Dodgy photos dog phytology

Image: Wikimedia Commons.

Image: Wikimedia Commons.

It has oft been claimed that a picture is worth a thousand words. In the case of certain images in Klementina Kakar et al.’s study entitled ‘CLASP-mediated cortical microtubule organization guides PIN polarization axis’ it seems quite clear that many more than a thousand words have been written about them. Why? The normally genteel world of botanical research has been shaken, stirred and shocked to its very core by a retraction of that paper – which purported to identify the molecular machinery that connects the organisation of microtubules to the regulation of the axis of polarisation of auxin-transporting PIN proteins (which membrane-sited molecules are needed for transport of the plant hormone auxin across plasma membranes and thereby help to maintain polarity of growth and development within the plant). Relating as it does to fundamental aspects of plant growth and development and such phenomena as gravitropism, this is an important finding and understandably published in a very high-impact and influential journal. So what’s gone awry? A retraction is, after all, a very serious state of affairs. Well, and in the words of the same four authors of the original paper, ‘after re-examination of this Letter [this is how Nature articles are formally described], concerns with some of the reported data were raised. It was found that two confocal images were near-identical in panels of Figure 3 and two confocal images were re-used in panels of Figure 4, and that some gel images were inappropriately generated by cutting and pasting of non-adjacent bands. Therefore, we feel that the most responsible action is to retract the paper. We sincerely apologize for any adverse consequences that may have resulted from the paper’s publication’. For more on this, visit the various items at the Retraction Watch* website. Fortunately – for those unaware of this from media reports, etc, but who might otherwise come across the article in their literature searches, the PubMed entry for the original Nature paper does make mention of its subsequent retraction, and provides a link to the retraction notice. Although I don’t know if the paper’s retracted status is indicated on all search engines… However, in the scrabble to find appropriate literature to cite in one’s work, one might overlook that notification. Is this therefore a weakness in the otherwise laudable retraction process/system whereby subsequent readers of those papers may not be aware of their retraction? Maybe we need a form of historical revisionism reminiscent of the rewriting of history in George Orwell’s classic novel Nineteen Eighty-Four to expunge such items from the record totally so that they’re never ever found…? Hmm, what would historians of science make of that? Do let us know!

* Retraction Watch is a blog that reports on retractions of scientific papers. Launched in August 2010 it is produced by science writers Ivan Oransky (executive editor of Reuters Health) and Adam Marcus (managing editor of Anesthesiology News).

[For more on the costs associated with retractions, check out Tracy Vence's commentary at The Scientist.  And with such sobering news, if you are concerned that retractions can unduly affect one’s career, Virginia Gewin has some words of comfort. But, if you want more retraction stories, why not check out last year’s ‘Top 10’? – Ed.]

Seeing the Forest and the Trees: Research on Plant Science Teaching and Learning

CBE Life Sci Educ The September issue of CBE—Life Sciences Education is a Special Focus edition on plant science education:

Plant Behavior. CBE Life Sci Educ September 2, 2014 13:363-368; doi:10.1187/cbe.14-06-0100
Plants are a huge and diverse group of organisms ranging from microscopic marine phytoplankton to enormous terrestrial trees. Stunning, and yet some of us take plants for granted. In this plant issue of LSE, WWW.Life Sciences Education focuses on a botanical topic that most people, even biologists, do not think about—plant behavior.

Book Review: Plant Biology for Young Children. CBE Life Sci Educ September 2, 2014 13:369-370; doi:10.1187/cbe.14-06-0093
My Life as a Plant is an activity book targeted toward helping young children see the importance, relevance, and beauty of plants in our daily lives. The book succeeds at introducing children to plant biology in a fun, inquiry-based, and appropriately challenging way.

Understanding Early Elementary Children’s Conceptual Knowledge of Plant Structure and Function through Drawings. CBE Life Sci Educ September 2, 2014 13:375-386; doi:10.1187/cbe.13-12-0230
We present the results of an early elementary study (K–1) that used children’s drawings to examine children’s understanding of plant structure and function.

Effects of a Research-Infused Botanical Curriculum on Undergraduates’ Content Knowledge, STEM Competencies, and Attitudes toward Plant Sciences. CBE Life Sci Educ September 2, 2014 13:387-396; doi:10.1187/cbe.13-12-0231
This research-infused botanical curriculum increased students’ knowledge and awareness of plant science topics, improved their scientific writing, and enhanced their statistical knowledge.

Connections between Student Explanations and Arguments from Evidence about Plant Growth. CBE Life Sci Educ September 2, 2014 13:397-409; doi:10.1187/cbe.14-02-0028
In an analysis of 22 middle and high school student interviews, we found that many students reinterpret the hypotheses and results of standard investigations of plant growth to match their own understandings. Students may benefit from instructional strategies that scaffold their explanations and inquiry about how plants grow.

Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in Brassica rapa Fast Plants. CBE Life Sci Educ September 2, 2014 13:410-424; doi:10.1187/cbe.13-12-0232
This study explores shifts in student word association and explanations of phenotypic variation through an integrative quantitative genetics unit using Brassica rapa Fast Plants.

Optimizing Learning of Scientific Category Knowledge in the Classroom: The Case of Plant Identification. CBE Life Sci Educ September 2, 2014 13:425-436; doi:10.1187/cbe.13-11-0224
The software program Visual Learning—Plant Identification offers a solution to problems in category learning, such as plant identification. It uses well-established learning principles, including development of perceptual expertise in an active-learning format, spacing of practice, interleaving of examples, and testing effects to train conceptual learning.

Attention “Blinks” Differently for Plants and Animals. CBE Life Sci Educ September 2, 2014 13:437-443; doi:10.1187/cbe.14-05-0080
We use an established paradigm in visual cognition, the “attentional blink,” to demonstrate that our attention is captured more slowly by plants than by animals. This suggests fundamental differences in how the visual system processes plants, which may contribute to plant blindness considered broadly.

 

AP1/SEP/AGL6 MADs-box genes in a basal eudicot

AP1/SEP/AGL6 MADs-box genes in a basal eudicot

AP1/SEP/AGL6 MADs-box genes in a basal eudicot

MADS-box transcriptional regulators play important roles during plant development. Sun et al. study structural and functional variation of FUL-like (AP1 subfamily), SEP-like and AGL6-like genes in the basal eudicot Epimedium sagittatum and provide a description of EsFUL-like, EsAGL2-1, EsAGL2-2 and EsAGL6-like function divergence and conservation in comparison to a selection of model core eudicots. The results highlight how organization in genomic segments containing A- and E-class genes in sequenced model species has resulted in similar topologies of AP1 and SEP-like gene trees.

Trends and concepts in fern classification (Invited Review)

Trends and concepts in fern classification (Invited Review)

Trends and concepts in fern classification (Invited Review)

Fern classification has been highly unstable in the past, largely because the morphological characters selected for emphasis in higher-level classifications have been variable. Christenhusz and Chase review the history of fern classification, and consider that some classifications based on single characteristics have been useful for identifying species but are highly artificial in terms of their views on relationships, whilst classifications using a suite of characters have been considered more ‘natural’, but with the advance of molecular phylogenetics many of these ‘natural’ groups are also been shown to be highly artificial. They highlight which groups/genera have taxonomic issues that remain to be clarified, and propose the use of broader family concepts. Progress in developing a consensus fern classification is reflected in a new proposed classification.

GPT2, seedling development and sugar signalling

GPT2, seedling development and sugar signalling

GPT2, seedling development and sugar signalling

GPT2,a glucose 6-phosphate/phosphate translocator, plays an important role in environmental sensing in mature leaves of Arabidopsis thaliana, and its expression has also been detected in arabidopsisseeds and seedlings. Dyson et al. study wild-type A. thaliana and a gpt2 T-DNA insertion knockout line, and find that plants lacking GPT2 expression are delayed in seedling establishment, specifically in the process of cotyledon greening (rather than germination). This phenotype cannot be rescued by glucose in the growth medium, with greening being hypersensitive to glucose. Germination itself is, however, hyposensitive to glucose in the gpt2 mutant. They conclude that endogenous sugar signals function in controlling germination and the transition from heterotrophic to autotrophic growth, and that the partitioning of glucose 6-phosphate, or related metabolites, between the cytosol and the plastid modulates these developmental responses.

Picture Perfect

Young Woman Taking Photos Of Sunflowers.

Are you a keen photographer? You are reading a botany blog, so we can speculate that you have at least a passing interest in plants! Over at photocrowd.com you can combine these two passions and throw in a little healthy creative competition, as they are currently running a photo contest to showcase your best images on the theme of ‘Seeds and fruit’ (entry closes Sept 19th 2014, midnight UK time, winners announced 25th September 2014).

Simply join photocrowd, and upload one or two images. By submitting your images into a contest you gain the right to see what other members have submitted on the same topic, and you can vote for your favourite images as part of the ‘Crowd vote’. You can choose to ‘love’, ‘like’ or ‘pass’ an image. The crowd votes are updated in real time, be warned – checking your current score and seeing what new images have been submitted can become a bit of an addiction! There is also an expert judge who choses their favourite image. In this contest the top voted pictures, as chosen by the crowd and expert, each win £50 of professional photo retouching.

Good luck!

This photo © Belahoche/BigStockPhoto.

Sesquiterpene lactones and herbivore resistance

Sesquiterpene lactones and herbivore resistance

Sesquiterpene lactones and herbivore resistance

Stereochemical variation is common in plant secondary metabolites, but its importance in mediating plant–herbivore interactions has received little attention. Ahern and Whitney  use common garden experiments with common cocklebur, Xanthium strumarium (Asteraceae), to examine relationships between stereochemical variation in sesquiterpene lactones, herbivore damage and plant fitness. They find that the stereochemistry of sesquiterpene lactone ring junctions helps explain variation in plant herbivore resistance, in turn influencing plant fitness. Their results indicate that subtle differences in stereochemistry may be a major, yet under-appreciated, determinant of the protective role of secondary metabolites.

The trees have it…

Image: Stefan Laube/Wikimedia Commons.

Image: Stefan Laube/Wikimedia Commons.

Trees, those magnificent, organic, large – sometimes huge – woody constructions continue to fascinate and inspire all who stop, stand and stare up (and up, and up…) at them. So here’s a selection of tree-based items to maintain – or maybe even initiate? – the phenomenon of arborifascination. But first a question: why did the three-toed sloth come down from the trees?

Answer: to defecate! Sloths are considered to be amongst the most, well, er, slothful of animals that, anecdotally, spend most of their time in trees, doing ‘not a lot’, apart from eating tree leaves [they are arboreal herbivores, after all; Tree Use No. (TUN) 1]. However, not only is this descent to the ground energy-consuming, it also exposes the sloth to potential predators; so why would they risk it? Work by Jonathan Pauli et al. may have the answer to this otherwise inexplicable behaviour. Three-toed sloths* harbour moths, inorganic nitrogen (N) and algae (e.g. green algae Trichophilus spp.) within their fur. The lipid-rich algae are eaten by the sloths and presumably supplement their diet of leaves. By leaving the tree for defecation, the fur-residing moths are transported to their oviposition (egg-laying) sites in sloth dung, which subsequently facilitates further moth colonisation of sloth fur. Since those moths are ‘portals for nutrients’, levels of inorganic N (potentially from moth excreta) in sloth fur increase, which in turn fuels algal growth. As the researchers conclude, ‘these linked mutualisms between moths, sloths and algae appear to aid the sloth in overcoming a highly constrained lifestyle’. Wow! I will never look at a three-toed sloth in quite the same way again.

Also challenging perceived wisdom is work by Marc Ancrenaz et al. Traditionally, orangutans (the world’s largest arboreal mammal) are assumed to be obligate arborealists, swinging seemingly effortlessly from tree to tree (TUN 2) as they navigate their lofty aerial neighbourhood. However, observations of terrestrial activity by these primates in the wild begs the question, why? Hitherto this activity was considered to be a response to habitat disturbance, but Ancrenaz et al. found no difference in instances of this behaviour in disturbed versus non-disturbed areas. They therefore propose that terrestrial locomotion is part of the Bornean orangutan’s natural behavioural repertoire and may increase their ability to cope with at least smaller-scale forest fragmentation, and to cross moderately open spaces in mosaic landscapes. So, it seems that even orangutans can have a bit too much of the ‘high life’ at times.

Finally, a terrestrial–aquatic organism that’s going up in the world. Reviewing evidence of tree-climbing activity in extant crocodilians (crocodiles and alligators), Vladimir Dinets et al. suggest it is much more widespread than previously considered and ‘might have multiple functions’, e.g. as an alternative site for thermoregulation (TUN 4), or increased detectability of prey (TUN 5). So, there you have it, ‘tons’ of alternative tree uses! Trees, helping to make the world an even more amazing place.

 

* Two-toed sloths don’t go in for this more energetic activity – and have lower densities of moths, lower N levels and reduced algal biomass in their fur…

Pollination by sexual deception in Pterostylis

Pollination by sexual deception in Pterostylis

Pollination by sexual deception in Pterostylis

Pterostylis is an Australasian terrestrial orchid genus of more than 400 species, most of which use a motile, touch-sensitive labellum to trap dipteran pollinators. The mode of attraction, however, is uncertain. Phillips et al. find that a single species of male gnat (Mycetophilidae) visits and pollinates the rewardless flowers of P. sanguinea, and that the gnats often show probing copulatory behaviour on the labellum, leading to its triggering and the temporary entrapment of the gnat in the flower. Pollen deposition and removal occurs as the gnat escapes from the flower via the reproductive structures. The labellum is the sole source of the chemical attractant involved. It is predicted that sexual deception will be widespread in the genus, although the diversity of floral forms suggests that other mechanisms may also operate.

Hydraulic integration in tree root vessels

Hydraulic integration in tree root vessels

Hydraulic integration in tree root vessels

Plants can adapt to their environment by varying the hydraulic integration of their xylem network. While much is known about xylem organization in aerial parts, roots have been less well studied. Johnson et al. measure xylem embolism resistance and connectivity in roots of two co-occurring tree species in a semi-arid habitat, Quercus fusiformis and Sideroxylon lanuginosum.They find that Quercus vessels are primarily solitary, while Sideroxylon xylem is highly connected, leading to resistant and vulnerable xylem networks, respectively. Pit membrane thickness plays less of a role in embolism resistance than expected, suggesting that xylem organization is an important trait that has yet to be fully explored.