Isolation of mRNA species related to the rooting induction in almond and apple through the differential display technique

Differential display of mRNA has been recently developed as a tool to detect and characterize changes in gene expression. We applied this technique to fruit trees plantlets induced to root in vitro, in order to isolate and study genes involved in root induction. A reproducible pattern of polymerase chain reaction (PCR) products was obtained, both in almond and apple, in vertical polyacrylamide gels stained with ethidium bromide. Differences in PCR fingerprinting were detected in mRNAs of basal part of either auxin induced or non induced microcuttings. Thus, we suggest that this technique can be used in woody species to detect changes among mRNA populations during root induction. This revised version was published online in July 2006 with corrections to the Cover Date.     

Characterization of a xylose-specific antiserum that reacts with the complex asparagine-linked glycans of extracellular and vacuolar glycoproteins

Antibodies were raised against carrot (Daucus carota) cell wall β-fructosidase that was either in a native configuration (this serum is called anti-βF₁) or chemically deglycosylated (anti-βF₂). The two antisera had completely different specificities when tested by immunoblotting. The anti-βF₁ serum reacted with β-fructosidase and many other carrot cell wall proteins as well as with many proteins in extracts of bean (Phaseolus vulgaris) cotyledons and tobacco (Nicotiana tabacum) seeds. It did not react with chemically deglycosylated β-fructosidase. The anti-βF₁ serum also reacted with the bean vacuolar protein, phytohemagglutinin, but not with deglycosylated phytohemagglutinin. The anti-βF₂ serum reacted with both normal and deglycosylated β-fructosidase but not with other proteins. These results indicate that the βF₂ antibodies recognize the β-fructosidase polypeptide, while the βF₁ antibodies recognize glycan sidechains common to many glycoproteins. We used immunoadsorption on glycoprotein-Sepharose columns and hapten inhibition of immunoblot reactions to characterize the nature of the antigenic site. Antibody binding activity was found to be associated with Man₃(Xyl)(GIcNAc)₂Fuc, Man₃(Xyl)(GIcNAc)₂, and Man(Xyl) (GIcNAc)₂ glycans, but not with Man₃(GIcNAc)₂. Treatment of phytohemagglutinin, a glycoprotein with a Man₃(Xyl)(GIcNAc)₂Fuc glycan, with Charonia lampas β-xylosidase (after treatment with jack-bean α-mannosidase) greatly diminished the binding between the antibodies and phytohemagglutinin. We conclude, therefore, that the antibodies bind primarily to the xyloseβ, 1→ 2mannose structure commonly found in the complex glycans of plant glycoproteins.     

Epithelio-mesenchymal interface and fibronectin in the differentiation of the rat mesonephric and paramesonephric ducts

Abstract. The distribution of fibronectin and the morphological differentiation of the genital ducts was studied in rat fetuses at ages from 15 to 21 days. Fibronectin was localized with the peroxidase-antiperoxidase and avidin-biotin method at the electron- and light-microscope level. In 15-day-old male and female fetuses, fibronectin was localized as a continuous lamella around the mesonephric duct and as a discontinuous lamella around the paramesonephric duct. During the differentiation of the female paramesonephric duct, the fibronectin layer became continuous and remained so after the age of 16 days. The fibronectin layer of the male mesonephric duct remained continuous at all ages. The accumulation of mesenchymal cells on the outer surface of the female mesonephric duct and the concomitant detachment of the fibronectin layer around the duct suggests that mesenchymal regulation plays a role in the regression of the mesonephric duct. In the regressing male paramesonephric duct fibronectin was simultaneously lost in the condensed periductal mesenchyme, the places of epithelio-mesenchymal contact, and the epithelial cytoplasmic protrusions towards the mesenchyme. Ultrastructurally, fibronectin was localized in the basal laminae, on the cell membrane in contact with the extracellular material, and on the surface of the fibrillar and flocculent extracellular material. In addition to auto- and heterophagy, epithelio-mesenchymal interactions seem to play an important role in the regression of the genital ducts, although in different ways in males and females. The present results give additional support to the theory of the possible migration of epithelial cells into the surrounding mesenchyme during the regression of the paramesonephric duct.     

Assessment of the efficiency of different control programs to reduce Trioza apicalis Först. (Triozidae: Hemiptera) feeding damage and the spread of “Candidatus Liberibacter solanacearum” on carrots (Daucus carota ssp. sativus L.)

The control of carrot psyllid Trioza apicalis Förster largely relies on chemical measures, and the current integrated pest management (IPM) strategy is based on pest scouting. The number of active ingredients available for psyllid control will further decline in the coming years. The need for alternative control measures is therefore urgent. In this work the efficiency of different control programs including a kaolin particle film and plant-derived, crude saponin extract, chemical control, insect net and IPM (kaolin in combination with insecticides) programs to reduce psyllid feeding damage, reproduction and the spread of “Candidatus Liberibacter solanacearum” (CLso) in carrots was studied. Each year in 2016–2018, four replicates of each treatment were randomised in a row-column design on a commercial carrot farm. After the treatments were executed, the psyllid nymphs and eggs were counted. At the harvest, the carrot roots and shoots were weighed, damages assessed, and samples were taken for CLso detection from 50 plants at each replicate. Kaolin treatment alone and in combination with insecticides effectively reduced the number of psyllid nymphs and eggs in all the years studied. Saponin was applied only on the first year, since it significantly increased the number of T. apicalis eggs compared to other treatments. The insect net was superior to other treatments in all the studied aspects in all the years. Under normal weather conditions, the highest root weight was harvested under the insect net, followed by the chemical control program consisting of pyrethroids, kaolin treatment, untreated control and saponin treatment. During extreme weather conditions, chemical control programs were not effective at protecting the carrots from psyllid feeding, which was reflected as low root yield. In all years, the carrot leaf damage percent negatively correlated with the root weight. Similarly, the shoot:root ratio increased as the leaf-curling percentage rose, which was even pronounced under drought stress. The effect of climatic stress should be considered when developing IPM strategies.     

Two Mechanisms Drive Changes in Boreal Peatland Photosynthesis Following Long-Term Water Level Drawdown: Species Turnover and Altered Photosynthetic Capacity

Ecosystems - Climate change and the related increases in evapotranspiration threaten to make northern peatlands drier. The carbon sink function in peatlands is based on the delicate balance between...     

Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays

MOTIVATION: Single nucleic polymorphisms (SNPs) are one of the most abundant genetic variations in the human genome. Recently, several platforms for high-throughput SNP analysis have become available, capable of measuring thousands of SNPs across the genome. Tools for analysing and visualizing these large genetic data sets in biologically relevant manner are rare. This hinders effective use of the SNP-array data in research on complex diseases, such as cancer. RESULTS: We describe a computational framework to analyse and visualize SNP-array data, and link the results in relevant databases. Our major objective is to develop methods for identifying DNA regions that likely harbour recessive mutations. Thus, the algorithms are designed to have high sensitivity and the identified regions are ranked using a scoring algorithm. We have also developed annotation tools that automatically query gene IDs, exon counts, microarray probe IDs, etc. In our case study, we apply the methods for identifying candidate regions for recessively inherited colorectal cancer predisposition and suggest directions for wet-lab experiments. AVAILABILITY: R-package implementation is available at http://www.ltdk.helsinki.fi/sysbio/csb/downloads/CohortComparator/     

Hepatitis C Virus Induces Epidermal Growth Factor Receptor Activation via CD81 Binding for Viral Internalization and Entry

While epidermal growth factor receptor (EGFR) has been shown to be important in the entry process for multiple viruses, including hepatitis C virus (HCV), the molecular mechanisms by which EGFR facilitates HCV entry are not well understood. Using the infectious cell culture HCV model (HCVcc), we demonstrate that the binding of HCVcc particles to human hepatocyte cells induces EGFR activation that is dependent on interactions between HCV and CD81 but not claudin 1. EGFR activation can also be induced by antibody mediated cross-linking of CD81. In addition, EGFR ligands that enhance the kinetics of HCV entry induce EGFR internalization and colocalization with CD81. While EGFR kinase inhibitors inhibit HCV infection primarily by preventing EGFR endocytosis, antibodies that block EGFR ligand binding or inhibitors of EGFR downstream signaling have no effect on HCV entry. These data demonstrate that EGFR internalization is critical for HCV entry and identify a hitherto-unknown association between CD81 and EGFR.