Search PubMed⌕ Search

Biomedical subjects

W Bains

Publications and source records attributed to W Bains.

50 records · Page 3Linked to original sources
PubMed1989

Similarity and divergence among rodent repetitive DNA sequences.

We have analyzed the sequence of 63 B1 and 71 B2 repetitive elements from published data base sequences. The sequences conform to previously published consensus sequences, but are not identical to them. The B2 sequences show seven regions of high variability between family members, which we show points to the B2 family containing subfamilies; no similar evidence is found for subfamilies of the B1 family. The comparisons show no evidence for the emergence of species-specific variants of B1 or B2 sequences since the separation of murine and hamster lines of descent, nor of their concerted evolution within species in the last 10 million years.

Animals↗
PubMed1988

A novel method for nucleic acid sequence determination.

We describe a novel sequencing methodology which should be readily and completely automated. The method relies on fragmentation of a nucleotide or deoxynucleotide sequence into short fragments, and subsequent quantitation of the fragments by hybridization to oligo-deoxynucleotides on a solid support. The original sequence may be reconstructed from the resulting table of fragment frequencies. We present a specific protocol which would allow practical implementation of this approach.

Base Sequence↗
PubMed1987

Codon distribution in vertebrate genes may be used to predict gene length.

I have analysed the coding regions of 96 eukaryotic genes for their use of iso-coding codons. Specific codons occur more frequently in specific positions in all members of some gene families than would be expected if codon choice was determined solely by the frequency of codon usage. In the absence of evidence a priori for selection for particular codons at particular positions, I term such co-occurring codons "coincident codons". Coincident codons are not confined to particular regions of genes, and their occurrence is not detectably linked with the location of introns in the genomic sequence. Their presence is partly but not completely explained by the exchange of sequence between similar functional genes within a species: homologous genes from different organisms also possess the same codons at some sites with greater than expected frequencies. The relative excess of coincident codons correlates well with the overall length of the genes analysed, but not with the length of mRNA or coding regions, or with qualitative features of gene structure or expression. This, and the unusual sequence environment of coincident codons, suggests that they are a feature of the overall secondary structure of the heterogeneous nuclear RNA. Such considerations suggest approaches for optimizing the expression of exogenous genes in eukaryotic systems, and for predicting the structure of genes for which only partial sequence data is available.

Actins↗
PubMed1987

Rate of base substitution in mammalian nuclear DNA is dependent on local sequence context.

We have analysed the pattern of base substitutions in 40 mammalian processed pseudogenes by comparing them with their cognate functional genes. We find that the rate of base substitution is dependent both on the nature of the mutating base and upon the bases which flank it. Among bases which are not members of CG dinucleotides, bases which are the 5' members of purine-pyrimidine or pyrimidine-purine dinucleotides mutate faster than 5' members of other dinucleotides. These data allow the mutational distance between genes to be estimated more accurately, and suggest some general properties of the mechanism of error prevention in mammalian nuclear DNA.

Animals↗
PubMed1987

Differential patterns of transcript accumulation during human myogenesis.

We evaluated the extent to which muscle-specific genes display identical patterns of mRNA accumulation during human myogenesis. Cloned satellite cells isolated from adult human skeletal muscle were expanded in culture, and RNA was isolated from low- and high-confluence cells and from fusing cultures over a 15-day time course. The accumulation of over 20 different transcripts was compared in these samples with that in fetal and adult human skeletal muscle. The expression of carbonic anhydrase 3, myoglobin, HSP83, and mRNAs encoding eight unknown proteins were examined in human myogenic cultures. In general, the expression of most of the mRNAs was induced after fusion to form myotubes. However, several exceptions, including carbonic anhydrase and myoglobin, showed no detectable expression in early myotubes. Comparison of all transcripts demonstrated little, if any, identity of mRNA accumulation patterns. Similar variability was also seen for mRNAs which were also expressed in nonmuscle cells. Accumulation of mRNAs encoding alpha-skeletal, alpha-cardiac, beta- and gamma-actin, total myosin heavy chain, and alpha- and beta-tubulin also displayed discordant regulation, which has important implications for sarcomere assembly. Cardiac actin was the only muscle-specific transcript that was detected in low-confluency cells and was the major alpha-actin mRNA at all times in fusing cultures. Skeletal actin was transiently induced in fusing cultures and then reduced by an order of magnitude. Total myosin heavy-chain mRNA accumulation lagged behind that of alpha-actin. Whereas beta- and gamma-actin displayed a sharp decrease after initiation of fusion and thereafter did not change, alpha- and beta-tubulin were transiently induced to a high level during the time course in culture. We conclude that each gene may have its own unique determinants of transcript accumulation and that the phenotype of a muscle may not be determined so much by which genes are active or silent but rather by the extent to which their transcript levels are modulated. Finally, we observed that patterns of transcript accumulation established within the myotube cultures were consistent with the hypothesis that myoblasts isolated from adult tissue recapitulate a myogenic developmental program. However, we also detected a transient appearance of adult skeletal muscle-specific transcripts in high-confluence myoblast cultures. This indicates that the initial differentiation of these myoblasts may reflect a more complex process than simple recapitulation of development.

Adult↗
PubMed1986

MULTAN: a program to align multiple DNA sequences.

I describe a computer program which can align a large number of nucleic acid sequences with one another. The program uses an heuristic, iterative algorithm which has been tested extensively, and is found to produce useful alignments of a variety of sequence families. The algorithm is fast enough to be practical for the analysis of large number of sequences, and is implemented in a program which contains a variety of other functions to facilitate the analysis of the aligned result.

Animals↗
PubMed1986

The multiple origins of human Alu sequences.

I have analyzed a collection of published human Alu sequences. The compiled sequences show several unexpected features, including a uniform pattern of divergence from their consensus sequence, a mutual divergence that is not correlated with their age, and common features in the genomic DNA flanking the 5' ends of the elements. I suggest that the Alu family of sequences derives from a large pool of precursors and not from a single precursor similar to the family consensus sequence, and that new elements integrate into the genome selectively at oligo-A-rich sites.

Base Sequence↗
PubMed1986

Codon usage in histone gene families of higher eukaryotes reflects functional rather than phylogenetic relationships.

The nucleic acid sequences coding for 23 H3 histone genes from a variety of species have been analyzed using a computer assisted alignment and analysis program. Although these histones are highly conserved within and between highly divergent species, they represent various classes of histones whose patterns of expression are distinctively regulated. Surprisingly, in dendrograms derived from these comparisons, H3 sequences cluster according to their modes of regulation rather than phylogenetically. These clusters are generated from highly distinctive patterns of codon usage within the functional gene classes. We suggest that one factor involved in specifying the differing codon usage patterns between functional classes is a difference in requirements for rapid translation of mRNA. In addition, the data presented here, together with structural and sequence information, suggest a heterodox evolutionary model in which genes related to the intron-bearing, basally expressed H3.3 vertebrate genes are the ancestors of the intronless H3.1 class of genes of higher eukaryotes. The H3.1 class must have arisen, therefore, following duplication of a primitive H3.3 gene, but prior to the plant-animal divergence. Implications of the data presented are discussed with regard to functional and evolutionary relationships.

Amino Acid Sequence↗
PubMed1984

Cardiac actin is the major actin gene product in skeletal muscle cell differentiation in vitro.

We examined the expression of alpha-skeletal, alpha-cardiac, and beta- and gamma-cytoskeletal actin genes in a mouse skeletal muscle cell line (C2C12) during differentiation in vitro. Using isotype-specific cDNA probes, we showed that the alpha-skeletal actin mRNA pool reached only 15% of the level reached in adult skeletal muscle and required several days to attain this peak, which was then stably maintained. However, these cells accumulated a pool of alpha-cardiac actin six times higher than the alpha-skeletal actin mRNA peak within 24 h of the initiation of differentiation. After cells had been cultured for an additional 3 days, this pool declined to 10% of its peak level. In contrast, over 95% of the actin mRNA in adult skeletal muscle coded for alpha-actin. This suggests that C2C12 cells express a pattern of sarcomeric actin genes typical of either muscle development or regeneration and distinct from that seen in mature, adult tissue. Concurrently in the course of differentiation the beta- and gamma-cytoskeletal actin mRNA pools decreased to less than 10% of their levels in proliferating cells. The decreases in beta- and gamma-cytoskeletal actin mRNAs are apparently not coordinately regulated.

Actins↗
PubMedDate not supplied

Mixed hybridization and conventional strategies for DNA sequencing.

Oligonucleotide hybridization can be used to sequence short regions of DNA. In this report, I examine the extent to which this method can be used to sequence genomic DNA, using simulation experiments performed on known human genomic DNA sequences, and show that segments of sequence of up to 800-bp length may be unambiguously sequenced using 65,536 mixed 11-mers. Conventional sequencing or hybridization to specific, longer oligonucleotides can extend this limit in a mixed strategy that can sequence 10-kb DNA sequences with 5-7 conventional sequencing reactions and hybridization to a mixed 12-mer probe array.

Algorithms↗