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Biomedical subjects

H Tyson

Publications and source records attributed to H Tyson.

17 recordsLinked to original sources
PubMed1992

A set of BASIC programs to evaluate relationships among protein sequences by optimum alignment and distance matrix analysis.

These six programs evaluate relationships among a number (> 2) of protein (or DNA) sequences. Program 1 automatically computes optimum alignments and total distances for all pairwise sequence combinations over any user desired range of the two gap penalties. Programs 2, 3 and 4 generate a square, symmetrical distance matrix, which can be exported for cluster analysis, or further analysed with programs 5 and 6 to give specific distances between sequences and extract sequence relationships. Data and results are exchanged among these programs, which are written in BASIC and compiled to run on Macintosh (68020/030/040) type machines with coprocessor and at least one MB of RAM. BASIC graphics commands or those for the Macintosh interface are avoided to facilitate use on other machines. Two groups of sequences are used to demonstrate (a) alignment, inter sequence distance calculation and dendrogram generation and (b) specific distance calculation and its usage in detecting sub groups of related sequences in dendrograms.

Algorithms↗
PubMed1992

Relationships between amino acid sequences determined through optimum alignments, clustering, and specific distance patterns: application to a group of scorpion toxins.

Optimum alignment in all pairwise combinations among a group of amino acid sequences generated a distance matrix. These distances were clustered to evaluate relationships among the sequences. The degree of relationship among sequences was also evaluated by calculating specific distances from the distance matrix and examining correlations between patterns of specific distances for pairs of sequences. The sequences examined were a group of 20 amino acid sequences of scorpion toxins originally published and analyzed by M.J. Dufton and H. Rochat in 1984. Alignment gap penalties were constant for all 190 pairwise sequence alignments and were chosen after assessing the impact of changing penalties on resultant distances. The total distances generated by the 190 pairwise sequence alignments were clustered using complete (farthest neighbour) linkage. The square, symmetrical input distance matrix is analogous to diallel cross data where reciprocal and parental values are absent. Diallel analysis methods provided analogues for the distance matrix to genetical specific combining abilities, namely specific distances between all sequence pairs that are independent of the average distances shown by individual sequences. Correlation of specific distance patterns, with transformation to modified z values and a stringent probability level, were used to delineate subgroups of related sequences. These were compared with complete linkage clustering results. Excellent agreement between the two approaches was found. Three originally outlying sequences were placed within the four new subgroups.

Amino Acid Sequence↗
PubMed1991

Outcomes of 1001 midwife-attended home births in Toronto, 1983-1988.

A retrospective descriptive study of 1001 midwife-attended home births in Toronto, Ontario, was carried out between January 1983 and July 1988. Interviews with 26 midwives and reviews of client records provided data on maternal age, socio-economic status, gestation, ruptured membranes, length of labor, episiotomies and perineal lacerations, transfer to hospital of mother or baby or both, infant resuscitation, and breastfeeding. Of 1001 planned home births, 361 involved primiparous women, of whom 245 (68%) remained at home and 116 (32%) required transfer of mother or baby to hospital during labor or the first four postpartum days. Of the 640 multiparous births, 591 (92%) women remained at home and 49 (8%) required transfer to hospital. Among women transferred, 91 had spontaneous vaginal births, 34 had forceps deliveries, and 35 had cesarean sections. Variables significantly associated with maternal transfer for both primiparas and multiparas were length of latent and active phases of the first stage of labor, length of the second stage of labor, and duration of ruptured membranes. Five neonates were transferred and two died, one each after birth at home and in hospital. There were no maternal deaths. The proportion of mothers breastfeeding without supplement at 28 days postpartum was 98.6 percent.

Adult↗
PubMed1986

Genetic control of acid phosphatase Rm and its relation to control of peroxidase Rm in flax (Linum) genotrophs.

Evidence from various workers has indicated that isozyme relative mobility (Rm) may not be defined solely by the corresponding structural gene but may also be modified by alleles at other loci. The instances of numerous, small ongoing temporal or tissue changes in Rm for certain enzyme systems in plants may be another aspect of this modification due to interactions between genes. A further possible example of Rm modification occurs in connection with environmentally (fertilizer treatment) induced heritable changes within particular completely inbred and genetically homogeneous plant genotypes. Fertilizer-induced, persistent relative mobility (Rm) shifts for peroxidases are controlled by two alleles at one locus, a dominant for faster Rm and a recessive for slower Rm; codominance is completely absent. There are similar Rm shifts in acid phosphatases, likewise stemming from molecular weight changes. This study examined genetic control of the acid phosphatase Rm shift and its relation to peroxidase Rm control. It showed that the environmentally induced heritable acid phosphatase Rm shift is controlled by an identical system of a dominant (faster) and recessive (slower) allele, closely linked to the locus controlling peroxidases. The Rm shifts for both these enzyme glycoproteins are unidirectional, with no codominance; at least 10 other nonidentified glycoproteins display the same unidirectional Rm shifts. The results suggest modification, possibly posttranslational or transcriptional, controlled by modifier loci. This supports indications in other organisms that small numbers of modifier loci may control widespread Rm changes in the protein products of a genome.

Acid Phosphatase↗
PubMed1985

Alignment of nucleotide or amino acid sequences on microcomputers, using a modification of Sellers' (1974) algorithm which avoids the need for calculation of the complete distance matrix.

A program to calculate optimum alignment between two sequences, which may be DNA, amino acid or other information, has been written in PASCAL. The Sellers' algorithm for calculating distance between sequences has been modified to reduce its demands on microcomputer memory space by more than half. Gap penalties and mismatch scores are user-adjustable. In 48 K of memory the program aligns sequences up to 170 elements in length; optimum alignment and total distance between a pair of sequences are displayed. The program aligns longer sequences by subdivision of both sequences into corresponding, overlapping sections. Section length and amount of section overlap are user-defined. More importantly, extension of this modification of Sellers' algorithm to align longer sequences, given hardware and compilers/languages capable of using a larger memory space (e.g. 640 K), shows that it is now possible to align, without subdivision, sequences with up to 700 elements each. The increase in computation time for this program with increasing sequence lengths aligned without subdivision is curvilinear, but total times are essentially dependent on hardware/language/compiler combinations. The statistical significance of an alignment is examined with conventional Monte Carlo approaches.

Amino Acid Sequence↗
PubMed1985

Isozyme relative mobility (Rm) changes related to leaf position; apparently smooth Rm trends and some implications.

Relative mobilities (Rm's) of peroxidase and acid phosphatase isozymes were examined in leaves of flax (Linum usitatissimum L.). The leaves were sampled from four equidistantly spaced positions from main stem base to apex in various genotypes. Rm's for the two slowest-migrating isozymes of each enzyme system changed in a simple, coherent fashion in leaves from stem bases toward apices. The Rm trends up the stem seen in two highly branched flax types were somewhat different from those in two sparsely branched types. The coherent Rm trends in the four types, suggesting a smooth continuum and a potentially large number of slightly different forms of these isozymes, are discussed in relation to other data for such Rm trends. In the study reported here, both enzyme systems behaved similarly. This fact and the simple Mendelian genetical system with no codominance controlling Rm's in flax peroxidases and acid phosphatases suggest posttranscriptional or posttranslational modifications as plausible mechanisms underlying the numerous, presumably small molecular changes generating the small, consistent changes in Rm's.

Acid Phosphatase↗
PubMed1984

Possible posttranslational modification, and its genetic control, in flax genotroph isozymes.

Environmentally induced flax genotrophs L and S show heritable shifts in the relative mobilities of peroxidase, esterase, and acid phosphatase isozymes, plus a number of nonspecific glycoproteins. All L isozymes migrated faster than corresponding S isozymes in 10% acrylamide gels. Various aspects of these shifts are reviewed here; it is proposed that posttranslational modification, probably of the carbohydrate moieties of these glycoproteins, underlies the shifts. This proposal is discussed in relation to the switch model for genotroph induction.

Acid Phosphatase↗
PubMed1984

Visualization of both peroxidase and acid phosphatase isozymes from flax (Linum) on the same gels.

The staining of both peroxidases (PERs) and acid phosphatases (APs) following electrophoresis on acrylamide gels is described. Scanning doubly stained gels at appropriate wavelengths reveals individual isozyme bands for both enzyme systems, giving essentially identical results to those obtained from separately run and stained gels. Collection of relative mobility (Rm) data is unaffected by such tandem staining. Few complications arise from overlapping PER and AP bands, or interactions between the two staining methods and PER or AP isozymes. Even if repeat scans of a gel at different wavelengths are needed to retrieve all isozyme information, dual staining provides distinct savings in time and sample material.

Acid Phosphatase↗
PubMed1983

Molecular weight differences in acid phosphatases of stem homogenates from L and S flax genotrophs.

Anionic acid phosphatase (AP) isozymes in stem homogenates of flax genotrophs L and S were examined electrophoretically. The banding pattern was similar in both genotrophs. Relative mobility (Rm) was faster in each band of L than in the corresponding band of S. These Rm shifts did not result from differences in the sample concentration or from differential rates of development. AP activity was the same in both genotrophs. The banding pattern of F1 hybrids resembled the parental pattern. No multiple banding was observed in any of the F1 bands. The Rm in the F1 hybrids showed a dominance of L. Plots of loge (Rm) against gel concentration were constructed. While the Y intercepts of the plots indicated some differences in free electrophoretic mobility, molecular conformation was the major factor underlying both the Rm differences between bands and the Rm shifts between L and S, for corresponding bands. Estimates of apparent molecular weight (MW) for the different bands ranged from 25,000 to 250,000, with a strong possibility that some bands were oligomeric forms of others. Apparent MW was, on average, 17% higher in S than L.

Acid Phosphatase↗
PubMed1982

Molecular weight and net charge of peroxidase isozymes in F1 hybrids between L and S flax genotrophs.

In the F1 hybrids between Durrant's L and Durrant's S flax genotrophs, the relative mobilities of the anionic peroxidase isozymes were essentially the same as those in the L parent. The isozymes in both parents and their F1's were compared over a range of acrylamide gel concentrations, with plots of log relative mobility against gel concentration. Plots of comparative mobility, relative to the internal standard hemoglobin, against concentration were also examined. Both approaches provided evidence that apparent molecular weight modifications underlay the shift in mobility between the parents and the resemblance of the F1's to L, the parent which was homozygous for the dominant alleles controlling the mobility shift for at least two of the isozymes.

Heterozygote↗
PubMed1982

A Pascal program for weighted least squares regression on a microcomputer.

Weighted least-squares regression has been programmed in Pascal for a microcomputer. A double precision Pascal compiler and the Motorola 6809 assembler produce a fast machine-code program occupying 22,000 bytes of memory when appended to the Pascal run-time module. Large data sets fit in the remaining memory. A regression with 72 observations and 24 parameters runs in 7 min, excluding optional print out of large matrices. The maximum dimensions of the design matrix, X, can be altered by modifying two Pascal constants. Minor changes to the Pascal source program will make it compatible with other Pascal compilers. The program optionally orthogonalises the X matrix to detect linearly-dependent columns in X, and/or generate orthogonal parameter estimates. After orthogonalizing X and fitting the model, the parameter estimates for the original X can be retrieved by the program. Regressions on a repeatedly reduced model are performed through elimination of columns in X until the minimum adequate model is obtained.

Computers↗
PubMed1982

A BASIC program for orthogonal polynomials and retrieval of regression coefficients for original model.

A fast, short method for calculating orthogonal polynomials has been programmed in BASIC. This is combined with the retrieval of b coefficients for the original, non-orthogonal model in, for example, a curvilinear regression. The program may be used alone, or in conjunction with a package of BASIC programs for weighted least-squares solutions, to which it forms an update. Transformation of the columns of an X, or design matrix, to orthogonal vectors can detect linear dependence among the columns, as well as supplying orthogonal polynomials for regression situations with unequal increments in x values, the values of the independent variable. Retrieval of the b coefficients for the original X matrix prior to transformation allows the user to insert any x value to obtain the corresponding predicted y (dependent variable) values.

Computers↗
PubMed1982

A BASIC program package for weighted least squares solutions using a microprocessor with disc memory.

The fitting of linear additive models to data by weighted least squares methods has been programmed in BASIC. By splitting up the matrix solution into several steps, the RAM memory space needed in a microprocessor by the corresponding programs was reduced, allowing room for larger matrices. Storage of intermediate products, and of subsequent programs in the sequence , was on a mini floppy dual-disc drive. Using an extended BASIC interpreter permitting several files to be open during a program, the program package compromised between computing time and problem size. Problems involving 1600 element matrices were run on a micro having 32000 bytes of memory, allowing for example, the fitting of a model with 22 parameters to 72 observations.

Computers↗