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The Week in Botany 29

January 8, 2018

They say January is the time for a fresh start. For me that's meant an emergency trip due to due flu for my breathing. So this week I'm catching up with what's happened as I compile the email. It's also meant I've not had chance to mention the deadline for the AoB PLANTS editor position, We have details on the post here, and the deadline is January 14. As always, for the stories below, we're using Twitter and followers of the @botanyone account to identify the big stories.

From Botany One

Just the four stories this week, due to illness.

Sex-specific morphology and physiology in Ceratodon purpureus
Separate sexes and biased sex ratios are common in bryophytes, yet little is known about how fine-scale, sex-specific morphological traits are correlated with physiology and population sex-ratios. Slate et al.analysed cellular, leaf, and canopy traits and photochemical measurements in the dioecious moss Ceratodon purpureus.

Good news for plant scientists who feel the need for speed
How fast does wheat need to be? You might look for taste and texture in a loaf, but why would anyone care about speed?

Scientists call for action to tackle a tree species invading Jamaica’s national parks
An Australian escapee from a botanical garden, now accounts for more than 10% of tree stems in a Jamaican National Park

Diving into the neglected world of seaweeds
The second edition of Seaweeds of Britain and Ireland by Francis Bunker et al. is an important addition to the recorded natural history of the coast and near-shore seas of the British Isles.

Call for Papers: Special issue on the Ecology and Evolution of Plant Reproduction

Botanists have long been fascinated by the extraordinary diversity in flowering plant reproductive patterns and have sought to understand theecological processes and genetic mechanisms influencing plant mating. Over the last five years, research progress in this discipline has rapidly accelerated. Important new insights in this field often combine elegant theoretical models with innovative field and laboratory experiments. Annals of Botany will release a Special Issue on the Ecology and Evolution of Plant Reproduction in January 2019, and it will highlight papers from 3 symposia at the XIX International Botanical Congress in Shenzhen, China. See the full call for papers for more information.

News and Views

Our plant health policy
There has been an increase in the rate at which harmful plant pests and diseases have become established in the UK. The RHS is making its policy public.
Royal Horticultural Society

Introducing #herbologyhunt
A twinge of envy as #WildflowerHour introduces its new scheme to get children hunting for herbs. A great idea and exactly the sort of thing we can't do at Botany One. If there are other locations running similar schemes, I'd love to know about them.

Molecular ecology, the flowchart
Jeremy Yoder returns to Rasmus Nielsen’s 2005 review of tests for recent natural selection in genetic data. Then he tried to cram everything molecular ecologists do into a single flowchart.
The Molecular Ecologist

The Extraordinary Catasetum Orchids
Orchids, in general, have perfect flowers in that they contain both male and female organs. However, in a family this large, exceptions to the rules are always around the corner. Take, for instance, orchids in the genus Catasetum. With something like 166 described species, this genus is rather unique in that individual plants produce either male or female flowers. What's more, the floral morphology of the individual sexes are so distinctly different from one another that some were originally described as distinct species. 
In Defense of Plants

From Hooch To Haute Cuisine: A Nearly Extinct Bootlegger's Corn Gets A Second Shot
For nearly a century, Jimmy Red corn was used by bootleggers to make moonshine whiskey. The variety nearly went extinct in the early 2000s, but two remaining ears of corn were used to revive it. Now, the heirloom corn is thriving in the South, and being used widely by chefs and distillers.
NPR: The Salt

Mark Lynas – Speech to the Oxford Farming Conference 2018
Five years ago, almost to this very day, I stood before you and offered an apology for my earlier anti-GMO activism. Today I want to do something different.
Mark Lynas / OFC

The latest cutting-edge technology changing our landscapes? Trees
The UK has been slow to embrace agroforestry, fearing trees compete for valuable space and water. In fact they can increase crop diversity as well as profits, as two pioneering Cambridgeshire farmers have found
The Guardian

The photosynthesis fix
As world food needs rise, so does the need for faster, more efficient plant growth. Bypassing an error-prone enzyme is one way to do it.
Knowable Magazine

Fighting Climate Change, One Laundry Load at a Time
Experts in the study of fungi are playing a bigger role in improving laundry detergents and, by extension, leading efforts to cut energy use.
NY Times

Camille Parmesan: ‘Trump’s extremism on climate change has brought people together’
The climate scientist on leaving the US to work in France – with funding from President Macron – and why she believes Trump’s decision to pull out of the Paris agreement will backfire on him. (Note: her co-authored review: Plants and climate change: complexities and surprises is available with free access)
The Guardian

Call for papers: Developing sustainable bioenergy crops for future climates

Rapid progress has been made over the last five years with respect to emerging new genomic technologies for crop improvement and this Annals of Botany Special Issue will be devoted to highlighting the latest findings and considering the potential of these technologies for the future deployment of bioenergy crops in the face of climate change. At the same time, cutting-edge research that provides insights into the complex plant traits underpinning drought tolerance and response to other abiotic and biotic stresses is required for these relatively new crops. Knowledge in this area will be brought together in this Special Issue, and there will be a focus on recent advances in high throughput phenotyping to unravel these complex responses. See the full call for papers for more information.

Scientific Papers

Semantic Network Analysis Reveals Opposing Online Representations of the Search Term “GMO”
Semantic network analysis is performed to characterize the presentation of the term “GMO (genetically modified organism),” a proxy for food developed from GE crops, on the web. Texts from three sources are analyzed: U.S. federal websites, top pages from a Google search, and online news titles. We found that the framing and sentiment (positive, neutral, or negative attitudes) of “GMO” varies across these sources.
Global Challenges

A Comprehensive Tool Set for Inducible, Cell Type-Specific Gene Expression in Arabidopsis
We generated a resource for inducible cell-type specific trans-activation based on the well-established combination of the chimeric GR-LhG4 transcription factor and the synthetic pOp promoter. Harnessing the flexibility of the GreenGate cloning system, we produced a comprehensive set of GR-LhG4 driver lines targeting most tissues in the Arabidopsis shoot and root with a strong focus on the indeterminate meristems. We show that, when combined with effectors under control of the pOp promoter, tight temporal and spatial control of gene expression is achieved.

Detection of the plant parasite Cuscuta reflexa by a tomato cell surface receptor
In a process analogous to defenses mounted against microbial infection, the host plant perceives a small-peptide signal from the parasitic plant and initiates defense responses. The candidate receptor isolated from the tomato plant provided partial protection when transferred to two other susceptible plant species.

Refined assessment and perspectives on the cumulative risk resulting from the dietary exposure to pesticide residues in the Danish population
The present study adds support to the evidence showing that adverse health effects of chronic pesticide residue exposure in the Danish population are very unlikely. The HI for pesticides for a Danish adult was on level with that of alcohol for a person consuming the equivalent of 1 glass of wine every seventh year.
Food and Chemical Toxicology

Phloem function and development — biophysics meets genetics
Evolution of the vascular tissues allowed plants to efficiently settle land, occupy new ecological niches, and thereby crucially shape earth's biosphere. Of the two conducting cell types in the plant vasculature, the tubular network of phloem sieve elements transports phloem sap from source to sink organs. Recent years have witnessed the identification of ever more regulators of sieve element differentiation, as well as a more detailed understanding of phloem physiology and function. From molecular regulators of the commitment to sieve element fate, to enzymatic executors of the differentiation process, the toolbox to investigate sieve element formation has been greatly enlarged. To connect the various players in different genetic layers, and thus to ultimately attain a comprehensive description and understanding of sieve element development at the molecular level, appears to be within reach.
Current Opinion in Plant Biology

Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina
Intermediate outcrossing rates are theoretically predicted to maintain effective selection against harmful alleles, but few studies have empirically tested this prediction with the use of genomic data. We used whole-genome resequencing data from alpine rock-cress to study how genetic variation and purifying selection vary with mating system. We find that populations with intermediate outcrossing rates have similar levels of genetic diversity as outcrossing populations, and that purifying selection against harmful alleles is efficient in mixed-mating populations. In contrast, self-fertilizing populations from Scandinavia have strongly reduced genetic diversity and accumulate harmful mutations, likely as a result of demographic effects of postglacial colonization. Our results suggest that mixed-mating populations can avoid some of the negative evolutionary consequences of high self-fertilization rates

Ten simple rules for biologists learning to program
As big data and multi-omics analyses are becoming mainstream, computational proficiency and literacy are essential skills in a biologist’s tool kit. All “omics” studies require computational biology: the implementation of analyses requires programming skills, while experimental design and interpretation require a solid understanding of the analytical approach. While academic cores, commercial services, and collaborations can aid in the implementation of analyses, the computational literacy required to design and interpret omics studies cannot be replaced or supplemented. However, many biologists are only trained in experimental techniques. We write these 10 simple rules for traditionally trained biologists, particularly graduate students interested in acquiring a computational skill set.
PLOS Computational Biology

Two genetic changes in cis-regulatory elements caused evolution of petal spot position in Clarkia
We identify the genetic differences between species in the genus Clarkia that are responsible for evolutionary change in an ecologically important element of floral colour patterns: spot position. The evolutionary shift in spot position was due to two simple genetic changes that resulted in the appearance of a transcription factor binding site mutation in the R2R3 Myb gene that changes spot formation. These genetic changes caused R2R3 Myb to be activated by a different transcription factor that is expressed in a different position in the petal. These results suggest that the regulatory rewiring paradigm is as applicable to plants as it is to animals, and support the hypothesis that cis-regulatory changes may often play a role in plant morphological evolution. (ReadCube Link)
Nature Plants

How land plant life cycles first evolved
This year marks the 100th anniversary of the first in a series of papers on the biota of a 407-million-year-old hot spring system that opened a window onto early life on land. The site near the village of Rhynie in Aberdeenshire, Scotland, is exceptional because fossilization occurred in microcrystalline silica (chert), preserving organisms to the cellular level and shedding light on community structure and interactions among the plants, arthropods, fungi, algae, and cyanobacteria. Recent research on these remarkable fossils and advances in understanding plant developmental genetics are beginning to reveal how major changes in life cycle had an early influence on the direction of plant evolution.


Next week and onwards

The plan was to use a quiet week after Christmas to make some small changes to the Botany One site. For example, I think I can improve how we highlight comments. However, there's now a bit of a backlog to deal with, so changes might be delayed. In the meantime time, comments, criticism, and help for blocked chests that don't involve honey, are all welcome @botanyone on Twitter. I hope a slightly fuller email will be with you next week.



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