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Biology

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Bergey's manual of determinative bacteriology.

Stiles, WalterLeach, William Parodi, Lorenzo Raimundo, Soriano, Alberto, tr., Escriche, B.Ferre, J. González-Cabrera, J. Herrero, S.

Mutations in Cu/Zn superoxide dismutase gene are associated with familial amyotrophic lateral sclerosis.

Daniel R. Rosen, Teepu Siddique, David Patterson, Denise A. Figlewicz, Peter Sapp, Afif Hentati, Donaldson Dh, Jun Goto, Jeremiah P. O'Regan, Han-Xiang Deng, Rahmani Z, Aldis Krizus, Diane McKenna-Yasek, Sandra M. Gaston, Ralph Berger, Rudolph E. Tanzi, John J. Halperin, R. Bergh, W.-Y. Hung, Thomas D. Bird, Gang Deng, Celestine Smyth, Nigel G. Laing, Edwin Soriano, Margaret A. Pericak–Vance, Jonathan L. Haines, Guy A. Rouleau, H. Robert Horvitz, Robert H. Brown

Notch signaling: cell fate control and signal integration in development.

Notch signaling defines an evolutionarily ancient cell interaction mechanism, which plays a fundamental role in metazoan development. Signals exchanged between neighboring cells through the Notch receptor can amplify and consolidate molecular differences,...

Bone marrow cells regenerate infarcted myocardium

Donald Orlic, Jan Kajstura, Stefano Chimenti, Igor Jakoniuk, Stacie M. Anderson, Baosheng Li, James M. Pickel, Ron McKay, Bernardo Nadal-Ginard, David M. Bodine, Annarosa Leri, Piero Anversa

INTERLEUKIN-10 AND THE INTERLEUKIN-10 RECEPTOR

▪ Abstract Interleukin-10 (IL-10), first recognized for its ability to inhibit activation and effector function of T cells, monocytes, and macrophages, is a multifunctional cytokine with diverse effects on most hemopoietic cell types. The principal...

Specificity of receptor tyrosine kinase signaling: Transient versus sustained extracellular signal-regulated kinase activation

A number of different intracellular signaling pathways have been shown to be activated by receptor tyrosine kinases. These activation events include the phosphoinositide 3-kinase, 70 kDa S6 kinase, mitogen-activated protein kinase (MAPK), phospholipase...

TCS: a computer program to estimate gene genealogies

Mark J. Clement, David Posada, Keith A. Crandall

Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells.

Estelle Bettelli, Yijun Carrier, Wenda Gao, Thomas Korn, Terry B. Strom, Mohamed Oukka, Howard L. Weiner, Vijay K. Kuchroo

MicroRNA signatures in human cancers

MicroRNA (miRNA ) alterations are involved in the initiation and progression of human cancer. The causes of the widespread differential expression of miRNA genes in malignant compared with normal cells can be explained by the location of these genes in...

Integrins: bidirectional, allosteric signaling machines.

In their roles as major adhesion receptors, integrins signal across the plasma membrane in both directions. Recent structural and cell biological data suggest models for how integrins transmit signals between their extracellular ligand binding adhesion...

Crystal structure of the nucleosome core particle at 2.8 A resolution

K Luger, Armin W. Mäder, Robin K. Richmond, David F. Sargent, Timothy J. Richmond

Standardisation of spirometry

[⇓][1] SERIES “ATS/ERS TASK FORCE: STANDARDISATION OF LUNG FUNCTION TESTING” Edited by V. Brusasco, R. Crapo and G. Viegi Number 2 in this Series [1]: #HASH#F13

World Reference Base for Soil Resources

Jozef Deckers, P. M. Driessen, O. Spaargaren

Regional Distribution of Circulating Blood During Submersion Asphyxia in the Duck

Regional blood flow distribution in ducks was estimated from fractional distribution of Rb86CI. A comparison was made between normally breathing ducks and submerged ducks. The data document that conspicuous changes in regional blood flow take place upon...

DnaSP, DNA polymorphism analyses by the coalescent and other methods

Summary: DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (∼5 Mb per sequence); (2) conducting a large number...

Tissue destruction by neutrophils.

WITH increasing frequency, the human neutrophil is being implicated as a mediator of tissue-destructive events in inflammatory diseases ranging from rheumatoid arthritis and myocardial reperfusion injury to respiratory distress syndromes, blistering skin...

A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1

A strong candidate for the 17q-linked BRCA1 gene, which influences susceptibility to breast and ovarian cancer, has been identified by positional cloning methods. Probable predisposing mutations have been detected in five of eight kindreds presumed to...

The genetic legacy of the Quaternary ice ages

The genetic legacy of the Quaternary ice ages

Untangling the ErbB signalling network

Yosef Yarden, Mark X. Sliwkowski

The heat-shock proteins.

Susan Lindquist, Elizabeth A. Craig

Room-temperature transistor based on a single carbon nanotube

Sander J. Tans, Alwin R. M. Verschueren, Cees Dekker

Intracellular signaling by hydrolysis of phospholipids and activation of protein kinase C.

Hydrolysis of inositol phospholipids by phospholipase C is initiated by either receptor stimulation or opening of Ca2+ channels. This was once thought to be the sole mechanism to produce the diacylglycerol that links extracellular signals to intracellular...

Statistical significance for genomewide studies

With the increase in genomewide experiments and the sequencing of multiple genomes, the analysis of large data sets has become com- monplace in biology. It is often the case that thousands of features in a genomewide data set are tested against some null...

Quantum dots for live cells, in vivo imaging, and diagnostics.

Research on fluorescent semiconductor nanocrystals (also known as quantum dots or qdots) has evolved over the past two decades from electronic materials science to biological applications. We review current approaches to the synthesis, solubilization,...

Diarrheagenic Escherichia coli

Escherichia coli is the predominant nonpathogenic facultative flora of the human intestine. Some E. coli strains, however, have developed the ability to cause disease of the gastrointestinal, urinary, or central nervous system in even the most robust...

|[alpha]|-Synuclein in Lewy bodies

Maria Grazia Spillantini, Virginia M.-Y. Lee, John Q. Trojanowski, Ross Jakes, Michel Goedert

Error and attack tolerance of complex networks

: Many complex systems, such as communication networks, display a surprising degree of robustness: while key components regularly malfunction, local failures rarely lead to the loss of the global information-carrying ability of the network. The stability...

A new method for sequencing DNA.

Maxam Am, Walter Gilbert

Alzheimer's disease: genes, proteins, and therapy.

Rapid progress in deciphering the biological mechanism of Alzheimer's disease (AD) has arisen from the application of molecular and cell biology to this complex disorder of the limbic and association cortices. In turn, new insights into fundamental aspects...

Ecological responses to recent climate change

There is now ample evidence of the ecological impacts of recent climate change, from polar terrestrial to tropical marine environments. The responses of both flora and fauna span an array of ecosystems and organizational hierarchies, from the species...

Genome Sequencing in Open Microfabricated High Density Picoliter Reactors

We describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel 60×60 mm 2 fibreoptic slide containing 1,600,000 individual...

The Dendritic Cell System and its Role in Immunogenicity

Dendritic cells are a system of antigen presenting cells that function to initiate several immune responses such as the sensitization ofMHC -restric­ ted T cells, the rejection of organ transplants, and the formation of T­ dependent antibodies. Dendritic...

Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands

James G. Herman, Jeremy R. Graff, Sanna Myöhänen, Barry D. Nelkin, Stephen B. Baylin

Akt Phosphorylation of BAD Couples Survival Signals to the Cell-Intrinsic Death Machinery

Growth factors can promote cell survival by activating the phosphatidylinositide-3′-OH kinase and its downstream target, the serine-threonine kinase Akt. However, the mechanism by which Akt functions to promote survival is not understood. We show that...

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.

Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA ( mtDNA ) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site,...

The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases

The cyclin-dependent kinase Cdk2 associates with cyclins A, D, and E and has been implicated in the control of the G1 to S phase transition in mammals. To identify potential Cdk2 regulators, we have employed an improved two-hybrid system to isolate human...

Electroluminescence in conjugated polymers

Richard H. Friend, R. W. Gymer, Andrew B. Holmes, J. H. Burroughes, R. N. Marks, C. Taliani, David K. Bradley, D.A. dos Santos, J. L. Bredas, M. Lögdlund, W. R. Salaneck

Phosphorylation Meets Ubiquitination: The Control of NF-κB Activity

NF-κB (nuclear factor-κB) is a collective name for inducible dimeric transcription factors composed of members of the Rel family of DNA-binding proteins that recognize a common sequence motif. NF-κB is found in essentially all cell types and is involved...

Involvement of chemokine receptors in breast cancer metastasis

Anja Müller, Bernhard Homey, Hortensia Soto, Nianfeng Ge, Daniel Catron, Matthew E. Buchanan, Terri McClanahan, Erin Murphy, Wei Yuan, Stephan N. Wagner, Jose Luis Barrera, Alejandro Mohar, Emma Verastegui, Albert Zlotnik

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

Motivation: When running experiments that involve multiple high density oligonucleotide arrays, it is important to remove sources of variation between arrays of non-biological origin. Normalization is a process for reducing this variation. It is common...

Epithelial-Mesenchymal Transitions in Development and Disease

Most adult tissues and organs arise from a series of conversions of epithelial cells to mesenchymal cells, through the epithelial to mesenchymal transition (EMT) and the reverse process (mesenchymal to epithelial transition [MET]). Epithelial cells establish...

Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation

Sophisticated 21st-century analyses of the signaling pathways that control cell growth have led researchers back to the seminal work of Otto Warburg, who discovered in the 1920s that tumor cells generate their energy in an unusual way—by switching from...

Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase.

Plasmid expression vectors have been constructed that direct the synthesis of foreign polypeptides in Escherichia coli as fusions with the C terminus of Sj26, a 26-kDa glutathione S -transferase (GST; EC 2.5.1.18) encoded by the parasitic helminth...

A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: polyethylenimine.

Otmane Boussif, Frank Lezoualc'h, Zanta Ma, Mergny Md, Barbara A. Demeneix, Jean-Paul Behr

A System for Stable Expression of Short Interfering RNAs in Mammalian Cells

Mammalian genetic approaches to study gene function have been hampered by the lack of tools to generate stable loss-of-function phenotypes efficiently. We report here a new vector system, named pSUPER, which directs the synthesis of small interfering...

The serial cultivation of human diploid cell strains

The isolation and characterization of 25 strains of human diploid fibroblasts derived from fetuses are described. Routine tissue culture techniques were employed. Other than maintenance of the diploid karyotype, ten other criteria serve to distinguish...

Antimicrobial peptides of multicellular organisms

Antimicrobial peptides of multicellular organisms

A Toll-like receptor recognizes bacterial DNA

Hiroaki Hemmi, Osamu Takeuchi, Taro Kawai, Tsuneyasu Kaisho, Hideki Sanjo, Makoto Matsumoto, Hermann Wagner, Kiyoshi Takeda, Shizuo Akira

Culture of Human Endothelial Cells Derived from Umbilical Veins. IDENTIFICATION BY MORPHOLOGIC AND IMMUNOLOGIC CRITERIA

Endothelial cells were isolated from freshly obtained human umbilical cords by collagenase digestion of the interior of the umbilical vein. The cells were grown in tissue culture as a homogeneous population for periods up to 5 mo and some lines were subcultured...

Taxonomic Note: A Place for DNA-DNA Reassociation and 16s rRNA Sequence Analysis in the Present Species Definition in Bacteriology

Because a natural entity “species” cannot be recognized as a group of strains that is genetically well separated from its phylogenetic neighbors, a pragmatic approach was taken to define a species by a polyphasic approach (L. G. Wayne, D. J. Brenner,...

Identification of human brain tumour initiating cells

Sheila K. Singh, Cynthia Hawkins, Ian D. Clarke, Jeremy A. Squire, Jane Bayani, Takuichiro Hide, R. Mark Henkelman, Michael D. Cusimano, Peter B. Dirks

Efficient selection for high-expression transfectants with a novel eukaryotic vector

We have developed a new expression vector which allows efficient selection for transfectants that express foreign genes at high levels. The vector is composed of a ubiquitously strong promoter based on the β-actin promoter, a 69% Subregion of the bovine...

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

Molecular structures and sequences are gen- erally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progres- sively shifted from the...

Surfing the p53 network

Bert Vogelstein, David Lane, Arnold J. Levine

Equilibrium points in n-person games

Equilibrium points in n-person games

Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins

Through the study of transcriptional activation in response to interferon alpha (IFN-alpha) and interferon gamma (IFN-gamma), a previously unrecognized direct signal transduction pathway to the nucleus has been uncovered: IFN-receptor interaction at the...

Chronic Parkinsonism in humans due to a product of meperidine-analog synthesis.

Four persons developed marked parkinsonism after using an illicit drug intravenously. Analysis of the substance injected by two of these patients revealed primarily 1-methyl-4-phenyl-1,2,5,6-tetrahydropyridine (MPTP) with trace amounts of 1-methyl-4-phenyl-4-propionoxy-piperidine...

Human Adipose Tissue Is a Source of Multipotent Stem Cells

Min Zhu, Peter Ashjian, Daniel A. De Ugarte, Jerry I. Huang, Hiroshi Mizuno, Zeni Alfonso, John K. Fraser, Prosper Benhaim, Marc H. Hedrick

In Vivo Gene Delivery and Stable Transduction of Nondividing Cells by a Lentiviral Vector

A retroviral vector system based on the human immunodeficiency virus (HIV) was developed that, in contrast to a murine leukemia virus-based counterpart, transduced heterologous sequences into HeLa cells and rat fibroblasts blocked in the cell cycle, as...

Multiple receptors for dopamine.

John W. Kebabian, Donald B. Calne

New perspectives in cell adhesion: RGD and integrins.

Rapid progress has been made in the understanding of the molecular interactions that result in cell adhesion. Many adhesive proteins present in extracellular matrices and in the blood contain the tripeptide arginine-glycine-aspartic acid (RGD) as their...

DAVID: Database for Annotation, Visualization, and Integrated Discovery

The distributed nature of biological knowledge poses a major challenge to the interpretation of genome-scale datasets, including those derived from microarray and proteomic studies. This report describes DAVID, a web-accessible program that integrates...

Multilineage Cells from Human Adipose Tissue: Implications for Cell-Based Therapies

Future cell-based therapies such as tissue engineering will benefit from a source of autologous pluripotent stem cells. For mesodermal tissue engineering, one such source of cells is the bone marrow stroma. The bone marrow compartment contains several...

A novel assay for apoptosis Flow cytometric detection of phosphatidylserine expression on early apoptotic cells using fluorescein labelled Annexin V

In the early stages of apoptosis changes occur at the cell surface, which until now have remained difficult to recognize. One of these plasma membrane alterations is the translocation of phosphatidylserine (PS) from the inner side of the plasma membrane...

Herbivores and the Number of Tree Species in Tropical Forests

A high number of tree species, low density of adults of each species, and long distances between conspecific adults are characteristic of many low-land tropical forest habitats. I propose that these three traits, in large part, are the result of the action...

THE GREEN FLUORESCENT PROTEIN

▪ Abstract In just three years, the green fluorescent protein (GFP) from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology. Its amazing ability...

Use of T7 RNA polymerase to direct expression of cloned genes.

Studier Fw, Rosenberg Ah, John J. Dunn, Dubendorff Jw

Chlorophyll fluorescence—a practical guide

typically written from a biophysicist’s or a molecular plant physiologist’s point of view (Horton and Bowyer, Chlorophyll fluorescence analysis has become one of 1990; Krause and Weis, 1991; Govindjee, 1995). The aim the most powerful and widely used...

PAML: a program package for phylogenetic analysis by maximum likelihood

PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such...

The Genome Sequence of Drosophila melanogaster

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined...

LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing.

Little is known about the protein constituents of autophagosome membranes in mammalian cells. Here we demonstrate that the rat microtubule‐associated protein 1 light chain 3 (LC3), a homologue of Apg8p essential for autophagy in yeast, is associated...

Biological identifications through DNA barcodes

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon...

Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.

Hanne Philbert Nielsen, Jacob Engelbrecht, Søren Brunak, G von Heijne

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae...

Reticular synthesis and the design of new materials

Omar M. Yaghi, Michael O'Keeffe, Nathan W. Ockwig, Hee K. Chae, Mohamed Eddaoudi, Jaheon Kim

Phosphorylation and Regulation of Akt/PKB by the Rictor-mTOR Complex

Deregulation of Akt/protein kinase B (PKB) is implicated in the pathogenesis of cancer and diabetes. Akt/PKB activation requires the phosphorylation of Thr308 in the activation loop by the phosphoinositide-dependent kinase 1 (PDK1) and Ser473 within the...

Akt Promotes Cell Survival by Phosphorylating and Inhibiting a Forkhead Transcription Factor

Survival factors can suppress apoptosis in a transcription-independent manner by activating the serine/threonine kinase Akt, which then phosphorylates and inactivates components of the apoptotic machinery, including BAD and Caspase 9. In this study, we...

ras Oncogenes in Human Cancer: A Review

Mutations in codon 12, 13, or 61 of one of the three ras genes, H- ras , K- ras , and N- ras , convert these genes into active oncogenes. Rapid assays for the detection of these point mutations have been developed recently and used to investigate the...

Mdm2 promotes the rapid degradation of p53.

Ygal Haupt, Ruth Maya, Anat Kazaz, Moshe Oren

Tight control of gene expression in mammalian cells by tetracycline-responsive promoters.

Control elements of the tetracycline-resistance operon encoded in Tn10 of Escherichia coli have been utilized to establish a highly efficient regulatory system in mammalian cells. By fusing the tet repressor with the activating domain of virion protein...

Crystal structure of the nucleosome core particle at 2.8|[thinsp]||[Aring]| resolution

Armin W. Mäder, Robin K. Richmond, David F. Sargent, Timothy J. Richmond

APE: Analyses of Phylogenetics and Evolution in R language

Summary: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well...

Some genetic consequences of ice ages, and their role in divergence and speciation

The genetic effects of pleistocene ice ages are approached by deduction from paleoenvironmental information, by induction from the genetic structure of populations and species, and by their combination to infer likely consequences. (1) Recent palaeoclimatic...

TESTING SIGNIFICANCE OF INCONGRUENCE

James S. Farris, Mari Källersjö, Arnold G. Kluge, Carol Bult

Trends, Rhythms, and Aberrations in Global Climate 65 Ma to Present

Since 65 million years ago (Ma), Earth's climate has undergone a significant and complex evolution, the finer details of which are now coming to light through investigations of deep-sea sediment cores. This evolution includes gradual trends of warming...

The clonal evolution of tumor cell populations.

It is proposed that most neoplasms arise from a single cell of origin, and tumor progression results from acquired genetic variability within the original clone allowing sequential selection of more aggressive sublines. Tumor cell populations are apparently...

Textbook of pollen analysis

Knut Faegri, Johannes Iversen

Toxic Potential of Materials at the Nanolevel

Nanomaterials are engineered structures with at least one dimension of 100 nanometers or less. These materials are increasingly being used for commercial purposes such as fillers, opacifiers, catalysts, semiconductors, cosmetics, microelectronics, and...

Adipose expression of tumor necrosis factor-alpha: direct role in obesity-linked insulin resistance

Tumor necrosis factor-alpha (TNF-alpha) has been shown to have certain catabolic effects on fat cells and whole animals. An induction of TNF-alpha messenger RNA expression was observed in adipose tissue from four different rodent models of obesity and...

RNA-Seq: a revolutionary tool for transcriptomics.

RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far...

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data....

THE NF-κB AND IκB PROTEINS: New Discoveries and Insights

▪ Abstract The transcription factor NF-κB has attracted widespread attention among researchers in many fields based on the following: its unusual and rapid regulation, the wide range of genes that it controls, its central role in immunological processes,...

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