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Preliminary analysis of two selected genomic regions of Buchnera aphidicola BCc, the primary endosymbiont of the cedar aphid Cinara cedri, has revealed a number of interesting features when compared with the corresponding homologous regions of the three B. aphidicola genomes previously sequenced, that are associated with different aphid species. Both regions exhibit a significant reduction in length...
The last 50 years of molecular genetics have produced an abundance of new discoveries and data that make it useful to revisit some basic concepts and assumptions in our thinking about genomes and evolution. Chief among these observations are the complex modularity of genome organization, the biological ubiquity of mobile and repetitive DNA sequences, and the fundamental importance of DNA rearrangements...
Only 5–6% of mammalian genomes are genes; the remainders are made up primarily of transposable elements and different types of simple sequence repeat (SSRs) (micro- and minisatellites and cryptic repeats), which tend to accumulate in organisms with larger genomes. SSRs are also found at the level of protein sequences and may or may not be encoded by SSRs at the DNA sequence level. Studies of proteins...
Recent large-scale studies of evolutionary changes in gene expression among mammalian species have led to the proposal that gene expression divergence may be neutral with respect to organismic fitness. Here, we employ a comparative analysis of mammalian gene sequence divergence and gene expression divergence to test the hypothesis that the evolution of gene expression is predominantly neutral. Two...
A family of functional neogenes called Mart, related to the gag gene of Sushi-like long terminal repeat retrotransposons from fish and amphibians, is present in the genome of human (11 genes) and other primates, as well as in mouse (11 genes), rat, dog (12 genes), cat, and cow. Mart genes have lost their capacity of retrotransposition through non-functionalizing rearrangements having principally affected...
We study short-range correlations in DNA sequences with methods from information theory and statistics. We find a persisting degree of identity between the correlation patterns of different chromosomes of a species. Except for the case of human and chimpanzee inter-species differences in this correlation pattern allow robust species distinction: in a clustering tree based upon the correlation curves...
To understand the process of bilaterian evolution, we estimated ancestral gene sets at the split of plant–animal–fungi and the divergence of bilaterian animals and from 1,236,790 non-redundant genes. We, then, examined how the numbers of the gene clusters have changed since the split. As a result, we estimated the numbers of gene clusters in the ancestral gene sets of plant–animal–fungi and bilaterian...
RNA-ligand binding often depends crucially on the local RNA secondary structure at the binding site. We develop here a model that quantitatively predicts the effect of RNA secondary structure on effective RNA-ligand binding activities based on equilibrium thermodynamics and the explicit computations of partition functions for the RNA structures. A statistical test for the impact of a particular structural...
A two-hybrid screen with the translation initiation factor, eIF(iso)4E from Arabidopsis, identified a clone encoding a lipoxygenase type 2 [Freire, M.A., et al., 2000. Plant lipoxygenase 2 is a translation initiation factor-4E-binding protein. Plant Molecular Biology 44, 129–140], and three cDNA clones encoding the homologue of the mammalian BTF3 factor, the β subunit of the nascent polypeptide-associated...
A subtractive hybridization approach was used to identify genes that are expressed at the beginning of gastrulation. We used tester DNA complimentary to RNA (cDNA) prepared from stages 6–7 embryos (gastrula) and excess driver cDNA from stages 2–4 embryos (syncytial blastoderm) to generate a gastrula-subtracted cDNA library. A reverse Northern blot procedure used to analyze 105 subtracted clones showed...
We identified eight genes of putative RGS proteins in skin of Medaka fish using PCR amplification with degenerate primers for the RGS domain of known RGS proteins. Then, we cloned a full-length cDNA for a new RGS protein. This RGS protein was similar to human RGS3 within the RGS domain, but other parts were unique among known RGS proteins. RT-PCR analysis demonstrated that this Medaka RGS3-like protein...
Saccharomyces cerevisiae Upf1p is a 971-amino-acid protein that is required for the nonsense-mediated mRNA decay (NMD) pathway, a pathway that degrades mRNAs with premature translational termination codons. We have identified a two-hybrid interaction between Upf1p and the nuclear pore (Nup) proteins, Nup100p and Nup116p. Both nucleoporins predominantly localize to the cytoplasmic side of the nuclear...
Although ambient levels of estradiol and synthesis of the osteoblast growth factor IGF-I are inversely related in vivo, estradiol has little or no direct effect on igf1 gene expression in rat osteoblasts in vitro. Rather, estradiol suppresses the effect of hormones that enhance igf1 expression through protein kinase A dependent activation of CCAAT enhancer binding protein (C/EBP) transcription factors...
Tripeptidyl-peptidase II (TPP II) is a ubiquitously expressed exopeptidase. The expression of this enzyme is increased, e.g. in some tumor cells, but the regulation of the expression of the gene has not been investigated previously. The gene encoding human TPP II (TPP2) is 82 kb and consists of 30 exons. An 8 kb NcoI fragment covering the 5′-flanking region of the TPP2 gene, including the initiation...
We have adopted a method of telomere-mediated chromosome fragmentation in order to demonstrate the alignment of contigs and determination of gaps. We established the order and orientation of four contigs of Candida albicans chromosome 5 and determined the sizes of three gaps between these contigs. We confirmed this proposed alignment of contigs, as well as gap sizes, by sequencing one gap and analyzing...
Extracellular regulated kinase 5 (ERK5) is an unusually large member of the MAP kinase family of signaling molecules that plays an important role in cellular proliferation, differentiation and survival. Recently, three transcriptional variants of murine Erk5 were described (mErk5-a, -b and -c) that result from alternate splicing across introns 1 and/or 2, the net effect of which is translation of...
Xyloglucan endotransglucosylase/hydrolases (XTH) are enzymes that catalyze the hydrolysis and transglycosylation of xyloglucan polymers in plant cell walls. Previously, we isolated a cDNA from mycorrhizal roots of Medicago truncatula that is predicted to encode an XTH [van Buuren, M.L., Maldonado-Mendoza, I.E., Trieu, A.T., Blaylock, L.A., Harrison, M.J., 1999. Novel genes induced during an arbuscular...
In humans three isoforms of 6-phosphofructo-1-kinase (PFK) exist. Among them platelet-type PFK (PFKP) is highly abundant in the brain. With its distinct allosteric properties PFKP is regarded to be the key enzyme for the regulation of glycolysis in this organ. We cloned 1.7 kb of the 5′ upstream promoter of the human PFKP gene and analyzed the promoter activity by deletion and mutation analysis using...
Natural antisense transcripts, because of their potential to form double-stranded RNA (dsRNA) molecules, recently emerged as a mechanism acting on eukaryotic gene regulation at multiple levels. CHRNA3 and CHRNA5, coding for α3 and α5 subunits of the neuronal nicotinic acetylcholine receptor, have been reported to overlap at their 3′ends in human and bovine genomes. In the present paper, four CHRNA3...
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