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Biology

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Quantum phase transition from a superfluid to a Mott insulator in a gas of ultracold atoms

Markus Greiner, Olaf Mandel, Tilman Esslinger, T. W. Hänsch, Immanuel Bloch

Comparison of the Ligand Binding Specificity and Transcript Tissue Distribution of Estrogen Receptors α and β

The rat estrogen receptor (ER) exists as two subtypes, ERα and ERβ, which differ in the C-terminal ligand binding domain and in the N-terminal transactivation domain. In this study we investigated the messenger RNA expression of both ER subtypes in...

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes...

A homochiral metal|[ndash]|organic porous material for enantioselectiveseparation and catalysis

Jung Soo Seo, Hyoyoung Lee, Sung Im Jun, Jinho Oh, Young Jin Jeon, Kimoon Kim

The Problem of Pattern and Scale in Ecology

It is argued that the problem of pattern and scale is the central problem in ecology, unifying population biology and ecosystems science, and marrying basic and applied ecology. Applied challenges, such as the prediction of the ecological causes and consequences...

Mechanisms of TGF-β Signaling from Cell Membrane to the Nucleus

TGF-β signaling controls a plethora of cellular responses and figures prominently in animal development. Recent cellular, biochemical, and structural studies have revealed significant insight into the mechanisms of the activation of TGF-β receptors...

Essential oils: their antibacterial properties and potential applications in foods—a review

In vitro studies have demonstrated antibacterial activity of essential oils (EOs) against Listeria monocytogenes, Salmonella typhimurium, Escherichia coli O157:H7, Shigella dysenteria, Bacillus cereus and Staphylococcus aureus at levels between 0.2...

Most mammalian mRNAs are conserved targets of microRNAs

MicroRNAs (miRNAs) are small endogenous RNAs that pair to sites in mRNAs to direct post-transcriptional repression. Many sites that match the miRNA seed (nucleotides 2–7), particularly those in 3 untranslated regions (3UTRs), are preferentially conserved....

Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells.

Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells.

The Phosphoinositide 3-Kinase Pathway

Phosphorylated lipids are produced at cellular membranes during signaling events and contribute to the recruitment and activation of various signaling components. The role of phosphoinositide 3-kinase (PI3K), which catalyzes the production of phosphatidylinositol-3,4,5-trisphosphate,...

HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor.

A cofactor for HIV-1 (human immunodeficiency virus-type 1) fusion and entry was identified with the use of a novel functional complementary DNA (cDNA) cloning strategy. This protein, designated “fusin,” is a putative G protein-coupled receptor with...

How useful is SBF in predicting in vivo bone bioactivity

The bone-bonding ability of a material is often evaluated by examining the ability of apatite to form on its surface in a simulated body fluid (SBF) with ion concentrations nearly equal to those of human blood plasma. However, the validity of this method...

SWISS-MODEL: an automated protein homology-modeling server

SWISS-MODEL (http://swissmodel.expasy.org) is a server for automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated modeling starting in 1993 and is the most widely-used free web-based automated...

Two simple media for the demonstration of pyocyanin and fluorescin

Elizabeth O. King, Martha K. Ward, Donald E. Raney

Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.

The advent of complete genetic linkage maps consisting of codominant DNA markers [typically restriction fragment length polymorphisms (RFLPs)] has stimulated interest in the systematic genetic dissection of discrete Mendelian factors underlying quantitative...

The origins and the future of microfluidics

The origins and the future of microfluidics

Microphysics of clouds and precipitation

Hans R. Pruppacher, James D. Klett

Climate and atmospheric history of the past 420,000 years from the Vostok ice core, Antarctica

Jean Robert Petit, Jean Jouzel, D. Raynaud, N. I. Barkov, Jean Marc Barnola, Isabelle Basile, Michael L. Bender, J. Chappellaz, M. Davis, Gilles Delaygue, M. Delmotte, V. M. Kotlyakov, M. Legrand, Vladimir Ya. Lipenkov, Claude Lorius, Laurence Pépin, C. Ritz, E. Saltzman, M. Stievenard

Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms

Masato Orita, Hiroyuki Iwahana, Kanazawa H, Kenshi Hayashi, Takao Sekiya

Efficient presentation of soluble antigen by cultured human dendritic cells is maintained by granulocyte/macrophage colony-stimulating factor plus interleukin 4 and downregulated by tumor necrosis factor alpha.

Summary Using granulocyte/macrophage colony-stimulating factor (GM-CSF) and interleukin 4 we have established dendritic cell (DC) lines from blood mononuclear cells that maintain the antigen capturing and processing capacity characteristic of immature...

Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries

A new and highly effective method, termed suppression subtractive hybridization (SSH), has been devel- oped for the generation of subtracted cDNA libraries. It is based primarily on a recently described technique called suppression PCR and combines normalization...

The nuclear RNase III Drosha initiates microRNA processing

Yoontae Lee, Jinju Han, Hyounjeong Choi, Jae-Kwang Kim, Jeongbin Yim, Junho Lee, Patrick Provost, Olof Rådmark, Sunyoung Kim, V. Narry Kim

The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers.

A series of plasmid vectors containing the multiple cloning site (MCS7) of M13mp7 has been constructed. In one of these vectors a kanamycin-resistance marker has been inserted into the center of the symmetrical MCS7 to yield a restriction-site-mobilizing...

A SIMPLE AND GENERAL METHOD FOR TRANSFERRING GENGS INTO PLANTS

Surface-sterilized leaf discs from petunia, tobacco and tomato were inoculated with an Agrobacterium tumefaciens strain containing a modified Ti plasmid with a chimaeric gene for kanamycin resistance. The discs were cultured for 2 days and then transferred...

STABLE ISOTOPES IN ECOSYSTEM STUDIES

and B J Peterson, Brian Fry

EXTINCTION RISK FROM CLIMATE CHANGE

Climate change over the past ~30 years has produced numerous shifts in the distributions and abundance of species and has been implicated in one species-level extinction. Using projections of species distributions for future climate scenarios, we assess...

Purity of the sacred lotus, or escape from contamination in biological surfaces

The microrelief of plant surfaces, mainly caused by epicuticular wax crystalloids, serves different purposes and often causes effective water repellency. Furthermore, the adhesion of contaminating particles is reduced. Based on experimental data carried...

Identification and inhibition of the ICE/CED-3 protease necessary for mammalian apoptosis

The protease responsible for the cleavage of poly(ADP-ribose) polymerase and necessary for apoptosis has been purified and characterized. This enzyme, named apopain, is composed of two subunits of relative molecular mass (M(r)) 17K and 12K that are derived...

Mesenchymal stem cells

Mesenchymal stem cells

Functional organization of the yeast proteome by systematic analysis of protein complexes

Most cellular processes are carried out by multiprotein complexes. The identification and analysis of their components provides insight into how the ensemble of expressed proteins (proteome) is organized into functional units. We used tandem-affinity...

The Biology of Vascular Endothelial Growth Factor

I. Introduction II. Biological Activities of VEGF III. Organization of the VEGF Gene IV. Properties of the VEGF Isoforms V. Regulation of VEGF Gene Expression A. Hypoxia B. Cytokines C. Differentiation and transformation VI. The VEGF Receptors A. Characterization...

Inhibition of vascular endothelial growth factor-induced angiogenesis suppresses tumour growth in vivo

K. Jin Kim, Bing Li, Jane Winer, Mark Armanini, Nancy Gillett, Heidi S. Phillips, Napoleone Ferrara

Prevention of Apoptosis by Bcl-2: Release of Cytochrome c from Mitochondria Blocked

Bcl-2 is an integral membrane protein located mainly on the outer membrane of mitochondria. Overexpression of Bcl-2 prevents cells from undergoing apoptosis in response to a variety of stimuli. Cytosolic cytochrome c is necessary for the initiation of...

Autophagy fights disease through cellular self-digestion

Noboru Mizushima, Beth Levine, Ana Maria Cuervo, Daniel J. Klionsky

T-COFFEE: A NOVEL METHOD FOR FAST AND ACCURATE MULTIPLE SEQUENCE ALIGNMENT

We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. The method is broadly based on the popular progressive...

DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development

The establishment of DNA methylation patterns requires de novo methylation that occurs predominantly during early development and gametogenesis in mice. Here we demonstrate that two recently identified DNA methyltransferases, Dnmt3a and Dnmt3b, are essential...

Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale

DNA microarrays containing virtually every gene of Saccharomyces cerevisiae were used to carry out a comprehensive investigation of the temporal program of gene expression accompanying the metabolic shift from fermentation to respiration. The expression...

Cloning of a novel receptor expressed in rat prostate and ovary

George G. J. M. Kuiper, Eva Enmark, Markku Pelto-Huikko, Stefan Nilsson, Jan Gustafsson

Mammalian protein metabolism.

H. N. Munro, J. B. Allison

Insulin-Like Growth Factors and Their Binding Proteins: Biological Actions*

I. Introduction THE insulin-like growth factors were discovered on the basis of their ability to stimulate cartilage sulfation and to replace the “sulfation factor activity” of GH, as determined using an in vivo assay, in an in vitro test system (1)....

Extension of Life-Span by Introduction of Telomerase into Normal Human Cells

Normal human cells undergo a finite number of cell divisions and ultimately enter a nondividing state called replicative senescence. It has been proposed that telomere shortening is the molecular clock that triggers senescence. To test this hypothesis,...

Serial Analysis of Gene Expression

The characteristics of an organism are determined by the genes expressed within it. A method was developed, called serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. To demonstrate...

A comprehensive analysis of protein|[ndash]|protein interactions in Saccharomyces cerevisiae

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HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5

Tatjana Dragic, Virginia M. Litwin, Graham P. Allaway, Scott R. Martin, Yaoxing Huang, Kirsten A. Nagashima, Charmagne Cayanan, Paul J. Maddon, Richard A. Koup, John P. Moore, William A. Paxton

A review of central 5-HT receptors and their function

It is now nearly 5 years since the last of the currently recognised 5-HT receptors was identified in terms of its cDNA sequence. Over this period, much effort has been directed towards understanding the function attributable to individual 5-HT receptors...

Glioma stem cells promote radioresistance by preferential activation of the DNA damage response

Shideng Bao, Qiulian Wu, Roger E. McLendon, Yueling Hao, Qing Shi, Anita B. Hjelmeland, Mark W. Dewhirst, Darell D. Bigner, Jeremy N. Rich

A New Concept for Macromolecular Therapeutics in Cancer Chemotherapy: Mechanism of Tumoritropic Accumulation of Proteins and the Antitumor Agent Smancs

We previously found that a polymer conjugated to the anticancer protein neocarzinostatin, named smancs, accumulated more in tumor tissues than did neocarzinostatin. To determine the general mechanism of this tumoritropic accumulation of smancs and other...

Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies

We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked...

PTEN, a Putative Protein Tyrosine Phosphatase Gene Mutated in Human Brain, Breast, and Prostate Cancer

Mapping of homozygous deletions on human chromosome 10q23 has led to the isolation of a candidate tumor suppressor gene, PTEN, that appears to be mutated at considerable frequency in human cancers. In preliminary screens, mutations of PTEN were detected...

Inhibition of glycogen synthase kinase-3 by insulin mediated by protein kinase B.

Darren A. E. Cross, Dario R. Alessi, Philip Cohen, Mirjana Andjelkovich, Brian A. Hemmings

The small GTP-binding protein rho regulates the assembly of focal adhesions and actin stress fibers in response to growth factors

Actin stress fibers are one of the major cytoskeletal structures in fibroblasts and are linked to the plasma membrane at focal adhesions. rho, a ras-related GTP-binding protein, rapidly stimulated stress fiber and focal adhesion formation when microinjected...

Heterozygous embryonic lethality induced by targeted inactivation of the VEGF gene

Napoleone Ferrara, Karen Carver-Moore, Helen Chen, Lucy Lu, Lyn Powell-Braxton, Kenneth J. Hillan, Mark Moore

Database resources of the National Center for Biotechnology Information.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank R � nucleic acid sequence database and the PubMed database of citations and abstracts for...

The limited in vitro lifetime of human diploid cell strains

This chapter discusses a study to examine that the finite lifetime of diploid cell strains in vitro may be an expression of aging or senescence at the cellular level. Human diploid cell strains WI-26, WI-38, and WI-44 were used. WI-26 was derived from...

Epigenetic programming by maternal behavior

Here we report that increased pup licking and grooming (LG) and arched-back nursing (ABN) by rat mothers altered the offspring epigenome at a glucocorticoid receptor (GR) gene promoter in the hippocampus. Offspring of mothers that showed high levels of...

Osteoclast differentiation and activation

William J. Boyle, W. Scott Simonet, David L. Lacey

High-efficiency transformation of mammalian cells by plasmid DNA.

We describe a simple calcium phosphate transfection protocol and neo marker vectors that achieve highly efficient transformation of mammalian cells. In this protocol, the calcium phosphate-DNA complex is formed gradually in the medium during incubation...

AKT/PKB Signaling: Navigating Downstream

Brendan D. Manning, Lewis C. Cantley

Chemokines — Chemotactic Cytokines That Mediate Inflammation

The attraction of leukocytes to tissues is essential for inflammation and the host response to infection. The process is controlled by chemokines, which are chemotactic cytokines. This review introduces the burgeoning family of cytokines, with special...

Mental Rotation of Three-Dimensional Objects

The time required to recognize that two perspective drawings portray objects of the same three-dimensional shape is found to be (i) a linearly increasing function of the angular difference in the portrayed orientations of the two objects and (ii) no shorter...

TOLL-LIKE RECEPTORS

▪ Abstract The innate immune system in drosophila and mammals senses the invasion of microorganisms using the family of Toll receptors, stimulation of which initiates a range of host defense mechanisms. In drosophila antimicrobial responses rely on...

Obesity as a medical problem

Obesity is now so common within the world's population that it is beginning to replace undernutrition and infectious diseases as the most significant contributor to ill health. In particular, obesity is associated with diabetes mellitus, coronary heart...

ARB: a software environment for sequence data.

The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user...

The Release of Cytochrome c from Mitochondria: A Primary Site for Bcl-2 Regulation of Apoptosis

In a cell-free apoptosis system, mitochondria spontaneously released cytochrome c, which activated DEVD-specific caspases, leading to fodrin cleavage and apoptotic nuclear morphology. Bcl-2 acted in situ on mitochondria to prevent the release of cytochrome...

Tumor cells secrete a vascular permeability factor that promotes accumulation of ascites fluid

Tumor ascites fluids from guinea pigs, hamsters, and mice contain activity that rapidly increases microvascular permeability. Similar activity is also secreted by these tumor cells and a variety of other tumor cell lines in vitro. The permeability-increasing...

The embryonic cell lineage of the nematode Caenorhabditis elegans.

The embryonic cell lineage of Caenorhabditis elegans has been traced from zygote to newly hatched larva, with the result that the entire cell lineage of this organism is now known. During embryogenesis 671 cells are generated; in the hermaphrodite 113...

The protein kinase family: conserved features and deduced phylogeny of the catalytic domains.

In recent years, members of the protein kinase family have been discovered at an accelerated pace. Most were first described, not through the traditional biochemical approach of protein purification and enzyme assay, but as putative protein kinase amino...

Osteoprotegerin: A Novel Secreted Protein Involved in the Regulation of Bone Density

A novel secreted glycoprotein that regulates bone resorption has been identified. The protein, termed Osteoprotegerin (OPG), is a novel member of the TNF receptor superfamily. In vivo, hepatic expression of OPG in transgenic mice results in a profound...

The expanding universe of T-cell subsets: Th1, Th2 and more

Since their discovery nearly ten years ago, T helper 1 (Th1) and Th2 subsets have been implicated in the regulation of many immune responses. In this article, Tim Mosmann and Subash Sad discuss the increasing number of T-cell subsets defined by cytokine...

An integrated map of genetic variation from 1,092 human genomes

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14...

Generation of germline-competent induced pluripotent stem cells.

Keisuke Okita, Tomoko Ichisaka, Shinya Yamanaka

Rapid and sensitive protein similarity searches

An algorithm was developed which facilitates the search for similarities between newly determined amino acid sequences and sequences already available in databases. Because of the algorithm's efficiency on many microcomputers, sensitive protein database...

ADDITIONAL MODULES FOR VERSATILE AND ECONOMICAL PCR-BASED GENE DELETION AND MODIFICATION IN SACCHAROMYCES CEREVISIAE

An important recent advance in the functional analysis of Saccharomyces cerevisiae genes is the development of the one-step PCR-mediated technique for deletion and modification of chromosomal genes. This method allows very rapid gene manipulations without...

Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals

Cells of a multicellular organism are genetically homogeneous but structurally and functionally heterogeneous owing to the differential expression of genes. Many of these differences in gene expression arise during development and are subsequently retained...

Rho, Rac, and Cdc42 GTPases regulate the assembly of multimolecular focal complexes associated with actin stress fibers, lamellipodia, and filopodia

Rho and rac, two members of the ras-related superfamily of small GTPases, regulate the polymerization of actin to produce stress fibers and lamellipodia, respectively. We report here that cdc42, another member of the rho family, triggers the formation...

Mammalian Neural Stem Cells

Neural stem cells exist not only in the developing mammalian nervous system but also in the adult nervous system of all mammalian organisms, including humans. Neural stem cells can also be derived from more primitive embryonic stem cells. The location...

Two CD95 (APO‐1/Fas) signaling pathways

Carsten Scaffidi, Simone Fulda, Anu Srinivasan, Feng Li, Kevin J. Tomaselli, Klaus-Michael Debatin, Peter H. Krammer, Marcus E. Peter

Segregation of a missense mutation in the amyloid precursor protein gene with familial Alzheimer's disease

A locus segregating with familial Alzheimer's disease (AD) has been mapped to chromosome 21, close to the amyloid precursor protein (APP) gene. Recombinants between the APP gene and the AD locus have been reported which seemed to exclude it as the site...

Internet: Diameter of the World-Wide Web

Réka Albert, Hawoong Jeong, Albert-László Barabási

An endotoxin-induced serum factor that causes necrosis of tumors

Elizabeth A. Carswell, Lloyd J. Old, Robert Kassel, Stephanie J. Green, N Fiore, B Williamson

Cell Death: Critical Control Points

Programmed cell death is a distinct genetic and biochemical pathway essential to metazoans. An intact death pathway is required for successful embryonic development and the maintenance of normal tissue homeostasis. Apoptosis has proven to be tightly interwoven...

Correlation between protein and mRNA abundance in yeast.

Steven P. Gygi, B. Robert Franza, Ruedi Aebersold

Characteristics of the Microplate Method of Enzyme-Linked Immunosorbent Assay for the Detection of Plant Viruses

SummarySome characteristics of a microplate method for the detection and assay of plant viruses using enzyme-labelled antibodies are described. The method enabled the highly sensitive detection of a number of morphologically different viruses in purified...

A Measure of Population Subdivision Based on Microsatellite Allele Frequencies

A new measure of the extent of population subdivision as inferred from allele frequencies at microsatellite loci is proposed and tested with computer simulations. This measure, called R(ST), is analogous to Wright's F(ST) in representing the proportion...

Atlas of Protein Sequence and Structure, 1966.

Robert T. Hersh, R. V. Eck, Margaret O. Dayhoff

Large-scale analysis of the yeast proteome by multidimensional protein identification technology.

We describe a largely unbiased method for rapid and large-scale proteome analysis by multidimensional liquid chromatography, tandem mass spectrometry, and database searching by the SEQUEST algorithm, named multidimensional protein identification technology...

The structure of haplotype blocks in the human genome.

Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. As part of The SNP Consortium Allele Frequency Projects, we characterized haplotype...

ASCORBATE AND GLUTATHIONE: Keeping Active Oxygen Under Control.

▪ Abstract To cope with environmental fluctuations and to prevent invasion by pathogens, plant metabolism must be flexible and dynamic. Active oxygen species, whose formation is accelerated under stress conditions, must be rapidly processed if oxidative...

Targeting of HIF-α to the von Hippel-Lindau Ubiquitylation Complex by O2-Regulated Prolyl Hydroxylation

Hypoxia-inducible factor (HIF) is a transcriptional complex that plays a central role in the regulation of gene expression by oxygen. In oxygenated and iron replete cells, HIF-α subunits are rapidly destroyed by a mechanism that involves ubiquitylation...

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of...

Tolerogenic dendritic cells.

▪ Abstract Dendritic cells (DCs) have several functions in innate and adaptive immunity. In addition, there is increasing evidence that DCs in situ induce antigen-specific unresponsiveness or tolerance in central lymphoid organs and in the periphery....

Normalizing mitochondrial superoxide production blocks three pathwaysof hyperglycaemic damage

Takeshi Nishikawa, Diane Edelstein, Xue Liang Du, Sho-ichi Yamagishi, Takeshi Matsumura, Yasufumi Kaneda, Mark A. Yorek, David A. Beebe, Peter J. Oates, Hans-Peter Hammes, Ida Giardino, Michael Brownlee

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