Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray

Background  

Unravelling the path from genotype to phenotype, as it is influenced by an organism's environment, is one of the central goals in biology. Gene expression profiling by means of microarrays has become very prominent in this endeavour, although resources exist only for relatively few model systems. As genomics has matured into a comparative research program, expression profiling now also provides a powerful tool for non-traditional model systems to elucidate the molecular basis of complex traits.     

Physiological traits associated with reductions in grain number in wheat and barley under waterlogging

Plant and Soil - Negative effects of waterlogging on wheat and barley yield are expressed mainly through reductions in grain number per plant. Physiological traits associated with reductions in...     

Clustering cancer gene expression data: a comparative study

Background  

The use of clustering methods for the discovery of cancer subtypes has drawn a great deal of attention in the scientific community. While bioinformaticians have proposed new clustering methods that take advantage of characteristics of the gene expression data, the medical community has a preference for using "classic" clustering methods. There have been no studies thus far performing a large-scale evaluation of different clustering methods in this context.     

Vitamin E activates CRABP-II gene expression in cultured human fibroblasts, role of protein kinase C

The treatment of human fibroblasts with different tocopherols in the presence of retinol caused an increase in cytoplasmic retinoic acid binding protein II (CRABP-II) mRNA and protein. The possibility of an involvement of protein kinase C (PKC) in the response to tocopherols was supported by the results obtained with the PKC-specific inhibitors, calphostin C and bisindolylmaleimide I. The effect of alpha-tocopherol was prevented by okadaic acid, suggesting that a protein phosphatase is responsible for PKC dephosphorylation produced by the presence of tocopherols. The results shown support the hypothesis that phosphorylation/dephosphorylation of RXRalpha via PKC may be involved in the regulation of CRABP-II gene expression.     

Induction of protection against the necrotrophic pathogens Phytophthora citrophthora and Alternaria solani in Lycopersicon esculentum Mill. by a novel synthetic glycoside combined with amines

1,2,3,4-tetra-O-acetyl-6-ethyladipate-beta- D-glucopyranose (TOGE), a glycoside derivative of adipic acid monoethyl ester and 1,2,3,4-tetra-O-acetyl-beta- D-glucopyranose, was synthesized and the resistance-inducing activity shown by TOGE-1 (TOGE plus furfurylamine) and TOGE-2 (TOGE plus 1,3-diaminepropane) was assayed. TOGE-1 and TOGE-2 protected tomato plants against two different fungal pathogens Phytophthora citrophthora and Alternaria solani. Foliar treatments at very low concentrations (2.5 mg l(-1) TOGE, 0.5 mg l(-1) amine) clearly reduced the disease incidence for both pathogens. TOGE-2 application was the most effective on intact plants as well as on detached leaves, reducing fungal growth by more than 46% with respect to control plants. On the other hand TOGE-1 treatment reduced fungal advance by 21%. These results demonstrate a high protective effect against fungal infections for both chemicals. A possible direct antimicrobial effect was discounted due to the weak activity observed in vitro against these pathogens at the low concentrations used in plants. TOGE-2 treatment clearly activates resistance against both pathogens and improves the protective effect previously shown by FGA mixture (adipic acid monoethyl ester, 1,2,3,4-tetra-O-acetyl-beta- D-glucopyranose and furfurylamine) [V. Flors et al. (2001) J Agric Food Chem 49:2569-2575]. The obtained results indicate that TOGE-1 and TOGE-2 act as resistance inducers. Although their mode of action is still unknown, pre-challenge studies have demonstrated the induction of the phenylpropanoid pathway and antioxidant activities. Both chemicals have demonstrated a beneficial effect on plant development, increasing chlorophyll and protein contents, photosynthetic rate and water-use efficiency. The improvement of plant growth and development produced by these treatments suggests crop tolerance to these chemicals, although effective formulations that are safe to humans must be developed before this technology can be used commercially.     

Phylogeny of the genus trichoderma based on sequence analysis of the internal transcribed spacer region 1 of the rDNA cluster

Sequences of the internal transcribed spacer region 1 (ITS1) of the ribosomal DNA were used to determine the phylogenetic relationships of species of Trichoderma sect. Pachybasium. To this end, 85 strains-including all the available ex-type strains-were analyzed. Parsimony analysis demonstrated that the section is nonmonophyletic, distributing the 85 strains among three main groups that were supported by bootstrap values. Group A comprises two clades (A1 and A2), with A1 including T. polysporum, T. piluliferum, and T. minutisporum, while A2 included T. hamatum, T. pubescens, and T. strigosum in addition to species previously included in sect. Trichoderma (i.e., T. viride, T. atroviride, and T. koningii). The ex-type strain of T. fasciculatum formed a separate branch basal to clade A. Clade B contained the sect. Pachybasium members T. harzianum, T. fertile, T. croceum, T. longipile, T. strictipile, T. tomentosum, T. oblongisporum, T. flavofuscum, T. spirale, and the anamorphs of Hypocrea semiorbis and H. cf. gelatinosa. Sequence differences among clades A1, A2, and B were in the same order of magnitude as between each of them and T. longibrachiatum, which was used as an outgroup in these analyses. Sequence differences within clades A1, A2, and B were considerably smaller: in some cases (i.e., T. virens and T. flavofuscum; T. strictipile and H. cf. gelatinosa), the ITS1-sequences were identical, suggesting conspecifity. In other cases (e.g., T. crassum and T. longipile; T. harzianum, T. inhamatum, T. croceum, T. fertile, and H. semiorbis; T. hamatum and T. pubescens; and T. viride, T. atroviride, and T. koningii) differences were in the range of 1-3 nt only, suggesting a very close phylogenetic relationship. The sequence of a previously described aggressive mushroom competitor group of T. harzianum strains (Th2) was strikingly different from that of the ex-type strain of T. harzianum and closely related species and is likely to be a separate species. Copyright 1998 Academic Press.     

Mutant actins that stabilise F-actin use distinct mechanisms to activate the SRF coactivator MAL

Nuclear accumulation of the serum response factor coactivator MAL/MKL1 is controlled by its interaction with G-actin, which results in its retention in the cytoplasm in cells with low Rho activity. We previously identified actin mutants whose expression promotes MAL nuclear accumulation via an unknown mechanism. Here, we show that actin interacts directly with MAL in vitro with high affinity. We identify a further activating mutation, G15S, which stabilises F-actin, as do the activating actins S14C and V159N. The three mutants share several biochemical properties, but can be distinguished by their ability to bind cofilin, ATP and MAL. MAL interaction with actin S14C is essentially undetectable, and that with actin V159N is weakened. In contrast, actin G15S interacts more strongly with MAL than the wild-type protein. Strikingly, the nuclear accumulation of MAL induced by overexpression of actin S14C is substantially dependent on Rho activity and actin treadmilling, while that induced by actin G15S expression is not. We propose a model in which actin G15S acts directly to promote MAL nuclear entry.     

Regulation of iNOS expression and glutathione levels in rat liver by oxygen tension

SNI-2011 induces the long-lasting increase in the amount of aquaporin-5 (AQP5) in apical plasma membranes (APMs) of rat parotid acini in a concentration-dependent manner. This induction was inhibited by p-F-HHSiD, U73122, TMB-8, or dantrolene but not by bisindolmaleimide or H-7, indicating that SNI-2011 acting at M(3) muscarinic receptors induced translocation of AQP5 via [Ca(2+)](i) elevation but not via the activation of protein kinase C. In contrast, acetylcholine induced a transient translocation of AQP5 to APMs. SNI-2011 induces long-lasting oscillations of [Ca(2+)](i) in the presence of extracellular Ca(2+). Thus, SNI-2011 induces a long-lasting translocation of AQP5 to APMs coupled with persistent [Ca(2+)](i) oscillations.