bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nomenclature of the Human Immunoglobulin Genes
Authors: Lefranc Marie‐Paule 
Published: June 2004

AbstractThe human immunoglobulins (Ig) are the products of three unlinked sets of genes: the immunoglobulin heavy (IGH), the immunoglobulin κ (IGK), and the immunoglobulin λ (IGL) genes, localized on chromosome 14 (14q32.33), 2 (2p12), and 22 (22q11.2), respectively. This appendix presents tabulated lists of the human immunoglobulin heavy, κ, and λ genes named in accordance with the International ImMunoGeneTics database (IMGT) and approved by the Human Genome Organization (HUGO) Nomenclature Committee in 1999. Three additional tables list corresponding nomenclatures for these genes.
Detection and Quantitation of Radiolabeled Proteins and DNA in Gels and Blots
Authors: Voytas Daniel , Ke Ning 
Published: June 2004

AbstractThis appendix presents procedures for visualizing and quantitating radiolabeled proteins or DNA separated by polyacrylamide gel electrophoresis or affixed to filter membranes. Autoradiography is the most common method by which this is accomplished; X‐ray film is the traditional recording medium. Film images can be analyzed by densitometry as described to obtain a quantitative measure of the radioactivity in the sample. The use of X‐ray films for autoradiography, however, suffers from lack of sensitivity and limited linear range. Protocols are provided for overcoming these limitations using fluorography and intensifying screens, both of which enhance the radioactive signal. Sensitivity and linear ranges of measurement can be greatly extended by using a phosphor imaging system, which also makes it much faster and easier to quantify radioactive samples.
Monoclonal Antibodies to Human Cell Surface Antigens
Authors: Stockinger Hannes , Majdic Otto , Knapp Walter , Swart Bernadette , Nicholson Ian , Zola Heddy 
Published: June 2004

AbstractThis appendix lists the cluster of differentiation (CD) designations for the nearly 300 different leukocyte surface molecules that have been assigned and approved by the nomenclature committee of the International Union of Immunological societies (IUIS).
Pulsed‐Field Gel Electrophoresis for Long‐Range Restriction Mapping
Authors: Gemmill Robert M. , Bolin Richard , Albertsen (LiDS prep) Hans , Tomkins Jeff P. , Wing Rod A. 
Published: June 2004

AbstractThis unit describes procedures for generating long‐range restriction maps of genomic DNA and for analysis of large insert clones. The basic protocol details restriction digestion of agarose‐embedded DNA, PFGE separation, Southern transfer, and hybridization. Support protocols describe the preparation of high‐molecular‐weight genomic DNA samples in agarose blocks and in agarose microbeads, respectively. Additional support protocols describe the preparation of DNA size standards from l phage and two yeast species, Saccharomyces cerevisiae and Schizosaccharomyces pombe. An alternative method of preparing S. cerevisiae size standards using lithium dodecyl sulfate (LiDS) solubilization is provided. The final protocol details the preparation of BAC DNA suitable for digestion, mapping, and sequencing.
Gene Identification: Methods and Considerations
Authors: Baxevanis Andreas D. 
Published: June 2004

AbstractThis unit introduces readers to some of the more commonly used techniques for gene identification. The author discusses the general problem behind accurately predicting genes in both prefinished and finished sequence data, provides a handson description of programs available in the public domain, and suggests strategies for how to best tackle the prediction problem at various stages of data generation and assembly.This unit introduces readers to some of the more commonly used techniques for gene identification.
Sequence Similarity Searching Using the BLAST Family of Programs
Authors: Wolfsberg Tyra G. , Madden Thomas L. 
Published: June 2004

AbstractDatabase sequence similarity searching is carried out thousands of times each day by researchers worldwide. This unit describes the BLAST (Basic Local Alignment Search Tool) family of sequence similarity search programs. It compares basic and advanced searches, discusses the BLAST algorithm, and presents the variety of databases that can be searched. Examples of various BLAST searches (e.g., BLASTP, BLASTX, BLASTN) are included. The unit also includes a discussion of different search strategies, such as filtering repeats and low‐complexity regions, and tips for analyzing genomic DNA, mRNA, and short sequences. Two unit appendices detail the BLAST parameters and sequence identifier syntax.
Accessing the Human Genome
Authors: Church Deanna , Pruitt Kim D. 
Published: June 2004

AbstractThe majority of the sequence for the human genome is now available. Regardless of the researcher's area of interest, it is quite likely that they will want to use some aspect of this data. This unit helps researchers achieve that goal. It presents the gene models available at NCBI, the UCSC Genome Browser, and Ensembl. It reviews the features and options available from the three web sites to query, display, and download the data. In addition, the unit illustrates how to query each of the databases in order to identify information, such as the genomic location of a novel cDNA, a BAC clone that contains a particular gene, and homologous human genes to a particular protein sequence from a different organism.
Preparation, Culture, and Analysis of Amniotic Fluid Samples
Authors: Meron Patricia Minehart 
Published: June 2004

AbstractThe describes an in situ method for the preparation, culture, harvest, and analysis of amniotic fluid samples. In this procedure, cells are grown and harvested for metaphase spreads on glass coverslips. The metaphase spreads are analyzed without being removed from the coverslips. describes a harvesting technique that yields higher‐resolution banding. describes a method for growing more cells by passaging cells from a backup monolayer culture. An describes a flask method for the preparation, culture, harvest, and analysis of amniotic fluid samples that can be used instead of the in situ method. Accompanying is that describes subculturing cells from flasks.
Multiplex PCR for Identifying Dystrophin Gene Deletions
Authors: Beggs Alan H. 
Published: June 2004

AbstractThe identification of dystrophin as the defective protein in patients with Duchenne and Becker muscular dystrophies (DMD and BMD) has allowed the development of sensitive and specific tests to establish a diagnosis and to aid in genetic counseling and prenatal diagnosis. The describes three complementary multiplex PCR assays that detect 26 dystrophin gene exons. The describes preparation and storage of stock PCR reaction mixes with primers for each of the three diagnostic assays. The is a modification of the for radioactive detection of duplications in males and deletions in carrier females.The identification of dystrophin as the defective protein in patients with Duchenne and Becker muscular dystrophies
Metaphase Harvest and Cytogenetic Analysis of Malignant Hematological Specimens
Authors: Cin Paola Dal 
Published: June 2004

AbstractCytogenetic analysis of malignant hematological disease is an important methodology used by clinicians and researchers, as observations of clonal chromosomal abnormalities have been shown to have both diagnostic and prognostic significance. The describes the culture, harvest, and preparation of chromosome spreads from bone marrow aspirates. Five alternate protocols describe adaptations of the for preparation of specimens from chronic lymphocytic leukemia (CLL) bone marrow, leukemic peripheral blood, CLL peripheral blood, post‐bone marrow transplant (post‐BMT) peripheral blood, and aplastic anemia bone marrow and peripheral blood. The modifications involve slightly different culture and harvest methods that are necessary to assure optimal results.
Oligonucleotide Arrays for Expression Monitoring
Authors: Byrne Michael C. , Whitley Maryann Z. , Follettie Maximillian T. 
Published: June 2004

AbstractThis unit provides protocols for the amplification and labeling of mRNA (and the necessary controls) for hybridization to oligonucleotide arrays. It also describes methods for processing and normalizing the raw gene expression data in preparation for clustering and further analysis.
Profiling Human Gene Expression with cDNA Microarrays
Authors: Jiang Yuan , Lueders John , Glatfelter Arthur , Gooden Chris , Bittner Michael 
Published: June 2004

AbstractAs a result of genomics initiatives worldwide, it has become increasingly easy to obtain cDNA clones representing the 3 ends of many human genes. This unit describes methods that allow these clones to be used as hybridization detectors in a highly parallel assay of gene expression. Protocols are provided for preparing cDNA microarrays, extracting RNA from cells of interest and preparing fluorescently labeled cDNA representations of the message pools, and hybridizing the labeled cDNAs to the microarrays.
Semliki Forest Virus and Sindbis Virus Vectors
Authors: Ehrengruber Markus U. , Lundstrom Kenneth 
Published: June 2004

AbstractSemliki Forest virus (SFV) and Sindbis virus (SIN) are two, positive‐strand RNA viruses of the alphavirus genus. Vectors for both have been developed to express high levels of foreign genes in vitro and in vivo. describes the preparation of packaged SFV and SIN replicons by co‐electroporation of helper and vector RNA into baby hamster kidney (BHK)‐21 cells. describes the activation of packaged SFV replicons with a‐chymotrypsin. provides a method for the infection of hippocampal slices. is a technique for the infection of primary cultures of dispersed neurons with infectious SFV and SIN replicons. The describes a method for the cotransfection of in vitro‐transcribed vector and helper RNA into BHK‐21 cells. describes determining the titers of infectious SFV and SIN replicon stocks, and for metabolic labeling of infected cells.
Production of Retroviral Vectors
Authors: Miller A. Dusty 
Published: June 2004

AbstractIn this unit, the basic protocol generates stable cell lines, which produce retroviral vectors that carry selectable markers. applies when the retroviral vector does not carry a selectable marker. presents rapidly generating retroviral vector preparations by transient transfection. describes construction of the retrovirus vectors. The methods for generating virus from retroviral vector plasmids rely on the use of packaging cells that synthesize all of the retroviral proteins but do not produce replication‐competent virus. One packaging cell line is transiently transfected to produce virus carrying the vector RNA that can be used to infect a second packaging cell line. Virus that carries a selectable marker can be titered and viral stocks can be tested for the presence of helper virus, as described. Vectors that contain sequence for alkaline phosphatase can be assayed histochemically.In this unit, the basic protocol generates stable cell lines, which produce retroviral vectors that carry selectable markers.
Particle‐Mediated Gene Delivery In Vivo and In Vitro
Authors: Yang Ning‐Sun , Burkholder Joseph , McCabe Dennis , Neumann Veronica , Fuller Deb 
Published: June 2004

AbstractParticle‐mediated or “gene gun” technology has been developed as a nonviral method for gene transfer into various mammalian tissues. Gene delivery is achieved by physical force: a strong shock wave is generated that accelerates DNA‐coated gold particles to high speeds, providing them with the momentum needed to penetrate the targeted cells. This unit describes general procedures for in vivo and in vitro DNA and RNA transfections by particle‐mediated delivery. The and an alternate protocol address in vivo delivery to mouse skin. In vitro delivery to cryopreserved and adherent cells is also described.
DNA Vaccination
Authors: Ulmer Jeffrey B. , Rappuoli Rino 
Published: June 2004

AbstractThis unit details some of the key methods for setting up and testing DNA vaccines in animal models. The basic procedures are discussed, as well as alternative methods that have been developed over the past several years. The gives step‐by‐step instructions for administering the DNA vaccine via intramuscular injection of the quadriceps muscle, while an alternate procedure details injection of the anterior tibialis.
Methods for Cancer Gene Therapy
Authors: Kwong Yok‐Lam , Chen Shu‐Hsia , Woo Savio L.C. 
Published: June 2004

AbstractFirst, the testing of therapeutic gene vectors in vitro is described. This is followed by a discussion of the administration of therapeutic vectors in vivo. Two methods for assessing the development of anti‐tumor immunity after cytokine gene therapy are provided. In addition, two methods for the generation of murine tumor models in syngeneic hostsone subcutaneous and one orthotopicare also included.
Laboratory Safety
Authors: Meisenhelder Jill , Semba Kentaro , Lunn George , Strober Warren 
Published: June 2004

AbstractPersons carrying out the protocols in this manual may encounter the following hazardous or potentially hazardous materials: (1) radioactive substances; (2) toxic chemicals and carcinogenic, mutagenic, or teratogenic reagents; and (3) pathogenic and infectious biological agents. Most governments regulate the use of these materials; it is essential that they be used in strict accordance with local and national regulations. Cautionary notes are included in many instances throughout the manual, and some specific guidelines are also provided in this appendix. However, users must proceed with the prudence and precautions associated with good laboratory practice, under the supervision of personnel responsible for implementing laboratory safety programs at their institutions and in compliance with designated guidelines of federal, state, and local officials.
Quantitation of DNA and RNA with Absorption and Fluorescence Spectroscopy
Authors: Gallagher Sean R. 
Published: June 2004

AbstractReliable quantitation of nanogram and microgram amounts of DNA and RNA in solution is essential to researchers in molecular biology. In addition to the traditional absorbance measurements at 260 nm, two more sensitive fluorescence techniques using Hoechst 33258 and ethidium bromide are presented in this appendix. These three procedures cover a range from 5 to 10 ng/ml DNA to 50 µg/ml DNA.
Internet Basics for Biologists
Authors: Baxevanis Andreas D. , Ouellette B.F. Francis 
Published: June 2004

AbstractWith the explosion of sequence and structural information available to researchers, the field of bioinformatics is playing an increasingly large role in the study of fundamental biomedical problems. The challenge facing computational biologists will be to aid in gene discovery and in the design of molecular modeling, site‐directed mutagenesis, and experiments of other types that can potentially reveal previously unknown relationships with respect to the structure and function of genes and proteins. This appendix begins with a review of the Internet and its terminology, also discussing major classes of Internet protocols, without becoming overly engaged in the engineering minutiae underlying these protocols. This appendix also discusses matters of connectivity, ranging from simple modem connections to digital subscriber lines (DSL). Finally, one of the most common problems that has arisen with the proliferation of Web pages throughout the worldWith the explosion of sequence and structural information available to researchers, the field of bioinformatics is playing.
Genetic Linkage Reference Maps: Access to Internet‐Based Resources
Authors: Haines Jonathan L. 
Published: June 2004

AbstractThe goal of this appendix is to introduce the reader to some of the most useful reference map resources now available through the World Wide Web (WWW). The maps presented in earlier versions of this appendix have been eliminated, since they are no longer updated and the most common methods of access and retrieval of up‐to‐date reference maps are now through the WWW. It should be noted that the very nature of the WWW is dynamic change. New sites appear and old ones disappear with somewhat disruptive regularity. The sites mentioned here are the most likely to remain stable, and thus to remain useful for the human gene mapper.
Double child burial from sunghir (Russia): Pathology and inferences for upper paleolithic funerary practices
Authors: Formicola Vincenzo , Buzhilova Alexandra P. 
Published: June 2004

AbstractThe double child burial from Sunghir (Russia) is a spectacular Mid Upper Palaeolithic funerary example dated to about 24,000 BP. A boy (Sunghir 2) and a girl (Sunghir 3), about 12–13 and 9–10 years old, respectively, were buried at the same time, head to head, covered by red ocher and ornamented with extraordinarily rich grave goods. Examination of the two skeletons reveals that the Sunghir 3 femora are short and exhibit marked antero‐posterior bowing. The two femora do not show any asymmetry in the degree of shortening and bowing. Bowing affects the whole diaphysis and shows a regularly incurved profile, with the highest point at midshaft. Pathology is confined to the femora, and no other part of this well‐preserved specimen shows abnormality. The isolated nature of the Sunghir 3 anomalies points to cases reported in the medical literature under the label of “congenital bowing of long bones” (CBLB). These are a group of rare conditions exhibiting localized, sometimes bilateral, bowing and shortening which are nonspecific and may result from different causes, including abnormalities of the primary cartilaginous anlage (i.e., the aggregation of cells representing the first trace of an organ). Localized ossification disturbances, possibly linked to a diabetic maternal condition, might explain the shortening and the coincidence of maximum midshaft curvature with the position of the primary ossification center, as well as the lack of involvement of other skeletal parts. This scenario, rather than other possibilities (early bilateral midshaft fracture, acute plastic bowing deformities, or faulty fetal posture), provides the most likely explanation for the Sunghir 3 femoral deformities. The intriguing combination of a pathological condition apparent since birth with a spectacular burial of unusually positioned young individuals of different sexes recalls significant aspects of the triple burial from the contemporary site of Dolní Věstonice (Moravia), evoking a patterned relationship between physical abnormality and extraordinary Upper Paleolithic funerary behavior. Am J Phys Anthropol, 2003. © 2003 Wiley‐Liss, Inc.
Effects of high static magnetic field exposure on different DNAs
Authors: Potenza Lucia , Cucchiarini Luigi , Piatti Elena , Angelini Umberta , Dachà Marina 
Published: June 2004

AbstractThe effects of magnetic fields produced by permanent magnets on different DNA sources were investigated in vivo and in vitro. Escherichia coli DNA, plasmid, and amplification products of different lengths were used as the magnetic field target. The in vivo assays did not reveal any DNA alterations following exposure, demonstrating the presence of cell dependent mechanisms, such as the repair system and the buffering action of the heat shock proteins DNA K/J (Hsp 70/40). The in vitro assays displayed interactions between the magnetic field and DNA, revealing principally that magnetic field exposure induces DNA alterations in terms of point mutations. We speculate that the magnetic field can perturb DNA stability interacting with DNA directly or potentiating the activity of oxidant radicals. This genotoxic effect of the magnetic field, however, is minimized in living organisms due to the presence of protective cellular responses. Bioelectromagnetics 25:352–355, 2004. © 2004 Wiley‐Liss, Inc.
0.2 T magnetic field inhibits angiogenesis in chick embryo chorioallantoic membrane
Authors: Ruggiero Marco , Bottaro Donald P. , Liguri Gianfranco , Gulisano Massimo , Peruzzi Benedetta , Pacini Stefania 
Published: June 2004

AbstractInhibition of angiogenesis is a major target in the fight against cancer and other diseases. Although the effects of static magnetic fields on cancer development and cell growth have been investigated, effects on angiogenesis have received no attention so far. In this study we report the effects on angiogenesis of exposure to 0.2 T static magnetic field. Angiogenesis was analyzed using the chick embryo chorioallantoic membrane assay. Exposure to 0.2 T static magnetic field was achieved by placing the eggs for 3 hr in the isocentre of the magnet of a sectorial magnetic resonance tomograph used in clinical practice. In sham exposed specimens treated with phosphate buffered saline (negative control), no significant vascular reaction was detectable; 3 hr exposure to 0.2 T static magnetic field did not affect the basal pattern of vascularization or chick embryo viability. Prostaglandin E1 and fetal calf serum elicited a strong angiogenic response in sham exposed eggs. This angiogenic response was significantly inhibited by 3 hr exposure to 0.2 T static magnetic field. These findings point to possible use of static magnetic field in inhibiting angiogenesis; this effect could be exploited for treatment of cancer and other diseases where excessive angiogenesis is involved. Bioelectromagnetics 25:390–396, 2004. © 2004 Wiley‐Liss, Inc.
A Series of Redox Active, Tetrathiafulvalene‐Based Amidopyridines and Bipyridines Ligands: Syntheses, Crystal Structures, a Radical Cation Salt and Group 10 Transition‐Metal Complexes
Authors: Devic Thomas , Avarvari Narcis , Batail Patrick 
Published: June 2004

AbstractAmidopyridine and −2,2′‐bipyridine derivatives of EDT‐TTF and BTM‐TTF (EDT=ethylenedithio, BTM=bis(thiomethyl), TTF=tetrathiafulvalene) have been synthesized and crystallographically characterized. In the solid state, the different supramolecular organization of all these donors results from the competition between the intermolecular interactions, that is, van der Waals, hydrogen‐bonding, π–π stacking, and donor–acceptor interactions. The electron‐donating properties of the new donors have been investigated by cyclic voltammetry measurements. A radical cation salt, formulated [EDT‐TTF‐CONH‐m‐Py].+[PF6]−, has been prepared by electrocrystallization and its crystal structure determined by X‐ray analysis. Square planar dicationic complexes with the same donor and MIIL2 fragments (M=Pd, Pt, L2=bis(diphenylphosphino)propane (dppp) or bis(diphenylphosphino)ethane (dppe)) have been synthesized and one of them, containing the Pd(dppp) unit, has been structurally characterized. The conformation of the complex in the crystalline state is anti, with the coexistence of the dl racemic pair of enantiomers.