Transcription profiling of fertilization and early seed development events in a solanaceous species using a 7.7 K cDNA microarray from Solanum chacoense ovules

<p>Abstract</p> <p>Background</p> <p>To provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 ESTs isolated from <it>Solanum chacoense </it>ovules bearing embryos from all developmental stages. Our aims were to: 1) identify genes expressed in a tissue-specific and temporal-specific manner; 2) define clusters of genes showing similar patterns of spatial and temporal expression; and 3) identify stage-specific or transition-specific candidate genes for further functional genomic analyses.</p> <p>Results</p> <p>We analyzed gene expression during <it>S. chacoense </it>embryogenesis in a series of experiments with probes derived from ovules isolated before and after fertilization (from 0 to 22 days after pollination), and from leaves, anthers, and styles. From the 6374 unigenes present in our array, 1024 genes were differentially expressed (≥ ± 2 fold change, p value ≤ 0.01) in fertilized ovules compared to unfertilized ovules and only limited expression overlap was observed between these genes and the genes expressed in the other tissues tested, with the vast majority of the fertilization-regulated genes specifically or predominantly expressed in ovules (955 genes). During embryogenesis three major expression profiles corresponding to early, middle and late stages of embryo development were identified. From the early and middle stages, a large number of genes corresponding to cell cycle, DNA processing, signal transduction, and transcriptional regulation were found. Defense and stress response-related genes were found in all stages of embryo development. Protein biosynthesis genes, genes coding for ribosomal proteins and other components of the translation machinery were highly expressed in embryos during the early stage. Genes for protein degradation were overrepresented later in the middle and late stages of embryo development. As expected, storage protein transcripts accumulated predominantly in the late stage of embryo development.</p> <p>Conclusion</p> <p>Our analysis provides the first study in a solanaceous species of the transcriptional program that takes place during the early phases of plant reproductive development, including all embryogenesis steps during a comprehensive time-course. Our comparative expression profiling strategy between fertilized and unfertilized ovules identified a subset of genes specifically or predominantly expressed in ovules while a closer analysis between each consecutive time point allowed the identification of a subset of stage-specific and transition-specific genes.</p

Hopf monoids from class functions on unitriangular matrices

We build, from the collection of all groups of unitriangular matrices, Hopf monoids in Joyal's category of species. Such structure is carried by the collection of class function spaces on those groups, and also by the collection of superclass function spaces, in the sense of Diaconis and Isaacs. Superclasses of unitriangular matrices admit a simple description from which we deduce a combinatorial model for the Hopf monoid of superclass functions, in terms of the Hadamard product of the Hopf monoids of linear orders and of set partitions. This implies a recent result relating the Hopf algebra of superclass functions on unitriangular matrices to symmetric functions in noncommuting variables. We determine the algebraic structure of the Hopf monoid: it is a free monoid in species, with the canonical Hopf structure. As an application, we derive certain estimates on the number of conjugacy classes of unitriangular matrices.Comment: Final Version, 32 pages, accepted in "Algebra and Number Theory

A toolbox for epitope-tagging and genome-wide location analysis in Candida albicans

<p>Abstract</p> <p>Background</p> <p><it>Candida albicans </it>is a diploid pathogenic fungus not yet amenable to routine genetic investigations. Understanding aspects of the regulation of its biological functions and the assembly of its protein complexes would lead to further insight into the biology of this common disease-causing microbial agent.</p> <p>Results</p> <p>We have developed a toolbox allowing <it>in vivo </it>protein tagging by PCR-mediated homologous recombination with TAP, HA and MYC tags. The transformation cassettes were designed to accommodate a common set of integration primers. The tagged proteins can be used to perform tandem affinity purification (TAP) or chromatin immunoprecipitation coupled with microarray analysis (ChIP-CHIP). Tandem affinity purification of <it>C. albicans </it>Nop1 revealed the high conservation of the small processome composition in yeasts. Data obtained with <it>in vivo </it>TAP-tagged Tbf1, Cbf1 and Mcm1 recapitulates previously published genome-wide location profiling by ChIP-CHIP. We also designed a new reporter system for <it>in vivo </it>analysis of transcriptional activity of gene <it>loci </it>in <it>C. albicans</it>.</p> <p>Conclusion</p> <p>This toolbox provides a basic setup to perform purification of protein complexes and increase the number of annotated transcriptional regulators and genetic circuits in <it>C. albicans</it>.</p

Characterization of Three Rice Basic/Leucine Zipper Factors, Including Two Inhibitors of EmBP-1 DNA Binding Activity

The promoter of the wheat Em gene contains elements with a CACGTG core sequence (G-boxes), which are recognized by EmBP-1, a wheat basic/leucine zipper (bZIP) protein. G-boxes are required for Em expression in response to the phytohormone abscisic acid and for transactivation by the Viviparous-1 protein (VP1) using transient expression systems. In order to identify other factors that are part of the transcriptional complex that associates with G-boxes, we have screened a rice (Oryza sativa) cDNA library with biotinylated EmBP-1. We have isolated osZIP-1a, a homolog of EmBP-1 and other plant G-box-binding factors. We show that EmBP-1 and osZIP-1a will preferentially heterodimerize in vitro. Overexpression of osZIP-1a in rice protoplasts can enhance expression from the Em promoter only in the presence of abscisic acid. Two other clones have been identified by screening with EmBP-1: osZIP-2a and osZIP-2b. These osZIP-2 factors represent a novel class of bZIP proteins with an unusual DNA-binding domain that does not recognize G-boxes. The osZIP-2 factors can heterodimerize with EmBP-1 and prevent it from binding to the Em promoter. Interestingly, osZIP-1a does not heterodimerize with the osZIP-2 factors and its DNA binding activity is unaffected by their presence. Thus, osZIP-2 factors may be involved in sequestering a particular group of G-box-binding factors into inactive heterodimers

Center of Mass Compensation during Gait in Hip Arthroplasty Patients: Comparison between Large Diameter Head Total Hip Arthroplasty and Hip Resurfacing

Objective. To compare center of mass (COM) compensation in the frontal and sagittal plane during gait in patients with large diameter head total hip arthroplasty (LDH-THA) and hip resurfacing (HR). Design. Observational study. Setting. Outpatient biomechanical laboratory. Participants. Two groups of 12 patients with LDH-THA and HR recruited from a larger randomized study and 11 healthy controls. Interventions. Not applicable. Main Outcome Measures. To compare the distance between the hip prosthetic joint center (HPJC) and the COM. The ratio (RHPJC-COM) and the variability (CVHPJC-COM) were compared between groups. Hip flexor, abductor, and adductor muscle strength was also correlated between groups while radiographic measurements were correlated with the outcome measures. Results. In the frontal plane, HR shows less variability than healthy controls at push-off and toe-off and RHPJC-COM is correlated with the muscle strength ratios (FRABD) at heel contact, maximal weight acceptance, and mid stance. In the sagittal plane, LDH-THA has a higher RHPJC-COM than healthy controls at push-off, and CVHPJC-COM is significantly correlated with FRFLEX. Conclusions. One year after surgery, both groups of patients, LDH-THA and HR, demonstrate minor compensations at some specific instant of the gait cycle, in both frontal and sagittal planes. However, their locomotion pattern is similar to the healthy controls

Transcriptional Regulation of Carbohydrate Metabolism in the Human Pathogen Candida albicans

Glycolysis is a metabolic pathway that is central to the assimilation of carbon for either respiration or fermentation and therefore is critical for the growth of all organisms. Consequently, glycolytic transcriptional regulation is important for the metabolic flexibility of pathogens in their attempts to colonize diverse niches. We investigated the transcriptional control of carbohydrate metabolism in the human fungal pathogen Candida albicans and identified two factors, Tye7p and Gal4p, as key regulators of glycolysis. When respiration was inhibited or oxygen was limited, a gal4tye7 C. albicans strain showed a severe growth defect when cultured on glucose, fructose or mannose as carbon sources. The gal4tye7 strain displayed attenuated virulence in both Galleria and mouse models as well, supporting the connection between pathogenicity and metabolism. Chromatin immunoprecipitation coupled with microarray analysis (ChIP-CHIP) and transcription profiling revealed that Tye7p bound the promoter sequences of the glycolytic genes and activated their expression during growth on either fermentable or non-fermentable carbon sources. Gal4p also bound the glycolytic promoter sequences and activated the genes although to a lesser extent than Tye7p. Intriguingly, binding and activation by Gal4p was carbon source-dependent and much stronger during growth on media containing fermentable sugars than on glycerol. Furthermore, Tye7p and Gal4p were responsible for the complete induction of the glycolytic genes under hypoxic growth conditions. Tye7p and Gal4p also regulated unique sets of carbohydrate metabolic genes; Tye7p bound and activated genes involved in trehalose, glycogen, and glycerol metabolism, while Gal4p regulated the pyruvate dehydrogenase complex. This suggests that Tye7p represents the key transcriptional regulator of carbohydrate metabolism in C. albicans and Gal4p provides a carbon source-dependent fine-tuning of gene expression while regulating the metabolic flux between respiration and fermentation pathways

Widespread occurrence of chromosomal aneuploidy following the routine production of Candida albicans mutants

It has come to our attention that approximately 35% of >100 published microarray datasets, where transcript levels were compared between two different strains, exhibit some form of chromosome-specific bias. While some of these arose from the use of strains whose aneuploidies were not known at the time, in a worrisome number of cases the recombinant strains have acquired additional aneuploidies that were not initially present in the parental strain. The aneuploidies often affected a different chromosome than the one harboring the insertion site. The affected strains originated from either CAI-4, RM1000, BWP17 or SN95 and were produced through a variety of strategies. These observations suggest that aneuploidies frequently occur during the production of recombinant strains and have an effect on global transcript profiles outside of the afflicted chromosome(s), thus raising the possibility of unintended phenotypic consequences. Thus, we propose that all Candida albicans mutants and strains should be tested for aneuploidy before being used in further studies. To this end, we describe a new rapid testing method, based on a multiplex quantitative PCR assay, that produces eight bands of distinct sizes from either the left or right arms of each C. albicans chromosome

A Conserved Domain of the viviparous-1 Gene Product Enhances the DNA Binding Activity of the bZIP Protein EmBP-1 and Other Transcription Factors

The maize VP1 protein is a seed-specific regulator of gene expression that effects the expression of a subset of abscisic acid (ABA)-regulated genes that are expressed during the maturation program of the seed. In addition, VP1 has pleiotropic effects on seed development that are not related to ABA. In transient expression assays, VP1 has been shown to transactivate gene expression through at least two distinct promoter elements: the G boxes from the ABA-inducible wheat Em gene and the SphI box from the maize C1 gene. We have investigated how VP1 can transactivate gene expression through diverse promoter elements by analyzing its association in vitro with EmBP-1, a factor that binds the Em promoter. We demonstrate that VP1 can greatly enhance the DNA binding activity of EmBP-1 in a gel retardation assay. This enhancing activity has also been observed on transcription factors as diverse as Opaque-2, Max, Sp1, and NF-kappaB. Deletion of a small but highly conserved region (BR2) in VP1 eliminates the enhancement in vitro as well as the ability of VP1 to transactivate Em gene expression in a transient expression assay. A 40-amino acid fragment from VP1 sandwiched between the maltose-binding protein and LacZ can confer the enhancement function to this fusion protein in vitro. A weak and relatively nonspecific interaction between BR2 and DNA is demonstrated by UV cross-linking. The in vitro properties we observe for VP1 might explain the regulatory effects of VP1 on a diverse set of genes and why mutations in the vp1 locus have pleiotropic effects

Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes

For Assembly 20 of the Candida albicans genome, the sequence of each of the eight chromosomes was determined, revealing new insights into gene family creation and dispersion, subtelomere organization, and chromosome evolution

Investigative approach to improve hot water system hydraulics through temperature monitoring to reduce building environmental quality hazard associated to Legionella

Several countries have promulgated control measures and design guidelines to limit the proliferation of Legionella within hot water distribution systems (HWDS). However, there is little information on how to assess and improve existing HWDS unable to maintain water temperatures >= 55 degrees C throughout the system. A 50-year old hot water system of a 10 story hospital was investigated in terms of temperature distribution and Legionella pneumophila prevalence. Concentrations of L. pneumophila were correlated with the maximum temperature reached at the tap, with a significant decrease observed at T >= 55 degrees C. Continuous temperature and flow monitoring was performed on the overall HWDS, characterizing the principal and secondary horizontal return loops for all 9 wings, and detailed investigations of the secondary vertical return loops was completed in Wing 3. Results indicated the system inability to systematically maintain desired operating temperatures of 55 degrees C. The deficient hydraulic distribution was the root cause of the poor temperature maintenance throughout the secondary loops, but defective devices were also identified as playing an important role in sectorial temperature failure. A simple stepwise investigative approach was developed to identify hydraulic deficiencies. The implementation of flow restrictions on identified recirculation loops and increased pumping efficiency was conducted within a short period of 2 months, with no major system upgrade. These corrective measures resulted in a balanced system with increased flow velocities (>0.2 m/s). As a result, the proportion of taps achieving 55 degrees C within 2 min increased from 11% to 74% and L. pneumophila prevalence decreased from 93.1% to 46.1% after 4 weeks. (C) 2016 The Authors. Published by Elsevier Ltd