Nuclear mitochondrial DNA activates replication in Saccharomyces cerevisiae

The nuclear genome of eukaryotes is colonized by DNA fragments of mitochondrial origin, called NUMTs. These insertions have been associated with a variety of germ-line diseases in humans. The significance of this uptake of potentially dangerous sequences into the nuclear genome is unclear. Here we provide functional evidence that sequences of mitochondrial origin promote nuclear DNA replication in Saccharomyces cerevisiae. We show that NUMTs are rich in key autonomously replicating sequence (ARS) consensus motifs, whose mutation results in the reduction or loss of DNA replication activity. Furthermore, 2D-gel analysis of the mrc1 mutant exposed to hydroxyurea shows that several NUMTs function as late chromosomal origins. We also show that NUMTs located close to or within ARS provide key sequence elements for replication. Thus NUMTs can act as independent origins, when inserted in an appropriate genomic context or affect the efficiency of pre-existing origins. These findings show that migratory mitochondrial DNAs can impact on the replication of the nuclear region they are inserted in.     

Functional Annotation,Genome Organization and Phylogeny of the Grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis>) Terpene Synthase Gene Family Based on Genome Assembly,FLcDNA Cloning,and Enzyme Assays

Background  

Terpenoids are among the most important constituents of grape flavour and wine bouquet, and serve as useful metabolite markers in viticulture and enology. Based on the initial 8-fold sequencing of a nearly homozygous Pinot noir inbred line, 89 putative terpenoid synthase genes (VvTPS) were predicted by in silico analysis of the grapevine (Vitis vinifera) genome assembly [1]. The finding of this very large VvTPS family, combined with the importance of terpenoid metabolism for the organoleptic properties of grapevine berries and finished wines, prompted a detailed examination of this gene family at the genomic level as well as an investigation into VvTPS biochemical functions.     

Rootstock genotype succession influences apple replant disease and root-zone microbial community composition in an orchard soil

Apple replant disease (ARD) is a soil-borne disease complex that affects young apple trees in replanted orchards, resulting in stunted growth and reduced yields. Newly developed rootstock genotypes with tolerance to ARD may help to control this disease. We determined the effects of rootstock genotype rotations during orchard renovation, by investigating root-zone soil microbial consortia and the relative severity of ARD on seven rootstock genotypes (M.9, M.26, G.30, G.41, G.65, G.935, and CG.6210) planted in soil where trees on four of those same rootstocks (M.9, M.26, G.30 and CG.6210) had grown for the previous 15 years. Rootstock genotyping indicated that genetic distances among rootstocks were loosely correlated with their differential responses to ARD. Root-zone fungal and bacterial community composition, assessed by DNA fingerprinting (T-RFLP), differed between M.26 and CG.6210. Soil bacterial communities were influenced most by which rootstock had grown in the soil previously, while fungal communities were influenced more by the current replanted rootstock. In a clone library of bacteria from M.26 and CG.6210 root-zone soil, β-Proteobacteria was the most abundant phylum (25% of sequences). Sequences representing the Burkholderia cepacia complex were obtained only from CG.6210 soil. Rootstock genotypes that were grown in the orchard soil previously affected subsequent ARD severity, but replanting with the same or closely related rootstocks did not necessarily exacerbate this disease problem. Our results suggest that genotype-specific interactions with soil microbial consortia are linked with apple rootstock tolerance or susceptibility to ARD.     

Prokaryotic aminopeptidase activity along a continuous salinity gradient in a hypersaline coastal lagoon (the Coorong, South Australia)

The relation between climatic parameters (relative air humidity) and the water activity of the Urmia Sea water determines the possible maximum evaporation of the lake. Using the Pitzer thermodynamic approach, the activity of the Urmia Lake water during evaporation was calculated and compared to the present relative air humidity above the water. Present climatic conditions allow the Urmia Sea water to evaporate down to water with activity of 0.55, corresponding to the lowest air humidity measured over the lake. This water activity falls in the range of halite precipitation, while carnalite precipitation starts at somewhat lower (a H₂O = 0.499) point. Our dynamic model predicts that for air humidity as low as 55% (reflecting present climate conditions), the Urmia Sea level may drop to as low as 1270 m (i. e., 1270 m above mean sea level). At that point, the lake water volume will have a volume of 11 km³. For the sake of comparison, at the beginning of 1990, the level of the lake was 1275 m, its volume was 25 km³, and its surface area was 5145 km².     

The inflammatory side of human chondrocytes unveiled by antibody microarrays

Although being largely used for pathobiological models of cartilage diseases such as osteoarthritis (OA), human chondrocytes are still enigmatic cells, in as much as a large part of their secretome is unknown. We took advantage of the recent development of antibody-based microarrays to study multiple protein expression by human chondrocytes obtained from one healthy and five osteoarthritic joints, in unstimulated conditions or after stimulation by the proinflammatory cytokines interleukin-1 (IL-1) or tumour necrosis factor (TNF). The secretion media of chondrocytes were incubated with array membranes consisting of 79 antibodies directed against cytokines, chemokines, and angiogenic or growth factors. Several proteins were identified as new secretion products of chondrocytes, including the growth or angiogenic factors EGF, thrombopoietin, GDNF, NT-3 and -4, and PlGF, the chemokines ENA-78, MCP-2, IP-10, MIP-3alpha, NAP-2, PARC, and the cytokines MIF, IL-12, and IL-16. Most of the newly identified chemokines were increased intensely after stimulation by IL-1 or TNF, as for other proteins of the array, including GRO proteins, GM-CSF, IL-6, IL-8, MIP-1beta, GCP-2, and osteoprotegerin. The up-regulation by cytokines suggested that these proteins may participate in the destruction of cartilage and/or in the initiation of chemotactic events within the joint during OA. In conclusion, the microarray approach enabled to unveil part of an as yet unexplored chondrocyte secretome. Our findings demonstrated that chondrocytes were equipped with a proinflammatory arsenal of proteins which may play an important part in the pathogenesis of OA and/or its drift towards an inflammatory, rheumatoid phenotype.     

A new computational efficient approach for trabecular bone analysis using beam models generated with skeletonized graph technique

Micro-finite element (FE) analysis is a well established technique for the evaluation of the elastic properties of trabecular bone, but is limited in its application due to the large number of elements that it requires to represent the complex internal structure of the bone. In this paper, we present an alternative FE approach that makes use of a recently developed 3D-Line Skeleton Graph Analysis (LSGA) technique to represent the complex internal structure of trabecular bone as a network of simple straight beam elements in which the beams are assigned geometrical properties of the trabeculae that they represent. Since an enormous reduction of cputime can be obtained with this beam modeling approach, ranging from approximately 1,200 to 3,600 for the problems investigated here, we think that the FE modeling technique that we introduced could potentially constitute an interesting alternative for the evaluation of the elastic mechanical properties of trabecular bone.     

Highly Significant Association between Two Common Single Nucleotide Polymorphisms in CORIN Gene and Preeclampsia in Caucasian Women

Preeclampsia is a frequent medical complication during pregnancy. Corin, a serine protease which activates pro-atrial natriuretic peptide, has recently been shown to be involved in the pathophysiology of preeclampsia. The aim of this study was to search for CORIN gene variations and their association to preeclampsia in Caucasian and African women. Our study population was composed of 571 pregnant women (295 with preeclampsia and 276 normotensive controls) matched for maternal and gestational age, and ethnic origin. The 22 exons of the CORIN gene were sequenced in a discovery sample (n = 260), where 31 single nucleotide polymorphisms were identified. In a replication sample (n = 311), 4 single nucleotide polymorphisms were tested. Two minor alleles (C for rs2271036 and G for rs2271037) were significantly associated to preeclampsia. Adjusted odds ratios [95% confidence interval] were 2.5 [1.2–3.8] (p = 0.007) and 2.3 [1.5–3.5] (p = 1.3×10⁻⁴), respectively. These associations were ethnic-specific, as only found in the Caucasian of subjects (odds ratio = 3.5 [1.8–6.6], p = 1.1×10⁻⁴; odds ratio = 3.1 [1.7–5.8], p = 2.1×10⁻⁴, for each single nucleotide polymorphism, respectively). The two single nucleotide polymorphisms are in almost perfect linkage disequilibrium (r² = 0.93). No specific association was found with severe preeclampsia, early-onset preeclampsia nor fetal growth retardation. In conclusion, this is the first report of a highly significant association between these two single nucleotide polymorphisms in CORIN gene and preeclampsia. Our findings further support the probability of a critical role of corin in preeclamspia pathophysiology at the uteroplacental interface.     

Fear-like behavioral responses in mice in different odorant environments: Trigeminal versus olfactory mediation under low doses

Odors can have repulsive effects on rodents based on two complementary adaptive behaviors: the avoidance of predator odors (potentially dangerous) and the avoidance of trigeminal stimulants (potentially noxious). The present study aimed to compare the behavioral effects on mice of odors according to their trigeminal properties and ecological significance. We used three different odors: 2,4,5-trimethylthiazoline (TMT: a fox feces odor frequently used to elicit fear-induced behaviors), toluene (a strong stimulant of the trigeminal system) and phenyl ethyl alcohol (PEA: a selective stimulant of the olfactory system). First, we checked preference and avoidance behaviors in mice with and without anosmia towards these odors to ensure their olfactory/trigeminal properties. Secondly, we used a standard test (open-field and elevated plus-maze) to assess the behaviors of mice when exposed to these odors. The results show that the anosmic and control mice both avoided TMT and toluene odors. In the open-field and the elevated plus-maze, mice exhibited "anxious" behaviors when exposed to TMT. Conversely, exposure to PEA induced "anxiolytic" effects confirmed by low blood corticosterone levels resulting from completion of the elevated plus-maze. Compared with TMT exposure, toluene exposure induced moderate "anxious" effects.