Holocentric Chromosomes of Luzula elegans Are Characterized by a Longitudinal Centromere Groove, Chromosome Bending, and a Terminal Nucleolus Organizer Region

The structure of holocentric chromosomes was analyzed in mitotic cells of Luzula elegans. Light and scanning electron microscopy observations provided evidence for the existence of a longitudinal groove along each sister chromatid. The centromere-specific histone H3 variant, CENH3, colocalized with this groove and with microtubule attachment sites. The terminal chromosomal regions were CENH3-negative. During metaphase to anaphase transition, L. elegans chromosomes typically curved to a sickle-like shape, a process that is likely to be influenced by the pulling forces of microtubules along the holocentric axis towards the corresponding microtubule organizing regions. A single pair of 45S rDNA sites, situated distal to Arabidopsis-telomere repeats, was observed at the terminal region of one chromosome pair. We suggest that the 45S rDNA position in distal centromere-free regions could be required to ensure chromosome stability. Copyright (C) 2011 S. Karger AG, Base

JunctionViewer: customizable annotation software for repeat-rich genomic regions

<p>Abstract</p> <p>Background</p> <p>Repeat-rich regions such as centromeres receive less attention than their gene-rich euchromatic counterparts because the former are difficult to assemble and analyze. Our objectives were to 1) map all ten centromeres onto the maize genetic map and 2) characterize the sequence features of maize centromeres, each of which spans several megabases of highly repetitive DNA. Repetitive sequences can be mapped using special molecular markers that are based on PCR with primers designed from two unique "repeat junctions". Efficient screening of large amounts of maize genome sequence data for repeat junctions, as well as key centromere sequence features required the development of specific annotation software.</p> <p>Results</p> <p>We developed JunctionViewer to automate the process of identifying and differentiating closely related centromere repeats and repeat junctions, and to generate graphical displays of these and other features within centromeric sequences. JunctionViewer generates NCBI BLAST, WU-BLAST, cross_match and MUMmer alignments, and displays the optimal alignments and additional annotation data as concise graphical representations that can be viewed directly through the graphical interface or as PostScript^®output.</p> <p>This software enabled us to quickly characterize millions of nucleotides of newly sequenced DNA ranging in size from single reads to assembled BACs and megabase-sized pseudochromosome regions. It expedited the process of generating repeat junction markers that were subsequently used to anchor all 10 centromeres to the maize map. It also enabled us to efficiently identify key features in large genomic regions, providing insight into the arrangement and evolution of maize centromeric DNA.</p> <p>Conclusions</p> <p>JunctionViewer will be useful to scientists who wish to automatically generate concise graphical summaries of repeat sequences. It is particularly valuable for those needing to efficiently identify unique repeat junctions. The scalability and ability to customize homology search parameters for different classes of closely related repeat sequences make this software ideal for recurring annotation (e.g., genome projects that are in progress) of genomic regions that contain well-defined repeats, such as those in centromeres. Although originally customized for maize centromere sequence, we anticipate this software to facilitate the analysis of centromere and other repeat-rich regions in other organisms.</p

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

The centromere is a functional chromosome domain that is essential for faithful chromosome segregation during cell division and that can be reliably identified by the presence of the centromere-specific histone H3 variant CenH3. In monocentric chromosomes, the centromere is characterized by a single CenH3-containing region within a morphologically distinct primary constriction. This region usually spans up to a few Mbp composed mainly of centromere-specific satellite DNA common to all chromosomes of a given species. In holocentric chromosomes, there is no primary constriction; the centromere is composed of many CenH3 loci distributed along the entire length of a chromosome. Using correlative fluorescence light microscopy and high-resolution electron microscopy, we show that pea (Pisum sativum) chromosomes exhibit remarkably long primary constrictions that contain 3-5 explicit CenH3-containing regions, a novelty in centromere organization. In addition, we estimate that the size of the chromosome segment delimited by two outermost domains varies between 69 Mbp and 107 Mbp, several factors larger than any known centromere length. These domains are almost entirely composed of repetitive DNA sequences belonging to 13 distinct families of satellite DNA and one family of centromeric retrotransposons, all of which are unevenly distributed among pea chromosomes. We present the centromeres of Pisum as novel ``meta-polycentric'' functional domains. Our results demonstrate that the organization and DNA composition of functional centromere domains can be far more complex than previously thought, do not require single repetitive elements, and do not require single centromere domains in order to segregate properly. Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function

Cytomolecular identification of individual wheat-wheat chromosome arm associations in wheat-rye hybrids

Chromosome pairing in the meiotic metaphase I of wheatrye hybrids has been characterized by sequential genomic and fluorescent in situ hybridization allowing not only the discrimination of wheat and rye chromosomes, but also the identification of the individual wheat and rye chromosome arms involved in the chromosome associations. The majority of associations (93.8%) were observed between the wheat chromosomes. The largest number of wheat-wheat chromosome associations (53%) was detected between the A and D genomes, while the frequency of B-D and A-B associations was significantly lower (32 and 8%, respectively). Among the A-D chromosome associations, pairing between the 3AL and 3DL arms was observed with the highest frequency, while the most frequent of all the chromosome associations (0.113/ cell) was found to be the 3DS-3BS. Differences in the pairing frequency of the individual chromosome arms of wheat-rye hybrids have been discussed in relation to the homoeologous relationships between the constituent genomes of hexaploid wheat

Tumor Necrosis Factor Alpha-Induced Interleukin-8 Production via NF- B and Phosphatidylinositol 3-Kinase/Akt Pathways Inhibits Cell Apoptosis in Human Hepatocytes

Tumor necrosis factor alpha (TNF-α) not only induces apoptotic signals but also causes antiapoptotic and regenerative responses in the liver. However, the molecular mechanism(s) of the latter events remains unclear. In the present study, we examined TNF-α-induced genes in Hc human normal (unsensitized) hepatocytes by cDNA microarray analysis. Interleukin-8 (IL-8) induction was the most pronounced of the upregulated genes. The IL-8 protein level was also increased. IL-8 belongs to the ELR-CXC chemokine family and appears to exert mitogenic and antiapoptotic functions in other cell systems. IL-8 expression by TNF-α was inhibited when two survival signals, nuclear factor κB (NF-κB) and phosphatidylinositol 3-kinase (PI3K)/Akt, were inhibited by a mutant form of inhibitor of NF-κB (IκB); by dominant negative (kinase-dead) Akt; or by treatment with LY 294002, an inhibitor of PI3K. TNF-α induced apoptosis in Hc cells that were sensitized by inhibition of NF-κB and PI3K activation. IL-8 administration protected mice against concanavalin A-induced hepatitis in vivo. IL-8 also rescued the sensitized Hc cells, at least in part, from TNF-α-induced apoptosis in vitro. TNF-α inhibited DNA synthesis in unsensitized Hc cells in the absence of serum. Exogenous IL-8 reversed, though anti-IL-8 neutralization antibody enhanced, growth inhibition by TNF-α. These results indicate that IL-8, the production of which is stimulated by TNF-α, inhibits apoptosis of sensitized hepatocytes and releases normal (unsensitized) hepatocytes from growth inhibition induced by TNF-α

XLF-Cernunnos promotes DNA ligase IV–XRCC4 re-adenylation following ligation

XLF-Cernunnos (XLF) is a component of the DNA ligase IV–XRCC4 (LX) complex, which functions during DNA non-homologous end joining (NHEJ). Here, we use biochemical and cellular approaches to probe the impact of XLF on LX activities. We show that XLF stimulates adenylation of LX complexes de-adenylated by pyrophosphate or following LX decharging during ligation. XLF enhances LX ligation activity in an ATP-independent and dependent manner. ATP-independent stimulation can be attributed to enhanced end-bridging. Whilst ATP alone fails to stimulate LX ligation activity, addition of XLF and ATP promotes ligation in a manner consistent with XLF-stimulated readenylation linked to ligation. We show that XLF is a weakly bound partner of the tightly associated LX complex and, unlike XRCC4, is dispensable for LX stability. 2BN cells, which have little, if any, residual XLF activity, show a 3-fold decreased ability to repair DNA double strand breaks covering a range of complexity. These findings strongly suggest that XLF is not essential for NHEJ but promotes LX adenylation and hence ligation. We propose a model in which XLF, by in situ recharging DNA ligase IV after the first ligation event, promotes double stranded ligation by a single LX complex

An epistatic mini-circuitry between the transcription factors Snail and HNF4\uce\ub1 controls liver stem cell and hepatocyte features exhorting opposite regulation on stemness-inhibiting microRNAs

Preservation of the epithelial state involves the stable repression of epithelial-to-mesenchymal transition program, whereas maintenance of the stem compartment requires the inhibition of differentiation processes. A simple and direct molecular mini-circuitry between master elements of these biological processes might provide the best device to keep balanced such complex phenomena. In this work, we show that in hepatic stem cell Snail, a transcriptional repressor of the hepatocyte differentiation master gene HNF4\uce\ub1, directly represses the expression of the epithelial microRNAs (miRs)-200c and-34a, which in turn target several stem cell genes. Notably, in differentiated hepatocytes HNF4\uce\ub1, previously identified as a transcriptional repressor of Snail, induces the miRs-34a and-200a, b, c that, when silenced, causes epithelial dedifferentiation and reacquisition of stem traits. Altogether these data unveiled Snail, HNF4\uce\ub1 and miRs-200a, b, c and-34a as epistatic elements controlling hepatic stem cell maintenance/differentiation. \uc2\ua9 2012 Macmillan Publishers Limited. All rights reserved

Traditional eye medicine use by newly presenting ophthalmic patients to a teaching hospital in south-eastern Nigeria: socio-demographic and clinical correlates

<p>Abstract</p> <p>Background</p> <p>This study set out to determine the incidence, socio-demographic, and clinical correlates of Traditional Eye Medicine (TEM) use in a population of newly presenting ophthalmic outpatients attending a tertiary eye care centre in south-eastern Nigeria.</p> <p>Methods</p> <p>In a comparative cross-sectional survey at the eye clinic of the University of Nigeria Teaching Hospital (UNTH), Enugu, between August 2004 - July 2006, all newly presenting ophthalmic outpatients were recruited. Participants' socio-demographic and clinical data and profile of TEM use were obtained from history and examination of each participant and entered into a pretested questionnaire and proforma. Participants were subsequently categorized into TEM- users and non-users; intra-group analysis yielded proportions, frequencies, and percentages while chi-square test was used for inter-group comparisons at P = 0.01, df = 1.</p> <p>Results</p> <p>Of the 2,542 (males, 48.1%; females, 51.9%) participants, 149 (5.9%) (males, 45%; females, 55%) used TEM for their current eye disease. The TEMs used were chemical substances (57.7%), plant products (37.7%), and animal products (4.7%). They were more often prescribed by non-traditional (66.4%) than traditional (36.9%) medicine practitioners. TEMs were used on account of vision loss (58.5%), ocular itching (25.4%) and eye discharge (3.8%). Reported efficacy from previous users (67.1%) and belief in potency (28.2%) were the main reasons for using TEM. Civil servants (20.1%), farmers (17.7%), and traders (14.1%) were the leading users of TEM. TEM use was significantly associated with younger age (p < 0.01), being married (p < 0.01), rural residence (p < 0.01), ocular anterior segment disease (p < 0.01), delayed presentation (p < 0.01), low presenting visual acuity (p < 0.01), and co-morbid chronic medical disease (p < 0.01), but not with gender (p = 0.157), and educational status (p = 0.115).</p> <p>Conclusion</p> <p>The incidence of TEM use among new ophthalmic outpatients at UNTH is low. The reasons for TEM use are amenable to positive change through enhanced delivery of promotive, preventive, and curative public eye care services. This has implications for eye care planners and implementers. To reverse the trend, we suggest strengthening of eye care programmes, even distribution of eye care resources, active collaboration with orthodox eye care providers and traditional medical practitioners, and intensification of research efforts into the pharmacology of TEMs.</p