Evidence from enzymatic and meta-analyses does not support a direct association between USP26 gene variants and male infertility.

Do men who carry mutations in USP26 have an increased risk of infertility? The association between mutations in USP26 gene and male infertility has been studied intensively. However, the results from different groups are controversial. In particular, biological function of the mutant proteins remains to be elucidated. In this study, we conducted a USP cleavage assay and a meta-analysis of the published literature (up to 31 May 2013) to evaluate the impact of five frequent mutations (NM_031907.1: c.363_364insACA, c.494T>C, c.1423C>T, c.1090C>T, c.1737G>A) on enzymatic activity of the USP26 and to assess the strength of the association between those mutations and male infertility. The USP cleavage assay showed that those mutations do not affect USP26 enzymatic activity. Moreover, the results of meta-analysis of ten case-control studies (in total 1716 patients and 2597 controls) revealed no significant association (P > 0.05) between USP26 mutations and male infertility. The pooled ORs were 1.58 (95% CI: 0.81, 3.10) for cluster mutations (c.363_364insACA, c.494T>C, c.1423C>T), 1.60 (95% CI: 0.93, 2.74) for c.1090 C>T and 2.64 (95% CI: 0.97, 7.20) for c.1737 G>A. Evidence from both enzymatic and meta-analyses does not support a direct association between USP26 variants and male infertility. Further research is necessary to study the biological function of USP26, which may provide clues as to the regulation of androgen receptor signalling.

Diagnostic performance of des-γ-carboxy prothrombin (DCP) for hepatocellular carcinoma: a bivariate meta-analysis.

Serum markers are needed to be developed to specifically diagnose Hepatocellular carcinoma (HCC). Des-γ-carboxy prothrombin (DCP) is a promising tool with limited expense and widely accessibility, but the reported results have been controversial. In order to review the performance of DCP for the diagnosis of HCC, the meta-analysis was performed. After a systematic review of relevant studies, the sensitivity, specificity, positive and negative likelihood ratios (PLR and NLR, respectively) were pooled using a bivariate meta-analysis. Potential between-study heterogeneity was explored by meta-regression model. The post-test probability and the likelihood ratio scattergram to evaluate clinical usefulness were calculated. Based on literature review of 20 publications, the overall sensitivity, specificity, PLR and NLR of DCP for the detection of HCC were 67% (95%CI, 58%-74%), 92% (95%CI, 88%-94%), 7.9 (95%CI, 5.6-11.2) and 0.36 (95%CI, 0.29-0.46), respectively. The area under the bivariate summary receiving operating characteristics curve was 0.89 (95%CI, 0.85-0.92). Significant heterogeneity was present. In conclusion, the major role of DCP is the moderate confirmation of HCC. More prospective studies of DCP are needed in future.

Specific protein-DNA and protein-protein interaction in the hig gene system, a plasmid-borne proteic killer gene system of plasmid Rts1.

The hig (host inhibition of growth) gene system of plasmid Rts1 belongs to the plasmid-encoded proteic killer gene family. Among the proteic killer genes described so far, hig is unique in that the toxin gene (higB) exists upstream of the antidote gene (higA). There are two promoters in the hig locus, Phig and PhigA, and only the former, which expresses both higB and higA genes, is negatively controlled by HigA and HigB proteins. In this study, we purified HigA protein by means of GST fusion. The electrophoretic mobility shift assay using the purified protein revealed that HigA specifically bound to the Phig region, but not to PhigA. The HigA-binding sequence was determined by DNase I footprinting assay to be a 56-bp sequence that completely covered the -35 and -10 boxes of Phig. The presence of two inverted repeats in the binding sequence and the identification of a dimer form of HigA by cross-linking experiment suggested that the protein bound to the Phig region as a dimer. HigB was purified as a GST fusion protein as well, though it was achieved only in the presence of HigA. HigA and GST-HigB formed a highly stable complex where the two proteins were present in an equimolar ratio.

Characterization of a novel synGAP isoform, synGAP-beta.

We cloned a cDNA encoding a novel synGAP, synGAP-d (GenBank(TM) accession number ), from a rat brain cDNA library. The clone consisted of 4801 nucleotides with a coding sequence of 3501 nucleotides, encoded a protein consisting of 1166 amino acids with >99% homology with 1092 amino acid overlaps to synGAP, and contained a 13-nucleotide insertion to the previously reported synGAP mRNAs, which suggested that the clone was a splice variant of synGAP. We also found that there are at least seven variants in the 3' portion of the synGAP mRNA and that they encoded five different protein isoforms. The coding sequence of these C-terminal variants were classified into alpha1, alpha2, beta1, beta2, beta3, beta4, and gamma, and synGAP-d was classified as the beta1 form. The previously reported synGAPs (synGAP-a, -b, and -c and p135synGAP) can be classified as the alpha1 isoform. All isoforms were expressed specifically in the brain. Unexpectedly, the beta isoform, which lacks a C-terminal PSD-95-binding motif ((S/T)XV), was more restricted to the postsynaptic density fraction than the motif-containing alpha1 isoform. The beta isoform did not interact with PSD-95 but specifically interacted with a nonphosphorylated alpha subunit of Ca(2+)/calmodulin-dependent protein kinase II through its unique C-terminal tail.

Identification of mRNAs localizing in the postsynaptic region.

Local protein synthesis using mRNAs readily distributed in the dendrites is believed to play an important role in maintaining the already expressed synaptic plasticity. To find proteins translated in the postsynaptic region, such as neuronal dendrites, we tried to identify the mRNAs associated with the postsynaptic density (PSD) fraction prepared from a rat's forebrain. The PSD-associated mRNAs were amplified by reverse transcriptase-based polymerase chain reaction (RT-PCR), separated by polyacrylamide gel electrophoresis, and sequenced. The database search revealed, among 130 mRNAs sequenced, 17 known and 108 unknown sequences, while five mRNAs were too short for the search. Of the mRNAs with unknown sequences, we selected 33 genes with a length longer than 150 bases, performed in situ hybridization, and found that at least 12 mRNA types were localized in the dendrites. These results suggest that a large number of mRNAs localize around the postsynaptic area of the neuronal cells in the central nervous system. In addition, our method proved efficient in identifying collectively the mRNAs localizing in the dendrites.

Gene product identification and promoter analysis of hig locus of plasmid Rts1.

The hig (host inhibition of growth) genes of plasmid Rts1 belong to the plasmid-encoded proteic killer gene family. Compared with other proteic killer genes described so far, hig is unique in that the toxic part (higB) exists upstream of the antidote gene (higA). Here we describe results of the promoter analysis of hig genes together with identification of the proteic gene products of higA and higB. Two promoters were identified in the hig locus; a stronger one, named Phig, is located upstream of higB and a weaker one, PhigA, is upstream of higA within the higB coding region. The Phig activity was negatively regulated by HigA and this regulation was augmented by HigB, whereas PhigA was not subjected to such a regulation.

A new plasmid-encoded proteic killer gene system: cloning, sequencing, and analyzing hig locus of plasmid Rts1.

A new proteic killer gene system, hig, was identified on the plasmid Rts1. The hig locus consisting of a higA and higB is directly related to the temperature sensitive host cell growth conferred by Rts1. We proved that higB encoding presumably a 92-amino-acid polypeptide inhibited segregation of plasmid free cells, and higA encoding a 104-amino-acid polypeptide suppressed the higB function both in cis and in trans.