Modern elite rice varieties of the 'Green Revolution' have retained a large introgression from wild rice around the Pi33 rice blast resistance locus

During the breeding process of cultivated crops, resistance genes to pests and diseases are commonly introgressed from wild species. The size of these introgressions is predicted by theoretical models but has rarely been measured in cultivated varieties. By combining resistance tests with isogenic strains, genotyping and sequencing of different rice accessions, it was shown that, in the elite rice variety IR64, the resistance conferring allele of the rice blast resistance gene Pi33 was introgressed from the wild rice Oryza rufipogon (accession IRGC101508). Further characterization of this introgression revealed a large introgression at this locus in IR64 and the related variety IR36. The introgressed fragment represents approximately half of the short arm of rice chromosome 8. This is the first report of a large introgression in a cultivated variety of rice. Such a large introgression is likely to have been maintained during backcrossing only if a selection pressure was exerted on this genomic region. The possible traits that were selected are discussed.     

Floral data from the mid-Cenozoic of central Pakistan

Floral remains are generally rare in the fossil record of Pakistan. We present here new discoveries of mid-Cenozoic wood and pollen of Oligocene deposits from central Pakistan. The palynological sample derives from claystone stratigraphically positioned above the wood fossils, but pollen and spores as well as the wood are all of Oligocene age. The three fossil wood samples derive from the top of the lower unit of the Chitarwata Formation, and the palynological sample comes from claystone situated in the middle unit of the formation. The wood samples are described and found to represent two species of the morphotaxon Terminalioxylon (Combretaceae): T. burmense Mädel-Angeliewa and Müller-Stoll [Madel-Angeliewa, E., Müller-Stoll, W.R., 1973. Kritische Studien über fossile Combretaceen-Hölzer: über Hölzer von Typus Terminalioxylon G. Schönfeld mit einer Revision der bisher zu Evodioxylon Chiarugi gestellten Arten. Palaeontographica 142B, 117–136.] and T. sulaimanense sp. nov. These fossils are close to modern species of Terminalia, which occur in moist deciduous or semi-evergreen tropical forests. The palynological assemblage is composed of a mixture of pollen and spore types from different origins. There is a dominance of hygrophilous ferns, pines, Amaranthaceae–Chenopodiaceae–Caryophylaceae, but also the occurrence of Palmae, which are typical of tropical rainforests. This assemblage suggests that the depositional system is set in a context of nearby mountains with a minimum altitude of 2000 to 2500 m and characterized by differentiated forest belts above the tropical lowland vegetation of lower elevations. Wood, pollen and spores support the view of a fluvial environment surrounded by a tropical forested habitat. The separate stratigraphic position of the pollen assemblage above the fossil wood could explain its slightly different, more varied, palaeoenvironmental signal.     

Direct protein-protein interaction between PLCgamma1 and the bradykinin B2 receptor--importance of growth conditions

Recently, we have described a novel protein-protein interaction between the G-protein coupled bradykinin B2 receptor and tyrosine phosphatase SHP-2 via an immunoreceptor tyrosine-based inhibition motif (ITIM) sequence located in the C-terminal part of the B2 receptor and the Src homology (SH2) domains of SHP-2. Here we show that phospholipase C (PLC)gamma1, another SH2 domain containing protein, can also interact with this ITIM sequence. Using surface plasmon resonance analysis, we observed that PLCgamma1 interacted with a peptide containing the phosphorylated form of the bradykinin B2 receptor ITIM sequence. In CHO cells expressing the wild-type B2 receptor, bradykinin-induced transient recruitment and activation of PLCgamma1. Interestingly, this interaction was only observed in quiescent and not in proliferating cells. Mutation of the key ITIM residue abolished this interaction with and activation of PLCgamma1. Finally we also identified bradykinin-induced PLCgamma1 recruitment and activation in primary culture renal mesangial cells.     

Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor

MOTIVATION: Identifying protein enzymatic or pharmacological activities are important areas of research in biology and chemistry. Biological and chemical databases are increasingly being populated with linkages between protein sequences and chemical structures. There is now sufficient information to apply machine-learning techniques to predict interactions between chemicals and proteins at a genome scale. Current machine-learning techniques use as input either protein sequences and structures or chemical information. We propose here a method to infer protein-chemical interactions using heterogeneous input consisting of both protein sequence and chemical information. RESULTS: Our method relies on expressing proteins and chemicals with a common cheminformatics representation. We demonstrate our approach by predicting whether proteins can catalyze reactions not present in training sets. We also predict whether a given drug can bind a target, in the absence of prior binding information for that drug and target. Such predictions cannot be made with current machine-learning techniques requiring binding information for individual reactions or individual targets.     

The migratory behavior of avian embryonic cells does not require phosphorylation of the fibronectin-receptor complex

When locomotory embryonic cells become stationary, they acquire new substratum-adhesion properties. In particular, the distribution of fibronectin receptors shifts from diffuse and highly mobile on the cell membrane to immobilized in close association with fibronectin molecules and cytoskeletal elements in focal contacts. Receptor phosphorylation has been proposed as a possible regulator of the interaction between the receptor and its intracellular and extracellular ligands. In the present study, we have compared the phosphorylation state of the fibronectin receptor in motile neural crest and somitic cells, in stationary somitic cells, and in Rous-sarcoma virus transformed-chick embryo fibroblasts, using immunoprecipitation following metabolic labeling. While no receptor phosphorylation was detected in motile embryonic cells, the beta subunit of the receptor was phosphorylated in stationary cells. This subunit was also highly phosphorylated in Rous-sarcoma virus-transformed chicken cells. These results suggest that phosphorylation of the fibronectin receptor cannot account for its distribution in the cell membrane and for the nature of the interactions between this receptor and its ligands in embryonic cells.     

Cyclic AMP-Dependent Protein Kinase Decreases γ-Aminobutyric AcidA Receptor-Mediated 36Q1− Uptake by Brain Microsacs

The effect of cyclic AMP (cAMP)-dependent protein phosphorylation on gamma-aminobutyric acidA (GABAA) receptor function was examined using isolated brain membrane vesicles (microsacs). Muscimol-stimulated 36Cl- uptake was studied in mouse brain microsacs permeabilized to introduce the catalytic subunit of cAMP-dependent protein kinase (PKA). At both submaximal and maximally effective concentrations of muscimol, PKA inhibited muscimol-stimulated 36Cl- uptake by approximately 25%. In parallel experiments, PKA and [gamma-32P]ATP were introduced into the microsacs, and we attempted to immunoprecipitate the entire GABAA receptor complex, under nondenaturing conditions, using an anti-alpha 1-subunit antibody. Data from such experiments show that PKA increases the phosphorylation of several microsac proteins, including a 66-kDa polypeptide specifically immunoprecipitated with the GABAA receptor anti-alpha 1 subunit antibody. Phosphopeptide mapping of the 66-kDa polypeptide demonstrated a 14-kDa fragment similar to that obtained with the purified, PKA-phosphorylated GABAA receptor. These results provide evidence that the catalytic subunit of PKA inhibits the function of brain GABAA receptors and demonstrate that this functional change is concomitant with an increase in protein phosphorylation.     

A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance

The completion of the genome sequences of both rice and Magnaporthe oryzae has strengthened the position of rice blast disease as a model to study plant-pathogen interactions in monocotyledons. Genetic studies of blast resistance in rice were established in Japan as early as 1917. Despite such long-term study, examples of cultivars with durable resistance are rare, partly due to our limited knowledge of resistance mechanisms. A rising number of blast resistance genes and quantitative trait loci (QTL) have been genetically described, and some have been characterized during the last 20 years. Using the rice genome sequence, can we now go a step further toward a better understanding of the genetics of blast resistance by combining all these results? Is such knowledge appropriate and sufficient to improve breeding for durable resistance? A review of bibliographic references identified 85 blast resistance genes and approximately 350 QTL, which we mapped on the rice genome. These data provide a useful update on blast resistance genes as well as new insights to help formulate hypotheses about the molecular function of blast QTL, with special emphasis on QTL for partial resistance. All these data are available from the OrygenesDB database.     

Lysophosphatidic acid and renal fibrosis

The development of fibrosis involves a multitude of events and molecules. Until now the majority of these molecules were found to be proteins or peptides. But recent data show significant involvement of the phospholipid lysophosphatidic acid (LPA) in the development of pulmonary, liver and renal fibrosis. The latest data on the role of LPA and the G-protein-coupled LPA1 receptor in the development of renal fibrosis will be discussed. LPA1-receptor activation was found to be associated with increased vascular leakage and increased fibroblast recruitment in pulmonary fibrosis. Furthermore, in renal fibrosis LPA1-receptor activation stimulates macrophage recruitment and connective tissue growth factor expression. The observations make this receptor an interesting alternative and new therapeutic target in fibrotic diseases.     

Determining the roles of the three alcohol dehydrogenases (AdhA,AdhB and AdhE) in Thermoanaerobacter ethanolicus during ethanol formation

Journal of Industrial Microbiology & Biotechnology - Thermoanaerobacter ethanolicus is a promising candidate for biofuel production due to the broad range of substrates it can utilize and its...     

Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis

We analyzed urinary polypeptides from individuals with neonatal ureteropelvic junction (UPJ) obstruction to predict which individuals with this condition will evolve toward obstruction that needs surgical correction. We identified polypeptides that enabled diagnosis of the severity of obstruction and validated these biomarkers in urine collected in a prospective blinded study. Using these noninvasive biomarkers, we were able to predict, several months in advance and with 94% precision, the clinical evolution of neonates with UPJ obstruction.