Untangling complex histories of genome mergings in high polyploids

Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated network-like histories, and the evolutionary history of many plant groups cannot be adequately represented by phylogenetic trees because of such reticulate events. The history of complex genome mergings within a high-polyploid species complex in the genus Cerastium (Caryophyllaceae) is here untangled by the use of a network algorithm and noncoding sequences of a low-copy number gene. The resulting network illustrates how hybridization and polyploidization have acted as key evolutionary processes in creating a plant group where high-level allopolyploids clearly outnumber extant parental genomes.     

Wnt4 action in gonadal development and sex determination

Wnt4 is a growth factor involved in multiple developmental processes such as the formation of the kidney, adrenal, mammary gland, pituitary and the female reproductive system. During mammalian embryogenesis, Wnt4 is expressed in the gonads of both sexes before sex determination events take place and is subsequently down-regulated in the male gonad. Inactivation of the Wnt4 gene in mice has revealed that it is involved at several steps of female reproductive development. Wnt4 is implicated in Müllerian duct regression, the formation of sex-specific vasculature, the inhibition of steroidogenesis and in sex-specific cell migration events. A mouse model of sex-reversal has partially unravelled the molecular pathways in which Wnt4 operates during the development of the female reproductive system. However, the specific molecular mechanism of action of Wnt4 during gonadal development remains unknown. This and downstream signaling pathways involved in Wnt4 action during female gonad development are reviewed and models of Wnt4 action are proposed for Müllerian duct formation, sex-specific vasculature development, and sex determination events. Further identification of critical downstream effectors of the Wnt4 signaling pathway in mouse models and in patients with sex-reversal conditions could help in understanding sex-reversal pathologies in humans.     

The CD44 standard/ezrin complex regulates Fas-mediated apoptosis in Jurkat cells

The transmembrane receptor CD44 conveys important signals from the extracellular microenvironment to the cytoplasm, a phenomena known as “outside-in” signaling. CD44 exists as several isoforms that result from alternative splicing, which differ only in the extracellular domain but yet exhibit different activities. CD44 is a binding partner for the membrane-cytoskeleton cross-linker protein ezrin. In this study, we demonstrate that only CD44 standard (CD44s) colocalizes and interacts with the actin cross-linkers ezrin and moesin using well-characterized cell lines engineered to express different CD44 isoforms. Importantly, we also show that the association CD44s-ezrin-actin is an important modulator of Fas-mediated apoptosis. The results highlight a mechanism by which signals from the extracellular milieu regulate intracellular signaling activities involved in programmed cell death. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

Boltzmann probability of RNA structural neighbors and riboswitch detection

MOTIVATION: We describe algorithms implemented in a new software package, RNAbor, to investigate structures in a neighborhood of an input secondary structure S of an RNA sequence s. The input structure could be the minimum free energy structure, the secondary structure obtained by analysis of the X-ray structure or by comparative sequence analysis, or an arbitrary intermediate structure. RESULTS: A secondary structure T of s is called a delta-neighbor of S if T and S differ by exactly delta base pairs. RNAbor computes the number (N(delta)), the Boltzmann partition function (Z(delta)) and the minimum free energy (MFE(delta)) and corresponding structure over the collection of all delta-neighbors of S. This computation is done simultaneously for all delta < or = m, in run time O (mn3) and memory O(mn2), where n is the sequence length. We apply RNAbor for the detection of possible RNA conformational switches, and compare RNAbor with the switch detection method paRNAss. We also provide examples of how RNAbor can at times improve the accuracy of secondary structure prediction. AVAILABILITY: http://bioinformatics.bc.edu/clotelab/RNAbor/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

GGtools: analysis of genetics of gene expression in bioconductor

This paper reviews the central concepts and implementation of data structures and methods for studying genetics of gene expression with the GGtools package of Bioconductor. Illustration with a HapMap+expression dataset is provided. Availability: Package GGtools is part of Bioconductor 1.9 (http://bioconductor.org). Open source with Artistic License.     

Extending assembly of short DNA sequences to handle error

Inexpensive de novo genome sequencing, particularly in organisms with small genomes, is now possible using several new sequencing technologies. Some of these technologies such as that from Illumina's Solexa Sequencing, produce high genomic coverage by generating a very large number of small reads ( approximately 30 bp). While prior work shows that partial assembly can be performed by k-mer extension in error-free reads, this algorithm is unsuccessful with the sequencing error rates found in practice. We present VCAKE (Verified Consensus Assembly by K-mer Extension), a modification of simple k-mer extension that overcomes error by using high depth coverage. Though it is a simple modification of a previous approach, we show significant improvements in assembly results on simulated and experimental datasets that include error. AVAILABILITY: http://152.2.15.114/~labweb/VCAKE     

Sphingosine 1-phosphate rapidly increases endothelial barrier function independently of VE-cadherin but requires cell spreading and Rho kinase

Sphingosine 1-phosphate (S1P) rapidly increases endothelial barrier function and induces the assembly of the adherens junction proteins vascular endothelial (VE)-cadherin and catenins. Since VE-cadherin contributes to the stabilization of the endothelial barrier, we determined whether the rapid, barrier-enhancing activity of S1P requires VE-cadherin. Ca(2+)-dependent, homophilic VE-cadherin binding of endothelial cells, derived from human umbilical veins and grown as monolayers, was disrupted with EGTA, an antibody to the extracellular domain of VE-cadherin, or gene silencing of VE-cadherin with small interfering RNA. All three protocols caused a reduction in the immunofluorescent localization of VE-cadherin at intercellular junctions, the separation of adjacent cells, and a decrease in basal endothelial electrical resistance. In all three conditions, S1P rapidly increased endothelial electrical resistance. These findings demonstrate that S1P enhances the endothelial barrier independently of homophilic VE-cadherin binding. Junctional localization of VE-cadherin, however, was associated with the sustained activity of S1P. Imaging with phase-contrast and differential interference contrast optics revealed that S1P induced cell spreading and closure of intercellular gaps. Pretreatment with latrunculin B, an inhibitor of actin polymerization, or Y-27632, a Rho kinase inhibitor, attenuated cell spreading and the rapid increase in electrical resistance induced by S1P. We conclude that S1P rapidly closes intercellular gaps, resulting in an increased electrical resistance across endothelial cell monolayers, via cell spreading and Rho kinase and independently of VE-cadherin.     

Biodegradation of phytane (2,6,10,14-tetramethylhexadecane) and accumulation of related isoprenoid wax esters by Mycobacterium ratisbonense strain SD4 under nitrogen-starved conditions

The accumulation of storage lipids during the biodegradation of 2,6,10,14-tetramethylhexadecane (phytane) by Mycobacterium ratisbonense strain SD4 grown under nitrogen-starved conditions was investigated. Detailed chemical analysis of intracellular metabolites revealed the existence of (at least) three different pathways for the catabolism of phytane, and the accumulation of significant proportions (39% of the total lipids) of several isoprenoid wax esters formed by condensation of oxidation products of the hydrocarbon. In contrast, triacylglycerols but no wax esters were accumulated by strain SD4 grown on hexadecane, the unbranched homologue of phytane.     

Testis-specific expression and genomic multiplicity of the rat Rtdpoz genes that encode bipartite TRAF- and POZ/BTB-domain proteins

Based on bioinformatics analysis, we previously hypothesized the existence of a bipartite TDPOZ protein family members of which carry the TRAF domain (TD) and POZ/BTB [Huang, C.-J., Chen, C.-Y., Chen, H.-H., Tsai, S.-F., Choo, K.-B., 2004. TDPOZ, a family of bipartite animal and plant proteins that contain the TRAF (TD) and POZ/BTB domains. Gene 324, 117-127.]. Conservation in animals and plants suggests important biological functions for the putative TDPOZ proteins. In this work, we report testis-specific expression of two new Tdpoz members, Rtdpoz-T1 and -T2, of the rat genome; the result clearly indicates that members of the hypothetical gene family are, indeed, expressed. T1 and T2 cDNA sequences were derived by rapid amplification of cDNA ends (RACE). The exons of the genes were determined by queries of the rat genome sequence draft and selectively confirmed in splicing assays. The results indicate that T1 and T2 share a common leader exon indicative of alternative splicing, and that the genes are uninterrupted by introns in their respective coding sequences. Database interrogations also reveal a combined 297 hits of Rtdpoz-like sequences on 7 chromosomes; however, the bulk of the hits (264) and 26 putative TDPOZ-encoding genes, including T1 and T2, are found in a approximately 2.5 Mb cluster in the Rn2_2148 supercontig on chromosome 2. Our data signify retrotransposition in the generation and expansion of the Rtdpoz repertoire in the rat genome. We also anticipate spatio-temporal-specific expression of many more TDPOZ members in the rat or other animals and plants.