Search results for "Macro"

Risk tables for discrimination tests

1993

Abstract Duo-trio and triangle test are often used in the food industry for the purpose of declaring two products non-distinguishable. In that situation, it is much more important to control the power of the test rather than the type 1 error risk. This paper makes available by e-mail a SAS ® macro, called BINRISKS, for computing type 1 and type 2 risks for any one-tailed binomial test and for any level of the percentage above chance to be detected. Using this macro, two sets of tables have been compiled. The first table includes for any total number of responses below 50, for any number of correct responses and for three levels of the percentage above chance to be detected, the correspondin…

Modeling of Particle Number Fluctuations in Entire Cells

2012

In a recent study we developed a method to model protein diffusion in cells [1], where special attention was given to generating from image data of the measured cell a realistic digital model cell in which protein dynamics were simulated. The method was shown to be well suited for modeling non-equilibrium situations that arise, e.g., in photobleaching experiments, and to be capable of producing more detailed information about protein motion than traditional modeling.Another experimental way to assess protein dynamics is to study fluctuations in the local protein number, as it is done, e.g., in fluorescence correlation spectroscopy (FCS), or in similar measurements that apply single-plane il…

Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits

2020

In this chapter, we describe how to use DarkHorse2.0 to search for xenologs in the genome of the cyanobacterium Synechococcus elongatus PCC 7942. DarkHorse is an implicit phylogenetic method that uses BLAST searches to identify proteins having close homologs of unexpected taxonomic affiliation. Once a set of putative xenologs are identified, Phylomizer is used to reconstruct phylogenetic trees. Phylomizer reproduces all the necessary steps to perform a basic phylogenetic analysis. The combined use of DarkHorse and Phylomizer allows the identification of genes incorporated into a given genome by HGT.

Furcocercous cercariae (Trematoda) from freshwater snails in Central Finland

2007

AbstractA total of eight species of furcocercous cercariae of four families (Strigeidae, Diplostomidae, Schistosomatidae and Sanguinicolidae), were found in 2005 in Lake Konnevesi in Central Finland in four snail species (Valvata macrostoma, Lymnaea stagnalis, Bathyomphalus contortus and Planorbarius corneus). Australapatemon burti (Miller, 1923), Australapatemon sp., Cotylurus brevis Dubois et Rausch, 1950, Cercaria spinulosa Ginetsinskaya, 1959 and Sanguinicola sp. are new species records for Finland. Ichthyocotylurus variegatus (Creplin, 1825) and Bilharziella polonica (Kowalewski, 1895) were first recorded as cercariae in Finland. The most common cercariae were A. burti (prevalence 13.3…

2015

Purpose: The aim of this study was to investigate the interaction and co-localization of novel interacting proteins with the Leber congenital amaurosis (LCA) associated protein aryl hydrocarbon receptor interacting protein-like 1 (AIPL1). Methods: The CytoTrapXR yeast two-hybrid system was used to screen a bovine retinal cDNA library. A novel interaction between AIPL1 and members of the family of EB proteins was confirmed by directed yeast two-hybrid analysis and co-immunoprecipitation assays. The localization of AIPL1 and the EB proteins in cultured cells and in retinal cryosections was examined by immunofluorescence microscopy and cryo-immunogold electron microscopy. Results: Yeast two-hy…

Detecting Protein Aggregation on Cells Surface: Concanavalin A Oligomers Formation

2009

A number of neurodegenerative diseases involve protein aggregation and amyloid formation. Recently evidence has emerged indicating small-transient prefibrillar oligomers as the primary pathogenic agents. Noteworthy, strict analogies exist between the behaviour of cells in culture treated with misfolded non-pathogenic proteins and in pathologic conditions, this instance together with the observation that the oligomers and fibrils are characterised by common structural features suggest that common mechanisms for cytotoxicity could exists and have to be perused in common interactions involved in aggregation.We here report an experimental study on ConcanavalinA (ConA) aggregation and its effect…

2013

Controlling the position of the nucleus is vital for a number of cellular processes from yeast to humans. In Drosophila nurse cells, nuclear positioning is crucial during dumping, when nurse cells contract and expel their contents into the oocyte. We provide evidence that in nurse cells, continuous filopodia-like actin cables, growing from the plasma membrane and extending to the nucleus, achieve nuclear positioning. These actin cables move nuclei away from ring canals. When nurse cells contract, actin cables associate laterally with the nuclei, in some cases inducing nuclear turning so that actin cables become partially wound around the nuclei. Our data suggest that a perinuclear actin mes…

Echovirus 1 infection depends on biogenesis of novel multivesicular bodies

2011

Summary Non-enveloped picornavirus echovirus 1 (EV1) clusters its receptor α2β1 integrin and causes their internalization and accumulation in α2β1 integrin enriched multivesicular bodies (α2-MVBs). Our results here show that these α2-MVBs are distinct from acidic late endosomes/lysosomes by several criteria: (i) live intra-endosomal pH measurements show that α2-MVBs are not acidic, (ii) they are not positive for the late endosomal marker LBPA or Dil-LDL internalized to lysosomes, and (iii) simultaneous stimulation of epidermal growth factor receptor (EGFR) and α2β1 integrin clustering leads to their accumulation in separate endosomes. EGFR showed downregulation between 15 min and 2 h, where…

Selenomethionine labeling of large biological macromolecular complexes: probing the structure of marine bacterial virus PM2.

2008

There is a need for improved tools for labeling protein species within large macromolecular assemblies. Here we describe a method for the efficient selenomethionine labeling of the membrane-containing bacterial virus PM2 for structural studies. By examining potential host cells a strain was found which was auxotrophic for methionine, and by performing a multiparameter search of conditions it was possible to derive a robust protocol which simultaneously minimized the toxic effects of the selenomethionine, so that a reasonable virus yield was maintained, whilst still achieving essentially complete labeling. This has allowed us to fingerprint the protein constituents of the virus in a relative…

2020

ObjectiveThe HBV HBx regulatory protein is required for transcription from the covalently closed circular DNA (cccDNA) minichromosome and affects the epigenetic control of both viral and host cellular chromatin.DesignWe explored, in relevant cellular models of HBV replication, the functional consequences of HBx interaction with DLEU2, a long non-coding RNA (lncRNA) expressed in the liver and increased in human hepatocellular carcinoma (HCC), in the regulation of host target genes and the HBV cccDNA.ResultsWe show that HBx binds the promoter region, enhances the transcription and induces the accumulation of DLEU2 in infected hepatocytes. We found that nuclear DLEU2 directly binds HBx and the…