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Latest Publications

Arabidopsis WRKY50 and TGA Transcription Factors Synergistically Activate Expression of PR1

front_plant_sci_logo.jpgRana M. F. Hussain, Arsheed H. Sheikh, Imran Haider, Mussa Quareshy and Huub J. M. Linthorst

Arabidopsis PR1 is a salicylic acid (SA) inducible marker gene for systemic acquired resistance (SAR). However, the regulation of PR1 in plants is poorly understood. In this study, we showed that AtWRKY50 transcription factor binds to two promoter elements of PR1 via its DNA binding domain. Using electrophoretic mobility shift assays (EMSA) it was established that AtWRKY50 and TGA2 or TGA5 simultaneously bind to the PR1 promoter. Taken together, these results support a role of AtWRKY50 in SA-induced expression of PR1.

Frontiers in Plant Science. June 2018

Fri 20 July 2018, 12:28 | Tags: Plant and Crop Science

Assays to monitor aggrephagy in Drosophila brain

methods_in_mol_biol.jpgJacomin Anne-Claire and Ioannis P. Nezis

Accumulation of ubiquitinated protein aggregates is a hallmark of most ageing-related neurodegenerative disorders. Autophagy has been found to be involved in the selective clearance of these protein aggregates, and this process is called aggrephagy. Here we provide two protocols for the investigation of protein aggregation and their removal by autophagy using western blotting and immunofluorescence techniques in Drosophila brain. Investigating the role of aggrephagy at the cellular and organismal level is important for the development of therapeutic interventions against ageing-related diseases.

Methods In Molecular Biology. Jun3 2018

Wed 18 July 2018, 07:43 | Tags: Biomedical Science

Bacterial expression, purification and biophysical characterization of the smallest plant reticulon isoform, RTNLB13

Protein E&P jun18Michael Chow, Meropi Sklepari, Lorenzo Frigerio, Ann M. Dixon  

Reticulons are a large family of integral membrane proteins that are ubiquitous in eukaryotes and play a key role in functional remodelling of the endoplasmic reticulum membrane. The reticulon family is especially large in plants, with the Arabidopsis thaliana genome containing twenty-one isoforms. Reticulons vary in length but all contain a conserved C-terminal reticulon homology domain (RHD) that associates with membranes. An understanding of the structure and membrane interactions of RHDs is key to unlocking their mechanism of function, however no three-dimensional structure has been solved.

We report here the first bacterial overexpression, purification, and biophysical investigation of a reticulon protein from plants, the RTNLB13 protein from A. thaliana.

Protein Expression & Purification. June 2018

Mon 16 July 2018, 08:11

Touching proteins with virtual bare hands : visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware

Comp aided Mol Design jun18Ratamero Erick Martins, Bellini Dom, Dowson Christopher G and Roemer Rudolf A  

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). In this work, we present a freely available software pipeline for visualising protein structures through VR.

Journal of Computer-aided Molecular Design June 2018

Thu 05 July 2018, 07:58 | Tags: Biomedical Science

The use of gas phase detection and monitoring of potato soft rot infection in store

Postharvest B&T jun18Rutolo Massimo F, Clarkson John P, Harper Glyn and Covington James A

Soft rot caused mainly by the bacterium Pectobacterium carotovorum is a major cause of potato post-harvest storage losses. This work reports on pre-symptomatic detection and monitoring of soft rot under laboratory and commercial research store conditions by means of an array of gas sensors

Results showed that a number of gas sensors could detect and monitor early soft rot development with considerable accuracy.

Postharvest Biology and Technology. June 2018

Mon 02 July 2018, 08:17 | Tags: Plant and Crop Science

MetQy – an R package to query metabolic functions of genes and genomes

bioinformatics.jpgAndrea Martinez-Vernon, Frederick Farrell, and Orkun S. Soyer

With the rapid accumulation of sequencing data from genomic and metagenomic studies, there is an acute need for better tools that facilitate their analyses against biological functions. To this end, we developed MetQy, an open–source R package designed for query–based analysis of functional units in [meta]genomes and/or sets of genes using the The Kyoto Encyclopedia of Genes and Genomes (KEGG). Furthermore, MetQy contains visualisation and analysis tools and facilitates KEGG’s flat file manipulation. Thus, MetQy enables better understanding of metabolic capabilities of known genomes or user–specified [meta]genomes by using the available information and can help guide studies in microbial ecology, metabolic engineering and synthetic biology.

Bioinformatics. June 2018

Fri 29 June 2018, 07:57 | Tags: Biotechnology

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