Archive for the ‘Botany’ Category

Coping with temperature fluctuations

November 18, 2011

How do plants manage to deal with temperature fluctuations? A nice commentary.

Mathematisation of …

March 30, 2010

Sexual attraction; here is the abstract:

Pollen tubes follow attractants secreted by the ovules. In a recent paper in BMC Plant Biology, Stewman and colleagues have quantified the parameters of this attraction and used them to calibrate a mathematical model that reproduces the process and enables predictions on the nature of the female attractant and the mechanisms of the male response.

Here is the last paragraph of the piece:

As with many other mathematical approaches to complex biological behavior, this new model from Stewman et al. [3] raises more questions than answers. But the fact that new approaches are contributing to a precise experimental description of the system [2,11,12] may make mathematical modeling an important tool for testing and selecting candidate molecules that may fit the in vivo biological profile of the final step of plant sexual attraction.

Here are the references in question:

[2] Dresselhaus T, Márton ML: Micropylar pollen tube guidance and burst: adapted from defense mechanisms? Curr Opin Plant Biol 2009, 12:773-780.

[3] Stewman SF, Jones-Rhoades M, Bhimalapuram P, Tchernookov M, Preuss D, Dinner AR: Mechanistic insights from a quantitative analysis of pollen tube guidance.

BMC Plant Biol 2010, 10:32.

[11] Márton M, Dresselhaus T: A comparison of early molecular fertilization mechanisms in animals and flowering plants. Sex Plant Reprod 2008, 21:37-52.

[12] Okuda S, Tsutsui H, Shiina K, Sprunck S, Takeuchi H, Yui R, Kasahara RD, Hamamura Y, Mizukami A, Susaki D, Kawano N, Sakakibara T, Namiki S, Itoh K, Otsuka K, Matsuzaki M, Nozaki H, Kuroiwa T, Nakano A, Kanaoka MM, Dresselhaus T, Sasaki N, Higashiyama T: Defensin-like polypeptide LUREs are pollen tube attractants secreted from synergid cells.

Nature 2009, 458:357-361.

Here is Reference 3. Have fun!

Quantum coherence and photosynethsis

October 14, 2009

An interesting paper:

Theoretical examination of quantum coherence in a photosynthetic system at physiological temperature

A Ishizaki and G R Fleming

The observation of long-lived electronic coherence in a photosynthetic pigment–protein complex, the Fenna–Matthews–Olson (FMO) complex, is suggestive that quantum coherence might play a significant role in achieving the remarkable efficiency of photosynthetic electronic energy transfer (EET), although the data were acquired at cryogenic temperature [Engel GS, et al. (2007) Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature 446:782–786]. In this paper, the spatial and temporal dynamics of EET through the FMO complex at physiological temperature are investigated theoretically. The numerical results reveal that quantum wave-like motion persists for several hundred femtoseconds even at physiological temperature, and suggest that the FMO complex may work as a rectifier for unidirectional energy flow from the peripheral light-harvesting antenna to the reaction center complex by taking advantage of quantum coherence and the energy landscape of pigments tuned by the protein scaffold. A potential role of quantum coherence is to overcome local energetic traps and aid efficient trapping of electronic energy by the pigments facing the reaction center complex.

Here is a commentary on the paper:

Some quantum weirdness in physiology

P G Wolynes

Quantum mechanics seems alien to physiology. Alarm bells go off in our heads when we hear even people of such genius as Sir Roger Penrose (1) invoke the weird coherence of quantum mechanical wave functions to explain biological function. Of course, it is only some of the “weirder” parts of quantum mechanics that bother us. Structural biochemistry is founded on the rigid geometrical relationships involved in chemical bonding that arise from quantum mechanics; the α-helix could only have been discovered by Pauling by acknowledging the power of quantum mechanical resonance to flatten the peptide bonding unit (2). Nevertheless, most modern biomolecular scientists view quantum mechanics much as deists view their God; it merely sets the stage for action and then classically understandable, largely deterministic, pictures take over. In this issue of PNAS Ishizaki and Fleming (3), by combining experimental and theoretical investigations, demonstrate that quantum coherence effects play a big role in light energy transport in photosynthetic green sulfur bacteria under physiological conditions. Quantum coherence allows a nonclassical simultaneous exploration of many paths of energy flow through the many chromophores of a light-harvesting complex, thereby significantly increasing the efficiency of the energy capture process, presumably helping the bacteria to survive in low light.

In search of Sanjeevani plant

September 10, 2009

In the latest column of Speaking of science, D Balasubramanian talks about this paper from the latest issue of Current science (pdf) and this commentary on it (pdf) from the same journal. Here is the abstract of the paper:

This article reports our attempt to explore the possible plants that could represent Sanjeevani – the mythical herb from the epic Ramayana. Our search was based on a set of criteria developed from the consistent details available from the epic on the names of the herb in different languages, its habitat, medicinal values and the ability to ‘resurrect’ life. Accordingly, from an initial list of potential candidate species, we have filtered two species on which initial studies can be focused. However, our search is not complete and hence not final, as there could be other approaches and accordingly, other suggestions as well for Sanjeevani.

Balasubramanian’s piece is also a nice summary of the work. Take a look!

Devil’s dung

July 31, 2009

I did not realise the amount of flavour that the uses of hing gives to our sambhar and rasam until, one day, I cooked them without hing and tasted the concoction. D Balasubramanian, in his latest column writes about the culinary and other uses of hing:

What gives it the pungent smell? It is the sulphides, the simplest of them being the one from the Kipp’s apparatus of high school chemistry lab.

The major component, 2-butyl 1-propenyl disulphide, is so “stinking” that the Europeans called it asafoetida – Asa from the Persian word for resin and foetida meaning ‘stinking’ in Latin. More colorfully it was called the devil’s dung – both for its shape and smell.

Ferula asafoetida is not grown in India, and is a native of Afghanistan, Iran, Turkmenistan and that region of central Asia.

Have a look!

On mebranes and core/shell structures

December 10, 2008

Latest PNAS carries a couple of very interesting articles; in the first, H J Lee et al by modelling membranes as fluid-lipid bilayers that are in mechanical equilibrium, show that the the externally applied force, pressure, tension and spontaneous curvature can directly be computed using the shape of the mebrane alone; they also report on their experiments with optical tweezers on vesicles to show how the computation is in agreement with experimental observations:

Recent advances have enabled 3-dimensional reconstructions of biological structures in vivo, ranging in size and complexity from single proteins to multicellular structures. In particular, tomography and confocal microscopy have been exploited to capture detailed 3-dimensional conformations of membranes in cellular processes ranging from viral budding and organelle maintenance to phagocytosis. Despite the wealth of membrane structures available, there is as yet no generic, quantitative method for their interpretation. We propose that by modeling these observed biomembrane shapes as fluid lipid bilayers in mechanical equilibrium, the externally applied forces as well as the pressure, tension, and spontaneous curvature can be computed directly from the shape alone. To illustrate the potential power of this technique, we apply an axial force with optical tweezers to vesicles and explicitly demonstrate that the applied force is equal to the force computed from the membrane conformation.

In the second, J Yin et al tackle what Darwin apprently identified as an issue that can “drive the sanest man mad”, namely, the pattern formation in fruits and vegetables:

Many natural fruits and vegetables adopt an approximately spheroidal shape and are characterized by their distinct undulating topologies. We demonstrate that various global pattern features can be reproduced by anisotropic stress-driven buckles on spheroidal core/shell systems, which implies that the relevant mechanical forces might provide a template underpinning the topological conformation in some fruits and plants. Three dimensionless parameters, the ratio of effective size/thickness, the ratio of equatorial/polar radii, and the ratio of core/shell moduli, primarily govern the initiation and formation of the patterns. A distinct morphological feature occurs only when these parameters fall within certain ranges: In a prolate spheroid, reticular buckles take over longitudinal ridged patterns when one or more parameters become large. Our results demonstrate that some universal features of fruit/vegetable patterns (e.g., those observed in Korean melons, silk gourds, ribbed pumpkins, striped cavern tomatoes, and cantaloupes, etc.) may be related to the spontaneous buckling from mechanical perspectives, although the more complex biological or biochemical processes are involved at deep levels.

Two very interesting pieces; take a look!

How science is done: the nuts-and-bolts edition

April 6, 2008

Karen James writes a BPR3 post on her own research:

It’s been over a month–that’s about seven thousand blog years–since my PLoS ONE paper came out and I’m only just now getting around to giving it a proper blog treatment. In defense of my tardiness, the paper is pretty small-fry in terms of its newsworthiness. It didn’t even get a press release (though maybe that’s a good thing). In other words, it’s still fresh to the blogosphere. Well, that’s my excuse at least.

At first I wondered: is this normal? Blogging on one’s own peer-reviewed research, that is? But Bora Zivkovic (PLoS ONE Online Community Manager/crazy uncle of the science blogging community) and Liz Allen (PLoS Director of Marketing and Business Development) have made it clear that giving my own paper the BPR3 treatment is not only normal, it is expected.

There are several ways I might approach writing this post. The most obvious is to simply summarise the paper In Plain English. Problem is, I’ve already done that by writing a news blurb for the Natural History Museum website, and I don’t really feel like repeating myself (though of course I will, but only to the extent to which it is necessary to tell my story).

A second approach is to critically analyse the paper. But you can see the problem with that right away: since I wrote it, I’ve already critically analysed it. Critical analysis necessarily belongs to someone who isn’t an author on the paper.

A third approach, and the one I am going to go with, is to tell the whole story of this project: the blood, sweat and occasional tears, not just the part that appears in the paper itself. This will be by far more interesting than a simple recap of the key findings of the paper itself (which, as I said, you can get elsewhere). Moreover, the whole story illuminates the reality of the scientific process in a way that’s intelligible to the non-scientist; well, that’s my aim anyways.

A must-read post; link via Bora who recommends the methodology strongly.

Asexual and sexual reproduction in plants!

March 19, 2008

D Balasubramanian, in his latest (fortnightly) column in the Hindu, Speaking of Science, describes some of the recent research carried out at CCMB, Hyderabad (and is getting published in Nature next week a couple of weeks ago) on the genetic altering of the sexual life of plants that can lead to sustained production of high yielding plants.

The issue?

Just as we would (if we could) choose our mates with desired qualities and traits, we choose, while farming, to cross plants with desired qualities in their offspring.

These qualities are high yield, pest resistance, better fruits, more beautiful flowers and so on. In agriculture and major food crops, such well-chosen crosses lead to high yielding hybrids. The Green Revolution is the result of such an exercise.

But farmers face a problem. Once they have a good hybrid, they wish to keep its genes and propagate them by self-fertilizing the hybrid, so that the cultivars have superior yields than the parental inbred lines

Sadly though, this hybrid vigour decreases with each generation of hybrid self crossing. The copies of the different genes in the hybrid separate from each other during germ cell production, and get reshuffled in each succeeding generation. As a result we need to cross the parental lines anew each time — not a satisfactory situation.

And, is there a way out? Seems to be, and that is precisely where the CCMB researchers lead by Dr. Imran Siddiqi come in:

But there is way out. This comes from a peculiar property of many plants (and some animals such as insects and fish). Some plants such as dandelion, some berries and grasses side-step the meiosis process altogether and their seeds reproduce clonally, asexually.

The entire gene pool of the mother is passed on straight to the daughter seed. This curious, but exciting, property is referred to as apomixis, the first step of which is called apomeiosis (the apo-referring to the missing of a component).

While berries and grasses do this, major crop plants do not; they reproduce sexually. If only they could be made apomictic, we could retain hybrid vigour forever, since no reshuffling of genes as in sexual reproduction kind would occur.

If we understand the genetic and cell biological basis behind apomeiosis, we could perhaps send wheat, rice and corn along the apomixis path and produce high yielding hybrid seeds.

What are the genes controlling apomixis? It is this important issue that has been elegantly addressed and identified by Dr. Imran Siddiqi and co-workers, using the sexually reproducing plant Arabidopsis.

They show that alteration in the gene called DYAD leads to apomeiosis, sending the plant into the asexual mode. The DYAD gene normally regulates the organisation of chromosomes during meosis. Plants with mutation in DYAD, however, give rise to seeds that contain the full set of genes from the parent.

A single gene, whose function is known, can lead to a plant becoming apomictic, when its function is tampered with! This is truly a path-finding discovery and we should applaud the group for this breakthrough.

A nice piece; take a look!

E K Janaki Ammal

June 10, 2007

The latest issue of Resonance carries a biographical sketch of EK Janaki Ammal, a botanist (pdf); though the sketch mentions that Ammal was elected to be a fellow of the Indian Academy of Sciences the year the academy was founded by Sir C V Raman, namely, in 1935, from this document, it is clear that she is actually one of the founding members of the academy (and, hence the first woman member of the academy). Here is a note with her photograph (pdf). Unfortunately, there does not seem to be much of information on her on the net (and, no wiki page too, though she is listed as an eminent Ezhava).

Golden guide to hallucinogenic plants

April 30, 2007

Hallucinogenic plants have been used by humans for ages; here is Wiki on one such Indian use in Vedic times, for example:

Soma (Sanskrit: सोमः), or Haoma (Avestan), from Proto-Indo-Iranian *sauma-, was a ritual drink of importance among the early Indo-Iranians, and the later Vedic and greater Persian cultures. It is frequently mentioned in the Rigveda, which contains many hymns praising its energizing or intoxicating qualities. In the Avesta, Haoma has an entire Yasht dedicated to it.

It is described as prepared by pressing juice from the stalks of a certain mountain plant, which has been variously hypothesized to be a psychedelic mushroom, cannabis, peganum harmala, or ephedra. In both Vedic and Zoroastrian tradition, the drink is identified with the plant, and also personified as a divinity, the three forming a religious or mythological unity.

Via B-squared, I now understand that the Golden Guide to Hallucinogenic Plants is available online. And, in case you are curious, the Golden Guide thinks that Soma is Amanita Muscaria–the mushroom, which, I first saw in Bavarian alps:

Recent studies suggest that this mushroom was the mysterious God- narcotic soma of ancient India. Thousands of years ago, Aryan conquerors, who swept across India, worshiped some, drinking it in religious ceremonies. Many hymns in the Indian Rig-Veda are devoted to soma and describe the plant and its effects.

PS:- By the way, if you followed the link above, and wondered about the mention of urine drinking in Rg Veda, this page gives some more information on the issue.