LABORATORY OF PLANT PHYSIOLOGY AND BIOPHYSICS

  • Cyanobacteria
    Cyanobacteria, also known as blue-green algae,
    obtain their energy through photosynthesis,
    making use of much the same pathways as plants.
    It is thought that modern plants arose through
    a symbiotic association with cyanobacteria,
    which have since evolved to form the chloroplasts
    of higher plants thus providing energy to the
    host. For these reasons, cyanobacteria have long
    been used as a model with which to study the
    process of photosynthesis.
  • Begonia
    Begonias represent one of the largest and most
    diverse genera among the angiosperms. Several
    Begonia species exhibit complex stomatal
    patterning and variable stomatal clustering,
    which may be important for their physiological
    adaptation to extreme wet environments such as
    around waterfalls, and is a focus of research
    in the Laboratory.
  • Water Scarcity
    Water scarcity and changes in the global
    environment are the most serious threats to
    global food security. Many parts of the USA,
    Australia and Asia as well as the mediterranean
    countries have seen substantial increases in
    water deficits over the past decade. Even in the
    UK, the demand for irrigation water has risen
    almost 10-fold in the past 20 years. Recurrence
    of the Dust Bowl phenomenon that devastated the
    American wheat belt is a real concern.
  • Oilseed rape
    Brassica napus is a major focus
    for translational research building on work
    from Arabidopsis. The leaves and stems are
    commonly eaten in Southeast Asia and are often
    found in asian groceries sold as tender greens.
    Over 60% of its cultivation in the EU currently
    goes into biodiesel production. Rapeseed demands
    substantial water and N fertilization, although
    newer varieties grown in Canada have been
    reported to be more drought-tolerant.
  • Broad Bean
    Vicia faba is familiar to us as the broad bean
    or butterbean. It is a robust, upright annual
    that grows well in cooler environments. It’s
    rounded, segmented leaves are easy to dissect
    by hand and have long been a favourite for
    research on stomatal guard cells and their
    control of gas exchange in plants. Data that
    comes from studies of Vicia remains the gold
    standard in the field of membrane transport
    and its control.
  • Arabidopsis Flowers
    The Arabidopsis genome was the first plant genome
    to be fully sequenced. This knowledge, together
    with a large body of mutational data, tools for
    genetic manipulation and access to closerelatives
    with varied physiological traits, greatly speeds
    fundamental research in the plant sciences.
  • Jungle Night
    Amorphophallus Paeoniifolius is one of a number
    of giant arums found in tropical central
    Americas. Its close relative, Amorphophallus
    titanium, produces the largest flower in the
    world, which can grow to over 2 meters in
    height. Like many giant arums, A. paeoniifolius
    grows from an elongated tuber. The leaf
    structure, stomatal organisation and venation,
    visible here, are well-adapted for highly humid
    environments.

Site-directed mutagenesis - SDM-Assist

SDM-Assist is a stand-alone application which allows SDM primer design in just 3 clicks without the need for an internet connection and will work on almost any Mac/Windows machine.



Key Features Include:


» Allows the user to generate and choose primers for SDM that contain a unique restriction site identity allowing for highly efficient identification of 'mutated clones' by a simple restriction digest.

» Suggested primer pairs are scored based on factors such as Tm, GC content, 5 prime and 3 prime-stability and secondary structure.

» Ability to custom choose and feed restriction enzymes to SDM-Assist for inserting silent restriction sites in the primers.

» All suggested primer sequences along with detailed information on them can be exported into an excel or text file.

» A useful reference tool in the display window of the programme, which logs the sequence of events and provides brief tips as you design the primer.

 

***DOWNLOAD SDM-ASSIST HERE (please read the INSTALLATIONS INSTRUCTIONS)***

-You can also download a useful HELPSHEET or view the tutorial video below-

For enquiries and further information about SDM-Assist, please e-mail christopher.grefen@glasgow.ac.uk







Watch the video tutorial below.





Key Notes



Installation Instructions

Installation Instructions

1. Installing the Adobe AIR package: If Adobe AIR is not installed on your machine you will be asked to install it first. Clicking the image will take care of AIR installation.

2. Installing SDM-Assist: After step 1 (or if AIR is already installed), SDM-Assist will be installed. You will be prompted to "Open" or "Save" the file. Select "Open" to proceed with installation.

3. In the options screen, you will be asked if you want to create a desktop icon. Please check this box so that the application icon is available on the desktop.

4. Uninstalling SDM-Assist: To uninstall from Windows, Go to Control Panel>Uninstall Program and select SDM-Assist. Click 'Uninstall'/'Remove' to remove the application. Note: If you get an Error #2032, try clearing the History cache and cookies on the browser. Alternately try using another browser (application not new window) to install the SDM-Assist.

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Restriction Enzyme Lists

Restriction Enzyme Lists

SDM-Assist allows you to customize the list of restriction enzymes used by it. To use a compatible file (tab separated RE Name and RE Sequence, one per line), simply drag n drop it onto the icon.

 

Download the list of Restriction Enzymes used by default

 



 

Download the complete list of supported Restriction Enzymes

 

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Terms of Use

Terms of Use

SDM-Assist is available free of charge for non-commercial use. For non-academic use, contact authors for permission. When publishing data generated resulting from use of the software, please cite:

Karnik A, Karnik R and Grefen C: SDM-assist software to design site-directed mutagenesis primers introducing "silent" restriction sites. BMC Bioinformatics 2013, 14:105; DOI: 10.1186/1471-2105-14-105

For a detailed description please refer to our paper : (Journal Page)

Software license: [CC BY-NC-ND]

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