How do so few control so many?

The separation of sister chromatids at the metaphase-to-anaphase transition is triggered by a protease called separase that is activated by the destruction of an inhibitory chaperone (securin). This process is mediated by a ubiquitin protein ligase called the anaphase-promoting complex or cyclosome (APC/C), along with a protein called Cdc20. It is vital that separase not be activated before every single chromosome has been aligned on the mitotic spindle. Kinetochores that have not yet attached to microtubules catalyze the sequestration of Cdc20 by an inhibitor called Mad2. Recent experiments shed important insight into how Mad2 molecules bound to centromeres through their association with a protein called Mad1 might be transferred to Cdc20 and thereby inhibit securin's destruction.     

Laws of biology: why so few?

Finding fundamental organizing principles is the current intellectual front end of systems biology. From a hydrogen atom to the whole cell level, organisms manage massively parallel and massively interactive processes over several orders of magnitude of size. To manage this scale of informational complexity it is natural to expect organizing principles that determine higher order behavior. Currently, there are only hints of such organizing principles but no absolute evidences. Here, we present an approach as old as Mendel that could help uncover fundamental organizing principles in biology. Our approach essentially consists of identifying constants at various levels and weaving them into a hierarchical chassis. As we identify and organize constants, from pair-wise interactions to networks, our understanding of the fundamental principles in biology will improve, leading to a theory in biology.     

Diacylglycerol kinases: why so many of them?

Diacylglycerol (DAG) kinase (DGK) modulates the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA. To date, ten mammalian DGK isozymes have been identified. In addition to the C1 domains (protein kinase C-like zinc finger structures) conserved commonly in all DGKs, these isoforms possess a variety of regulatory domains of known and/or predicted functions, such as a pair of EF-hand motifs, a pleckstrin homology domain, a sterile alpha motif domain and ankyrin repeats. Beyond our expectations, recent studies have revealed that DGK isozymes play pivotal roles in a wide variety of signal transduction pathways conducting development, neural and immune responses, cytoskeleton reorganization and carcinogenesis. Moreover, there has been rapidly growing evidence indicating that individual DGK isoforms exert their specific roles through interactions with unique partner proteins such as protein kinase Cs, Ras guanyl nucleotide-releasing protein, chimaerins and phosphatidylinositol-4-phosphate 5-kinase. Therefore, an emerging paradigm for DGK is that the individual DGK isoforms assembled in their own signaling complexes should carry out spatio-temporally segregated tasks for a wide range of biological processes via regulating local, but not global, concentrations of DAG and/or PA.     

Why so few?

Nobel Prize Women in Science: Their struggles and momentous discoveries (1998). S. Bertsch McGrayne. Carol Publishing Group, 448 pp. $19.95 paper ISBN 0806520256.     

Toxin–antitoxin systems: why so many,what for?

Toxin-antitoxin (TA) systems are small genetic modules that are abundant in bacterial genomes. Three types have been described so far, depending on the nature and mode of action of the antitoxin component. While type II systems are surprisingly highly represented because of their capacity to move by horizontal gene transfer, type I systems appear to have evolved by gene duplication and are more constrained. Type III is represented by a unique example located on a plasmid. Type II systems promote stability of mobile genetic elements and might act at the selfish level. Conflicting hypotheses about chromosomally encoded systems, from programmed cell death and starvation-induced stasis to protection against invading DNA and stabilization of large genomic fragments have been proposed.     

Replication origins: why do we need so many?

During the G1 phase of the cell cycle, replication origins are prepared to fire, a process that is referred to as origin licensing. It was often pondered what a cell's fate would be if not all of its replication origins were licensed and subsequently activated during S phase. One obvious prediction was that S phase would simply be prolonged. As it turns out, however, the consequences are much more complex. A short G1 phase enforced by premature entry into S phase, or other events that negatively affect origin licensing, will ultimately compromise the cell's ability to complete DNA replication before entering mitosis. As a result, the cell becomes genomically unstable when it attempts to repair unreplicated DNA during anaphase. Thus, the density of active replication origins in the chromosomes of eukaryotic cells determines S phase dynamics and chromosome stability during mitosis.     

Multiple chaperonins in bacteria – why so many?

A significant proportion of bacteria express two or more chaperonin genes. Chaperonins are a group of molecular chaperones, defined by sequence similarity, required for the folding of some cellular proteins. Chaperonin monomers have a mass of c . 60 kDa, and are typically found as large protein complexes containing 14 subunits arranged in two rings. The mechanism of action of the Escherichia coli GroEL protein has been studied in great detail. It acts by binding to unfolded proteins and enabling them to fold in a protected environment where they do not interact with any other proteins. GroEL can assist the folding of many proteins of different sizes, sequences, and structures, and homologues from many different bacteria can functionally replace GroEL in E. coli . What then are the functions of multiple chaperonins? Do they provide a mechanism for cells to increase their general chaperoning ability, or have they become specialized to take on specific novel cellular roles? Here I will review the genetic, biochemical, and phylogenetic evidence that has a bearing on this question, and show that there is good evidence for at least some specificity of function in multiple chaperonin genes.     

Two-component systems in Pseudomonas aeruginosa: why so many?

Screening the Pseudomonas aeruginosa genome has led to the identification of the highest number of putative genes encoding two-component regulatory systems of all bacterial genomes sequenced to date (64 and 63 encoding response regulators and histidine kinases, respectively). Sixteen atypical kinases, among them 11 devoid of an Hpt domain, and three independent Hpt modules were retrieved. These data suggest that P. aeruginosa possesses complex control strategies with which to respond to environmental challenges.     

Bumblebee sex ratios: why do bumblebees produce so many males?

Sex investment ratios in populations of bumblebees are male biased, which contradicts theoretical predictions. Male-biased investment ratios in eusocial Hymenoptera are assumed to be non-stable for both the queen and her workers. In this paper, we show that male-biased sex allocation does not necessarily decrease fitness in the bumblebee Bombus terrestris. A male-biased investment ratio can be the result of an optimal allocation of resources when resources are scarce if (i) there is a large cost difference between male and female production, (ii) there is uncertainty about the amount of resources a colony can invest, and (iii) only a proportion of the investment made in an individual can be reused. This resource allocation then leads to split sex ratios depending on the amount of resources available to a bumblebee colony: colonies under low resource conditions will show a male-biased investment ratio, whereas colonies under high resource conditions allocate more resources towards females. However, the extent to which bumblebee populations show a male-biased sex allocation cannot be explained by cost differences between male and female production alone. In a recent paper, A. F. G. Bourke argued that male-biased investment ratios in bumblebee populations are a by-product of the occurrence of protandry (males emerge before females). Here we will extend Bourke''s argument and show that within a protandrous population, both protandrous and protogynous (females emerge before males) colonies exist. The existence of protandrous and protogynous colonies results in split sex ratios in time, because protogynous colonies rely on males produced by protandrous colonies (partial protandry).     

The Azores diversity enigma: why are there so few Azorean endemic flowering plants and why are they so widespread?

Aim Endemism in the flora of the Azores is high (33%) but in other respects, notably the paucity of evolutionary radiations and the widespread distribution of most endemics, the flora differs markedly from the floras of the other Macaronesian archipelagos. We evaluate hypotheses to explain the distinctive patterns observed in the Azorean endemic flora, focusing particularly on comparisons with the Canary Islands. Location Azores archipelago. Methods Data on the distribution and ecology of Azorean endemic flowering plants are reviewed to ascertain the incidence of inter‐island allopatric speciation and adaptive, ecological speciation. These are contrasted with patterns for the Canary Islands. Patterns of endemism in the Azores and Canaries are further investigated in a phylogenetic context in relation to island age. beast was used to analyse a published molecular dataset for Pericallis (Asteraceae) and to investigate the relative ages of Azorean and Canarian lineages. Results There are few examples of inter‐island allopatric speciation in the Azorean flora, despite the considerable distances between islands and sub‐archipelagos. In contrast, inter‐island allopatric speciation has been an important process in the evolution of the Canary Islands flora. Phylogenetic data suggest that Azorean endemic lineages are not necessarily recent in origin. Furthermore, in Pericallis the divergence of the Azorean endemic lineage from its closest relative pre‐dates the radiation of a Canarian herbaceous clade by inter‐island allopatric speciation. Main conclusions The data presented do not support suggestions that hypotheses pertaining to island age, age of endemic lineages and ecological diversity considered individually explain the lack of radiations and the widespread distribution of Azorean endemics. We suggest that palaeoclimatic variation, a factor rarely considered in macroecological studies of island diversity patterns, may be an important factor. Palaeoclimatic data suggest frequent and abrupt transitions between humid and arid conditions in the Canaries during the late Quaternary, and such an unstable climate may have driven the recent diversification of the flora by inter‐island allopatric speciation, a process largely absent from the climatically more stable Azores. Further phylogenetic/phylogeographic analyses are necessary to determine the relative importance of palaeoclimate and other factors in generating the patterns observed.     

Why are there so few smart mammals (but so many smart birds)?

The expensive brain hypothesis predicts an interspecific link between relative brain size and life-history pace. Indeed, animals with relatively large brains have reduced rates of growth and reproduction. However, they also have increased total lifespan. Here we show that the reduction in production with increasing brain size is not fully compensated by the increase in lifespan. Consequently, the maximum rate of population increase (rmax) is negatively correlated with brain mass. This result is not due to a confounding effect of body size, indicating that the well-known correlation between rmax and body size is driven by brain size, at least among homeothermic vertebrates. Thus, each lineage faces a 'grey ceiling', i.e. a maximum viable brain size, beyond which rmax is so low that the risk of local or species extinction is very high. We found that the steep decline in rmax with brain size is absent in taxa with allomaternal offspring provisioning, such as cooperatively breeding mammals and most altricial birds. These taxa thus do not face a lineage-specific grey ceiling, which explains the far greater number of independent origins of large brain size in birds than mammals. We also predict that (absolute and relative) brain size is an important predictor of macroevolutionary extinction patterns.     

Ten years of AFLP in ecology and evolution: why so few animals?

Researchers in the field of molecular ecology and evolution require versatile and low-cost genetic typing methods. The AFLP (amplified fragment length polymorphism) method was introduced 10 years ago and shows many features that fulfil these requirements. With good quality genomic DNA at hand, it is relatively easy to generate anonymous multilocus DNA profiles in most species and the start-up time before data can be generated is often less than a week. Built-in dynamic, yet simple modifications make it possible to find a protocol suitable to the genome size of the species and to screen thousands of loci in hundreds of individuals for a relatively low cost. Until now, the method has primarily been applied in studies of plants, bacteria and fungi, with a strong bias towards economically important cultivated species and their pests. In this review we identify a number of research areas in the study of wild species of animals where the AFLP method, presently very much underused, should be a very valuable tool. These aspects include classical problems such as studies of population genetic structure and phylogenetic reconstructions, and also new challenges such as finding markers for genes governing adaptations in wild populations and modifications of the protocol that makes it possible to measure expression variation of multiple genes (cDNA-AFLP) and the distribution of DNA methylation. We hope this review will help molecular ecologists to identify when AFLP is likely to be superior to other more established methods, such as microsatellites, SNP (single nucleotide polymorphism) analyses and multigene DNA sequencing.     

Do tigers displace leopards? If so, why?

We investigated predictions concerning the competitive relationships between tigers Panthera tigris and leopards Panthera pardus in Bardia National Park, Nepal, based on spatial distributions of scats and territorial markings (sign), analyses of scat content and census of wild ungulate prey. Medium-sized ungulates, in particular chital Axis axis, was the main food of both predators, but leopards consumed significantly larger proportions of domestic animals, small mammals, and birds than tigers. Tiger sign were never found outside the park, while leopard sign occurred both inside and outside, and were significantly closer to the park border than tiger sign. Significantly higher prey densities at locations of tiger sign than that of leopards were mainly due to a preference of the latter species for the park border areas. Our results imply that interference competition––and not competition for food––was a limiting factor for the leopard population, whose distribution was restricted to the margins of the tiger territories. We suggest that the composition of the prey base is a key factor in understanding the different results and interpretations reported in studies on tiger/leopard coexistence. There are two potential mechanisms that link interference competition and prey: (1) low abundance of large ungulate prey decreases foraging efficiency of tigers, leading to increased energetic stress and aggression towards leopards; and (2) increased diet overlap due to scarcity of large prey leads to increased encounter rates and increased levels of interference competition.     

Why are so many trees hollow?

In many living trees, much of the interior of the trunk can be rotten or even hollowed out. Previously, this has been suggested to be adaptive, with microbial or animal consumption of interior wood producing a rain of nutrients to the soil beneath the tree that allows recycling of those nutrients into new growth via the trees roots. Here I propose an alternative (non-exclusive) explanation: such loss of wood comes at very little cost to the tree and so investment in costly chemical defence of this wood is not economic. I discuss how this theory can be tested empirically.     

Female call preferences in tree-hole frogs: why are there so many unattractive males?

In tree-hole frogs, Metaphrynella sundana, the fundamental call frequency varies widely between males. In field playback experiments, females strongly preferred calls from the lower range of frequencies found in the population. There was no correlation, however, between male size and call frequency, as is normally the case for anurans, so large males were not necessarily more attractive to females. Presence or absence of upper harmonics in the call had no effect on female choice. Tree holes with shallow air columns were more often used by calling frogs, and were presumably more common, than deep holes. Since male M. sundana actively exploit the resonant properties of tree holes for mate attraction, and high frequencies match comparatively shallow holes, the benefits of attaining acoustic matching probably select for high-frequency calls. In addition, males with high-frequency calls may be heard from a greater distance in the vicinity of torrent streams. Since the level of such noise in the forest varies in time and space, different frequencies may prove optimal in different contexts, thereby preserving the observed variation within the population. Having an ‘unattractive’ high-frequency call should be potentially beneficial only when calling males do not congregate, a condition that our data suggest is fulfilled in this system.