DNA binding proteins

reconstructionists often determine pre-collision conditions based on post-collision evidence. Energy-based speed calculations for skidding vehicles are commonly used and have been the basis for numerous theoretical and experimental works. The simplest analysis technique, "skid-to-stop" is fairly well understood, however the more complex circumstance of a spinning trajectory is less well understood. This paper will describe a series of experiments conducted to evaluate the frictional values applicable to a spinning vehicle as it rotates and translates without brake application.

In eukaryotes, the recognition of the DNA postreplication errors and initiation of the mismatch repair is carried out by two MutS homologs: MutSa and MutSb. MutSa recognizes base mismatches and 1 to 2 unpaired nucleotides whereas MutSb recognizes longer insertion-deletion loops (IDLs) with 1 to 15 unpaired nucleotides as well as certain mismatches. Results from molecular dynamics simulations of native MutSb:IDL-containing DNA and MutSa:mismatch DNA complexes as well as complexes with swapped DNA substrates provide mechanistic insight into how the differential substrate specificities are achieved by MutSa and MutSb, respectively. Our simulations results suggest more extensive interactions between MutSb and IDL-DNA and between MutSa and mismatch-containing DNA that suggest corresponding differences in stability. Furthermore , our simulations suggest more expanded mechanistic details involving a different degree of bending when DNA is bound to either MutSa or MutSb and a more likely opening of the clamp domains when noncognate substrates are bound. The simulation results also provide detailed information on key residues in MutSb and MutSa that are likely involved in recognizing IDL-DNA and mismatch-containing DNA, respectively.

The DNA damage response triggered by bacterial cytolethal distending toxins (CDTs) is associated with activation of the actin-regulating protein RhoA and phosphorylation of the downstream-regulated mitogen-activated protein kinase (MAPK) p38, which promotes the survival of intoxicated (i.e. cells exposed to a bacterial toxin) cells. To identify the effectors of this CDT-induced survival response, we screened a library of 4492 Saccharomyces cerevisiae mutants that carry deletions in nonessential genes for reduced growth following inducible expression of CdtB. We identified 78 genes whose deletion confers hypersensitivity to toxin. Bioinformatics analysis revealed that DNA repair and endocytosis were the two most overrepresented signaling pathways. Among the human orthologs present in our data set, FEN1 and TSG101 regulate DNA repair and endocytosis, respectively, and also share common interacting partners with RhoA. We further demonstrate that FEN1, but not TSG101, regulates cell sur...

Libraries of compounds are increasingly becoming commercially available for the use of individual academic laboratories. A high-throughput system based on a stably integrated transcriptional reporter was used to screen a library of random compounds to identify agents that conferred robust augmentation of a signal transduction pathway. A novel histone deacetylase (HDAC) inhibitor, termed scriptaid, conferred the greatest effect, a 12- to 18-fold augmentation. This facilitation of transcriptional events was generally applicable to exogenous gene constructs, including viral and cellular promoters, different cell lines and reporter genes, and stably integrated and transiently introduced sequences. Scriptaid did not interfere with a further induction provided by stimulation of the cognate signal transduction pathway (transforming growth factor beta/Smad4), which implied the functional independence of ligand-stimulated transcriptional activation and histone acetylation states in this syst...

We describe the identification and structural characterization of a novel family of Arabidopsis genes related to ATL2 which encode a variant of the RING zinc finger domain, known as RING-H2. Analysis of genes selected by us and of sequences from Arabidopsis stored in databases permitted the prediction of several RING-H2 proteins that contain highly homologous RING domains. The ATL gene family is represented by fifteen sequences that contain, in addition to the RING, a transmembrane domain which is located in most of them towards the N-terminal end. Transgenic Arabidopsis seedlings carrying the ATL2 promoter fused to the GUS reporter gene revealed that the expression of ATL2 is rapidly induced after exposure to chitin or inactivated crude cellulase preparations. Rapid induction of transcript accumulation of another member of the ATL family was also observed under the same conditions. These results suggest that some ATLs may be involved in the early stages of the defense response triggered in plants in response to pathogen attack.

Behçet's disease (BD) is an immune-mediated and complex disease which has been associated with HLA class I molecules although other genes such as IL23R and IL10 have also been involved in the susceptibility to BD. Recently, an association of variants of the JAK1 and TNFAIP3 genes with the disease has been reported in the Chinese Han population. The aim of the present work was to asses whether the association described in Asian populations is replicated in Europeans. This study includes a total of 1155 Spanish subjects of European origin (372 BD and 783 unrelated healthy individuals). Patients were recruited from different hospitals and controls were collected in the same geographic regions and they matched with patients in age and gender. A total of five SNPs, two in the JAK1 gene: rs2780815 and rs310241 and the other three in the TNFAIP3: rs10499194, rs9494885 and rs610604, were included in this study. The genotyping of these SNPs was performed using a real time PCR system (Taq...

Trichothiodystrophy (TTD) is a rare autosomal recessive disorder characterized by brittle hair with reduced sulfur content, ichthyosis, peculiar face, and mental and growth retardation. Clinical photosensitivity is present in approximately 50% of TTD patients but is not associated with an elevated frequency of cancers. Previous complementation studies show that the photosensitivity in nearly all of the studied patients is due to a defect in the same genetic locus that underlies the cancer-prone genetic disorder xeroderma pigmentosum group D (XP-D). Nucleotide-sequence analysis of the ERCC2 cDNA from three TTD cell strains (TTD1V1, TTD3VI, and TTD1RO) revealed mutations within the region from amino acid 713-730 and within previously identified helicase functional domains. The various clinical presentations and DNA repair characteristics of the cell strains can be correlated with the particular mutations found in the ERCC2 locus. Mutations of Arg658 to either His or Cys correlate with...

Abstract Abstract. The highly conserved basic helix-loop-helix transcription factor Hand plays a crucial role in cardiogenesis, limb formation and other developmental processes of vertebrates. Humans, mice and other higher vertebrates have two related genes, dHand (also known as Hand2, Hed, Thing2) and eHand (also known as Hand1, Hxt, Thing1), whereas fish and Drosophila have only a single hand gene. We cloned Drosophila hand and studied the embryonic expression in detail by using various tissue-specific markers that allowed us to analyze the identity of hand-expressing cells. We found hand to be expressed in the entire heart, including all cardioblasts and pericardial cells, in the progenitors of the circular visceral muscles, the lymph gland and garland cells, and in a few cells in the CNS. The expression of Drosophila hand starts after the inductive activity of the early regulators in these tissues, e.g. Tinman and Bagpipe, suggesting a role of Hand in differentiation rather than in tissue determination. In many aspects the expression pattern of Drosophila hand resembles the patterns of its vertebrates orthologues, for instance in cardiac tissues. We assume that Hand proteins might play a highly conserved role throughout evolution. Electronic Supplementary Material is available if you access this article at http://dx.doi.org/10.1007/s00427-002-0268-6. On that page (frame on the left side), a link takes you directly to the supplementary material.