-PCR analyses of clinical and environmental isolates of the different genomospecies. In most cases, each strain gave a unique fingerprint, illustrating genetic heterogeneity at the genomospecies level. However, some homogeneity in fragment sizes was seen among strains within a genomospecies which was not apparent in strains from different genomospecies. This study therefore complements and supports the current classification of Aeromonas into genomospecies. These results also show that RAPD-PCR has the potential to differentiate between the genomospecies of Aeromonas.
Aeromonas↗
Reconsideration of the use of peer sociometrics for evaluating social-skills training. Implications of an idiographic assessment of temporal stability.
Social-skills training studies using sociometric procedures as dependent measures have often yielded mixed results as to the improvement of the subjects. Failure to document improvement in peer acceptance subsequent to behavior change has led some to question the validity of social-skills interventions, whereas others have questioned the psychometric properties of the measures themselves. This study examined the temporal stability of the two major types of peer measures used in social-skills interventions studies; peer-nomination measures of liking and peer-rating measures of liking. Subjects were 87 children in three fourth-grade and two fifth-grade classrooms. Temporal stability was assessed across time intervals of 2,6, and 8 weeks. Temporal stability was examined as it traditionally has been at the group level (using Pearson product-moment correlations), and at the level at which data are normally examined for change in social-skills interventions, at the level of the individual child (using phi and Cramer's V coefficients). Assessed at the group level, the three types of peer measures were generally moderately to highly stable. Stability coefficients for individual children's scores on the peer measures, however, indicated instability at the level of the individual child. These problems regarding stability at the individual, idiographic level may be especially relevant when sociometric procedures are used as dependent measures in individual subject design studies. Conceptual and practical implications of the findings for the assessment of social-skills interventions are discussed.
Behavior Therapy↗
In vitro assessment of prosthetic valve function in mitral valve replacement with chordal preservation techniques.
BACKGROUND AND AIM OF THE STUDY: The importance of chordal preservation techniques in maintaining improved left ventricular function after mitral valve replacement has been well documented clinically. Currently, the choice of prosthetic valve used in chordal preservation is dependent upon the surgeon's preference. However, the transvalvular flow characteristics of common, clinically used prosthetic valves may be influenced by the mitral subvalvular apparatus, and may result in degraded valve function. The goal of this study was to perform an in vitro evaluation of the influence of chordal preservation on the transvalvular and left ventricular flow patterns of common valve prostheses. METHODS: Tissue and mechanical valves have been evaluated under physiologic pulsatile flow with anterior and/or posterior chordal preservation. Flow patterns were assessed by 2-D planar flow visualization, pulsed wave Doppler velocity measurements, 2-D echocardiography, and selected color Doppler flow mapping. Based on changes in transvalvular and left ventricular flow patterns, favorable prosthetic valve/chordal preservation combinations were identified. Additionally, valve orientation was varied to determine optimal orientation. RESULTS: Baseline results without chordal preservation indicate that the anti-anatomic orientation is preferred for the bileaflet valve design while the tilting disc valve should be oriented with the major axis toward the posterior (free) wall of the ventricle, corroborating published conclusions by other investigators. Some form of flow restriction is observed in all test cases with chordal preservation due to the presence of the subvalvular tissue. In general, bioprostheses showed less flow restriction then the mechanical valves, particularly with lateral flow expansion. This flow restriction may influence pressure recovery downstream of the mechanical valves tested. Increased flow constriction is observed with anterior and posterior chordal preservation. CONCLUSIONS: This study favors the use of the St. Jude Medical bileaflet valve orientated in the anti-anatomic position, or the Carpentier-Edwards pericardial valve with chordal preservation.
Bioprosthesis↗
Evaluation of an HIV/AIDS education program for family-based foster care providers.
Because individuals with mental retardation have recently been identified as a group at-risk for developing HIV infection, HIV/AIDS training programs for service providers working with this population are critical. In this study an HIV/AIDS education program for family-based foster care providers was described and evaluated. The results indicate that although these service providers had some prior knowledge about HIV and AIDS, there were significant improvements in knowledge following the training. Implications of these findings for individuals with mental retardation were discussed.
Acquired Immunodeficiency Syndrome↗
Velocity measurements and flow patterns within the hinge region of a Medtronic Parallel bileaflet mechanical valve with clear housing.
BACKGROUND AND AIMS OF THE STUDY: During recent clinical trials the Medtronic Parallel bileaflet mechanical heart valve was found to have an unacceptable number of valves with thrombus formation when implanted in the mitral position. Thrombi were observed in the hinge region and also in the upstream portion of the valve housing in the vicinity of the hinge. It was hypothesized that the flow conditions inside the hinge may have contributed to the thrombus formation. METHODS: In order to investigate the flow structures within the hinge, laser Doppler anemometry (LDA) measurements were conducted in both steady and pulsatile flow at approximately 70 predetermined sites within the hinge region of a 27 mm Medtronic Parallel mitral valve with transparent housing. The pulsatile flow velocity measurements were animated in time using a graphical software package to visualize the hinge flow field throughout the cardiac cycle. RESULTS: The LDA measurements revealed that mean forward flow velocities through the hinge region were on the order of 0.10-0.20 m/s. In the inflow channel, a large vortical structure was present during diastole. Upon valve closure, peak reverse velocity reached 3 m/s close to the housing wall in the inflow channel. This area also experienced high turbulent shear stresses (> 6000 dynes/cm2) during the leakage flow phase. A disturbed, vortical flow was again present in the inflow channel after valve closure, while slightly above the leaflet peg and relief the flow was essentially stagnant. The high turbulent stresses near the top of the inflow channel, combined with a persistent vortex, implicate the inflow channel of the hinge as a likely region of thrombus formation. CONCLUSIONS: This experimental investigation revealed zones of flow stagnation in the inflow region of the hinge throughout the cardiac cycle and elevated turbulent shear stress levels in the inflow region during the leakage flow phase. These fluid mechanic phenomena are most likely a direct result of the complex geometry of the hinge of this valve. Although the LDA measurements were conducted at only a limited number of sites within the hinge, these results suggest that the hinge design can significantly affect the washout capacity and thrombogenic potential of the Medtronic Parallel bileaflet mechanical heart valve. The use of LDA within the confines of the hinge region of a mechanical heart valve is a new application, made possible by recent advances in manufacturing technologies and a proprietary process developed by Medtronic that allowed the production of a transparent valve housing. Together, these modalities represent a new method by which future valve designs can be assessed before clinical trials are initiated.
Evaluation Studies as Topic↗
An in vitro investigation of the retrograde flow fields of two bileaflet mechanical heart valves.
BACKGROUND AND AIM OF THE STUDY: Fluid stresses occurring in retrograde flow fields during valve closure may play a significant role in thrombogenesis. The squeeze flow and regurgitant jets can cause damage to formed blood elements due to high levels of turbulent shear stress. The aim of this study was to characterize in detail the spatial structure and temporal behavior of the retrograde flow fields of the St. Jude Medical and Medtronic Parallel bileaflet mechanical heart valves. METHODS: Three-component, coincident laser Doppler anemometry (LDA) velocity measurements were obtained facilitating the determination of the full Reynolds stress tensor and the principal stresses in the valve flow fields. The experiments were performed in the Georgia Tech aortic flow chamber under physiologic pulsatile flow conditions. Data were collected over several hundred cardiac cycles for subsequent phase window averaging and generation of mean velocity and turbulence statistics over 20 ms intervals. A region approximately 8 mm x 10 mm was mapped 1.0 mm upstream of one hinge of each valve with an incremental resolution of 0.13-0.25 mm. Animation of the data allowed the visualization of the flow fields and a quantitative display of mean velocity and turbulent stress values. RESULTS: In the St. Jude Medical squeeze flow, the peak turbulent shear stress was 800 dynes/cm2 and the peak reverse velocity was 0.60 m/s. In the Medtronic Parallel squeeze flow, the peak turbulent shear stress was 1,000 dynes/cm2 and the peak velocity 0.70 m/s. The leakage jet fields of the two valves were very different: in the case of the St. Jude Medical valve, turbulent shear stresses reached 1,800 dynes/cm2 and peak jet velocity was 0.80 m/s; in the case of the Medtronic Parallel valve, turbulent shear stresses reached 3,690 dynes/cm2 and the peak jet velocity was 1.9 m/s. CONCLUSIONS: The retrograde flow fields of these two bileaflet mechanical heart valves appear to be design-dependent. The elevated turbulent shear stresses generated by both valve designs may indicate a propensity for blood element damage during the reverse flow phase of the cardiac cycle, but the extent of flow disturbance was twice as high with the Medtronic Parallel than with the St. Jude Medical valve. This research should yield a better understanding of the significance of retrograde flow to the functionality and potential thrombogenicity of bileaflet mechanical heart valves and aid in the development of new designs.
Heart Valve Prosthesis↗
Schistosoma mansoni: patterns of codon usage and bias.
Codon usage and bias has been examined in 20 genes of Schistosoma mansoni. Significant heterogeneity was detected in the patterns of codon usage and bias among genes by metric multidimensional scaling and three general indicators of bias (GC3S, Nc and B). In keeping with observations on sporozoan parasites, codon usage bias was observed to be dependent on the overall base composition of the genes analysed, which in turn was reflected in the types of codons that were over or under-represented in the sequences.
Animals↗
Codon usage and bias among individual genes of the coccidia and piroplasms.
Codon usage has been analysed in individual gene sequences, derived from a variety of parasitic protozoa in the class Sporozoa of the phylum Apicomplexa using metric multidimensional scaling. The two groups of codon usage patterns detected reflect the two main subgroups of organisms studied (the coccidia and the piroplasms), and it is the pattern of usage of synonymous codons that has the largest influence on overall codon usage in the individual genes, rather than being the pattern of amino acid composition of the gene product. The magnitude of the codon usage bias in the sequences was determined using three commonly used indices-NC, GC3S and B. In general, although relatively low levels of codon usage bias were detected in these gene sequences, codon usage bias does explain at least some of the codon usage patterns observed. Codon usage bias was observed to be dependent on the overall base composition of the genes analysed, which in turn was reflected in the types of codons that were either over- or under-represented in the nucleotide sequences. In keeping with observations on prokaryotic organisms, it is speculated that the codon usage patterns detected in these parasitic protozoa are the result of directional mutation pressure on the base composition of the genomic DNA.
Animals↗
Contributions to the phylogeny of Platyhelminthes based on partial sequencing of 18S ribosomal DNA.
Partial sequencing of the 18S ribosomal DNA gene of one nemertean and 13 free-living and parasitic Platyhelminthes (556 nucleotides), and of one nemertean and 20 Platyhelminthes (556 nucleotides) was used to test several hypotheses concerning the phylogenetic relationships of Platyhelminthes. The following conclusions were reached: the Neodermata is monophyletic; Trematoda (Aspidogastrea and Digenea) is monophyletic, although a sister group relationship of the Aspidogastrea and all other Neodermata cannot be definitely ruled out; the Cestoda comprising the Eucestoda, Amphilinidea and Gyrocotylidea is monophyletic; it is unresolved whether the Monogenea is paraphyletic; neither Gyrocotylidea and Monopisthocotylea nor Gyrocotylidea and Monogenea as a whole are sister groups; Anoplodiscus is a monopisthocotylean monogenean; none of Proseriata, Pterastericolidae/Umagillidae, Kalyptorhynchia, Rhabdocoela as a whole, Dalyelliida or the Temnocephalidae is the sister group of the Neodermata; there is some evidence that a larger taxon consisting of Proseriata, Tricladida and Rhabdocoela may be the sister group of the Neodermata but definitive evidence for a sister group relationship between the Neodermata and any turbellarian taxon is lacking; Rhabdocoela and Lecithoepitheliata are not closely related; it is unresolved whether the Rhabdocoela is monophyletic; Umagillidae, Pterastericolidae and Temnocephalidae belong to one monophylum; the Temnocephalidae are very close to the dalyelliids; Tricladida and Rhabdocoela are sister groups, the exact position of the Catenulida and Nemertini in relation to the Platyhelminthes has not been resolved, although Catenulida and Lecithoepitheliata may belong to one clade.
Animals↗
Detection and characterization of DNA polymerase activity in Toxoplasma gondii.
A DNA polymerase activity has been detected and characterized in crude extracts from tachyzoites of Toxoplasma gondii. The enzyme has a sedimentation coefficient of 6.4 S, corresponding to an approximate molecular weight of 150,000 assuming a globular shape. Like mammalian DNA polymerase alpha, the DNA polymerase of T. gondii was sensitive to N-ethylmaleimide and inhibited by high ionic strength. However, the enzyme activity was not inhibited by aphidicolin which is an inhibitor of mammalian DNA polymerases alpha, delta and epsilon and also cytosine-beta-D-arabinofuranoside-5'-triphosphate which is an inhibitor of alpha polymerase. The activity was inhibited by 2',3'-dideoxythymidine-5'-triphosphate which is an inhibitor of mammalian DNA polymerase beta and gamma. Magnesium ions (Mg2+) were absolutely required for activity and its optimal concentration was 6 mM. The optimum potassium (K+) concentration was 50 mM and a higher concentration of K+ markedly inhibited the activity. Activity was optimal at pH 8. Monoclonal antibodies against human DNA polymerase alpha did not bind to DNA polymerase of T. gondii. Thus the T. gondii enzyme differs from the human enzymes and may be a useful target for the design of toxoplasmacidal drugs.
Animals↗