Decreased expression of specific genes in yeast cells lacking histone H1

Chromatin plays an important role in regulating eukaryotic gene expression. Chromatin is composed of DNA wrapped around a nucleosome core (consisting of two copies of the well conserved histones H2A, H2B, H3, and H4) and a more variable linker histone H1. Various in vitro and in vivo studies have implicated histone H1 as a repressor of gene expression or as an activator, but its exact role is still unclear. Sequencing of the yeast genome has led to the identification of a putative histone H1 gene. Biochemical studies demonstrated that yeast does indeed possess a bona fide histone H1. However, deletion of the unique yeast H1 gene is not associated with any phenotypes, and it was questioned whether it plays any role. To address this issue, we performed whole-genome microarray analysis to identify genes that are affected by H1 removal. Surprisingly, deletion of the gene encoding histone H1 does not result in increased gene expression but rather in a modest reduction. Northern blot analysis of selected genes confirmed the results obtained with the microarray analysis. A similar effect was observed with an integrated lacZ reporter. Thus, our data demonstrate that removal of yeast histone H1 only results in decreased gene expression.     

Survey of transposable elements from rice genomic sequences

Oryza sativa L. (domesticated rice) is a monocotyledonous plant, and its 430 Mb genome has been targeted for complete sequencing. We performed a high-resolution computer-based survey for transposable elements on 910 Kb of rice genomic DNA sequences. Both class I and II transposable elements were present, contributing 19.9% of the sequences surveyed. Class II elements greatly outnumbered class I elements (166 versus 22), although class I elements made up a greater percentage (12.2% versus 6.6%) of nucleotides surveyed. Several Mutator-like elements (MULEs) were identified, including rice elements that harbor truncated host cellular genes. MITEs (miniature inverted-repeat transposable elements) account for 71.6% of the mined transposable elements and are clearly the predominant type of transposable element in the sequences examined. Moreover, a putative Stowaway transposase has been identified based on shared sequence similarity with the mined MITEs and previously identified plant mariner-like elements (MLEs). Members of a group of novel rice elements resembling the structurally unusual members of the Basho family in Arabidopsis suggest a wide distribution of these transposons among plants. Our survey provides a preview of transposable element diversity and abundance in rice, and allows for comparison with genomes of other plant species.     

Muscle palmitate uptake and binding are saturable and inhibited by antibodies to FABPPM

Studies show that uptake of long-chain fatty acids (LCFA) across the plasma membranes (PM) may occur partly via a carrier-mediated process and that the plasma membrane fatty acid-binding protein (FABP_PM) may be a component of this system. To test the hypothesis that FABP_PM is involved in transsarcolemmal transport of LCFA in muscle, we measured palmitate uptake in giant sarcolemmal vesicles and palmitate binding to PM proteins in rat muscles, (1) in the presence of increasing amounts of unbound palmitate and (2) in the absence or presence of antibody to FABP_PM. Both palmitate uptake and binding were found to be saturable functions of the unbound palmitate concentration with calculated V_max values of 10.5 ± 1.2 pmol/mg protein/15 sec and 45.6 ± 2.9 nmol/mg protein/15 min and K_m values of 12.8 ± 3.8 and 18.4 ± 1.8 nmol/L, respectively. The V_max values for both palmitate uptake and binding were significantly decreased by 75-79% in the presence of a polyclonal antibody to the rat hepatic FABP_PM. Antibody inhibition was found to be dose-dependent and specific to LCFA. Glucose uptake was not affected by the presence of the antibody to FABP_PM. Palmitate uptake and binding were also inhibited in the presence of trypsin and phloretin. These results support the hypothesis that transsarcolemmal LCFA transport occurs in part by a carrier-mediated process and that FABP_PM is a component of this process in muscle.     

Inheritance of stomatal conductance in cotton (Gossypium barbadense)

Stomatal conductance in improved Pima cotton cultivars (Gossypium barbadense) has been previously shown to be positively associated with heat resistance and yield potential. In the present study we determined the mode of inheritance of stomatal conductance in crosses of six G. barbadense parents varying in origin, degree of agronomic development and stomatal conductance. Parents included a primitive tropical cotton (B368), two obsolete cultivars (St Vincent V135, Pima 32), one modern commercial line (Pima S-6) and two elite genotypes of the Pima germplasm (P70, P73). These lines showed distinct differences in stomatal conductance, under greenhouse and field conditions. The primitive B368 had the lowest conductance, and the elite lines the highest. Generation means analysis was used to quantify genetic effects in the crosses P70 × St Vincent V135, Pima S-6 × B368, Pima S-6 × Pima 32, P73 × Pima 32 and P73 × Pima S-6. Best-fit models of the inheritance of stomatal conductance varied in complexity from a simple additive-dominance model in the cross P70 × St. Vincent V135 to models displaying digenic epistatic interactions in the remaining crosses. Significant additive mean effects for stomatal conductance were detected in all crosses. Dominance mean effects were significant in the crosses P73 × Pima 32 and P73 × Pima S-6. Broadsense heritability estimates of stomatal conductance were relatively low (0.16–0.44) in all crosses except Pima S-6 × B368 (0.74). Results also show that the mode of inheritance of stomatal conductance is multigenic, and may have maternal as well as nuclear components. Recouping higher stomatal conductance levels from genetically wider crosses appears feasible and could proceed at a moderate rate. Fixing higher levels of stomatal conductance in populations from crosses of elite germplasm may be more difficult because of the presence of dominant mean effects and digenic epistatic interactions.     

Phylogenetic studies of the genus <Emphasis Type="Italic">Cebus</Emphasis>(Cebidae-Primates) using chromosome painting and G-banding

Background  

Chromosomal painting, using whole chromosome probes from humans and Saguinus oedipus, was used to establish karyotypic divergence among species of the genus Cebus, including C. olivaceus, C. albifrons, C. apella robustus and C. apella paraguayanus. Cytogenetic studies suggested that the species of this genus have conservative karyotypes, with diploid numbers ranging from 2n = 52 to 2n = 54.     

Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase

Pattern recognition receptors (PRRs) play a key role in plant and animal innate immunity. PRR binding of their cognate ligand triggers a signaling network and activates an immune response. Activation of PRR signaling must be controlled prior to ligand binding to prevent spurious signaling and immune activation. Flagellin perception in Arabidopsis through FLAGELLIN‐SENSITIVE 2 (FLS2) induces the activation of mitogen‐activated protein kinases (MAPKs) and immunity. However, the precise molecular mechanism that connects activated FLS2 to downstream MAPK cascades remains unknown. Here, we report the identification of a differentially phosphorylated MAP kinase kinase kinase that also interacts with FLS2. Using targeted proteomics and functional analysis, we show that MKKK7 negatively regulates flagellin‐triggered signaling and basal immunity and this requires phosphorylation of MKKK7 on specific serine residues. MKKK7 attenuates MPK6 activity and defense gene expression. Moreover, MKKK7 suppresses the reactive oxygen species burst downstream of FLS2, suggesting that MKKK7‐mediated attenuation of FLS2 signaling occurs through direct modulation of the FLS2 complex.     

Anonymous nuclear DNA markers in the American oyster and their implications for the heterozygote deficiency phenomenon in marine bivalves

A puzzling population-genetic phenomenon widely reported in allozyme surveys of marine bivalves is the occurrence of heterozygote deficits relative to Hardy-Weinberg expectations. Possible explanations for this pattern are categorized with respect to whether the effects should be confined to protein-level assays or are genomically pervasive and expected to be registered in both protein- and DNA-level assays. Anonymous nuclear DNA markers from the American oyster were employed to reexamine the phenomenon. In assays based on the polymerase chain reaction (PCR), two DNA-level processes were encountered that can lead to artifactual genotypic scorings: (a) differential amplification of alleles at a target locus and (b) amplification from multiple paralogous loci. We describe symptoms of these complications and prescribe methods that should generally help to ameliorate them. When artifactual scorings at two anonymous DNA loci in the American oyster were corrected, Hardy-Weinberg deviations registered in preliminary population assays decreased to nonsignificant values. Implications of these findings for the heterozygote-deficit phenomenon in marine bivalves, and for the general development and use of PCR-based assays, are discussed.      

Phylogenetic analysis of the tenascin gene family: evidence of origin early in the chordate lineage

Background  

Tenascins are a family of glycoproteins found primarily in the extracellular matrix of embryos where they help to regulate cell proliferation, adhesion and migration. In order to learn more about their origins and relationships to each other, as well as to clarify the nomenclature used to describe them, the tenascin genes of the urochordate Ciona intestinalis, the pufferfish Tetraodon nigroviridis and Takifugu rubripes and the frog Xenopus tropicalis were identified and their gene organization and predicted protein products compared with the previously characterized tenascins of amniotes.