Biomedical subjects

H Tyson

Publications and source records attributed to H Tyson.

At least 19 recordsLinked to original sources

PubMed1995

Codon usage in plant peroxidase genes.

Codon preference and asymmetry in usage in the DNA sequences encoding the mature enzyme protein of 24 plant peroxidases from 12 different species were examined. Codon usage in highly conserved/non-conserved areas of the sequences was analysed, as well as possible deficiency/excess in CpG dinucleotides in the pairs of codon positions. Sequence relationships displayed by overall codon usage, dinucleotide frequencies within codons, and amino acid sequences were also studied. The main findings were: (1) Monocots clustered separately from dicots for overall codon usage and dinucleotide frequencies in codon positions 2 and 3, with six and seven clusters respectively discernible among these 24 peroxidase sequences. The monocot/dicot distinction disappeared in the four clusters among the mature protein amino acid sequences. Overall codon usage in sequences from monocotyledon and dicotyledon species differed, the monocots favouring codons with C or G in the third position. (2) Codon usage was biassed in many sequences, asymmetry was particularly noticeable in the monocots. (3) For repeated amino acids within conserved areas, codon preference appeared dependent on the order in which the repeated amino acid occurred, so that its usage of synonymous codons frequently balanced out.

Amino Acid Sequence↗

PubMed1994

Molecular evolution of a Y-chromosomal repetitive sequence family in the genus Mus.

A 522-base-long Y-chromosomal sequence was isolated from a BALB/c genomic library and was designated "BF046." It is repeated about 200 times in the male genome, and a difference was detected between the Mus musculus musculus and the M. m. domesticus type Y chromosomes. BF046-related sequences were present over the entire length of the Y chromosome as visualized by in situ hybridization. Southern blot analysis against DNAs isolated from eight species in the genus Mus showed that BF046-related sequences were amplified in the Y chromosomes of three closely related species: M. musculus, M. spicilegus, and M. spretus. To gain insight into the stability of the BF046 sequence family, we isolated 18 additional clones from these three mouse species and compared their sequences. The M. musculus sequences differed from the M. spicilegus and M. spretus sequences by two indels. The remaining parts of the sequences were very similar, but both parsimony and distance-based analytical methods divided the sequences into the same four subgroups, with each species having its own subgroup(s). Thus, the Y chromosomes of M. musculus, M. spicilegus, and M. spretus can be distinguished from one another.

Animals↗

PubMed1994

cDNA sequence and tissue-specific expression of an anionic flax peroxidase.

A flax (Linum usitatissimum L.) lambda gt10 cDNA library was screened with a probe coding for the amino terminus of a flax peroxidase. The probe was generated by PCR amplification of the library with one of the lambda gt10 sequencing primers and a mixed oligonucleotide derived from a well-conserved amino acid region (distal heme ligand) found in all plant peroxidases. A positive clone (FLXPER2) was isolated and characterized. The cDNA contains 1153 nucleotides, excluding the poly(A) tail, and encodes a mature protein of 297 amino acids with a molecular mass of 31.9 kDa. The mature protein's amino acid sequence contains three highly conserved regions, two of which contain histidine ligands for the heme group. The deduced amino acid sequence has nine cysteine residues. Eight are identically located to those of horseradish C peroxidase, which participate in four disulfide bridges; these cysteines are highly conserved in all plant peroxidases. One potential N-glycosylation site (Asn-X-Thr/Ser) is present. The predicted pI value of 4.5 identifies FLXPER2 as an anionic peroxidase. Northern blot analysis shows that its mRNA expression is unique to stem tissue. Amino acid sequence comparisons show high similarity between FLXPER2 and peanut, rice, and tobacco peroxidases.

Amino Acid Sequence↗

PubMed1993

A Macintosh BASIC program for fitting linear additive models to data by weighted least squares methods, with automatic elimination of redundant parameters from the model.

A BASIC program for fitting linear additive models to data with weighted or unweighted least squares methods and matrix procedures is described. Written and compiled to run on Macintosh II type machines (68020/68030/68040) with coprocessor (68881/68882), the program fits the model supplied by the user as an X or design matrix and provides the option of making the model's parameters orthogonal. Predicted values plus regression and residual terms are calculated. For the weighted fit, the significance of the residual term is evaluated and redundant parameters sequentially and automatically removed until a minimum adequate model is achieved. An appropriate design matrix allows weighted fitting of models for multiway analyses of variance (e.g. factorial, nested and split plot), simple or multiple linear or curvilinear regression, combinations of these in covariance analyses, and genetic analyses (including diallel cross analyses). Sums of squares for individual parameters and orthogonal comparisons can be calculated by the program.

Least-Squares Analysis↗

PubMed1993

cDNA sequence, expression, and transcript stability of a cold acclimation-specific gene, cas18, of alfalfa (Medicago falcata) cells.

The nucleotide sequence of a full-length cDNA, the deduced amino acid sequence, and the regulation of expression of a cold acclimation-specific gene, cas18, in cell suspension cultures of a freezing-tolerant cultivar of alfalfa (Medicago falcata cv Anik) have been determined. The deduced polypeptide, CAS18, is relatively small (17.6 kD), is highly hydrophilic, is rich in glycine and threonine, and contains two distinctive repeat elements. It exhibits homology with members of the LEA/RAB/dehydrin family of proteins, which accumulate in response to abscisic acid (ABA) or water stress. It is intriguing that cas18 is induced by neither ABA nor water stress. The cas18 cDNA hybridizes to three transcripts of 1.6, 1.4, and 1.0 kb, and the cDNA characterized here corresponds to the 1.0-kb transcript. The expression of this gene is about 30-fold greater in cold-acclimated cells than in nonacclimated cells. Although the accumulation of transcripts during cold acclimation is relatively slow, their disappearance during deacclimation is dramatically rapid, becoming undetectable in less than 5 h. Studies of nuclear run-on transcription show that cold acclimation enhances the transcription of this gene nearly 9-fold. The stability of cas18-detectable transcripts during deacclimation is considerably increased if transcription is inhibited with cordycepin. It therefore appears that low temperature regulates the expression of cas18 at both the transcriptional and posttranscriptional levels.

Acclimatization↗

PubMed1993

Comparison of mouse Y-chromosomal repetitive sequences isolated from Mus musculus, M. spicilegus, and M. spretus.

The mouse Y chromosome is rich in repetitive sequences. We describe a new highly male-specific BALB/c mouse sequence named 142-5. The distribution of 142-5 related sequences, which appeared to be repeated at least 100 times in the male genome of Mus musculus, was visualized on the Y chromosome by in situ hybridization. Their accumulation patterns in the genus Mus showed that the sequences evolved quickly and suggested that they might prove useful for detecting genetic differences between closely related species. To test this hypothesis, we isolated 20 additional sequences from three mouse species (M. musculus, M. spicilegus, and M. spretus) and compared their nucleotide sequences using three different computer programs. It was found that the sequences were remarkably similar but could be divided into four subgroups, and that each species had a distinct set or sets of sequences that were amplified in the Y chromosome.

Animals↗

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↗

PubMed1988

Elimination of Differences in the Mobility of Flax Isoperoxidases on PAGE by Digestion with alpha-Mannosidase.

In the flax (Linum usitatissimum) genotype Stormont cirrus, anodic peroxidases from the genotroph S migrate more slowly on PAGE and SDS-PAGE than the corresponding peroxidases from the genotroph L. When purified isoperoxidases S2 and L2 were digested with alpha-mannosidase, the difference in mobility was eliminated. Treatment with alpha-fucosidase and beta-xylosidase also altered the mobility of S2 and L2, but affected the sensitivity to the action of endo-beta-N-acetylglucosaminidase H of only S2. Our results suggest differences in posttranslational processing of the carbohydrate moiety between S and L isoperoxidases. These differences were also found in other S and L glycoenzymes (anodic acid phosphatases) as well as in the peroxidases of other flax genotypes.

Journal Article↗

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↗