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The article presents the work of biochemist Julie Theriot and her research team in combining a large-scale study using microscopy with mathematical modelling. Her group is determined by an interplay between membrane tension and the distribution of actin filaments for certain cell types, shape and thus movement. Theriot explains that for those eukaryotic cells that do not have a cell wall, shape is intrinsically connected to the inner mechanics that facilitate cell movement. Theriot embraces the applied mathematics involved in the work as she mentioned the whole reason for her existence is to make cell biology a more quantitative science.

The article discusses about the research in science done by North American countries. Topics include the researchers and budget allocated for nature science and life science in the U.S. and Canada, National Institutes of Health of the countries, and the research profiles of Harvard University in Massachusetts and University of Toronto in Canada. Several charts of the research efficiency and strengths of U.S. and Canada, and articles published in journals of the universities.

Evaluates the periodical 'Macromolecular Bioscience.' Journal format; Sections; Presentation of papers; Periodical layout.

The article offers information to biologists who wish to submit their papers to the journal "Nature." The journal aspires to publish papers that are not only interesting and thought-provoking, but reproducible and useful. To be published, materials and reagents need to be carefully described and readily available to interested scientists.

The article presents statistics concerning Spanish authors and researchers contributing to "Nature." 32 percent of researchers working in Spain have contributed to papers in the periodical in 2006. 86 percent of papers in the periodical with contributing authors from Spain are related to biological sciences.

The article discusses the scientific publishing contributions of North America to the Nature Index database in 2014. Topics cited include the region's article and weight fractional count, the pattern of top five institutions' relative subject area distribution and collaborativeness and top three country collaborations, the initiative of the Canadian government to launch the Canadian High Arctic Research Station, and percentage of life science research in the U.S.

The article focuses on the career of biologist Alina Vrabioiu. After finishing high school in Romania, she went to the U.S. and studied at the Massachusetts Institute of Technology. After receiving PhD in biology from Harvard University, she co-authored a paper with her adviser, professor Tim Mitchison.

Presents various research on biological sciences published between July and September 2005 issue of the journal "Nature."

The article discusses the science research done by North and Western Europe. Topics include the research and finance of Germany, the research and development initiative of the European Union, and the researcher strength of various European countries. Great Britain leading in researches in life sciences, and those conducted by universities across Europe are also mentioned. Several charts listing the research detains of the European nations are also given.

The article reviews two Web sites tinyurl.com from Nature Network and www.connotea.org from Connotea.

The author reflects on the pitfalls on the massive amounts of data on the genome studies of biologists. The author states that scientists are making many careless errors such as the high number of corrections on the research paper on life sciences. The author also mentions that the scientific errors are driven by the pressure of generating surprising results and quick publishing. Moreover, the importance of training on experimental method and collaboration with good statisticians is recommended.

The article provides information about "Nature" in South Africa. There are submissions to "Nature" coming from South African since January 2006. 15 authors who are working in South Africa have published original research in "Nature" in the past year. 75 percent of papers published in "Nature" that have contributing authors from South Africa have been in biological sciences.

The article offers information about a list of articles related to biological sciences that can be downloaded in the Nature's top ten Web sites. The articles are in portable document format. One article was written by Monica Bricelj on how genetic mutations of a protein in clams can lead to the accumulation of toxins and increase the risk of poisoning in humans.

Discusses the importance of publishing research papers. Challenges faced by the researcher in publishing the research; Need to convince peer reviewers of the contribution of the research to the collective knowledge; Achievement of a researcher if his or her work get published.

The article presents research papers related to life sciences which are published in various journals in the U.S. An astronomy research regarding galaxies has determined the two structures of two distant and massive galaxies that seem to have formed early in the history of the universe. A cancer biology research has found that a molecular switch silences a neural development gene in the most common type of brain cancer. A botany research has found that interactions with other plant species may influence the arrangement of flowers' structure.

The article comments on the difference between theory and application in conservation biology. The gap between conservation biologists and practitioners lies between their form of actions, wherein the former writes and publish papers while the latter make decisions through their personal experiences and acquired knowledge.

The article discusses intentions to include a "Turning Points" series in the journal "Nature Cell Biology." It will report the pivotal reasons why individual scientists decided upon their biology research careers. It says the Nautilus blog introduces these autobiographical essays. It invites readers to suggest biologists that they'd like to be featured.

The article reports on the inquiry of a research team led by Tae Kook Kim of the Korea Advanced Institute of Science and Technology (KAIST) in Taejon on two articles published in "Science and Nature Chemical Biology" on imaging living cells. Tae Kook Kim reported a new method for imaging living cells that used magnetized nanoparticles. KAIST's investigation is still going but has released some preliminary findings that the scientific truth of the papers was in question. The journal's editor said that the KAIST investigation team told him that the authors wanted to pull back the paper as soon as possible.

This article presents excerpts of articles published previously in the journal "Nature." According to an article published in the August 27, 1955 issue of the journal, there is something very depressing about contemporary biological journals. Paper after paper records observations or experiments, analyses them cautiously, and in a timid and tentative way compares them with previous observations and experiments on the same theme. Only rarely does the writer disclose how his work is related to the broad panorama of biology. According to an article published in the August 24, 1905 issue of the journal,a somewhat lamentable aspect of modern science is the vast array of unorganized facts which are awaiting coordination. This is too often because they have been amassed without any definite idea of the purpose which they may serve.

The article reports on development related to research. Researchers from the University of Bonn showed that inhibiting cannabinoid receptors either genetically or chemically enhances skin hypersensitivity to allergens in mice. Meanwhile, researchers at the University of Texas analyzed 133 samples of yellow fever virus to examine RNA sequences. A team at the European Molecular Biology Laboratory showed that transcription factor called Bsx regulates the level of spontaneous physical activity.

The article focuses on evolutionary biology. Despite the comforting certainty of textbooks and 150 years of argument, the true relationships of the major groups of animals remain contentious. In the late 1990s, a series of controversial papers used molecular evidence to propose a radical rearrangement of animal phylum. Traditional trees group together phyla of bilaterally symmetrical animals that possess a body cavity lined with mesodermal tissue, the coelom, as Coelomata. Those without a true coelom are classified as Acoelomata and Pseudocoelomata.

The article presents excerpts of research papers published in previous issues of the journal "Nature." An article published in the March 23, 1905 issue of the journal discussed the contents of the book "Die Kalahari." Another article published in the March 26, 1955 issue of the journal presented the views of scientist J.R. Oppenheimer on issues related to communication.

The article discusses animal origin research by researcher Samrat Mondol and his colleagues of India's National Centre for Biological Sciences in Bangalore through endangered species deoxyribonucleic acid (DNA) analysis which would help in reducing illegal animal trade.

Sensitive probing of temperature variations on nanometre scales is an outstanding challenge in many areas of modern science and technology. In particular, a thermometer capable of subdegree temperature resolution over a large range of temperatures as well as integration within a living system could provide a powerful new tool in many areas of biological, physical and chemical research. Possibilities range from the temperature-induced control of gene expression and tumour metabolism to the cell-selective treatment of disease and the study of heat dissipation in integrated circuits. By combining local light-induced heat sources with sensitive nanoscale thermometry, it may also be possible to engineer biological processes at the subcellular level. Here we demonstrate a new approach to nanoscale thermometry that uses coherent manipulation of the electronic spin associated with nitrogen-vacancy colour centres in diamond. Our technique makes it possible to detect temperature variations as small as 1.8 mK (a sensitivity of 9 mK Hz−1/2) in an ultrapure bulk diamond sample. Using nitrogen-vacancy centres in diamond nanocrystals (nanodiamonds), we directly measure the local thermal environment on length scales as short as 200 nanometres. Finally, by introducing both nanodiamonds and gold nanoparticles into a single human embryonic fibroblast, we demonstrate temperature-gradient control and mapping at the subcellular level, enabling unique potential applications in life sciences. [ABSTRACT FROM AUTHOR]

Experience from different fields of life sciences suggests that accessible, complete reference maps of the components of the system under study are highly beneficial research tools. Examples of such maps include libraries of the spectroscopic properties of molecules, or databases of drug structures in analytical or forensic chemistry. Such maps, and methods to navigate them, constitute reliable assays to probe any sample for the presence and amount of molecules contained in the map. So far, attempts to generate such maps for any proteome have failed to reach complete proteome coverage. Here we use a strategy based on high-throughput peptide synthesis and mass spectrometry to generate an almost complete reference map (97% of the genome-predicted proteins) of the Saccharomyces cerevisiae proteome. We generated two versions of this mass-spectrometric map, one supporting discovery-driven (shotgun) and the other supporting hypothesis-driven (targeted) proteomic measurements. Together, the two versions of the map constitute a complete set of proteomic assays to support most studies performed with contemporary proteomic technologies. To show the utility of the maps, we applied them to a protein quantitative trait locus (QTL) analysis, which requires precise measurement of the same set of peptides over a large number of samples. Protein measurements over 78 S. cerevisiae strains revealed a complex relationship between independent genetic loci, influencing the levels of related proteins. Our results suggest that selective pressure favours the acquisition of sets of polymorphisms that adapt protein levels but also maintain the stoichiometry of functionally related pathway members. [ABSTRACT FROM AUTHOR]

The transference of post-dentary jaw elements to the cranium of mammals as auditory ossicles is one of the central topics in evolutionary biology of vertebrates. Homologies of these bones among jawed vertebrates have long been demonstrated by developmental studies; but fossils illuminating this critical transference are sparse and often ambiguous. Here we report the first unambiguous ectotympanic (angular), malleus (articular and prearticular) and incus (quadrate) of an Early Cretaceous eutriconodont mammal from the Jehol Biota, Liaoning, China. The ectotympanic and malleus have lost their direct contact with the dentary bone but still connect the ossified Meckel's cartilage (OMC); we hypothesize that the OMC serves as a stabilizing mechanism bridging the dentary and the detached ossicles during mammalian evolution. This transitional mammalian middle ear narrows the morphological gap between the mandibular middle ear in basal mammaliaforms and the definitive mammalian middle ear (DMME) of extant mammals; it reveals complex changes contributing to the detachment of ear ossicles during mammalian evolution. [ABSTRACT FROM AUTHOR]

The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for three-dimensional (3D) structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography, or by scanning a series of thin sections through the sample, as in confocal microscopy. Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning ‘curved’ and graphein meaning ‘writing’), which under certain circumstances enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is in principle determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 Å resolution, and a single poliovirus at 2–3 nm resolution, from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we also provide a preliminary demonstration that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. With further development, this approach of obtaining complete 3D structure information from a single view could find broad applications in the physical and life sciences. [ABSTRACT FROM AUTHOR]

The article reports that the study of functioning groups of molecules is an important frontier of biology at reductionist and holistic levels. Systems biology couples the acquisition of comprehensive, high definition data sets to the construction of quantitative models and computer simulations. In the past five years, systems-biology institutes, departments and initiatives have been springing up across the globe. New journals have been launched, including, The Institution of Electrical Engineers' "Systems Biology" and Nature Publishing Group's "Molecular Systems Biology."

The article presents a biographical sketch of Carole Moquin-Pattey, head of unit, European Medical Research Councils, Strasbourg, France. Moquin-Pattey's career is marked by a series of double lives--art and science, chemistry and biology, adaptability and obstinacy. It has led her from work in a hospital pharmacy to heading the European Medical Research Councils (EMRC), via plant biology, marine chemistry and membership of the French ethics committee. Her efforts eventually secured her a postdoctorate in the United States.

In materials science and biology, optical near-field microscopies enable spatial resolutions beyond the diffraction limit, but they cannot provide the atomic-scale imaging capabilities of electron microscopy. Given the nature of interactions between electrons and photons, and considering their connections through nanostructures, it should be possible to achieve imaging of evanescent electromagnetic fields with electron pulses when such fields are resolved in both space (nanometre and below) and time (femtosecond). Here we report the development of photon-induced near-field electron microscopy (PINEM), and the associated phenomena. We show that the precise spatiotemporal overlap of femtosecond single-electron packets with intense optical pulses at a nanostructure (individual carbon nanotube or silver nanowire in this instance) results in the direct absorption of integer multiples of photon quanta (nħω) by the relativistic electrons accelerated to 200 keV. By energy-filtering only those electrons resulting from this absorption, it is possible to image directly in space the near-field electric field distribution, obtain the temporal behaviour of the field on the femtosecond timescale, and map its spatial polarization dependence. We believe that the observation of the photon-induced near-field effect in ultrafast electron microscopy demonstrates the potential for many applications, including those of direct space-time imaging of localized fields at interfaces and visualization of phenomena related to photonics, plasmonics and nanostructures. [ABSTRACT FROM AUTHOR]

The article focuses on the impact of evolutionary developmental biology insights and the mind sciences on the understanding of human capacity to think and the ways in which human mind constrains cultural expressions. It notes that there are no gaps in the dispersion of mental capacities throughout the species or of potential cultural forms. It points out that developments in evolutionary developmental biology and mind sciences have two gaps, the gap representing psychological discontinuity between humans and other animals and the gap representing cultural discontinuities within possible cultural forms.

This article focuses on research highlights of chemical biology. First article focuses onlight-switchable activity. An enzyme has been given light-switchable activity by having one of its key amino acids replaced with a 'photocaged' version. The tRNA molecule carries the amino acid to the cell's protein-synthesizing machinery, the ribosome, where it is stitched into the growing protein chain. Another article focuses on structural biology. Although X-ray crystallography has been used to elucidate the molecular mechanisms of many biological processes, it rarely reveals the exact position of important hydrogen atoms. Low-temperature neutron structures of other proteins have been solved.

The article discusses systems biology, a modern approach and increasingly adopted by pharmaceutical companies. Systems biology is about collecting unprecedented amounts of data from cell and making sense of it through mathematical models. The system has many advocates and it wider adoption seems to be inevitable. Industry analysts at PriceWaterhouseCoopers predict that systems biology will have become more prevalent by 2020. However, some people in the industry and academe remain hesitant about systems biology.

As arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood. Here we report the sequencing and analysis of the ∼98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole-genome phylogenetic analysis suggests that placozoans belong to a ‘eumetazoan’ clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome shows conserved gene content, gene structure and synteny in relation to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signalling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages. [ABSTRACT FROM AUTHOR]

We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation. [ABSTRACT FROM AUTHOR]

Stomatal pores, formed by two surrounding guard cells in the epidermis of plant leaves, allow influx of atmospheric carbon dioxide in exchange for transpirational water loss. Stomata also restrict the entry of ozone — an important air pollutant that has an increasingly negative impact on crop yields, and thus global carbon fixation and climate change. The aperture of stomatal pores is regulated by the transport of osmotically active ions and metabolites across guard cell membranes. Despite the vital role of guard cells in controlling plant water loss, ozone sensitivity and CO2 supply, the genes encoding some of the main regulators of stomatal movements remain unknown. It has been proposed that guard cell anion channels function as important regulators of stomatal closure and are essential in mediating stomatal responses to physiological and stress stimuli. However, the genes encoding membrane proteins that mediate guard cell anion efflux have not yet been identified. Here we report the mapping and characterization of an ozone-sensitive Arabidopsis thaliana mutant, slac1. We show that SLAC1 (SLOW ANION CHANNEL-ASSOCIATED 1) is preferentially expressed in guard cells and encodes a distant homologue of fungal and bacterial dicarboxylate/malic acid transport proteins. The plasma membrane protein SLAC1 is essential for stomatal closure in response to CO2, abscisic acid, ozone, light/dark transitions, humidity change, calcium ions, hydrogen peroxide and nitric oxide. Mutations in SLAC1 impair slow (S-type) anion channel currents that are activated by cytosolic Ca2+ and abscisic acid, but do not affect rapid (R-type) anion channel currents or Ca2+ channel function. A low homology of SLAC1 to bacterial and fungal organic acid transport proteins, and the permeability of S-type anion channels to malate suggest a vital role for SLAC1 in the function of S-type anion channels. [ABSTRACT FROM AUTHOR]

The Sir2 deacetylase regulates chromatin silencing and lifespan in Saccharomyces cerevisiae. In mice, deficiency for the Sir2 family member SIRT6 leads to a shortened lifespan and a premature ageing-like phenotype. However, the molecular mechanisms of SIRT6 function are unclear. SIRT6 is a chromatin-associated protein, but no enzymatic activity of SIRT6 at chromatin has yet been detected, and the identity of physiological SIRT6 substrates is unknown. Here we show that the human SIRT6 protein is an NAD+-dependent, histone H3 lysine 9 (H3K9) deacetylase that modulates telomeric chromatin. SIRT6 associates specifically with telomeres, and SIRT6 depletion leads to telomere dysfunction with end-to-end chromosomal fusions and premature cellular senescence. Moreover, SIRT6-depleted cells exhibit abnormal telomere structures that resemble defects observed in Werner syndrome, a premature ageing disorder. At telomeric chromatin, SIRT6 deacetylates H3K9 and is required for the stable association of WRN, the factor that is mutated in Werner syndrome. We propose that SIRT6 contributes to the propagation of a specialized chromatin state at mammalian telomeres, which in turn is required for proper telomere metabolism and function. Our findings constitute the first identification of a physiological enzymatic activity of SIRT6, and link chromatin regulation by SIRT6 to telomere maintenance and a human premature ageing syndrome. [ABSTRACT FROM AUTHOR]

In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human intervention, it is necessary to encode within the biopolymer sequences the reaction pathways by which self-assembly occurs. Nucleic acids show promise as a design medium for engineering dynamic functions, including catalytic hybridization, triggered self-assembly and molecular computation. Here, we program diverse molecular self-assembly and disassembly pathways using a ‘reaction graph’ abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif. Molecular programs are executed for a variety of dynamic functions: catalytic formation of branched junctions, autocatalytic duplex formation by a cross-catalytic circuit, nucleated dendritic growth of a binary molecular ‘tree’, and autonomous locomotion of a bipedal walker. [ABSTRACT FROM AUTHOR]

The Earth’s mantle transition zone could potentially store a large amount of water, as the minerals wadsleyite and ringwoodite incorporate a significant amount of water in their crystal structure. The water content in the transition zone can be estimated from the electrical conductivities of hydrous wadsleyite and ringwoodite, although such estimates depend on accurate knowledge of the two conduction mechanisms in these minerals (small polaron and proton conductions), which early studies have failed to distinguish between. Here we report the electrical conductivity of these two minerals obtained by high-pressure multi-anvil experiments. We found that the small polaron conductions of these minerals are substantially lower than previously estimated. The contributions of proton conduction are small at temperatures corresponding to the mantle transition zone and the conductivity of wadsleyite is considerably lower than that of ringwoodite for both mechanisms. The dry model mantle shows considerable conductivity jumps associated with the olivine–wadsleyite, wadsleyite–ringwoodite and post-spinel transitions. Such a dry model explains well the currently available conductivity–depth profiles obtained from geoelectromagnetic studies. We therefore conclude that there is no need to introduce a significant amount of water in the mantle transition to satisfy electrical conductivity constraints. [ABSTRACT FROM AUTHOR]

The long-standing assumption that messenger RNA (mRNA) degradation in Escherichia coli begins with endonucleolytic cleavage has been challenged by the recent discovery that RNA decay can be triggered by a prior non-nucleolytic event that marks transcripts for rapid turnover: the rate-determining conversion of the 5′ terminus from a triphosphate to a monophosphate. This modification creates better substrates for the endonuclease RNase E, whose cleavage activity at internal sites is greatly enhanced when the RNA 5′ end is monophosphorylated. Moreover, it suggests an explanation for the influence of 5′ termini on the endonucleolytic cleavage of primary transcripts, which are triphosphorylated. However, no enzyme capable of removing pyrophosphate from RNA 5′ ends has been identified in any bacterial species. Here we show that the E. coli protein RppH (formerly NudH/YgdP) is the RNA pyrophosphohydrolase that initiates mRNA decay by this 5′-end-dependent pathway. In vitro, RppH efficiently removes pyrophosphate from the 5′ end of triphosphorylated RNA, irrespective of the identity of the 5′-terminal nucleotide. In vivo, it accelerates the degradation of hundreds of E. coli transcripts by converting their triphosphorylated 5′ ends to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. That the action of the pyrophosphohydrolase is impeded when the 5′ end is structurally sequestered by a stem-loop helps to explain the stabilizing influence of 5′-terminal base pairing on mRNA lifetimes. Together, these findings suggest a possible basis for the effect of RppH and its orthologues on the invasiveness of bacterial pathogens. Interestingly, this master regulator of 5′-end-dependent mRNA degradation in E. coli not only catalyses a process functionally reminiscent of eukaryotic mRNA decapping but also bears an evolutionary relationship to the eukaryotic decapping enzyme Dcp2. [ABSTRACT FROM AUTHOR]

Listeria monocytogenes is an intracellular bacterial pathogen that replicates rapidly in the cytosol of host cells during acute infection. Surprisingly, these bacteria were found to occupy vacuoles in liver granuloma macrophages during persistent infection of severe combined immunodeficient (SCID) mice. Here we show that L. monocytogenes can replicate in vacuoles within macrophages. In livers of SCID mice infected for 21 days, we observed bacteria in large LAMP1+ compartments that we termed spacious Listeria-containing phagosomes (SLAPs). SLAPs were also observed in vitro, and were found to be non-acidic and non-degradative compartments that are generated in an autophagy-dependent manner. The replication rate of bacteria in SLAPs was found to be reduced compared to the rate of those in the cytosol. Listeriolysin O (LLO, encoded by hly), a pore-forming toxin essential for L. monocytogenes virulence, was necessary and sufficient for SLAP formation. A L. monocytogenes mutant with low LLO expression was impaired for phagosome escape but replicated slowly in SLAPs over a 72 h period. Therefore, our studies reveal a role for LLO in promoting L. monocytogenes replication in vacuoles and suggest a mechanism by which this pathogen can establish persistent infection in host macrophages. [ABSTRACT FROM AUTHOR]

Most eukaryotic genes are interrupted by non-coding introns that must be accurately removed from pre-messenger RNAs to produce translatable mRNAs. Splicing is guided locally by short conserved sequences, but genes typically contain many potential splice sites, and the mechanisms specifying the correct sites remain poorly understood. In most organisms, short introns recognized by the intron definition mechanism cannot be efficiently predicted solely on the basis of sequence motifs. In multicellular eukaryotes, long introns are recognized through exon definition and most genes produce multiple mRNA variants through alternative splicing. The nonsense-mediated mRNA decay (NMD) pathway may further shape the observed sets of variants by selectively degrading those containing premature termination codons, which are frequently produced in mammals. Here we show that the tiny introns of the ciliate Paramecium tetraurelia are under strong selective pressure to cause premature termination of mRNA translation in the event of intron retention, and that the same bias is observed among the short introns of plants, fungi and animals. By knocking down the two P. tetraurelia genes encoding UPF1, a protein that is crucial in NMD, we show that the intrinsic efficiency of splicing varies widely among introns and that NMD activity can significantly reduce the fraction of unspliced mRNAs. The results suggest that, independently of alternative splicing, species with large intron numbers universally rely on NMD to compensate for suboptimal splicing efficiency and accuracy. [ABSTRACT FROM AUTHOR]

The article presents an analysis about the prospect of human cloning. Several scholars expressed their disappointments pertaining the moral psychology as well as their worries at the advent of in vitro fertilization treatment. In this context, an overview about a new picture of the emotion that underlies such responses to biology called disgust put together by a loose band of interdisciplinary psychologists and neuroscientists is given.

Advances in technology have allowed chemical sampling with high spatial resolution and the manipulation and measurement of individual molecules. Adaptation of these approaches to lab-on-a-chip formats is providing a new class of research tools for the investigation of biochemistry and life processes. [ABSTRACT FROM AUTHOR]

Understanding the molecular genetic basis of adaptations provides incomparable insight into the genetic mechanisms by which evolutionary diversification takes place. Whether the evolution of common traits in different lineages proceeds by similar or unique mutations, and the degree to which phenotypic evolution is controlled by changes in gene regulation as opposed to gene function, are fundamental questions in evolutionary biology that require such an understanding of genetic mechanisms. Here we identify novel changes in the molecular structure of a sodium channel expressed in snake skeletal muscle, tsNaV1.4, that are responsible for differences in tetrodotoxin (TTX) resistance among garter snake populations coevolving with toxic newts. By the functional expression of tsNaV1.4, we show how differences in the amino-acid sequence of the channel affect TTX binding and impart different levels of resistance in four snake populations. These results indicate that the evolution of a physiological trait has occurred through a series of unique functional changes in a gene that is otherwise highly conserved among vertebrates. [ABSTRACT FROM AUTHOR]

Complex networks have been studied extensively owing to their relevance to many real systems such as the world-wide web, the Internet, energy landscapes and biological and social networks. A large number of real networks are referred to as‘scale-free’because they show a power-law distribution of the number of links per node. However, it is widely believed that complex networks are not invariant or self-similar under a length-scale transformation. This conclusion originates from the‘small-world’property of these networks, which implies that the number of nodes increases exponentially with the‘diameter’of the network, rather than the power-law relation expected for a self-similar structure. Here we analyse a variety of real complex networks and find that, on the contrary, they consist of self-repeating patterns on all length scales. This result is achieved by the application of a renormalization procedure that coarse-grains the system into boxes containing nodes within a given‘size’. We identify a power-law relation between the number of boxes needed to cover the network and the size of the box, defining a finite self-similar exponent. These fundamental properties help to explain the scale-free nature of complex networks and suggest a common self-organization dynamics. [ABSTRACT FROM AUTHOR]

Understanding the capacity of natural populations to adapt to their local environment is a central topic in evolutionary biology. Phenotypic differences between populations may have a genetic basis, but showing that they reflect different adaptive optima requires the quantification of both gene flow and selection. Good empirical data are rare. Using data on a spatially structured island population of great tits (Parus major), we show here that a persistent difference in mean clutch size between two subpopulations only a few kilometres apart has a major genetic component. We also show that immigrants from outside the island carry genes for large clutches. But gene flow into one subpopulation is low, as a result of a low immigration rate together with strong selection against immigrant genes. This has allowed for adaptation to the island environment and the maintenance of small clutches. In the other area, however, higher gene flow prevents local adaptation and maintains larger clutches. We show that the observed small-scale genetic difference in clutch size is not due to divergent selection on the island, but to different levels of gene flow from outside the island. Our findings illustrate the large effect of immigration on the evolution of local adaptations and on genetic population structure. [ABSTRACT FROM AUTHOR]

Presents an introduction to the December 23, 2004 issue of the journal "Nature."

All inferences in comparative biology depend on accurate estimates of evolutionary relationships. Recent phylogenetic analyses have turned away from maximum parsimony towards the probabilistic techniques of maximum likelihood and bayesian Markov chain Monte Carlo (BMCMC). These probabilistic techniques represent a parametric approach to statistical phylogenetics, because their criterion for evaluating a topology-the probability of the data, given the tree-is calculated with reference to an explicit evolutionary model from which the data are assumed to be identically distributed. Maximum parsimony can be considered nonparametric, because trees are evaluated on the basis of a general metric-the minimum number of character state changes required to generate the data on a given tree-without assuming a specific distribution. The shift to parametric methods was spurred, in large part, by studies showing that although both approaches perform well most of the time, maximum parsimony is strongly biased towards recovering an incorrect tree under certain combinations of branch lengths, whereas maximum likelihood is not. All these evaluations simulated sequences by a largely homogeneous evolutionary process in which data are identically distributed. There is ample evidence, however, that real-world gene sequences evolve heterogeneously and are not identically distributed. Here we show that maximum likelihood and BMCMC can become strongly biased and statistically inconsistent when the rates at which sequence sites evolve change non-identically over time. Maximum parsimony performs substantially better than current parametric methods over a wide range of conditions tested, including moderate heterogeneity and phylogenetic problems not normally considered difficult. [ABSTRACT FROM AUTHOR]

Understanding the emergence of cooperation is a fundamental problem in evolutionary biology. Evolutionary game theory has become a powerful framework with which to investigate this problem. Two simple games have attracted most attention in theoretical and experimental studies: the Prisoner's Dilemma and the snowdrift game (also known as the hawk-dove or chicken game). In the Prisoner's Dilemma, the non-cooperative state is evolutionarily stable, which has inspired numerous investigations of suitable extensions that enable cooperative behaviour to persist. In particular, on the basis of spatial extensions of the Prisoner's Dilemma, it is widely accepted that spatial structure promotes the evolution of cooperation. Here we show that no such general predictions can be made for the effects of spatial structure in the snowdrift game. In unstructured snowdrift games, intermediate levels of cooperation persist. Unexpectedly, spatial structure reduces the proportion of cooperators for a wide range of parameters. In particular, spatial structure eliminates cooperation if the cost-to-benefit ratio of cooperation is high. Our results caution against the common belief that spatial structure is necessarily beneficial for cooperative behaviour. [ABSTRACT FROM AUTHOR]