bluuebunny/crossref_metadata_2025_split huggingface dataset:
Animal Models of IgA Nephropathy
Authors: Emancipator Steven N. 
Published: June 2004

AbstractIgA nephropathy (IgAN) is a form of immune complex glomerulonephritis that occurs spontaneously in humans. This unit describes the induction of active disease in inbred mice, utilizing inert proteins or a common viral pathogen as the inciting antigen. An alternate protocol is offered for the induction of disease in rats by noninfectious protein antigens. Support protocols are presented for the evaluation of the extent of disease, for preparation of infectious and inactivated suspensions of viral stock, and for quantification of the virus.
Autoimmune Ovarian Disease Induced by Immunization with Zona Pellucida (ZP3) Peptide
Authors: Tung Kenneth , Agersborg Sally , Bagavant Harini , Garza Kristine , Wei Kevin 
Published: June 2004

AbstractAutoimmune ovarian disease is a known cause of human premature ovarian failure. An experimental murine model can be created by immunization with a peptide of ZP3, an ovary‐specific glycoprotein. Mice injected with the ZP3 peptide develop histological evidence of ovarian inflammation (oophoritis), as well as antibody to the zona pellucida and T cell responses to the peptide. This unit describes the immunologic properties of the ZP3 peptides, the method of active autoimmune oophoritis induction, and the evaluation and semiquantitation of ovarian pathology. Surgical manipulations of the ovaries have been instrumental in the novel application of this autoimmune model; thus the most useful operations are also detailed. Surgical procedures are included for adult oophrectomy, neonatal ovariectomy, and implantation of ovarian grafts into mice without endogenous ovaries.
Affinity‐Based Biosensors for Biomolecular Interaction Analysis
Authors: Gunnarsson Kerstin 
Published: June 2004

AbstractThis overview presents an introduction to affinity‐based biosensors, most notably the BIACORE. These biosensors detect molecular interactions by immobilizing one of the interactants (the ligand or target molecule) on the surface of a sensor chip. A solution containing the other interactant is then applied to the chip. Binding of analyte to the surface results in a response proportional to the mass bound. A discussion of sensor chips and practical applications is also provided.
Animal Models of Mycobacteria Infection
Authors: Orme Ian M. , Roberts Alan D. 
Published: June 2004

AbstractThis unit describes the infection of mice and guinea pigs with mycobacteria via the aerogenic route, or of mice via the intravenous route, as well as necropsy methods for the determination of mycobacterial loads within target organs. Additionally, methods for cultivating mycobacteria and preparing stocks are described. The protocols outlined are primarily used for M. tuberculosis, but can also be used for the study of other opportunistic Mycobacterial species.
Helicobacter Animal Models
Authors: Nedrud John G. , Blanchard Thomas G. 
Published: June 2004

AbstractIn this unit, protocols for growing Helicobacter organisms on plates or in liquid cultures are presented, followed by protocols for infecting mice with Helicobacter felis and H. pylori and for infecting ferrets with H. mustelae. Also, a procedure is described for adapting an H. pylori isolate to growth in mice. Support protocols describe methods for quantifying numbers of Helicobacter organisms, and how to create a growth curve for Helicobacter cultures. One important technique in investigating Helicobacter infection is assaying the disease processes that occur in the stomach, and a protocol is provided for preparing tissue sections for this purpose. It is also important to confirm that organisms recovered from tissue samples are, in fact, Helicobacter species, and a support protocol describes morphological and biochemical tests for this purpose. Helicobacter bacteria produce large amounts of the enzyme urease, and a support protocol describes how to perform a rapid urease test on animal‐tissue biopsies. Assays of Helicobacter‐specific immune responses require appropriate antigens, and preparation of both Helicobacter lysates and outer‐membrane proteins are detailed for use in these assays.
Influenza Virus
Authors: Cottey Robert , Rowe Cheryl A. , Bender Bradley S. 
Published: June 2004

AbstractThis unit contains several methods for infecting mice with influenza virus. It also includes protocols needed to propagate influenza virus in hen eggs, quantitate virus titers (in tissue culture medium and in influenza‐infected mouse serum), and adopt human isolates of influenza for growth in mice. Methods for measuring the 50% mouse lethal dose are also included. Finally, protocols for generating anti‐influenza cytotoxic T lymphocytes (CTL) from splenocyte precursors and harvesting pulmonary CTL following respiratory tract challenge of mice with influenza virus are provided.
Mouse 4T1 Breast Tumor Model
Authors: Pulaski Beth A. , Ostrand‐Rosenberg Suzanne 
Published: June 2004

AbstractThe 4T1 mammary carcinoma is a transplantable tumor cell line that is highly tumorigenic and invasive and, unlike most tumor models, can spontaneously metastasize from the primary tumor in the mammary gland to multiple distant sites including lymph nodes, blood, liver, lung, brain, and bone The 4T1 tumor has several characteristics that make it a suitable experimental animal model for human mammary cancer. First, tumor cells are easily transplanted into the mammary gland so that the primary tumor grows in the anatomically correct site, as described in this unit. Second, as in human breast cancer, 4T1 metastatic disease develops spontaneously from the primary tumor. Also, the progressive spread of 4T1 metastases to the draining lymph nodes and other organs is very similar to that of human mammary cancer. In this unit, a protocol describes surgical removal of the primary tumor, so that metastatic disease can be studied in an animal setting comparable to the clinical situation where the primary tumor is surgically removed, and metastatic foci remain intact. Another advantage of 4T1 is its resistance to 6‐thioguanine. This property enables precise quantitation of metastatic cells, even when they are disseminated and at sub‐microscopic levels in distant organs, as described here.
Nomenclature of the Human T Cell Receptor Genes
Authors: Lefranc Marie‐Paule 
Published: June 2004

AbstractThe human T cell receptors (TcR) α‐β and γ‐δ are the products of four sets of genes on two chromosomes: T cell receptors α (TRA) and δ (TRD) on chromosome 14 at 14q11.2, T cell receptor β (TRB) on chromosome 7 at 7q35, and T cell receptor γ (TRG) on chromosome 7 at 7p15‐p14. This appendix presents tabulated lists of the human TcR α, β, γ, and δ genes named in accordance with the International ImMunoGeneTics database and approved by the Human Genome Organization Nomenclature Committee in 1999. Two additional tables list corresponding nomenclatures for these genes.
Nomenclature and Serology of HLA Class I and Class II Alleles
Authors: McCluskey James , Kanaan Carmel , Diviney Mary 
Published: June 2004

AbstractThis overview presents nomenclature and serology information on human leucocyte antigens, or HLA molecules, which are encoded by a cluster of genes linked on the short arm of chromosome 6. This region is known as the major histocompatibility coclass II molecules based upon their structure, tissue distribution, and source of peptide antigen, as well as upon their interactions with T cell subsets.
Monitoring Cell Growth
Authors: Strober Warren 
Published: June 2004

AbstractThis appendix provides two protocols for monitoring cell growth. Counting cells using a hemacytometer is tedious but it allows one to effectively distinguish live cells from dead cells (using Trypan Blue exclusion). In addition, this procedure is less subject to errors due to cell clumping or heterogeneity of cell size. The use of an electronic cell counter is quicker and easier than counting cells using a hemacytometer. However, an electronic cell counter as currently constructed does not distinguish live from dead cells in a reliable fashion and is subject to error due to the presence of cell clumps. Overall, the electronic cell counter is best reserved for repetitive and rapid counting of fresh peripheral blood cells and should be used with caution when counting cell populations derived from tissues.
Labeling Cells in Microtiter Plates for Determination of [3H]Thymidine Uptake
Authors: Shevach Ethan M. 
Published: June 2004

AbstractA number of protocols in Current Protocols in Immunology use as their end‐point the determination of cell proliferation by determining the incorporation of [3H]thymidine into cellular DNA. This appendix presents a protocol in which the radioactive label is added during the last 4 to 24 hr of the culture. A semiautomated cell harvesting apparatus is then used to lyse the cells with water and precipitate the labeled DNA on glass fiber filters. The filter pads are then dried and counted by standard liquid scintillation counting techniques in a scintillation counter.
Cryopreservation of Cells
Authors: Yokoyama Wayne M. 
Published: June 2004

AbstractLaboratories interested in working with in vitro cultured cells must be able to freeze and thaw cell lines. Such capabilities are necessary to maintain the constancy of the cells since prolonged culture may result in phenotypic and genotypic changes. In addition, cell freezing minimizes problems with contamination as well as the overall expense of maintaining cell lines for long periods. Finally, freezing of cells provides a method of making cell lines available to other laboratories since frozen cells are readily shipped to distant points. This appendix describes how cell lines can be frozen for long‐term storage and thawed for growth in a tissue culture vessel.
Collection of Clinical and Epidemiological Data for Linkage Studies
Authors: Farrer Lindsay 
Published: June 2004

AbstractAccurate assessment of the genetic basis for a disorder is necessary to determine if linkage studies will be meaningful. This unit provides an overview of key concepts and presents guidelines for collecting diagnostic, epidemiological, and genealogical data from potential study participants. The commentary discusses methods for evaluating evidence of genetic versus environmental influences in a disease and for assessing individual pedigrees.
Model‐Free Tests for Genetic Linkage
Authors: Amos Christopher I. 
Published: June 2004

AbstractThis unit covers statistical methods of linkage analysis that do not require assuming a detailed genetic model as is required for standard lod score analysis. The unit has been updated to include the latest methods in sib‐pair analysis as well as relative‐ pair analysis, including the NPL method used in GENEHUNTER and GENEHUNTER PLUS.
Analysis of Gene‐Gene Interactions
Authors: Moore Jason H. 
Published: June 2004

AbstractThe goal of this unit is to introduce gene‐gene interactions or epistasis as a significant complicating factor in the search for disease susceptibility genes. This unit begins with an overview of gene‐gene interactions and why they are likely to be common; then, it reviews several statistical and computational methods for detecting and characterizing genes whose effects are dependent on other genes. The focus of this unit is genetic association studies of discrete and quantitative traits since most of the methods for detecting gene‐gene interactions have been developed specifically for these study designs.
Construction of Small‐Insert Libraries from Genomic DNA
Authors: Hudson Thomas J. 
Published: June 2004

AbstractConstruction of small‐insert genomic libraries involves ligation of a size‐selected insert to vector DNA. In this unit, vector DNA is prepared by digestion with a restriction endonuclease followed by phosphatase treatment to dephosphorylate the vector ends. Insert DNA is prepared by complete digestion of DNA with a compatible 4‐base‐cutting restriction endonuclease (e.g., AluI, HaeIII, RsaI, or Sau3A), as such frequently cutting endonucleases give the highest fragment number in the desired range. Alternatively, fragments may be generated by sonication of genomic DNA. Once the fragments have been generated, they are size selected on an agarose gel. The portion of the gel containing DNA of the desired size is excised and the DNA released from the agarose by digestion with b‐agarase. Insert and vector DNAs are then ligated with T4 DNA ligase and used to transform competent Escherichia coli cells to create a small‐insert library.
Chromosome Banding Techniques
Authors: Schreck Rhona R. , Distèche Christine M. 
Published: June 2004

AbstractChromosome banding techniques produce a series of consistent landmarks along the length of metaphase chromosomes that allow for both recognition of individual chromosomes within a genome and identification of specific segments of individual chromosomes. These landmarks facilitate assessment of chromosome normalcy, identification of sites of chromosome breaks and alterations, and location of specific genes. This unit covers these basic banding techniques (Q‐banding, G‐banding, and R‐banding), which produce virtually identical patterns of bands along the length of human chromosomes, although the bands and polymorphic regions highlighted may differ with each technique. These techniques highlight reproducible landmarks along the length of the chromosome and specialized staining techniques can be used to highlight particular regions of chromosomes, such as heterochromatic and repeated‐sequence segments. These specialized techniques, nucleolar organizer region (NOR) staining, centromeric heterochromatin staining (C‐banding), methylated satellite DNA staining (distamycin‐DAPI banding), and replication banding are also presented in this unit.
Morphology Antibody Chromosome Technique for Determining Phenotype and Genotype of the Same Cell
Authors: Knuutila Sakari 
Published: June 2004

AbstractThe morphology antibody chromosome (MAC) technique is a powerful combination of methods that permits analysis of both phenotype and genotype on a single interphase or mitotic cell as a basis for lineage analysis of neoplastic and normal cells. This unit describes MAC with sequential phenotypic analysis using antibody and an alkaline phosphatase anti‐alkaline phosphatase (APAAP) complex and genotypic analysis using in situ hybridization with either enzymatic or fluorescence detection. Alternate methods for phenotypic analysis are also described, which include the use of horseradish peroxidase‐conjugated antibodies, fluorochrome‐conjugated antibodies, May‐Grunwald‐Giemsa cytochemical staining, and Sudan black B cytochemical staining. An additional protocol describes G‐ and C‐banding as alternatives to in situ hybridization (ISH) for genotyping MAC specimens. Support protocols describe methods for preparing specimenscytospin preparations, in situ cultures, paraffin‐embedded or cryostat sections, and blood and bone marrow smears. describes a procedure for chromosome painting of previously GTG‐banded slides.
Principles and Applications of PRINS in Cytogenetics
Authors: Koch Jørn 
Published: June 2004

AbstractPRINS (PRimed IN Situ labeling) is a technique that traditionally has been used for the detection of tandemly repeated target sequences in chromosomes and nuclei (“in situ”) by oligonucleotide probes. With a simple short procedure rendering virtually 100% of potential targets labeled, such sequences can be detected down to a target size of a few hundred bases. More recently it has been found that single‐copy sequences can also be detected at high sensitivity, if signals are enhanced with the Tyramide system. This unit provides protocols for basic PRINS or dideoxy‐PRINS (ddPRINS), and for combinatorial labeling (combining PRINS with FISH). These protocols are also applicable after immunostaining, provided that the antibody has been “secured” at the site by fixation in (para)formaldehyde.
Generating Subclones from Large‐Insert Genomic Clones
Authors: Monaco Anthony P. , Larin Zoia 
Published: June 2004

AbstractThis unit provides a simple protocol for generating a partial‐digest sublibrary of yeast DNA containing a YAC of interest. The starting material is high‐molecular‐weight chromosomal DNA embedded in agarose plugs. Many genome equivalents of these YAC subclones in bacteriophage or cosmid vectors can be plated and screened by hybridization with total human DNA to identify clones that originate from the human portion of the YAC. The human‐positive clones can be picked into 96‐well microtiter plates for spotting on membranes. Once stored in ordered arrays, the YAC subclones can be constructed into contigs using an end‐probe or Alu‐PCR hybridization strategy, or a gel fingerprinting technique.This unit provides a simple protocol for generating a partial‐digest sublibrary of yeast DNA containing a YAC of interest.
Sequence Databases: Integrated Information Retrieval and Data Submission
Authors: Weisemann Jane M. , Boguski Mark S. , Ouellette B.F. Francis 
Published: June 2004

AbstractThis unit describes the NCBI's Entrez database browser. Entrez integrates DNA and protein sequence data, threedimensional structures, and taxonomic information with its associated abstracts and citations contained in PubMed (MEDLINE). It is possible to search the Entrez information space using conventional search queries (authors, gene names, map location) as well as by bibliographic associations (articles that are related to one another) and sequence homology. Also described are the procedures for submission of new data, updates, and corrections to the sequence databases.
Detection of Mutations by Denaturing Gradient Gel Electrophoresis
Authors: Børresen‐Dale Anne‐Lise , Hovig Eivind , Smith‐Sørensen Birgitte 
Published: June 2004

AbstractThis unit describes the procedure for determining the melting profile for a given PCR‐amplified sequence by perpendicular denaturing gradient gel electrophoresis (DGGE) and, using that information, for developing a screening assay based on either parallel DGGE, CDGE (Constant Denaturant Gel Electrophoresis), or TTGE (Temporal /Temperature Gradient Electrophoresis). Four support protocols describe techniques for pouring perpendicular and parallel denaturing gradient gels, constant denaturant gels, and temporal temperature gradient gels.
Detection of Mutations by Fluorescence‐Assisted Mismatch Analysis (FAMA)
Authors: Tosi Mario , Verpy Elisabeth , Meo Tommaso 
Published: June 2004

AbstractFluorescence‐assisted mismatch analysis (FAMA) methodology uses bifluorescent double‐stranded DNA substrates to maximize the reliability and sensitivity of mutation‐scanning procedures that rely on cleavage of mismatches using chemical. This unit presents a nested PCR procedure to fluorescently label each DNA strand, followed by chemical cleavage to detect the point mutations. Fluorescent end labeling with strand‐specific fluorophores, electrophoretic separation of cleavage products in an automated Perkin‐Elmer ABI 373 or 377 DNA sequencer and analysis using the Perkin‐Elmer GENESCAN software expands sensitivity by highlighting weak signals through superimposition of strand‐specific fluorescence electropherograms for different samples.
Overview of Clinical Cytogenetics
Authors: Korf Bruce R. 
Published: June 2004

AbstractThis unit provides an introduction to clinical cytogenetics. It opens with indications for prenatal and postnatal chromosome analysis, followed by a brief discussion of the applications of fluorescence in situ hybridization (FISH). It suggests tissue sources for prenatal and postnatal analysis, and closes with a review of numerical and structural chromosome abnormalities. This unit provides an introduction to clinical cytogenetics
Diagnosis of Microdeletion Syndromes by Fluorescence in situ Hybridization (FISH)
Authors: Shaffer Lisa G. 
Published: June 2004

AbstractThis unit opens with an overview of microdeletions and methods for their detection. It goes on to describe a vast array of autosomal microdeletion syndromes, X‐linked microdeletion syndromes, and microduplication syndromes. The final portion of the unit offers guidance for detecting such syndromes with Fluorescence in situ Hybridization (FISH).
Serial Analysis of Gene Expression (SAGE)
Authors: Blackshaw Seth , Kim Jae B. , Croix Brad St. , Polyak Kornelia 
Published: June 2004

AbstractThis unit provides a protocol for performing serial analysis of gene expression (SAGE). SAGE involves the generation of short fragments of DNA, or tags, from a defined point in the sequence of all cDNAs in the sample analyzed. This short tag, because of its presence in a defined point in the sequence, is typically sufficient to uniquely identify every transcript in the sample. SAGE allows one to generate a comprehensive profile of gene expression in any sample desired from as little as 100,000 cells or 1 ug of total RNA. SAGE generates absolute, rather than relative, measurements of RNA abundance levels, and this fact allows an investigator to readily and reliably compare data to those produced by other laboratories, making the SAGE data set increasingly useful as more data is generated and shared.
Production of High‐Titer Lentiviral Vectors
Authors: Zufferey Romain , Trono Didier 
Published: June 2004

AbstractConventional retroviral vectors are useful for gene delivery because of their large cloning capacity and ability to integrate into the chromosome of the target cell. However, their inability to transduce nondividing cells limits their utility. In contrast, lentiviruses, a retrovirus subfamily, can infect both non‐replicating and dividing cells. This unit describes the production of human immunodeficiency virus‐derived vectors by transient transfection of 293T cells. In addition, the multiple safeguards engineered into the latest version of HIV‐based vectors are described.Conventional retroviral vectors are useful for gene delivery because of their large cloning capacity and ability to integrate.
Gene Delivery Using Helper Virus–Free HSV‐1 Amplicon Vectors
Authors: Fraefel Cornel 
Published: June 2004

AbstractHerpes simplex virus type 1 (HSV‐1)‐based amplicon vectors contain only ˜1% of the viral genome. Consequently, replication and packaging of amplicons depend on helper functions provided either by replication‐defective mutants of HSV‐1 (helper viruses) or by replication‐competent, but packaging‐defective, HSV‐1 genomes. Sets of cosmids that overlap and represent the entire HSV‐1 genome can form, via homologous recombination, circular replication‐competent viral genomes, which give rise to infectious virus progeny. If the DNA cleavage/packaging signals are deleted, reconstituted virus genomes are not packageable, but still provide all the helper functions required for the packaging of cotransfected amplicon DNA. Resulting stocks of packaged amplicon vectors are free of contaminating helper virus. The basic protocol describes the cotransfection of amplicon and cosmid DNA into 2‐2 cells and the harvesting of packaged vector particles. Support protocols describe preparing cosmid DNA and methods for determining the titers of amplicon stocks.
Gene Transfer to Arteries
Authors: Akyürek Levent M. , San Hong , Nabel Elizabeth G. , Singh Ripudamanjit , Simari Robert D. 
Published: June 2004

AbstractThis unit provides a set of protocols for introducing recombinant genes into normal, injured, and atherosclerotic arteries. The protocols include animal preparation, surgical techniques, and delivery systems. Protocols describe gene delivery to normal, injured, and stented porcine iliofemoral arteries, employing a double balloon infusion catheter to deliver the vector. Another basic protocol describes gene delivery to atherosclerotic arteries using a hyperlipidemic double‐injury rabbit model, and requires surgical exposure of the artery and instillation of the gene vector via a catheter. Additional protocols describe gene delivery to normal and injured murine carotid and femoral arteries. An describes a percutaneous method for arterial gene delivery. These protocols may be adapted to deliver genes to either injured or noninjured atherosclerotic arteries.