How Tough are Sclerophylls?

Fracture toughness was estimated for a 'least tough' path inthe leaves of woody species from three sclerophyllous plantcommunities. Most of the species from Mediterranean, tropicalheath forest and lowland tropical rain forest habitats had verytough leaves, with toughness generally 600-1300 J m^-2, whichis two to four times higher than soft-leaved tropical pioneertrees. The toughest leaf (2032 J m^-2), Parishia insignis, camefrom the canopy of the lowland rain forest. Leaves from theshaded understorey of the rain forest did not appear any lesstough than those from the canopy.Copyright 1993, 1999 AcademicPress Leaf fracture toughness, sclerophylly, Mediterranean vegetation, tropical forest     

How repetitive are genomes?

Background  

Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index of repetitiveness, I _r, which can be computed in time proportional to the length of the sequences analyzed. We apply it to 336 genomes from all three domains of life.     

How reticulated are species?

Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree‐like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.     

How antigenic are antigenic peptides?

Most of a protein surface is potentially antigenic, consisting of numerous overlapping domains each complementary to antibody-combining sites. These domains may include peptide sequences that are demonstrably antigenic but only when antibodies from the appropriate host individuals and species are used. Methods for locating antigenic peptide sequences are described in which hydrophilic polyamide supports are used for peptide synthesis, then solid-phase radioimmunoassay with antisera and protein A. Most antigenic domains, however, comprise amino acid side chains contributed by two or more nearby polypeptide chains. Such domains can be identified by comparing the cross-reactivities of groups of very closely related proteins towards monoclonal antibodies raised to one of them. Such studies, using myoglobins, have identified a number of residues not previously shown to be antigenic and have provided a guide for the choice of synthetic peptides which are likely to carry several immunodominant side chains. One such peptide corresponding to residues (72–89) of beef myoglobin has been shown, using CD and antibodies to the parent protein, to have interesting conformational and antigenic properties. The peptide (25–55) is also antigenic.     

How essential are nonessential genes?

Gene essentiality in bacteria has been identified in silico, focusing on gene persistence, or experimentally, focusing on the growth of knockouts in rich media. Comparing 55 genomes of Firmicutes and Gamma-proteobacteria to identify the genes which, while persistent among genomes, do not lead to a lethal phenotype when inactivated, we show that the characteristics of persistence, conservation, expression, and location are shared between persistent nonessential (PNE) genes and experimentally essential genes. PNE genes show an overrepresentation of genes related to maintenance and stress response. This outlines the limits of current experimental techniques to define gene essentiality and highlights the essential role of genes implicated in maintenance which, although dispensable for growth, are not dispensable from an evolutionary point of view. Firmicutes and Gamma-proteobacteria are mostly differing in the construction of the cell envelope, DNA replication and proofreading, and RNA degradation. In addition to suggesting functions for persistent genes that had until now resisted identification, we show that these genes have many characters in common with experimentally identified essential genes. They should then be regarded as truly essential genes.     

How ancient are ancient asexuals?

Ancient asexual animal groups, such as bdelloid rotifers and darwinuloid ostracods, are excellent model organisms to study the effects of long-term asexuality. However, the absolute length of time that these groups have been fully asexual is mostly ignored. In the case of the darwinuloid ostracods, the fossil record shows that sexual reproduction disappeared almost completely after the end of Permian mass extinction (ca. 245 Myr ago), although several putative records of males from the Mesozoic obscure the exact time-frame of obligate asexuality in darwinuloids. Here, we re-examine the Mesozoic darwinuloid records, with regard to the reproductive mode of the assemblages. Three criteria to distinguish males in fossil populations (lack of brood pouch, position of muscle scars and size dimorphism) are used here to test for the presence of males in darwinuloid assemblages. A large, well-preserved assemblage of Darwinula leguminella (Forbes 1885) from the latest Jurassic (ca. 145 Myr ago) of England is found to be markedly variable in size and shape, but nevertheless turns out to be an all female assemblage. The exceptional preservation of the material also allows the re-assignment of this species to the extant darwinuloid genus Alicenula. All other putative dimorphic darwinuloid records from the Mesozoic are re-examined using the same criteria. The hypothesis that these assemblages represent bisexual populations is rejected for all post-Triassic (ca. 208 Myr ago) records.     

How clonal are human mitochondria?

Phylogenetic trees constructed using human mitochondrial sequences contain a large number of homoplasies. These are due either to repeated mutation or to recombination between mitochondrial lineages. We show that a tree constructed using synonymous variation in the protein coding sequences of 29 largely complete human mitochondrial molecules contains 22 homoplasies at 32 phylogenetically informative sites. This level of homoplasy is very unlikely if inheritance is clonal, even if we take into account base composition bias. There must either be 'hypervariable' sites or recombination between mitochondria. We present evidence which suggests that hypervariable sites do not exist in our data. It therefore seems likely that recombination has occurred between mitochondrial lineages in humans.     

How old are bacterial pathogens?

Only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. The global genetic diversity of Helicobacter pylori, which infects human stomachs, parallels that of its human host. The time to the most recent common ancestor (tMRCA) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence within H. pylori against major ancient human migrations. Similarly, genomic reconstructions of Mycobacterium tuberculosis, the cause of tuberculosis, from ancient skeletons in South America and mummies in Hungary support estimates of less than 6000 years for the tMRCA of M. tuberculosis. Finally, modern global patterns of genetic diversity and ancient DNA studies indicate that during the last 5000 years plague caused by Yersinia pestis has spread globally on multiple occasions from China and Central Asia. Such tMRCA estimates provide only lower bounds on the ages of bacterial pathogens, and additional studies are needed for realistic upper bounds on how long humans and animals have suffered from bacterial diseases.     

How safe are microbiology texts ?

Eleven practical microbiology books intended or recommended for schools have been evaluated for safety. A number of the texts are unsatisfactory and suggest techniques and, or organisms which are potentially dangerous. The authors consider that one book should be withdrawn. A code of recommendations to authors and publishers is included and it is suggested that professional societies should monitor future books.     

How many species are there?

How many species are there is a question receiving more attention from biologists and reasons for this are suggested. Different methods of answering this question are examined and include: counting all species; extrapolations from known faunas and regions; extrapolations from samples; methods using ecological models; censusing taxonomists' views. Most of these methods indicate that global totals of 5 to 15 million species are reasonable. The implications of much higher estimates of 30 million species or more are examined, particularly the question of where these millions of species might be found.     

How perennial are perennial plants?

Trade-offs involving life span are important in the molding of plant life histories. However, the empirical examination of such patterns has so far been limited by the fact that information on life span is mainly available in terms of discrete categories; annuals, semelparous perennials and iteroparous perennials. We used transition matrix models to project continuous estimates of conditional life spans from published information on size- or stage-structured demography for 71 perennial plant species. The projected life span ranged from 4.3 to 988.6 years and more than half of the species had a life span of more than 35 years. Woody plants had on average a projected life span more than four times as long as non-woody plants. Life spans were higher in forests than in open habitats and individuals of non-clonal species tended to have a longer life span than ramets of clonal species. Self-incompatible plants on average lived longer than self-compatible plants. There were no clear relations between life span and geographical region, dispersal syndrome, pollination mode, seed size or the presence of a seed bank. We conclude that accurate estimates of life span are central to understand how longevity is correlated to other traits within the group of perennial plants.     

How many birds are there?

Attempts to assess the magnitude of global biodiversity have focused on estimating species richness. However, this is but one component of biodiversity, and others, such as numbers of individuals or biomass, are at least as poorly known and just as important to quantify. Here, we use a variety of methods to estimate the global number of individuals for a single taxon, birds. The different methods yield surprisingly consistent estimates of a global bird population of between 200 billion and 400 billion individuals (1 billion=109). We discuss some of the implications of this figure.     

How are tonoplast proteins degraded?

Protein turnover is fundamental both for development and cellular homeostasis. The mechanisms responsible for the turnover of integral membrane proteins in plant cells are however still largely unknown. Recently, considerable attention has been devoted to the degradation of plasma membrane proteins. We have now studied the turnover of a tonoplast protein, the potassium channel TPK1, in fully differentiated Arabidopsis leaf cells and showed that its degradation occurs upon internalization into the vacuole. Here, we discuss the possible mechanisms and triggering events involved.