Weeding the Gems - Page 63 of 67 - the GARNet community blog

High-throughput, cheap, reliable DNA extraction method

Categories: methods, Summary for non-specialists

Comments: No Comments

Published on: September 11, 2012

Highlighted article: Zhanguo Xin and Junping Chen (2012) A high throughput DNA extraction method with high yield and quality. Plant Methods 2012, 8:26 doi:10.1186/1746-4811-8-26

Judging by the fact that it was accessed 1400 times in less than a month, the DNA extraction method described by Xin and Chen in last month’s Plant Methods must be worth a look.

Having had a look, I can tell you it seems to be an invaluable method for cheap, reliable high-throughput DNA extraction. It works on seeds and leaves from a number of plants, and according to the abstract, one person can manage 192 extractions in a working day. Using the price estimation in the paper, this would cost about £13 in total for consumables.

The protocol is clear and easy to follow, setting out exactly what reagents, consumables and equipment you will need so there will be no panicked begging of microtitr plates from a friend halfway through the extraction. As well as standard lab equipment which should be accessible to most researchers, you will need MagAttract Suspension G. MagAttract provides the simple, efficient clean up step, while the rest of the protocol is based on a traditional CTAB extraction method.

Female Plant Scientists on ‘Women in Science’

by Charis Cook

Categories: guest blogger, Women in Science

Tags: Women in Science

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Published on: September 6, 2012

A snapshot of the Smithsonian Institute’s Women In Science archives

This post on ‘Women in Science’ is ghost written by several women working in science, either in research or in science policy. I asked them to give me their thoughts, and as some of them wanted to be anonymous, I collected the common ideas and put them into this blog post. Thank you to everyone who contributed.

Why are there so few women at the highest levels of academia, for example as Heads of School, Directors of Institutes, or Fellows of the Royal Society?

As in many other pieces on women in science, a common response to this question was that an academic career is not family friendly. Day-to-day working life is difficult to manage with a family as a very successful academic career involves unsociable hours and a huge workload. In fact, a study out last week showed that many scientists work all night and through weekends. For many reasons, women are more likely than men to see their families as a more important focus for their time and energy than their careers.

Two of the women I asked pointed out very practical problems of combining family life and research. Firstly, if a woman takes a career break for her children, when she returns to work she may be excluded from grants and fellowships for early career scientists, which set a maximum number of years from PhD graduation to be eligible for the funding. Secondly, a woman who takes ordinary maternity leave and returns to work straight away will probably find maintaining the same level of output as before her pregnancy difficult. Strength of publication record is important for senior scientific positions, so a drop and/or gap in publications caused by maternity leave and subsequent out-of-hours time devoted to a baby may delay or prevent her making applications for more senior positions.

A second theme, again commonly discussed and relevant whether a woman has family commitments or not, is that male dominance at the highest levels of academia is self-perpetuating. Some women, consciously or otherwise, are put off staying in research and aiming for the top positions by the very fact that there are few women at those high levels. Equally, women may not be recommended or headhunted for top positions, not maliciously but automatically, simply because they do not fit the norm.

As in many professions, in academia the lack of women in senior positions is partially due to more men than women forcing their way to the top. The scientists who contributed to this piece thought that women are less likely than men to self-promote, to ask for a promotion, or to apply for the top job. This is the feeling of successful women in other professions too. One of the women I asked felt that women are judged more harshly than men by men and women alike, being seen as aggressive or manipulative if they use the same methods as men to get to the top.

Do you think the programs and awards that encourage ‘women in science’ in some way are necessary, and doing a good job? (more…)

Funding round-up: Deadlines in Autumn 2012

by Charis Cook

Categories: funding, UKPSF

Tags: BBSRC, funding, outreach, UKPSF

Comments: 1 Comment

Published on: September 4, 2012

A number of grant deadlines are coming up this autumn, from big fellowship grants to funding for development of methodology or for outreach. Many of them are bi-annual, so if you are interested you may want to prepare for a Spring 2013 application instead.

For more funding opportunities, other news and an events calendar, go to the UK Plant Sci website.

Nitrogen Ideas lab: deadline 7 September. You only have 3 days to apply for this but the application form is very short, and $12M funding from the BBSRC and NSF is available for projects that come out of the ideas lab, which will be held in Crewe (UK) from 3-7 December.

Fellowships for established researchers

scheme: Deadline 5 October. This is funded by the Royal Society, Engineering and Physical Sciences Research Council, Natural Environment Research Council, Rolls-Royce plc and Astra Zeneca as well as the BBSRC. It is for the transfer of knowledge between industry and academia. Fellowships can run for 2 years full time, or 4 years part time, during which the fellow will establish personal and corporate links between the 2 sectors of work.

The Leverhulme Trust Visiting Professorships: Deadline 11 October. This programme may last three to ten months and funding is dependent on requirement. This is to enable overseas academics with excellent research and teaching skills to spend time at a UK University for the enrichment of the host university, and for the visiting academic.

Leverhulme Trust Research Fellowships: Deadline 8 November. Up to £45 000 for a fellowship of between 3 and 24 months is available for experienced researchers of any discipline. Researchers who have been prevented from doing original research by routine duties should apply for this fellowship.

BBSRC Partnering Awards: Deadline 14 November. Funding to set up partnership links between the UK and one of Japan, China, Indis, the USA, or Brazil. Both single partnerships and consortia are eligible, and partnerships may last up to 4 years.

Doctoral programme

BBSRC BRIC doctoral programme: Deadline 11 October. This four year scholarship is to support new PhD students with interest in the bioprocessing industry. Students will receive £5000 per annum for training and development.

Grants for researchers of any level

Biochemical Society Eric Reid Fund for Methodology: Deadline 1 November. Members of the Biochemical Society may apply for up to £1800 for developing or carrying out a new method, testing the feasibility of a new idea, and other methodology-led projects.

BBSRC International Workshops: Deadline 14 November. Current BBSRC grant holders or researchers at BBSRC funded institutions can apply for approximately £10k of funding for a workshop to involve another country.

Technology Strategy Board Synthetic Biology competition: Briefing event 15 October; Deadline for registration 14 November; deadline for submission 21 November. Up to £6.5M will be invested. Eligible projects will demonstrate the feasibility of a new synthetic biology approach in the creation of novel or improved products or processes. Projects must be collaborative and business-led. The BBSRC is involved in this initiative, and more information can be found in this BBSRC leaflet.

Agricultural Economics Society Prize Essay Competition: Deadline 30 November. £1000 will be awarded to the best essay on any aspect of agricultural economics. Entrants must be within six years of graduation, or under 30 for non-graduates.

Royal Society Brian Mercer Feasibility Award: Rolling bias. Initial support of up to £30 000 is provided to the winner of the grant, to test the technical and economic feasibility of commercializing an aspect of their scientific research.

Outreach grant

British Ecological Society Outreach grants: Deadline 17 September. Up to £2000 is available to support projects that promote ecology to the public. If mid-September is too close, the next deadline is in March 2013.

NGS and the tomato genome

by Charis Cook

Categories: methods, teaching resources, Workshops

Tags: GARNet workshop

Comments: No Comments

Published on: August 31, 2012

In May, a consortium of researchers from 14 nations finally finished sequencing and annotating the tomato genome. They started in 2003 without the benefit of next generation sequencing (NGS), but in 2008 when there was no end in sight, the consortium took up three methods of NGS: Illumina, SOLiD, and 454. Four years later, the project was complete.

Annotation of the tomato genome is still ongoing, but much of the annotated genome can be found at the Sol Genomics Network.

What else can next generation sequencing do? The next GARNet workshop, Tools and Technologies to Advance Plant Research, is a day dedicated to exploring the opportunites presented by NGS. Speakers will speak on a range of ways they have used NGS, including chromatin mapping, RNA sequencing, and generation of new Arabidopsis mutant lines.

Teaching Resources

Tomato: Decoded video from Science 360

Solanaceae school activities from the Sol Genomics network

Teaching resources from the University of Leicester including two ‘sequencing’ activities for 14-16s

Method: New and improved multiplex PCR

by Charis Cook

Categories: methods, Summary for non-specialists

Tags: methods, PCR, Plant Methods, summary for non-specialists

Comments: No Comments

Published on: August 30, 2012

Highlighted article: Daxing Wen and Chuqing Zhang (2012) Universal Multiplex PCR: a novel method of simultaneous amplification of multiple DNA fragments. Plant Methods 8:32 (Online preview) doi: 10.1186/1746-4811-8-32

Background

Multiplex PCR allows amplification of multiple targets in a single PCR experiment. It is possible to amplify several sections of a single template, or to amplify different templates using a number of primer sets. If there are multiple primers in a reaction, it can be difficult optimise the PCR reaction to maximise the efficiency of every primer, and it is likely that some cross-hybridisation and mis-priming will occur.

Figure 3B from Wen and Zhange (2012). A comparison of multiplex PCR (Lanes 1-4) and universal multiplex PCR (lanes 5-8), using the same primers with universal adaptors. The band intensity from traditional PCR is very variable, but it is consistently strong when the universal adaptors are used.

Image credit: BioMed Central

The Method

Wen and Zhang from Shandong Agricultural University have devised a way around the inconveniences of multiplex PCR to develop a universal multiplex PCR method. ‘Universal adaptors’ are linked to specific primers, making the annealing temperature of the adaptor-primer structures 70°C. (more…)

Links for Women in Science (and family men too)

by Charis Cook

Categories: funding, resource, Women in Science

Tags: Athena Charter, funding, grants, Women in Science

Comments: 1 Comment

Published on: August 28, 2012

Some institutions which support women in science and family-friendly working practices

At the University where I did my PhD, male PIs far outnumbered female PIs in the School of Biological Sciences. The Head of School and all the Heads of Departments were male. The faculty lists of other universities show a similar story – and this is in life sciences, the science subject most dominated by girls at A-level. Gender balance among fellows of Royal Society is even more skewed, perhaps reflecting the wider scope of the Society, at 5% female.

These unbalanced ratios are not seen at school, university or even at post-doc level, so there is a time early in academic careers when more women than men leave academic research. The UK Resource Centre for Women in SET and the Royal Society of Chemistry commissioned a report to find out why. The report concluded that the lack of women in many areas of academia can seem isolating and off-putting; and an academic career demands a working life dictated by experiments and deadlines, with no room for part-time work or career breaks. The report also notes that both men and women are put off by the difficulties of life in academia, but more men than women are happy to make the sacrifices.

There are organisations and individuals calling for change, and providing support for female researchers at all stages of their careers. I have collected them below – feel free to get in touch if you know of any others.

Please note that many of these funds are available to men who require flexible working times and support for dependants. Most of them are not open now, but call for proposals annually or bi-annually. (more…)

Coming up soon

by Charis Cook

Categories: resource, UKPSF, Workshops

Tags: conferences, events, resources, UKPSF, workshops

Comments: No Comments

Published on: August 27, 2012

These are just a few of the events listed on the UKPSF Events Calender.

Register now for the GARNet New Technologies to Advance Plant Research workshop: http://www2.warwick.ac.uk/fac/sci/lifesci/news/newtech

Warwick Crop Centre are holding an Open Afternoon on 19^th September. Visitors will be able to view the facilities, including field and glasshouse trials, and learn about the research and training opportunities.

Also on 19^th September, EBI are holding a training course for PhD students and post-docs to train them to use the new PhytoPath resource.

The BBSRC funded Wheat Improvement Strategic Programme are running a course on wheat genetics at the John Innes Centre on 19-22 November 2012. There are only 10 places available but it will be a good introduction to cereals research and crop breeding for undergraduates, postgraduates or junior breeders. Apply here until 1 October.

There will be an international meeting on Imaging in Cell Biology in Windsor Great Park on 14-17 October. There are free places for graduate students and post-docs.

The International Symposium on Plant Photobiology will be held in Edinburgh in June 2013. To mark the launch of the event, a special launch price is available until 2 September – book early to get the good rate!

And something else…

Help GARNet assess the use of new Arabidopsis lines by doing a very short survey on MAGIC lines.

New open access resource for plant pest and disease management, detailed on PlantSci.

PLoS ONE have put together an impressive collection of all their synthetic biology papers.

NGS and root endophyte assembly cues

by Charis Cook

Categories: Summary for non-specialists, teaching resources, Workshops

Tags: endophyte, microbiology, plant-microbe interactions, teaching resources

Comments: No Comments

Published on: August 24, 2012

Cologne and Sanssouci, close to Golm: what effect do the soils at these two historic locations have on the local plant roots?

Highlighted article: Davide Bulgarelli, Matthias Rott, Klaus Schlaeppi, Emiel Ver Loren van Themaat, Nahal Ahmadinejad, Federica Assenza, Philipp Rauf, Bruno Huettel, Richard Reinhardt, Elmon Schmelzer, Joerg Peplies, Frank Oliver Gloeckner, Rudolf Amann, Thilo Eickhorst, and Paul Schulze-Lefert (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota Nature 488:91

Background

Although plant-microbe and plant-soil dynamics are widely studied areas of plant science, up until now there has been no broad picture of plant endophytic systems: which phyla are common endophytes; how the populations form; and what affects them. Endophytes colonise plant tissues, where unlike pathogens they do not cause harm or an immune response, and unlike endosymbionts they do not live inside plant cells or have an obvious mutually beneficial relationship with the plant. A recent review on bacterial endophytes is this one by Reinhold-Hurek and Hurek (2011).

Here, Bulgarelli et al. use an Arabidopsis system to shed light on the specifics of below ground plant-bacteria interactions, and set out a methodology for future investigations into other plants and soil types. This study and another article in the same issue of Nature by Lundberg et al. use next generation sequencing (NGS) to show similar cues for assembly of root endophytes. (more…)

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