Laminin-121—Recombinant expression and interactions with integrins

Laminin-121, previously referred as to laminin-3, was expressed recombinantly in human embryonic kidney (HEK) 293 cells by triple transfection of full-length cDNAs encoding mouse laminin α1, β2 and γ1 chains. The recombinant laminin-121 was purified using Heparin-Sepharose followed by molecular sieve chromatography and shown to be correctly folded by electron microscopy and circular dichroism (CD). The CD spectra of recombinant laminin-121 were very similar to those of laminin-111 isolated from Engelbreth-Holm-Swarm tumor (EHS-laminin) but its T_m value was smaller than EHS-laminin and recombinant lamnin-111 suggesting that the replacement of the β chain reduced the stability of the coiled-coil structure of laminin-121. Its binding to integrins was compared with EHS-laminin, laminin-3A32 purified from murine epidermal cell line and recombinantly expressed laminins-111, -211 and -221. Laminin-121 showed the highest affinity to α6β1 and α7β1 integrins and furthermore, laminin-121 most effectively supported neurite outgrowth. Together, this suggests that the β2 laminins have higher affinity for integrins than the β1 laminins.     

CEQer: A Graphical Tool for Copy Number and Allelic Imbalance Detection from Whole-Exome Sequencing Data

Copy number alterations (CNA) are common events occurring in leukaemias and solid tumors. Comparative Genome Hybridization (CGH) is actually the gold standard technique to analyze CNAs; however, CGH analysis requires dedicated instruments and is able to perform only low resolution Loss of Heterozygosity (LOH) analyses. Here we present CEQer (Comparative Exome Quantification analyzer), a new graphical, event-driven tool for CNA/allelic-imbalance (AI) coupled analysis of exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection. This data is used to build mixed statistical/heuristic models allowing the identification of CNA/AI events. To test our tool, we initially used in silico generated data, then we performed whole-exome sequencing from 20 leukemic specimens and corresponding matched controls and we analyzed the results using CEQer. Taken globally, these analyses showed that the combined use of comparative digital exon quantification and LOH/AI allows generating very accurate CNA data. Therefore, we propose CEQer as an efficient, robust and user-friendly graphical tool for the identification of CNA/AI in the context of whole-exome sequencing data.     

Phosphatidylinositol 4-phosphate 5-kinase Iγ_v6, a new splice variant found in rodents and humans

Phosphatidylinositol 4-phosphate 5-kinase Iγ (PIP5KIγ) is subject to extensive C-terminal splice variation, with four variants, PIP5KIγ_v1, 2, 4 and 5, described in humans Schill and Anderson (2009) [7]. Here firstly, we report a new rodent splice variant, which includes the exon that was previously unique to the rodent neuron-specific PIP5KIγ93 Giudici et al. (2006) [6], but which omits the C-terminal exon of PIP5KIγ93; this new variant shows a wide tissue expression pattern in mouse. Secondly, we show that in humans there is an alternative splicing site 78 nucleotides from the start of exon 16c, such that humans additionally express both PIP5KIγ93 (which we now call PIP5KIγ_v3) specifically in brain and, again expressed more widely, the new variant described here, which we now name PIP5KIγ_v6.     

On the mechanism of action of bonellin on the sea urchin egg

In this paper we report on the mechanism of action of bonellin on sea urchin eggs. Bonellin acts in the same way as porphyrins, ie, by causing the crosslinking of membrane proteins and the peroxocompounds formation. A possible role of membrane organization related to cleavage formation is discussed.     

Efficiency of natural and engineered bacterial strains in the degradation of 4-chlorobenzoic acid in soil slurry

Two bacterial strains, the natural isolate Arthrobacter sp. FG1 and the engineered strain Pseudomonas putida PaW340/pDH5, were compared for their efficiency in the degradation of 4-chlorobenzoic acid in a slurry phase system. The recombinant strain was obtained by cloning the Arthrobacter sp. FG1 dehalogenase encoding genes in P. putida PaW340. In the slurry inoculated with pre-adapted cultures of Arthrobacter sp. FG1, the 4-chlorobenzoic acid degradation was found to be slower than that observed in the slurry inoculated with the recombinant strain P. putida PaW340/pDH5, regardless of the presence or absence of soil indigenous bacteria. Slurry inoculated with mixed cultures of Arthrobacter sp. FG1 and the 4-hyroxybenzoic acid degrader P. putida PaW340 did not show any improvement in 4-chlorobenzoic acid degradation.     

Large-gauge needle biopsy in diagnosing malignant breast neoplasia

This paper is concerned with large-gauge needle biopsies of suspicious breast neoplasia performed within a three-year period (22nd June 1999 through 21st December 2001). Within that time 262 large-gauge needle biopsies as well as cytological punctions were performed with the aim of diagnosing benign and malignant neoplasia. In the same three-year period 29 malignant breast tumors were diagnosed. In one of the patients a clinically and PHD verified alteration was found which pointed to Mb. Padget, while in another patient an atypical ductal hyperplasia was confirmed by a pathohistological test.     

Likelihood-ratio tests for hidden Markov models

We consider hidden Markov models as a versatile class of models for weakly dependent random phenomena. The topic of the present paper is likelihood-ratio testing for hidden Markov models, and we show that, under appropriate conditions, the standard asymptotic theory of likelihood-ratio tests is valid. Such tests are crucial in the specification of multivariate Gaussian hidden Markov models, which we use to illustrate the applicability of our general results. Finally, the methodology is illustrated by means of a real data set.     

Wine colour adsorption phenotype: an inheritable quantitative trait loci of yeasts

AIMS: In this work, a population of 88 descendants derived from three wine strains of Saccharomyces cerevisiae was tested for the enological trait 'wine colour adsorption' (WCA) to evaluate its inheritability. METHODS AND RESULTS: The WCA phenotype was tested on plate agar medium specifically formulated for the purpose. After 10 days of anaerobic incubation at 28 degrees C, a computer-assisted assessment of WCA aptitude of the yeasts was carried out. The biomass colour -- ranging from white to dark brown -- reflects the adsorption of grape pigments: white and dark brown biomass colour corresponds to low and high adsorption, respectively. In order to confirm biomass colour results, microvinification trials using red must were performed, and the obtained wines were analysed. CONCLUSIONS: The analysis of the progeny demonstrated that the enological trait WCA is inheritable and polygenic. SIGNIFICANCE AND IMPACT OF THE STUDY: A way to describe the polygenic effect of the WCA trait has been found, also showing that this trait is inheritable. The impact of the work revolves more around the large-scale screening method, which could then assist in breeding wine yeast, and can also be used as a scientific tool to investigate WCA trait.