Mutagenicity of 4-nitroquinoline N-oxide after its complexation with copper(II) 2-chlorophenoxyacetate

Using the Ames test withSalmonella typhimurium strains TA97, TA100 and TA102 it was found that the mutagenicity of 4-nitroquinoline N-oxide was much lower than that of the tetrakis[μ-2-chlorophenoxyacetato(1−)-O,O′]bis(4-nitroquinoline N-oxide-O)dicopper(II) complex. This work was supported by theMinistry of Education of the Slovak Republic in Grant no. 95/5195/416.     

Dust emission of chromium from chromite ore processing residue disposal areas in the vicinity of Krasnogorskii Village in Chelyabinsk oblast

The chromium content of soil, dust, and plants near an open-pit mine used to store self-decomposing chromite ore processing residue (COPR) of the Chelyabinsk Electrometallurgical Combine was studied by synchrotron radiation X-ray fluorescence analysis (SRXFR).     

Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human sperm

Background

Male-factor infertility is a common condition, and etiology is unknown for a high proportion of cases. Abnormal epigenetic programming of the germline is proposed as a possible mechanism compromising spermatogenesis of some men currently diagnosed with idiopathic infertility. During germ cell maturation and gametogenesis, cells of the germ line undergo extensive epigenetic reprogramming. This process involves widespread erasure of somatic-like patterns of DNA methylation followed by establishment of sex-specific patterns by de novo DNA methylation. Incomplete reprogramming of the male germ line could, in theory, result in both altered sperm DNA methylation and compromised spermatogenesis.

Methodology/Principal Finding

We determined concentration, motility and morphology of sperm in semen samples collected by male members of couples attending an infertility clinic. Using MethyLight and Illumina assays we measured methylation of DNA isolated from purified sperm from the same samples. Methylation at numerous sequences was elevated in DNA from poor quality sperm.

Conclusions

This is the first report of a broad epigenetic defect associated with abnormal semen parameters. Our results suggest that the underlying mechanism for these epigenetic changes may be improper erasure of DNA methylation during epigenetic reprogramming of the male germ line.     

Tandem repeats over the edit distance

MOTIVATION: A tandem repeat in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats occur in the genomes of both eukaryotic and prokaryotic organisms. They are important in numerous fields including disease diagnosis, mapping studies, human identity testing (DNA fingerprinting), sequence homology and population studies. Although tandem repeats have been used by biologists for many years, there are few tools available for performing an exhaustive search for all tandem repeats in a given sequence. RESULTS: In this paper we describe an efficient algorithm for finding all tandem repeats within a sequence, under the edit distance measure. The contributions of this paper are two-fold: theoretical and practical. We present a precise definition for tandem repeats over the edit distance and an efficient, deterministic algorithm for finding these repeats. AVAILABILITY: The algorithm has been implemented in C++, and the software is available upon request and can be used at http://www.sci.brooklyn.cuny.edu/~sokol/trepeats. The use of this tool will assist biologists in discovering new ways that tandem repeats affect both the structure and function of DNA and protein molecules.     

Exposing the third chromosome of Burkholderia cepacia complex strains as a virulence plasmid

The Burkholderia cepacia complex (Bcc) consists of 17 closely related species of opportunistic bacterial pathogens, which are particularly problematic for cystic fibrosis patients and immunocompromised individuals. Bcc genomes consist of multiple replicons, and each strain sequenced to date has three chromosomes. In addition to genes thought to be essential for survival, each chromosome carries at least one rRNA operon. We isolated three mutants during a transposon mutagenesis screen that were non-pathogenic in a Caenorhabditis elegans infection model. It was demonstrated that these mutants had lost chromosome 3 (c3), and that the observed attenuation of virulence was a consequence of this. We constructed a c3 mini-replicon and used it to cure c3 from strains of several Bcc species by plasmid incompatibility, resulting in nine c3-null strains covering seven Bcc species. Phenotypic characterization of c3-null mutants revealed that they were attenuated in virulence in multiple infection hosts (rat, zebrafish, C. elegans, Galleria mellonella and Drosophila melanogaster), that they exhibited greatly diminished antifungal activity, and that c3 was required for d-xylose, fatty acid and pyrimidine utilization, as well as for exopolysaccharide production and proteolytic activity in some strains. In conclusion, we show that c3 is not an essential chromosomal element, rather a large plasmid that encodes virulence, secondary metabolism and other accessory functions in Bcc bacteria.     

Both the RGS Domain and the Six C-Terminal Amino Acids of Mouse Axin Are Required for Normal Embryogenesis

Axin is a negative regulator of canonical Wnt signaling, which promotes the degradation of β-catenin, the major effector in this signaling cascade. While many protein-binding domains of Axin have been identified, their significance has not been evaluated in vivo. Here, we report the generation and analysis of mice carrying modified Axin alleles in which either the RGS domain or the six C-terminal amino acids (C6 motif) were deleted. The RGS domain is required for APC-binding, while the C6 motif has been implicated in the activation of c-Jun N-terminal kinase, but is not required for the effects of Axin on the Wnt/β-catenin pathway, in vitro. Both mutant Axin alleles caused recessive embryonic lethality at E9.5–E10.5, with defects indistinguishable from those caused by a null allele. As Axin-ΔRGS protein was produced at normal levels, its inability to support embryogenesis confirms the importance of interactions between Axin and APC. In contrast, Axin-ΔC6 protein was expressed at only 25–30% of the normal level, which may account for the recessive lethality of this allele. Furthermore, many Axin^ΔC6/ΔC6 embryos that were heterozygous for a β-catenin null mutation survived to term, demonstrating that early lethality was due to failure to negatively regulate β-catenin.     

Functional and structural diversity of the human Dickkopf gene family

Wnt proteins influence many aspects of embryonic development, and their activity is regulated by several secreted antagonists, including the Xenopus Dickkopf-1 (xDkk-1) protein. xDkk-1 inhibits Wnt activities in Xenopus embryos and may play a role in induction of head structures. Here, we characterize a family of human Dkk-related genes composed of Dkk-1, Dkk-2, Dkk-3, and Dkk-4, together with a unique Dkk-3 related protein termed Soggy (Sgy). hDkks 1-4 contain two distinct cysteine-rich domains in which the positions of 10 cysteine residues are highly conserved between family members. Sgy is a novel secreted protein related to Dkk-3 but which lacks the cysteine-rich domains. Members of the Dkk-related family display unique patterns of mRNA expression in human and mouse tissues, and are secreted when expressed in 293T cells. Furthermore, secreted hDkk-2 and hDkk-4 undergo proteolytic processing which results in cleavage of the second cysteine-rich domain from the full-length protein. Members of the human Dkk-related family differ not only in their structures and expression patterns, but also in their abilities to inhibit Wnt signaling. hDkk-1 and hDkk-4, but not hDkk-2, hDkk-3 or Sgy, suppress Wnt-induced secondary axis induction in Xenopus embryos. hDkk-1 and hDkk-4 do not block axis induction triggered either by Xenopus Dishevelled (Xdsh) or Xenopus Frizzled-8 (Xfz8), both of which function to transduce signals from Wnt ligands. Thus, hDkks 1 and 4 may inhibit Wnt activity by a mechanism upstream of Frizzled. Our findings highlight the structural and functional heterogeneity of human Dkk-related proteins.