Is the future biology Shakespearean or Newtonian?

"Cells do not care about mathematics" thus concluded a biologist friend after a discussion on the future of biology. And indeed, why should they care? But if we exchange the word "cell" with "rock", "Moon" or "electrons", do we have to change the sentence also? Starting from this line of thought, we review some recent developments in understanding the stochastic behavior of biological systems. We emphasize the importance of a molecular Signal Generator in the study of genetic networks.     

Population density of the Réunion Grey White-eye Zosterops borbonicus within the summit ecosystems of Réunion,Mascarene Islands

Assessing population density is crucial for studying the ecology and evolutionary biology of species as well as for conservation purposes. Here we used point count methods to infer population density in a single-island endemic passerine bird, the Réunion Grey White-eye Zosterops borbonicus, that displays striking evidence of differentiation at a small spatial scale. Population density was estimated at 5.17 birds ha^?1 (CL 4.85–5.50), a value somewhat higher than previously believed. This estimation provides the first detailed estimation of bird population density in the vulnerable summit ecosystems of Réunion and will possibly allow a better understanding of the evolutionary causes of this plumage colour variation.     

The Cape element in the Afrotemperate flora: from Cape to Cairo?

The build-up of biodiversity is the result of immigration and in situ speciation. We investigate these two processes for four lineages (Disa, Irideae p.p., the Pentaschistis clade and Restionaceae) that are widespread in the Afrotemperate flora. These four lineages may be representative of the numerous clades which are species rich in the Cape and also occur in the highlands of tropical Africa. It is as yet unclear in which direction the lineages spread. Three hypotheses have been proposed: (i) a tropical origin with a southward migration towards the Cape, (ii) a Cape origin with a northward migration into tropical Africa, and (iii) vicariance. None of these hypotheses has been thoroughly tested. We reconstruct the historical biogeography of the four lineages using likelihood optimization onto molecular phylogenies. We find that tropical taxa are nested within a predominantly Cape clade. There is unidirectional migration from the Cape into the Drakensberg and from there northwards into tropical Africa. The amount of in situ diversification differs between areas and clades. Dating estimates show that the migration into tropical East Africa has occurred in the last 17 Myr, consistent with the Mio-Pliocene formation of the mountains in this area.     

Is the Legume Nodule a Modified Root or Stem or an Organ sui generis?

The legume nodule, which houses nitrogen-fixing rhizobia, is a unique plant organ. Its homology with lateral roots has been inferred by a comparison with other nitrogen-fixing nodules, especially those formed on actinorhizal plants in response to Frankia inoculation or on Parasponia roots following inoculation with Bradyrhizobium species. These nodules are clearly modified lateral roots in terms of their structure and development. However, legume nodules differ from lateral roots and these other nodules in their developmental origin, anatomy, and patterns of gene expression, and, consequently, several other evolutionary derivations, including from stems, wound or defense responses, or the more ancient vesicular-arbuscular mycorrhizal symbiosis, have been postulated for the legume nodule. In this review, we first present a broad view of the legume family showing the diversity of nodulation occurrence and types in the different subfamilies and particularly within the subfamily Papilionoideae. We then define the typological and molecular criteria used to discriminate the basic organs — root, stem, leaf— of the plant. Finally, we discuss the possible origins of the legume nodule in terms of these typological and molecular bases.     

Is plasma membrane lipid composition defined in the exocytic or the endocytic pathway?

Compared with intracellular membranes, the plasma membrane is rich in cholesterol and sphingomyelin. How does this distinct composition arise? Here David Allan and Karl-Josef Kallen take a critical view of the belief that these lipids arrive at the plasma membrane via vesicular traffic from the Golgi complex and propose instead that they may be accreted in the endocytic recycling pathway.     

Animal or Plant: Which Is the Better Fog Water Collector?

Occasional fog is a critical water source utilised by plants and animals in the Namib Desert. Fog basking beetles (Onymacris unguicularis, Tenebrionidae) and Namib dune bushman grass (Stipagrostris sabulicola, Poaceae) collect water directly from the fog. While the beetles position themselves optimally for fog water collection on dune ridges, the grass occurs predominantly at the dune base where less fog water is available. Differences in the fog-water collecting abilities in animals and plants have never been addressed. Here we place beetles and grass side-by-side in a fog chamber and measure the amount of water they collect over time. Based on the accumulated amount of water over a two hour period, grass is the better fog collector. However, in contrast to the episodic cascading water run-off from the grass, the beetles obtain water in a steady flow from their elytra. This steady trickle from the beetles' elytra to their mouth could ensure that even short periods of fog basking--while exposed to predators--will yield water. Up to now there is no indication of specialised surface properties on the grass leafs, but the steady run-off from the beetles could point to specific property adaptations of their elytra surface.     

Is mPTP the gatekeeper for necrosis, apoptosis, or both?

Permeabilization of the mitochondrial membranes is a crucial step in apoptosis and necrosis. This phenomenon allows the release of mitochondrial death factors, which trigger or facilitate different signaling cascades ultimately causing the execution of the cell. The mitochondrial permeability transition pore (mPTP) has long been known as one of the main regulators of mitochondria during cell death. mPTP opening can lead to matrix swelling, subsequent rupture of the outer membrane, and a nonspecific release of intermembrane space proteins into the cytosol. While mPTP was purportedly associated with early apoptosis, recent observations suggest that mitochondrial permeabilization mediated by mPTP is generally more closely linked to events of late apoptosis and necrosis. Mechanisms of mitochondrial membrane permeabilization during cell death, involving three different mitochondrial channels, have been postulated. These include the mPTP in the inner membrane, and the mitochondrial apoptosis-induced channel (MAC) and voltage-dependent anion-selective channel (VDAC) in the outer membrane. New developments on mPTP structure and function, and the involvement of mPTP, MAC, and VDAC in permeabilization of mitochondrial membranes during cell death are explored. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.     

Is nitric oxide luteolytic or antiluteolytic?

Nitric oxide (NO) has been reported to be luteolytic based on treatment of cows in vivo with an inhibitor of nitric oxide synthase (NOS-produces NO), which delayed the decline in progesterone by two to three days [Jaroszewki J, Hansel, W. Intraluteal administration of a nitric oxide synthase blocker stimulates progesterone, oxytocin secretion and prolongs the life span of the bovine corpus luteum. Proc Soc Exptl Biol Med 2000;224:50-5; Skarzynski D, Jaroszewki J, Bah, M, et al. Administration of nitric oxide synthase inhibitor counteracts prostaglandin F(2alpha)-induced luteolysis in cattle. Biol Reprod 2003;68:1674-81]. The objective of this experiment was to determine the effect of a long acting NO donor or a NOS inhibitor infused chronically into the interstitial tissue of the ovarian vascular pedicle adjacent to the ovary with a corpus luteum on secretion of progesterone during the ovine estrous cycle. Ewes were treated either with Vehicle (N=5); Diethylenetriamine (DETA-control for DETA-NONOate; N=5); (Z)-1-[2-(2-aminoethyl)-N-(2-ammonioethyl) amino]diazen-1-ium-1,2-diolate (DETA-NONOate-long acting NO donor; N=6); or l-nitro-arginine methyl ester (l-NAME-NOS inhibitor; N=6) every 6 h from 24:00 h (0 h) on day 8 through 18:00 h on day 18 of the estrous cycle. Jugular venous blood was collected every 6h for analysis for progesterone and corpora lutea were collected at 18:00 h on day 18 and weighed. Weights of corpora lutea were heavier (P< or =0.05) in DETA-NONOate-treated ewes when compared to Vehicle, DETA, or l-NAME-treated ewes, which did not differ amongst each other (P> or =0.05). Profiles of progesterone in jugular venous blood on days 8-18 differed (P< or =0.05) in DETA-NONOate-treated ewes when compared to Vehicle, DETA, or l-NAME-treated ewes did not differ (P> or =0.05) amongst each other. It is concluded that NO is not luteolytic during the ovine estrous cycle, but may instead be antiluteolytic and prevent luteolysis.     

Is it a paradox or misinterpretation?

The paradox recently raised by Wang and Yuan (Proteins 2000;38:165-175) in protein structural class prediction is actually a misinterpretation of the data reported in the literature. The Bayes decision rule, which was deemed by Wang and Yuan to be the most powerful method for predicting protein structural classes based on the amino acid composition, and applied by these investigators to derive the upper limit of prediction rate for structural classes, is actually completely the same as the component-coupled algorithm proposed by previous investigators (Chou et al., Proteins 1998;31:97-103). Owing to lack of a complete or near-complete training data set, the upper limit rate thus derived by these investigators might be both invalid and misleading. Clarification of these points will further stimulate investigation of this interesting area.     

Is ADHD adaptive or non-adaptive behavior?

The evolutionary approach to the issue of ADHD derives from the assumption that what is regarded as a pathological phenomenon today was once an adaptive response to the conditions of life in the ancestral stages of human development. The paper argues against this conception on the basis of the clinical picture of ADHD. The author believes that in the previous "natural" conditions the ADHD syndrome was even more of a maladaptation than in the "protective" conditions of present-day life.     

Is human thioredoxin monomeric or dimeric?

We have examined the molecular weight and rotational correlation time of human thioredoxin by analytical ultracentrifugation and NMR spectroscopy, respectively. Two variants of human thioredoxin were studied, namely human thioredoxin identical in amino acid sequence to the one whose NMR structure we previously determined (C62A, C69A, C73A, M74T) and human thioredoxin (C62A, C69A, C73A, M74) containing the wild-type amino acid methionine at position 74. In both cases, the experimental data indicate that the predominant species is monomeric and we find no evidence for the existence of a well-defined dimeric form as was observed in the recently reported crystal structure (Weichsel et al., 1996) of human thioredoxin and the C73S mutant.