Using GEFs to deorphanize odorant receptors

Odorant perception is initiated when odorants activate uniquecombinations of odorant receptors (ORs) expressed in the ciliaof olfactory sensory neurons in the nose (Buck and Axel 1991;Malnic et al. 1999). One of the greatest challenges in the olfactoryscience is to correlate ORs with their ligands (to deorphanizethe ORs). The determination of OR–ligand pairs shouldreveal how the OR family is used to generate diverse odorantperceptions (Keller et al. 2007, Menashi et al. 2007). However,these studies are complicated     

What hypothesis tests are not: a reply to Johnson

We are sorry that Johnson's pleasure at reading our recent paper(Colegrave and Ruxton, 2003) was so short-lived. Johnson (2005)is correct that the definition of the P value that we use inthe paper is incorrect, and we are grateful     

UV Effects in Aquatic Organisms and Ecosystems. Edited by Helbling, E. W. and Zagarese, H. (2003) The Royal Society of Chemistry, Springer Verlag, Cambridge, UK. $290.00. ISBN 0-854-04301-2.

All Earthly events can be eventually blamed on the Sun. Is itnot? There is no doubt that solar radiation is a fundamental forcein nature. At least two earlier books have dealt with the premisethat solar ultraviolet radiation (UVR) penetrating our wateryplanet profoundly impacts both the living as well as the non-livingcomponents (Calkins, 1982; De Mora et al., 2000). Today, inan     

On hotshots and lotteries: are the best males on larger leks better than expected?

Leks are clusters of males that hold territories containingno special resources except for the males themselves (Höglundand Alatalo, 1995). Among hypotheses put forth to explain whysuch clusters form, the hotshot hypothesis posits that leksform by males that would otherwise receive little attentionfrom females taking up positions next to males that would receivea great deal of female attention in any case (Beehler and Foster,1988; Höglund and Alatalo, 1995). Although this ideamight well be true, we still face the task of evaluating theevidence. In this note I question the efficacy of testing forhotshots by observing the success of males at leks of different sizes. Several authors have noted that the males most successful inattracting mates on larger leks are more successful than thebest males on smaller leks (Westcott and Smith, 1997     

Confronting complexity: reply to Le Quere and Flynn

Complexity pervades ecology. The search for unifying laws thereforeentails that ‘biologists work very close to the frontierbetween bewilderment and understanding’ (Medawar, 1969).One approach to developing ecological theory is to abandon simplicityat the outset and operate at the highest appropriate organizationallevel (Dunbar, 1980). On this basis, Le Quéré(Le Quéré, 2006) issues a plea for inclusion ofplankton functional types (PFTs) in plankton models because‘we will not understand ecology until we     

What's in a name? Are MSG and umami the same?

The Japanese word `umami' has a long past. It was already inuse during the Edo period (Tokugawa Shogunate) of Japanese history,which ended in 1868 (Mason, 1993). In Japanese, `umami' oftenconnotes a cognitive category (Yamaguchi and Ninomiya, 1998) oftaste, or perhaps flavor, with definitions that include deliciousness, flavor,relish,     

Sequence gaps join mice and men: phylogenetic evidence from deletions in two proteins

Recent nuclear sequence analyses have provided evidence thatprimates and rodents are more closely related than previouslybelieved (Madsen et al. 2001 ; Murphy et al. 2001a, 2001b ).This proposal is difficult to reconcile with morphological insights(Liu et al. 2001 ; Novacek 2001 ) and is not generally supportedby current mitochondrial sequence data (Reyes, Pesole, and Saccone2000 ; Nikaido et al. 2001 ; Arnason et al. 2002 ; Janke etal. 2002 ). Moreover, the supporting data and analyses havebeen criticized on methodological grounds (Rosenberg and Kumar2001 ). Here we report deletions in two nuclear protein-codinggenes that lend independent support     

What hypothesis tests are not: a response to Colegrave and Ruxton

It is always flattering to see one's work cited by others. Notonly does it boost the ego, but it provides a satisfying feelingthat one's efforts are both appreciated and contributing tothe advance of science. So I was pleased when a colleague pointedout that Colegrave and Ruxton (2003) had cited a recent paperof mine, "The insignificance of statistical significance testing"(Johnson, 1999). In that article I argued, as did Colegraveand Ruxton, that confidence intervals often are much more informativethan are p values associated with hypothesis tests. My pleasure, alas, was short-lived.     

New directions of post-rice genome sequencing

Rice (Oryza sativa L.) is one of the most important staple foodsand it has been estimated that 50% of the human population dependson it as the main source of nutrition. It is particularly importantfor people living in the monsoon areas of Asia, where it hasa long history of cultivation. On April 2002, two groups, Syngentaand the Beijing Genome Institute, reported draft sequences ofjaponica and indica varieties, respectively (Goff et al. 2002,Yu et al. 2002) and, in December of the     

Reply to: European barn swallows use melanin pigments to color their feathers brown

McGraw et al. (2004) have recently presented evidence that barnswallow (Hirundo rustica) feathers from the forehead and throatdo not     

Reply to Horizons Article 'Some ideas about the role of lipids in the life cycle of Calanus finmarchicus' Irigoien (2004): II

Recently, Irigoien (Irigoien, 2004) suggested a conceptual modelof the role of lipids in the life cycle of the marine copepodCalanus finmarchicus. As he pointed out, lipids accumulatedbefore     

Microsatellite variation, repeat array length, and population history of Plasmodium vivax

A recent paper (Leclerc et al. 2004) described limited variationin dinucleotide microsatellites from Plasmodium vivax, suggestingvery recent bottlenecks or genome-wide selective events. Wedescribe patterns of variation in 11 dinucleotide microsatellitesin P. vivax populations from Colombia, India, and Thailand.We find abundant variation with heterozygosity of 0.64, 0.76,and 0.77, respectively, in the three countries. The discrepancybetween these two studies results is simply explained by thedifferences in the size of repeat arrays. The microsatellitesstudied by Leclerc et al. (2004) have very few repeats (median5.5, range 4–13) and so would not be expected to be variable.Plasmodium vivax microsatellites show comparable levels of variationto those in Plasmodium falciparum when repeat array length istaken into account and provide no support for recent bottlenecksor widespread selective purging     

Plant ecology. * Schulze ED, Beck E, Muller-Hohenstein K. 2005. Berlin/Heidelberg: Springer. $89{middle dot}95 (hardback). 702 pp.

This book (a translation fromSchulze et al., 2002) is one of the most comprehensive textbooksof plant ecology so far. The authors aim to ‘for the firsttime bring together and clearly organize the large subdisciplinesof plant ecology’ and, to a large extent they have succeeded.The book is well written, and its more than 500 illustrationsare beautifully laid out and well chosen to help the readerunderstand the theory. It is clearly suitable not only     

Reply to Horizons Article 'Castles built on sand: dysfunctionality in plankton models and the inadequacy of dialogue between biologists and modellers' Flynn (2005). Shiny mathematical castles built on grey biological sands

Two discussion papers (Harte, 2002; Flynn, 2005) give me theopportunity to debate two common views about biology: (i) biologyis a grey science and (ii) biologists only look for complexity,not large unifying theories (that can be used in models).

1. Biology is not a grey science—all you need to know abouthow an organism works, what it does and even how it got to behere today are written inside the organism in a very precisedigital code called DNA (and we are learning to read it). Thereare two reasons why biology is usually considered as a greyscience. There is one that exact science practitioners tendto accept: that the expression of the instructions is flexiblein relation to the physical environment, phenotypic plasticity.The other is one that modellers tend     

Reply to Horizons Article 'Some ideas about the role of lipids in the life cycle of Calanus finmarchicus' Irigoien (2004): I

The biotic and abiotic factors that modulate the life historyof C. finmarchicus are not well described, and Xabier Irigoien(Irigoien, 2004) suggests some interesting hypotheses aboutwhat role lipids might play. He does, however, make some questionableassumptions about the role of lipids during overwintering. First,he states that ‘lipid storage determines the     

Higher sensitivity to perithreshold odors when sitting than when supine may be correlated with postural differences in locus coeruleus activity

Lundström et al. (2007) report an effect of posture onperithreshold odor sensitivity, which they found to be higherwhen sitting than when lying down (consistent with earlier workdescribed in Lundstrom et al. 2006). The explanation for thisresult focused on cognitive mechanisms, with support seen inthere being     

Synchrony, asynchrony, and temporally random mating: a new method for analyzing breeding synchrony

Much research has focused on understanding breeding synchronyin animals and its relationship to such issues as mating systemsand extrapair copulations in birds (Birkhead and Biggins, 1987;Emlen and Oring, 1977; Knowlton, 1979; Stutchbury and Morton,1995). To empirically examine synchrony, one needs an appropriatemeasure of the degree of synchrony in a population. Kempenaers(1993) presented an index of breeding synchrony (modified fromBjörklund and Westman, 1986) that has gained wide use asa simple representation of the degree to which breeding is synchronizedamong animals. This synchrony index (SI) is calculated as follows:

where F is the totalnumber of breeding females in the population; f_i,p is the numberof fertile females, excluding     

Valerie Andersen (1959 2007)

Valérie Andersen formally began her career in oceanographywith a PhD from the Université de Pierre et Marie Curiein 1985. Her thesis (Andersen, 1985a) was centred on the developmentof numerical models of the pelagic food web. However, it wasfirmly based on her experimental studies of salps (Andersen,1985b, 1986, 1989; Andersen and Nival, 1986) and data she gatheredon cruises in the N.W. Mediterranean Sea (Andersen and