PubMed Health⌕ Search

Biomedical subjects

F Farrelly

Publications and source records attributed to F Farrelly.

9 recordsLinked to original sources
PubMed2005

Shear stress fluctuations in the granular liquid and solid phases.

We report on experimentally observed shear stress fluctuations in both granular solid and fluid states, showing that they are non-Gaussian at low shear rates, reflecting the predominance of correlated structures (force chains) in the solidlike phase, which also exhibit finite rigidity to shear. Peaks in the rigidity and the stress distribution's skewness indicate that a change to the force-bearing mechanism occurs at the transition to fluid behavior, which, it is shown, can be predicted from the behavior of the stress at lower shear rates. In the fluid state stress is Gaussian distributed, suggesting that the central limit theorem holds. The fiber bundle model with random load sharing effectively reproduces the stress distribution at the yield point and also exhibits the exponential stress distribution anticipated from extant work on stress propagation in granular materials.

Journal Article↗
PubMed1983

Rearranged mitochondrial genes in the yeast nuclear genome.

We have found a contiguous DNA sequence in the yeast nuclear genome with extensive homology to non-contiguous yeast mitochondrial DNA sequences. Closely linked to this nuclear sequence in some, but not all, yeast strains is a tandem pair of transposable (Ty) elements. Certain features of the content and organization of this nuclear DNA sequence suggest that it may have originated from petite mitochondrial DNA which integrated into the nuclear genome.

Base Sequence↗
PubMed1983

Transcriptional analysis of the Saccharomyces cerevisiae mitochondrial var1 gene: anomalous hybridization of RNA from AT-rich regions.

A family of mitochondrial RNAs hybridizes specifically to the var1 region on Saccharomyces cerevisiae mitochondrial DNA (Farrelly et al., J. Biol. Chem. 257:6581-6587, 1982). We constructed a fine-structure transcription map of this region by hybridizing DNA probes containing different portions of the var1 region and some flanking sequences to mitochondrial RNAs isolated from var1-containing petites. We also report the nucleotide sequence of more than 1.2 kilobases of DNA flanking the var1 gene. Our primary findings are: (i) The family of RNAs we detect with homology to var1 DNA is colinear with the var1 gene. Their direction of transcription is olil to cap, as it is for most other mitochondrial genes. (ii) Extensive hybridization anomalies are present, most likely due to the high A-T (A-U) content of the hybridizing species and to the asymmetric distribution of their G-C residues. An important conclusion is that failure to detect transcripts from A-T-rich regions of the yeast mitochondrial genome by standard blot transfer hybridizations cannot be interpreted to mean that such sequences, which are commonly supposed to be spacer DNA, are noncoding or lack direct function in the expression of mitochondrial genes.

Base Composition↗
PubMed1982

Characterization of transcripts from the Var1 region on mitochondrial DNA of Saccharomyces cerevisiae.

We have identified transcripts with sequence homology to the var1 region on yeast mtDNA. In wild type, and in cytoplasmic petite strains retaining the var1 region, we detect four RNA species, 19 S, 16 S, 14 S, and 13 S, which hybridize to var1 DNA probes. The 16 S RNA is by far the most abundant of these RNAs in wild type cells. We also observe hybridization of the 15 S rRNA and a 10 S RNA species to var1 DNA probes. This hybridization is most likely due to the presence in these RNAs of a GC-rich cluster which has near perfect sequence homology to a GC-rich cluster in the var1 region. We find that the 16 S RNA, estimated to be 2000 to 2100 nucleotides long, varies in size in direct correspondence with the size of var1 polypeptide; it is about 100 nucleotides longer in strains with the var1 (44,000) allele than in strains with var1 (40,000). The amount of the 16 S RNA also varies in correspondence with the amount of var1 polypeptide made; it is increased in an oxi-3 mit- strain (CAD245) which makes about 10 times more var1 protein than wild type, and is barely detected in PZ200, a strain with very low levels of mitochondrial protein synthesis harboring two mutations within var1. We have purified the 16 S RNA following chromatography over oligo(dT) cellulose columns. When the RNA is end-labeled and hybridized to a HincII digest of wild type mtDNA, we observe hybridization only to the fragment containing the entire var1 region, HincII fragment 10.

DNA Restriction Enzymes↗
PubMed1981

Trans action and the var1 determinant region on yeast mitochondrial DNA. Specific labeling of mitochondrial translation products in zygotes.

We have studied the specification of the apparent molecular weight form of the var1 polypeptide by the var1 determinant region located on mitochondrial DNA of Saccharomyces cerevisiae. A complementation assay has been developed whereby mitochondrial translation products can be labeled selectively in zygotes with 35SO42-. The procedure takes advantage of the fact that met- cys- grande (rho +) strains are unable to incorporate 35SO42- into protein. When such a strain is crossed with a met+ cys petite (rho -) and cells of the mating mixture are labeled with 35SO42- in the presence of cycloheximide under conditions where glycolysis is inoperative, only mitochondrial translation products within zygotes are labeled. Using this procedure with petites containing the var1 determinant region, we find that as much as 75% of the total polypeptide synthesized in zygotes is the form specified by the petite var1 allele. Moreover, mitochondria containing mixed mitochondrial genomes (rho + and rho -) can be isolated from zygotes, and both the rho + and rho - var1 alleles are expressed in vitro. From these results and the analysis of discriminating petites in which var1 recombination can be distinguished from complementation, we conclude that the var1 determinant can specify the apparent molecular weight form of the var1 polypeptide in trans.

Ammonium Sulfate↗