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Biology

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Protein measurement with the folin phenol reagent

Oliver H. Lowry, Nira J. Rosebrough, A. Lewis Farr, Rose J. Randall

Molecular cloning : a laboratory manual

Sambrook J, Edward F. Fritsch, Tom Maniatis

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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...

Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a...

Current protocols in molecular biology

R E Kingston, David D. Moore, J. L. Smith

The CLUSTAL_X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools

CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the...

The evolution of cooperation

Cooperation in organisms, whether bacteria or primates, has been a difficulty for evolutionary theory since Darwin. On the assumption that interactions between pairs of individuals occur on a probabilistic basis, a model is developed based on the concept...

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of...

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

SummarySome simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide...

A simple salting out procedure for extracting DNA from human nucleated cells

Shirley A. Miller, Dale D. Dykes, Herbert F. Polesky

AFLP: a new technique for DNA fingerprinting

A novelDNAfingerprinting technique called AFLPis described. TheAFLPtechnique isbasedon the selective PCRamplification ofrestriction fragments fromatotal digest ofgenomicDNA.Thetechnique involves threesteps: (i) restriction oftheDNA and ligation ofoligonucleotide...

MRBAYES: Bayesian inference of phylogenetic trees

Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Selina S. Dwight, David A. Davis, David P. Hill, John J. Matese, Martin Ringwald, R. M. Harris, Kara Dolinski, Stephen J. P. Blake, Nicquet M.J. Blake, Magnus J. E. Richardson, Nia C S Lewis, Hope C. Ball, P. H. Butler, J. Michael Cherry, Michael Ashburner, S. W. Lewis, David Botstein, R. Sherlock, Andrea J. Richardson, John J. Eppig, L. Michele Issel, G P Rubin, Andrew Kasarskis

High resolution two-dimensional electrophoresis of proteins.

High resolution two-dimensional electrophoresis of proteins.

Dendritic cells and the control of immunity

Jacques Banchereau, Ralph M. Steinman

Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors

Three kinds of improvements have been introduced into the M13-based cloning systems. (1) New Escherichia coli host strains have been constructed for the E. coli bacteriophage M13 and the high-copy-number pUC-plasmid cloning vectors. Mutations introduced...

PRIMER DIRECTED ENZYMATIC AMPLIFICATION OF DNA WITH A THERMOSTABLE DNA POLYMERASE

A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction. The enzyme, isolated from Thermus aquaticus, greatly simplifies the procedure and, by enabling the amplification reaction to be performed...

MrBayes 3: Bayesian phylogenetic inference under mixed models

Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different...

Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors

SummaryDifferentiated cells can be reprogrammed to an embryonic-like state by transfer of nuclear contents into oocytes or by fusion with embryonic stem (ES) cells. Little is known about factors that induce this reprogramming. Here, we demonstrate induction...

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome....

A comprehensive set of sequence analysis programs for the VAX

John Devereux, Paul Haeberli, Oliver Smithies

Ordered mesoporous molecular sieves synthesized by a liquid-crystal template mechanism

C.T. Kresge, Michael E. Leonowicz, Wieslaw J. Roth, James C. Vartuli, Jeffrey S. Beck

DNA POLYMORPHISMS AMPLIFIED BY ARBITRARY PRIMERS ARE USEFUL AS GENETIC MARKERS

John G. K. Williams, Anne R. Kubelik, Kenneth J. Livak, J. Antoni Rafalski, Scott V. Tingey

Embryonic Stem Cell Lines Derived from Human Blastocysts

Human blastocyst-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express cell surface markers that characterize primate embryonic stem cells but do not characterize other early...

A low-viscosity epoxy resin embedding medium for electron microscopy.

A low-viscosity embedding medium based on ERL-4206 is recommended for use in electron microscopy. The composition is: ERL-4206 (vinyl cyclo-hexene dioxide) 10g, D.E.R. 736 (diglycidyl ether of polypropylene glycol) 6 g, NSA (nonenyl succinic anhydride)...

Cluster analysis and display of genome-wide expression patterns

A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is de- scribed that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression. The output is displayed graphically,...

The value of the world's ecosystem services and natural capital

Robert Costanza, Rudolf de Groot, Stephen Farberk, Monica Grasso, Bruce Hannon, Karin E. Limburg, Shahid Naeem, José M. Paruelo, Robert G. Raskin, Paul Suttonkk, Marjan van den Belt

Improved tools for biological sequence comparison.

William R. Pearson, David J. Lipman

MUSCLE: multiple sequence alignment with high accuracy and high throughput

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation...

Positional cloning of the mouse obese gene and its human homologue.

Yiying Zhang, Ricardo Proenca, Margherita Maffei, Marisa Barone, Lori Leopold, J. Friedman

Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors

Successful reprogramming of differentiated human somatic cells into a pluripotent state would allow creation of patient- and disease-specific stem cells. We previously reported generation of induced pluripotent stem (iPS) cells, capable of germline transmission,...

The Sequence of the Human Genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence...

Human breast cancer : correlation of relapse and survival with amplification of the HER-2/neu oncogene

The HER-2/neu oncogene is a member of the erbB-like oncogene family, and is related to, but distinct from, the epidermal growth factor receptor. This gene has been shown to be amplified in human breast cancer cell lines. In the current study, alterations...

Biodiversity hotspots for conservation priorities

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Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation...

Two-Dimensional Gas of Massless Dirac Fermions in Graphene

Quantum electrodynamics (resulting from the merger of quantum mechanics and relativity theory) has provided a clear understanding of phenomena ranging from particle physics to cosmology and from astrophysics to quantum chemistry1, 2, 3. The ideas underlying...

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products

We have developed a simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s). In this procedure, recombination requires the phage λ Red recombinase, which is...

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating...

The genetical evolution of social behaviour. I.

A genetical mathematical model is described which allows for interactions between relatives on one another's fitness. Making use of Wright's Coefficient of Relationship as the measure of the proportion of replica genes in a relative, a quantity is found...

PCR protocols: a guide to methods and applications.

Michael A. Innis, David H. Gelfand, John Sninsky, Thomas J. White

Targeted gene expression as a means of altering cell fates and generating dominant phenotypes

even-skipped represses wingless and transforms cells that would normally secrete naked cuticle into denticle secreting cells. The GAL4 system can thus be used to study regulatory interactions during embryonic development. In adults, targeted expression...

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood

The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle,...

Population biology of plants

John L. Harper, Begon, M.Harper, J.L.Towsend, C.R.

Manual of clinical microbiology

Patrick R. Murray, Ellen Jo Baron, James H. Jorgensen, Michael A. Pfaller, Robert H. Yolken

Isolation of Putative Progenitor Endothelial Cells for Angiogenesis

Putative endothelial cell (EC) progenitors or angioblasts were isolated from human peripheral blood by magnetic bead selection on the basis of cell surface antigen expression. In vitro, these cells differentiated into ECs. In animal models of ischemia,...

Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells

Sayda M. Elbashir, Jens Harborth, Winfried Lendeckel, Abdullah Yalcin, Klaus Weber

A general method applicable to the search for similarities in the amino acid sequence of two proteins.

A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed. From these findings it is possible to determine whether significant homology exists between the proteins. This information is used to...

PHYLOGENIES AND THE COMPARATIVE METHOD

Recent years have seen a growth in numerical studies using the comparative method. The method usually involves a comparison of two phenotypes across a range of species or higher taxa, or a comparison of one phenotype with an environmental variable. Objectives...

The Pfam protein families database

Pfam is a widely used database of protein families, currently containing more than 13 000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam. ...

A novel potent vasoconstrictor peptide produced by vascular endothelial cells

Masashi Yanagisawa, Hiroki Kurihara, Sadao Kimura, Yoko Tomobe, Mieko Kobayashi, Youji Mitsui, Yoshio Yazaki, Katsutoshi Goto, Tomoh Masaki

Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana

Summary The Agrobacterium vacuum infiltration method has made it possible to transform Arabidopsis thaliana without plant tissue culture or regeneration. In the present study, this method was evaluated and a substantially modified transformation method...

Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray

A high-capacity system was developed to monitor the expression of many genes in parallel. Microarrays prepared by high-speed robotic printing of complementary DNAs on glass were used for quantitative expression measurements of the corresponding genes....

ESTIMATION OF AVERAGE HETEROZYGOSITY AND GENETIC DISTANCE FROM A SMALL NUMBER OF INDIVIDUALS

The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the...

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

Gene-expression analysis is increasingly important in biological research, with real-time reverse transcription PCR (RT-PCR) becoming the method of choice for high-throughput and accurate expression profiling of selected genes. Given the increased sensitivity,...

A SIMPLE TECHNIQUE FOR QUANTITATION OF LOW LEVELS OF DNA DAMAGE IN INDIVIDUAL CELLS

Human lymphocytes were either exposed to X-irradiation (25 to 200 rads) or treated with H2O2 (9.1 to 291 μM) at 4 °C and the extent of DNA migration was measured using a single-cell microgel electrophoresis technique under alkaline conditions. Both...

Significance analysis of microarrays applied to the ionizing radiation response

Microarrays can measure the expression of thousands of genes to identify changes in expression between different biological states. Methods are needed to determine the significance of these changes while accounting for the enormous number of genes.We...

Molecular portraits of human breast tumours

Charles M. Perou, Therese Sørlie, Michael B. Eisen, Matt van de Rijn, Stefanie S. Jeffrey, Christian A. Rees, Jonathan R. Pollack, Douglas T. Ross, Hilde Johnsen, Lars A. Akslen, Øystein Fluge, Alexander Pergamenschikov, Cheryl F. Williams, Shirley Zhu, Per Eystein Lønning, Anne-Lise Børresen-Dale, Patrick O. Brown, David Botstein

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit...

Translating the Histone Code

Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA. Distinct histone...

Haploview: analysis and visualization of LD and haplotype maps

Summary: Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity....

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.

We predict regulatory targets of vertebrate microRNAs (miRNAs) by identifying mRNAs with conserved complementarity to the seed (nucleotides 2–7) of the miRNA. An overrepresentation of conserved adenosines flanking the seed complementary sites in mRNAs...

A genetic model for colorectal tumorigenesis

Eric R. Fearon, Bert Vogelstein

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical...

Functional rafts in cell membranes

Kai Simons, Elina Ikonen

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

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Mathematical model for studying genetic variation in terms of restriction endonucleases.

A mathematical model for the evolutionary change of restriction sites in mitochondrial DNA is developed. Formulas based on this model are presented for estimating the number of nucleotide substitutions between two populations or species. To express the...

Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia

Two new methods were used to establish a rapid and highly sensitive prenatal diagnostic test for sickle cell anemia. The first involves the primer-mediated enzymatic amplification of specific beta-globin target sequences in genomic DNA, resulting in the...

A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.

A series of yeast shuttle vectors and host strains has been created to allow more efficient manipulation of DNA in Saccharomyces cereuisiae. Transplacement vectors were constructed and used to derive yeast strains containing nonreverting his3, trpl, leu2...

The neutral theory of molecular evolution.

The neutral theory of molecular evolution.

Fast and accurate short read alignment with Burrows–Wheeler transform

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which...

EGFR Mutations in Lung Cancer: Correlation with Clinical Response to Gefitinib Therapy

Receptor tyrosine kinase genes were sequenced in non–small cell lung cancer (NSCLC) and matched normal tissue. Somatic mutations of the epidermal growth factor receptor gene EGFR were found in 15of 58 unselected tumors from Japan and 1 of 61 from the...

Sequence and organization of the human mitochondrial genome

S.W. Anderson, B. G. Barrell, M H de Bruijn, A. R. Coulson, Jacques Drouin, I. C. Eperon, Donald P. Nierlich, Roe Ba, F. Sanger, P.H. Schreier, Andrew J. H. Smith, Rodger Staden, I.G. Young

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

Motivation: DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the...

The biology of VEGF and its receptors

Napoleone Ferrara, Hans-Peter Gerber, Jennifer LeCouter

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considereble biological interest.

Mitochondria and apoptosis : Apoptosis

Douglas R. Green, John C. Reed

WAF1, a potential mediator of p53 tumor suppression

Wafik S. El-Deiry, Takashi Tokino, Victor E. Velculescu, Daniel B. Levy, Ramon Parsons, Jeffrey M. Trent, David Lin, W. Edward Mercer, Kenneth W. Kinzler, Bert Vogelstein

Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing.

Fred C. Tenover, Robert D. Arbeit, Patricia A. Mickelsen, David H. Persing, B. Swaminathan

Plant Products as Antimicrobial Agents

The use of and search for drugs and dietary supplements derived from plants have accelerated in recent years. Ethnopharmacologists, botanists, microbiologists, and natural-products chemists are combing the Earth for phytochemicals and “leads” which...

The Sequence Alignment/Map format and SAMtools

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style,...

Pluripotency of mesenchymal stem cells derived from adult marrow

We report here that cells co-purifying with mesenchymal stem cells—termed here multipotent adult progenitor cells or MAPCs—differentiate, at the single cell level, not only into mesenchymal cells, but also cells with visceral mesoderm, neuroectoderm...

Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I.

Circular (e.g. simian virus 40) and linear (e.g. λ phage) DNAs have been labeled to high specific radioactivities (>108 cts/min per μg) in vitro using deoxynucleoside [α-32P]triphosphates (100 to 250 Ci/mmol) as substrates and the nick translation...

Mfold web server for nucleic acid folding and hybridization prediction

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...

Rapid and efficient site-specific mutagenesis without phenotypic selection

This chapter focuses on rapid and efficient site-specific mutagenesis without phenotypic selection. The deliberate alteration of DNA sequences by in vitro mutagenesis has become a widely used and invaluable means of probing the structure and function...

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