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W M Fitch

Publications and source records attributed to W M Fitch.

At least 73 records · Page 4Linked to original sources
PubMed1986

The estimate of total nucleotide substitutions from pairwise differences is biased.

A nomographic method is presented that estimates the number of nucleotide substitutions since the common ancestor of two nucleotide sequences with no assumption about the proportion of transition and transversion substitutions except that it is constant over time. Of two previous methods of estimating this number, that of M. Kimura (Proc. natn. Acad. Sci. U.S.A. 78, 454-458 (1981) obtains the same result, and is thus confirmed by this work, while that of W. M. Brown, E. M. Prager, A. Wang & A. C. Wilson (J. molec. Evol. 18, 225-239 (1982] does not get the same result. The method presented here also obtains the fraction of all substitutions that are transitions. If one has three or more homologous sequences to compare, one can test the validity of the model by examining the constancy of the estimated proportion of substitutions that are transitions across the various pairs of sequences in a simple visual way. The method is general for any pair of mutually exclusive nucleotide substitutional categories, not just transitions and transversions. Mitochondrial data provide evidence that, for this and probably other current models correcting for superimposed substitutions, one or more of the underlying assumptions is incorrect. This is because there is some unknown systematic bias affecting this evolutionary process. It is suggested that at least part of the bias arises from incorrectly assuming that all sites are variable. In the absence of evidence that this bias is not present in other data, all estimates of the number of substitutions based upon pairs of sequences and current methods of estimating superimposed substitutions at a single site should be viewed as uncertain.

Animals↗
PubMed1986

Epidemiology of influenza C virus in man: multiple evolutionary lineages and low rate of change.

The nucleotide sequences of nonstructural protein (NS) genes of human influenza C viruses isolated between 1947 and 1983 were determined and compared. Assuming constant evolutionary rates, the extent of nucleotide differences among NS genes does not correspond to the isolation years of the strains. This suggests that more than one gene lineage is present in the population. Furthermore, examination of the eight C virus NS gene sequences by the maximum parsimony method (W. M. Fitch, 1971, Syst. Zool. 20, 406-416) yielded phylogenetic trees that were grossly different from those obtained using the hemagglutinin genes for the same eight isolates. This result is compatible with the idea of reassortment of genes in nature across lineages of influenza C viruses. The sequence analysis also suggests that nucleotide substitutions occur at a lower rate in the C virus NS genes than in influenza A virus NS genes.

Amino Acid Sequence↗
PubMed1986

Molecular evolution of pancreatic-type ribonucleases.

Amino acid sequences of 39 mammalian ribonucleases have been used to construct trees by the maximum parsimony procedure. These trees are in fairly good agreement with the biological classification of the species involved. In the branching order of the six investigated eutherian mammalian orders, the edentates diverge first, followed, probably, by the primates. No definite conclusions can be drawn about the order of divergence of the perissodactyls, the rodents, and the group consisting of artiodactyls plus cetaceans. Nucleic acid sequences of part of the messenger RNAs of rat pancreatic and bovine seminal ribonuclease were compared. Both messengers have a second stop codon at position 129, which is in agreement with the addition of four residues at the C-terminus in several other ribonucleases. Turtle pancreatic ribonuclease and human angiogenin differ from each other and from the mammalian ribonucleases at 55%-70% of the amino acid positions; they share a number of structural features. Mammalian nonsecretory ribonucleases are homologous to the pancreatic ribonucleases in sequence regions where the active-site histidine residues are located.

Amino Acid Sequence↗
PubMed1985

The biological significance of G-T/G-U mispairing in nucleic acid secondary structure.

We have computed the expected distribution of the potential for hairpin-like secondary structures with small loops (3-20 bases) and uninterrupted stems and compared that to the distribution observed in the complete genomes of seven DNA viruses from animals, plants and bacteria, as well as a bacterial plasmid. The formation of G-T mismatches in the stems of these structures was allowed. Furthermore we have analyzed the distribution of the potential for such structures along the genetic maps of these genomes, specifically around the start sites of known genes. Our data reveal that the potential for mismatch containing structures with stem length exceeding eight base pairs is over-represented and non-randomly distributed, but to a much lesser degree than that for perfect structures of equal size. Moreover, the potential for both types of structures is preferentially located near functional start codons. From this we deduce that in general G-T/G-U containing nucleic acid secondary structures are biologically relevant, though possibly less significant than perfect ones.

Bacteriophage phi X 174↗
PubMed1985

Evolution in inbred strains of mice appears rapid.

Genetic variation at 97 loci in ten commonly used inbred strains of mice is greatly in excess of that expected under current assumptions. Evidence against all of the readily apparent explanations is presented and the possibility of early selection for heterozygosity or of conversion is suggested. The common ancestor of these strains is estimated to have occurred about 150 years ago.

Animals↗
PubMed1984

Avian retrovirus pp32 DNA binding protein. Preferential binding to the promoter region of long terminal repeat DNA.

The avian retrovirus pp32 protein possesses DNA endonuclease activity and unique DNA binding properties. An improved purification procedure was developed for pp32, resulting in a severalfold increase in the yield of this virion protein. By use of the nitrocellulose filter binding assay, the protein retains approximately 2-fold more supercoiled (form I) DNA molecules than equivalent linear duplex DNA molecules. Single-stranded DNA is only slightly preferred over double-stranded DNA for pp32 binding. The pp32 DNA binding sites on form I pBR322 DNA which contained an insert of avian retrovirus long terminal repeat (LTR) DNA were determined. A preformed protein-DNA complex was digested with one of several different multicut restriction enzymes and filtered through nitrocellulose filters. Fragments containing viral LTR DNA sequences and plasmid DNA containing promoter sequences for the ampicillin and tetracycline genes, sequences for the "left-end" inverted repeat of transposon 3, and sequences encompassing the carboxyl terminus of the beta-lactamase gene were preferentially retained on the filter by pp32. Partial mapping of pp32 DNA binding sites on LTR DNA was accomplished by generation of deletions in LTR DNA sequences. The pp32 protein preferentially bound viral DNA fragments which contain the viral promoter (TATTTAA) and the adjacent "R" repeat sequences. Computer analysis revealed that three of the four plasmid DNA fragments retained by pp32 contained LTR DNA promoter-like sequences (one mismatch only) which were part of statistically significant and thermodynamically stable hairpin structures.

Animals↗
PubMed1984

Amino acid sequences of lower vertebrate parvalbumins and their evolution: parvalbumins of boa, turtle, and salamander.

One major parvalbumin each was isolated from the skeletal muscle of two reptiles, a boa snake, Boa constrictor, and a map turtle, Graptemys geographica, while two parvalbumins were isolated from an amphibian, the salamander Amphiuma means. The amino acid sequences of all four parvalbumins were determined from the sequences of their tryptic peptides, which were ordered partially by homology to other parvalbumins. Phylogenetic study of these and 16 other parvalbumin sequences revealed that the turtle parvalbumin belongs to beta lineage, while the salamander sequences belong, one each, to the alpha and beta lineages defined by Goodman and Pechère (1977). Boa parvalbumin, however, while belonging to the beta lineage, clusters within the fish in all reasonably parsimonious trees. The most parsimonious trees show many parallel or back mutations in the evolution of many parvalbumin residues, although the residues responsible for Ca2+ binding are very well conserved. These most parsimonious trees show an actinopterygian rather than a crossoptyrigian origin of the tetrapods in both the alpha and beta groups. One of two electric eel parvalbumins is evolving more than 10 times faster than its paralogous partner, suggesting it may be on its way to becoming a pseudogene. It is concluded that varying rates of amino acid replacement, much homoplasy, considerable gene duplication, plus complicated lineages make the set of parvalbumin sequences unsuitable for systematic study of the origin of the tetrapods and other higher-taxa divergence, although it may be suitable within a genus or family.

Amino Acid Sequence↗
PubMed1983

Calculating the expected frequencies of potential secondary structure in nucleic acids as a function of stem length, loop size, base composition and nearest-neighbor frequencies.

A formula is derived to estimate the expected frequency of potential secondary structure of a given stem length and loop size in a random sequence of nucleotides of known length and composition. An example is provided using the SV40 sequence which shows significant non-randomness in stem length but whose significance is reduced by more than six orders of magnitude by taking nearest neighbor frequencies into account.

Base Composition↗
PubMed1983

Evolutionary relationships of vertebrate lactate dehydrogenase isozymes A4 (muscle), B4 (heart), and C4 (testis).

The amino acid sequence variation among seven lactate dehydrogenase isozymes from dogfish muscle, chicken muscle and heart, pig muscle and heart, and mouse and rat testes were compared with respect to the whole lactate dehydrogenase polypeptide chain as well as their four functional domains. The coenzyme-binding domain is more conserved than the substrate-binding domain. The sequence of the loop and helix alpha D region of testicular LDH-C4 isozymes is very different from those of somatic LDH-A4 and LDH-B4 isozymes, while the NH2-terminal arm is extremely variable. The most parsimonious phylogenetic tree among these seven vertebrate lactate dehydrogenase sequences clearly indicates that the LDH-A4 and LDH-B4 isozymes are more closely related to each other than either to the LDH-C4 isozymes.

Amino Acid Sequence↗
PubMed1983

Random sequences.

The comparison of protein or nucleic acid sequences frequently leads to observations whose improbability can be tested only by Monte Carlo techniques that require randomizing the sequences being compared. Two decisions need to be made. One is whether one demands a resulting random sequence to have the properties of the original sequence (a shuffled sequence) or only expects it to have them (a representative sequence). The second decision concerns the properties of the sequence of which two are composition and nearest-neighbor frequencies. It is shown that biased nearest-neighbor frequencies can significantly affect the probability of observing a given result. Methods for producing random sequences according to these decisions are given.

Amino Acid Sequence↗
PubMed1983

Mapping the order of DNA restriction fragments.

A straightforward method was designed for mapping the order of DNA restriction fragments obtained by a double and two single digestions, without the necessity of using a computer or a radioactive label. All possible solutions compatible with a pre-set level of error in the determination of sequence lengths are obtained. The primary assumptions are given, and the appropriate modifications of the algorithm are presented as a function of any assumptions one is unable (or unwilling) to make. Use of the method in connection with end-labeled fragments is also described.

Chromosome Mapping↗
PubMed1983

Optimal sequence alignments.

Current theory is adequate to the task of finding an optimal alignment between two character strings such as nucleic acids. Most algorithms currently in use must fail to find the homologous alignment between a set of codons for the chicken alpha- and beta-hemoglobin sequence when it is in fact discoverable by a more general treatment of gaps. Fundamental reasons for this are discussed.

Journal Article↗
PubMed1983

Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus.

The kanamycin resistance gene from Staphylococcus aureus has been sequenced and its structure compared with similar genes isolated from Streptomyces fradiae and from two transposons, Tn5 and Tn903, originally isolated from Klebsiella pneumoniae and Salmonella typhimurium, respectively. The genes are all homologous but, since their common ancestor, have undergone extensive divergence, with more than 43% divergence between the closest pair. The phylogeny of the genes cannot be made congruent to the phylogeny of the taxa from which they were isolated without requiring rather improbable differences in rates. One is therefore led to conclude that there have been multiple occurrences of gene transfer between these species. Thus, although they are homologous, they are neither orthologous nor paralogous. It is suggested that homologous genes of this type be called xenologous.

Amino Acid Sequence↗
PubMed1982

Evolutionary selection for perfect hairpin structures in viral DNAs.

Several recent discoveries have pointed to nucleic acid secondary structure as an additional dimension in gene expression. Further evidence for the formation of hairpins in RNA is the fact that cruciforms exist in negatively supercoiled DNAs. As potential binding sites for proteins, these structures have been proposed to play a part in the regulation of various crucial reactions, such as replication, transcription, or RNA processing. As any random nucleotide sequence can self-anneal with an approximately 50% chance of forming some Watson-Crick-type base pairs, it is difficult to assess which, if any, of all possible hairpin-like secondary structures may be biologically relevant. We have computed the expected distribution of perfectly base-paired structures as a function of loop size and stem length and compared it with the distribution observed in the complete genome of eight DNA viruses from animals, plants and bacteria. We report here that hairpins having six or more consecutive base pairs in the stem are not distributed randomly long the genome, occur much more often than chance would predict, and are particularly over-represented in regions that appear to have regulatory significance. The average loop size was found to decrease with an increase in stem length. These results support our previous hypothesis that these structures are biologically relevant.

Bacteriophages↗
PubMed1982

Isolation and amino acid sequence of a monomeric hemoglobin in heart muscle of the bullfrog, Rana catesbeiana.

A monomeric heme-containing protein was isolated from heart muscles of the bullfrog, Rana catesbeiana, by gel filtration on Sephadex G-75 followed by DE52 ion-exchange column chromatography. The protein is composed of 132 amino acid residues and has Mr = 14,000 estimated by gel filtration on Sephadex G-50. This is the shortest heme globin so far known. The complete amino acid sequence of the apoprotein was deduced from the amino acid sequences of cyanogen bromide fragments and tryptic peptides. In order to align its amino acid sequence with other proteins in the globin superfamily (Hunt, L. T., Hurst-Calderone, S., and Dayhoff, M. O. (1978) Atlas of Protein Sequence and Structure, Vol. 5, Suppl. 3, 229-249, National Biomedical Research Foundation, Washington, D.C.), three gaps common to alpha-hemoglobin are required plus three more gaps unique in this protein. Of the latter, one is at the end of the EF region, the second near the beginning of the H-region, and the third is at the COOH terminus. With 62 amino acid residues in common, the amino acid sequence of this monomer is more homologous to the alpha-hemoglobin of the tadpole of R. catesbeiana (Maruyama, T., Watt, K. W. K., and Riggs, A. (1980) J. Biol. Chem. 255, 3285-3293), than to any other globin. A phylogenetic study of it and other globins clearly reveals that it arose via a gene duplication of hemoglobin near the time of the duplication that gave rise to the alpha and beta genes. But residues in contact with the heme group are rather conserved while the residues in the alpha 1 beta 1, alpha 1 beta 2 subunit contact regions are significantly substituted, frequently reverting to a myoglobin-like residue. The absence of this monomeric protein from the blood and the absence of myoglobin in heart muscle may indicate the protein functions as a myoglobin.

Amino Acid Sequence↗