DNA

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

8 typically slower than ϳ1 km s −1 ) might differ significantly from what is assumed by current modelling efforts 27 . The expected equation-of-state differences among small bodies (ice versus rock, for instance) presents another dimension of study; having recently adapted our code for massively parallel architectures (K. M. Olson and E.A, manuscript in preparation), we are now ready to perform a more comprehensive analysis.

The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system. The programs available and the conditions for transfer are described.

The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is https://www.bioinfo.rpi.edu/applications/ mfold. This URL will be referred to as 'MFOLDROOT'.

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure, and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall the project provides new insights into the organization and regulation of our genes and genome, and an expansive resource of functional annotations for biomedical research.

Graphene sheets-one-atom-thick two-dimensional layers of sp 2 -bonded carbon-are predicted to have a range of unusual properties. Their thermal conductivity and mechanical stiffness may rival the remarkable in-plane values for graphite (,3,000 Wm 21 K 21 and 1,060 GPa, respectively); their fracture strength should be comparable to that of carbon nanotubes for similar types of defects 1-3 ; and recent studies have shown that individual graphene sheets have extraordinary electronic transport properties 4-8 . One possible route to harnessing these properties for applications would be to incorporate graphene sheets in a composite material. The manufacturing of such composites requires not only that graphene sheets be produced on a sufficient scale but that they also be incorporated, and homogeneously distributed, into various matrices. Graphite, inexpensive and available in large quantity, unfortunately does not readily exfoliate to yield individual graphene sheets. Here we present a general approach for the preparation of graphene-polymer composites via complete exfoliation of graphite 9 and molecular-level dispersion of individual, chemically modified graphene sheets within polymer hosts. A polystyrene-graphene composite formed by this route exhibits a percolation threshold 10 of ,0.1 volume per cent for room-temperature electrical conductivity, the lowest reported value for any carbon-based composite except for those involving carbon nanotubes 11 ; at only 1 volume per cent, this composite has a conductivity of ,0.1 S m 21 , sufficient for many electrical applications 12 . Our bottom-up chemical approach of tuning the graphene sheet properties provides a path to a broad new class of graphenebased materials and their use in a variety of applications.

Human lymphocytes were either exposed to X-irradiation (25 to 200 rads) or treated with HzOz (9.1 to 291 u&f) at 4°C and the extent of DNA migration was measured using a singlecell microgel electrophoresis technique under alkaline conditions. Both agents induced a significant increase in DNA migration, beginning at the lowest dose evaluated. Migration patterns were relatively homogeneous among cells exposed to X-rays but heterogeneous among cells treated with HzOz. An analysis of repair kinetics following exposure to 200 rads X-rays was conducted with lymphocytes obtained from three individuals. The bulk of the DNA repair occurred within the first IS min, while all of the repair was essentially complete by 120 min after exposure. However, some cells demonstrated no repair during this incubation period while other cells demonstrated DNA migration patterns indicative of more damage than that induced by the initial irradiation with X-rays. This technique appears to be sensitive and useful for detecting damage and repair in single cells. @ IYXX Academic Press. Inc.

A method is presented for the rapid isolation of high molecular weight plant DNA (50,000 base pairs or more in length) which is free of contaminants which interfere with complete digestion by restriction endonucleases. The procedure yields total cellular DNA (i.e. nuclear, chloroplast, and mitochondrial DNA). The technique is ideal for the rapid isolation of small amounts of DNA from many different species and is also useful for large scale isolations.

A simple mathematical method is developed to estimate the number of nucleotide substitutions per site between two DNA sequences, by extending Kimura's (1980) two-parameter method to the case where a G+C-content bias exists. This method will be useful when there are strong transition-transversion and G+C-content biases, as in the case of Drosophila mitochondrial DNA.

Causal attribution of recent biological trends to climate change is complicated because non-climatic influences dominate local, short-term biological changes. Any underlying signal from climate change is likely to be revealed by analyses that seek systematic trends across diverse species and geographic regions; however, debates within the Intergovernmental Panel on Climate Change (IPCC) reveal several definitions of a 'systematic trend'. Here, we explore these differences, apply diverse analyses to more than 1,700 species, and show that recent biological trends match climate change predictions. Global meta-analyses documented significant range shifts averaging 6.1 km per decade towards the poles (or metres per decade upward), and significant mean advancement of spring events by 2.3 days per decade. We define a diagnostic fingerprint of temporal and spatial 'sign-switching' responses uniquely predicted by twentieth century climate trends. Among appropriate long-term/large-scale/multi-species data sets, this diagnostic fingerprint was found for 279 species. This suite of analyses generates 'very high confidence' (as laid down by the IPCC) that climate change is already affecting living systems.

We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform.

The ability of a 650 base pair section of the mitochondrial cytochrome c oxidase I (COI) gene to provide species-level identifications has been demonstrated for large taxonomic assemblages of animals such as insects, birds, and fishes, but not for the subphylum Crustacea, one of the most diverse groups of arthropods. In this study, we test the ability of COI to provide identifications in this group, examining two disparate levels in the taxonomic hierarchy -orders and species. The first phase of our study involved the development of a sequence profile for 23 dominant crustacean orders, based upon the analysis of 150 species, each belonging to a different family. The COI amino acid data placed these taxa into cohesive assemblages whose membership coincided with currently accepted boundaries at the order, superorder, and subclass levels. Species-level resolution was subsequently examined in an assemblage of Decapoda and in representatives of the genera Daphnia (Cladocera) and Gammarus (Amphipoda). These studies revealed that levels of nucleotide sequence divergence were from 19 to 48 times greater between congeneric species than between individuals of a species. We conclude that sequence variation in the COI barcode region will be very effective for discriminating species of Crustacea.

DNA sequence data are generally interpreted as favouring Kimura's neutral theory but not without dissent and often with a great deal of controversy with respect to molecular clocks, DNA polymorphism, adaptive evolution, and gene genealogy. Although the theory serves as a guiding principle, many issues concerning mutation, recombination, and selection remain unsettled. Of particular importance is the need for more knowledge about the function and structure of molecules.

Unique DNA sequences can be determined directly from mouse genomic DNA. A denaturing gel separates by size mixtures of unlabeled DNA fragments from complete re-striction and partial chemical cleavages of the entire genome. These lanes of DNA are transferred ...

Genome-wide association studies have identified hundreds of genetic variants associated with complex human diseases and traits, and have provided valuable insights into their genetic architecture. Most variants identified so far confer relatively small increments in risk, and ...

The long-standing challenge of designing and constructing new crystalline solid-state materials from molecular building blocks is just beginning to be addressed with success. A conceptual approach that requires the use of secondary building units to direct the assembly of ordered frameworks epitomizes this process: we call this approach reticular synthesis. This chemistry has yielded materials designed to have predetermined structures, compositions and properties. In particular, highly porous frameworks held together by strong metal-oxygen-carbon bonds and with exceptionally large surface area and capacity for gas storage have been prepared and their pore metrics systematically varied and functionalized. The deconstruction of diamond and lonsdaleite. a, diamond; b, lonsdaleite ('hexagonal diamond'). The units outlined in red are the natural tiles for these structures.

On activation, T cells undergo distinct developmental pathways, attaining specialized properties and effector functions. T-helper (T H ) cells are traditionally thought to differentiate into T H 1 and T H 2 cell subsets. T H 1 cells are necessary to clear intracellular pathogens and T H 2 cells are important for clearing extracellular organisms 1,2 . Recently, a subset of interleukin (IL)-17-producing T (T H 17) cells distinct from T H 1 or T H 2 cells has been described and shown to have a crucial role in the induction of autoimmune tissue injury 3-5 . In contrast, CD4 1 CD25 1 Foxp3 1 regulatory T (T reg ) cells inhibit autoimmunity and protect against tissue injury 6 . Transforming growth factor-b (TGF-b) is a critical differentiation factor for the generation of T reg cells 7 . Here we show, using mice with a reporter introduced into the endogenous Foxp3 locus, that IL-6, an acute phase protein induced during inflammation 8,9 , completely inhibits the generation of Foxp3 1 T reg cells induced by TGF-b. We also demonstrate that IL-23 is not the differentiation factor for the generation of T H 17 cells. Instead, IL-6 and TGF-b together induce the differentiation of pathogenic T H 17 cells from naive T cells. Our data demonstrate a dichotomy in the generation of pathogenic (T H 17) T cells that induce autoimmunity and regulatory (Foxp3 1 ) T cells that inhibit autoimmune tissue injury.

insight review articles NATURE | VOL 414 | 15 NOVEMBER 2001 | www.nature.com 353 E nergy can be stored in different forms: as mechanical energy (for example, potential energy or rotation energy of a flywheel); in an electric or magnetic field (capacitors and coils, respectively); as chemical energy of reactants and fuels (batteries, petrol or hydrogen); or as nuclear fuel (uranium or deuterium). Chemical and electric energy can be transmitted easily because they both involve electronic Coulomb interaction. Chemical energy is based on the energy of unpaired outer electrons (valence electrons) eager to be stabilized by electrons from other atoms. The hydrogen atom is most attractive because its electron (for charge neutrality) is accompanied by only one proton. Hydrogen thus has the best ratio of valence electrons to protons (and neutrons) of all the periodic table, and the energy gain per electron is very high.

Normal somatic cells invariably enter a state of irreversibly arrested growth and altered function after a finite number of divisions. This process, termed replicative senescence, is thought to be a tumor-suppressive mechanism and an underlying cause of aging. There is ample evidence that escape from senescence, or immortality, is important for malignant transformation. By contrast, the role of replicative senescence in organismic aging is controversial. Studies on cells cultured from donors of different ages, genetic backgrounds, or species suggest that senescence occurs in vivo and that organismic lifespan and cell replicative lifespan are under common genetic control. However, senescent cells cannot be distinguished from quiescent or terminally differentiated cells in tissues. Thus, evidence that senescent cells exist and accumulate with age in vivo is lacking. We show that several human cells express a f3-galactosidase, histochemically de-

Simple and reproducible fingerprints of complex genomes can be generated using single arbitrarily chosen primers and the polymerase chain reaction (PCR). No prior sequence information is required. The method, arbitrarily primed PCR (AP-PCR), involves two cycles of low stringency amplification followed by PCR at higher stringency. We show that strains can be distinguished by comparing polymorphisms in genomic fingerprints. The generality of the method is demonstrated by application to twenty four strains from five species of Staphylococcus, eleven strains of Streptococcus pyogenes and three varieties of Oryza sativa (rice). METHODS Strains S. aureus, ISP-8, isolated from human. ATCC 8432, from bird.

DNA can be sequenced by a chemical procedure that breaks a terminally laleled DNA molecule partially at each repetition of a base. The lengths of the labeled fragments then identify thepositions of thatse. We describe reactions that cleave DNA Preferentially at guanines, at adenines, at cy

First described by David Hilbert in 1891, the Hilbert curve is a one-dimensional fractal trajectory that densely fills higher-dimensional space without crossing itself. A new method for reconstructing the three-dimensional architecture of the human genome, described on page 289, reveals a polymer analog of Hilbert's curve at the megabase scale.

All ecosystems are exposed to gradual changes in climate, nutrient loading, habitat fragmentation or biotic exploitation. Nature is usually assumed to respond to gradual change in a smooth way. However, studies on lakes, coral reefs, oceans, forests and arid lands have shown that smooth change can be interrupted by sudden drastic switches to a contrasting state. Although diverse events can trigger such shifts, recent studies show that a loss of resilience usually paves the way for a switch to an alternative state. This suggests that strategies for sustainable management of such ecosystems should focus on maintaining resilience.

The conductor-like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, and electronic properties in solution for any chemical system that can be studied in vacuo. Particular attention is devoted to large systems requiring suitable iterative algorithms to compute the solvation charges: the fast multipole method (FMM) has been extensively used to ensure a linear scaling of the computational times with the size of the solute. A number of test applications are presented to evaluate the performances of the method.

letters to nature NATURE | VOL 411 | 31 MAY 2001 | www.nature.com 603 sequenced following ampli®cation from the DNA of ten CD patients and two unaffected individuals. Of 35 identi®ed SNPs, SNP 1±11, selected for their rare-allele frequencies greater than 0.08, were typed on 1,272 members of the 235 CD families. SNP 12 and 13 were further identi®ed by sequencing the 11 exons of the candidate IBD1 gene in 50 CD patients (SNP 1±13, GenBank accession numbers G67943±G67955, are submitted to dbSNP of the National Center for Biotechnology Information) and typed on the same group of individuals. To search for rare variant alleles, we subsequently investigated the 11 exons of 457 CD patients, 159 ulcerative colitis patients and 103 unaffected unrelated individuals. All variant alleles were con®rmed by sequencing a second independent ampli®cation product.

Despite their importance for urban planning [1], traffic forecasting [2], and the spread of biological [3, 4, 5] and mobile viruses [6], our understanding of the basic laws governing human motion remains limited thanks to the lack of tools to monitor the time resolved location of individuals. Here we study the trajectory of 100, 000 anonymized mobile phone users whose position is tracked for a six month period. We find that in contrast with the random trajectories predicted by the prevailing Lévy flight and random walk models [7], human trajectories show a high degree of temporal and spatial regularity, each individual being characterized by a time independent characteristic length scale and a significant probability to return to a few highly frequented locations. After correcting for differences in travel distances and the inherent anisotropy of each trajectory, the individual travel patterns collapse into a single spatial probability distribution, indicating that despite the diversity of their travel history, humans follow simple reproducible patterns. This inherent similarity in travel patterns could impact all phenomena driven by human mobility, from epidemic prevention to emergency response, urban planning and agent based modeling. Given the many unknown factors that influence a population's mobility patterns, ranging from means of transportation to job and family imposed restrictions and priorities, human trajectories are often approximated with various random walk or diffusion models [7, 8]. Indeed, early measurements on albatrosses, bumblebees, deer and monkeys [9, 10] and more recent ones on marine predators [11] suggested that animal trajectory is approximated by a Lévy flight [12, 13], a random walk whose step size ∆r follows a power-law distribution P (∆r) ∼ ∆r −(1+β) with β < 2. While the Lévy statistics for some animals require further study [14], Brockmann et al. [7] generalized this finding to humans, documenting that the distribution of distances between consecutive sight

We have analyzed 5,088 bacterial 16S rRNA gene sequences from the distal intestinal (cecal) microbiota of genetically obese ob͞ob mice, lean ob͞؉ and wild-type siblings, and their ob͞؉ mothers, all fed the same polysaccharide-rich diet. Although the majority of mouse gut species are unique, the mouse and human microbiota(s) are similar at the division (superkingdom) level, with Firmicutes and Bacteroidetes dominating. Microbial-community composition is inherited from mothers. However, compared with lean mice and regardless of kinship, ob͞ob animals have a 50% reduction in the abundance of Bacteroidetes and a proportional increase in Firmicutes. These changes, which are division-wide, indicate that, in this model, obesity affects the diversity of the gut microbiota and suggest that intentional manipulation of community structure may be useful for regulating energy balance in obese individuals. energy balance͞obesity ͉ host-microbial interactions ͉ intestinal bacterial diversity ͉ ob͞ob mice ͉ phylogenetics Freely available online through the PNAS open access option.