bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sham Feeding in Rats with Chronic, Reversible Gastric Fistulas
Authors: Smith Gerard P. 
Published: June 2004

AbstractSham feeding occurs when ingested food is prevented from accumulating in the stomach and small intestine by surgical intervention. Sham feeding permits the investigation of the orosensory controls of meal size in the absence of postingestive controls. This unit details preoperative preparation, surgery, postoperative care and maintenance, and test procedures for the simplest and most widely used method, which involves implantation of a gastric cannula in a rat to provide a chronic, reversible gastric fistula.
Conditioned Flavor Aversions: Assessment of Drug‐Induced Suppression of Food Intake
Authors: Riley Anthony L. 
Published: June 2004

AbstractAdministration of a drug following ingestion of a novel food or solution often suppresses subsequent intake of the new food or solution. This suppression is associative, in that consumption is not suppressed when there is no temporal relationship between consumption and drug administration. The robust nature of aversion learning has made this procedure a sensitive and widely used behavioral index of drug side effects. The procedures described in this unit are suitable for work with rodents, and may require modifications, e.g., in presentation of the ingesta and drug for other species. Familiar and novel foods may be used instead of solutions, with similar results.
Measurement of Startle Response, Prepulse Inhibition, and Habituation
Authors: Geyer Mark A. , Swerdlow Neal R. 
Published: June 2004

AbstractThe startle response is comprised of a constellation of reflexes elicited by sudden, relatively intense stimuli. The startle reflex is useful for studying fundamental properties of nervous function ranging from neurophysiological and anatomical relationships within the pons and reticular formation to forebrain regulation of complex behavioral states and cognitive processes. This unit presents protocols for measurement of the startle response in rats to acoustic stimuli, along with modifications encompassing an experimental manipulation such as drug treatment and measures of habituation of startle; a method for measuring prepulse inhibition (PPI) of startle; and specialized rat handling and calming techniques that supplement the startle protocols.
Rodent Models of Depression: Learned Helplessness Using a Triadic Design in Rats
Authors: Durgam Robert C. 
Published: June 2004

AbstractCertain types of human depression are precipitated by stressful life events, and vulnerable individuals experiencing these stressors may develop clinical depression. Understanding the neurobiology of stress vulnerability (depression) as well as stress resiliency (coping) is critical for guiding the development of novel pharmacotherapeutic agents for stress‐related disorders such as depression in humans. The use of a triadic design (escapable shock, yoked‐inescapable shock and restrained control) allows the investigator to examine the various sequella of stress exposure, while manipulating and quantifying the impact of psychological dynamics of stress such as active behavioral coping (i.e., stress control). Both escape and yoked subjects are exposed to the identical amount, intensity, pattern and duration of stress. The critical distinction between these two groups is that the escape group has the opportunity to terminate the shock stress by turning a wheel at the front of a chamber, while wheel‐turning for the yoked subject is of no consequence. Any difference observed between the escape and yoked subjects is a result of the effects of coping, rather than stress exposure per se. The restrained group is included to control for the effects of handling. Any differences between this group and the escape and yoked subjects reflects the impact of stress per se.
Rodent Models of Depression: Learned Helplessness Induced in Mice
Authors: Anisman Hymie , Merali Zul 
Published: June 2004

AbstractUncontrollable stressors induce a variety of behavioral disturbances that are in many ways reminiscent of the symptoms that characterize clinical depression. These deficits are evident across a range of species, including mice. Given the increasing focus on genetic techniques involving mice to identify the mechanisms subserving these behavioral disturbances (e.g., recombinant, knockout, and transgenic strains), it is of particular interest to provide a detailed description of the method to induce behavioral deficits in response to uncontrollable stressors. This unit describes the procedure used to assess the effects of controllable and uncontrollable shock on subsequent shock escape performance in mice using an escape‐delay procedure.
Fear‐Potentiated Startle in Mice
Authors: Falls William A. 
Published: June 2004

AbstractPavlovian fear conditioning is frequently used to assess the behavioral, physiological, genetic and molecular correlates of learning and memory. In the typical Pavlovian conditioned fear procedure a neutral stimulus, such as a tone, is paired with a mildly aversive stimulus such as a foot shock. The tone conditioned stimulus (CS) comes to elicit a variety of behaviors that are indicative of learned fear. One of the more prominent of these behaviors is a potentiated acoustic startle response. While fear‐potentiated startle in mice is qualitatively similar to that in rats, the stimulus parameters and procedures for producing optimum fear‐potentiated startle in mice differ considerably from those used in rats. Procedures outlined in this unit include initial assessment of startle, fear conditioning and fear‐potentiated startle testing. Special attention is paid to the parameters that affect the magnitude of fear‐potentiated startle and procedures designed to systematically examine these parameters are included.
Traumatic Brain Injury in the Rat Using the Fluid‐Percussion Model
Authors: Ling Geoffrey S.F. , Garcia‐Pinto Patricia 
Published: June 2004

AbstractTraumatic brain injury is a leading cause of death and disability, particularly among young adults. During closed head trauma, the injury process is initiated by the impact of the brain against the inner table of the calvarium. Subsequently, there is prompt initiation of a complex biochemical, cellular, and physiological injury cascade that may take days to complete. From a functional standpoint, this culminates in neurologic dysfunction and, if severe, death. This unit describes an impact‐induced brain trauma model in rats which replicates nonpenetrating head injury. It does not model either penetrating or ischemic brain injuries.
Preclinical Models of Hepatic Encephalopathy
Authors: Basile Anthony S. , Mullen Kevin 
Published: June 2004

AbstractParkinson's disease is a neurodegenerative disease in which pigmented midbrain neurons progressively die producing a dopamine (DA) deficit in the striatum which manifests as an akinetic movement disorder. Experimentally induced striatal DA depletion in animals is a valid model of parkinsonism. The capacity of certain substances to damage catecholaminergic neurones has been used for a long time to produce DA deficiency in animals. This unit focuses on methods for inducing parkinsonism using the neurotoxins MPTP and 6‐hydroxy dopamine and methods for evaluating the animals. Other models are briefly reviewed.
Rodent Models of Global Cerebral Ischemia
Authors: O'Neill Michael J. , Clemens James A. 
Published: June 2004

AbstractBrain damage after stroke and head injury remains a huge clinical problem. In stroke, the initial cause of the damage is a blockage in a blood vessel (often the middle cerebral artery) and this sets off several pathways that ultimately lead to cell death. Recent studies have demonstrated that several new mechanisms are involved in neuronal death and this has led to an increase in research into novel molecules that might prevent brain damage or improve recuperation post‐stroke. There are several models of global cerebral ischemia. Two of the most widely‐used models are discussed in detail in UNIT here, the gerbil bilateral carotid artery occlusion (BCAO) model and rat 4‐vessel occlusion (4‐VO) model. Additionally, several models of focal cerebral ischemia have been developed to mimic the effects of human stroke. The rationale behind the use of animal models, the various types of models and advantage and disadvantages of each model are presented.
Overview of Rodent Models for Obesity Research
Authors: Tschöp Matthias , Heiman Mark L. 
Published: June 2004

AbstractAnimal obesity models differ widely in type and extent of obesity. They are either based on environmental factors (e.g., high‐fat diet‐induced obesity), spontaneous mutants (i.e., ob/ob mice), genetically engineered animals (e.g., mice with melanocortin receptor subtype‐4 gene disruption (knock‐out), or mechanical intervention (e.g., chemical lesion of the ventromedial hypothalamus). This unit reviews available rodent models to study obesity and attempts to highlight the greatest utility for each model.
Models of Neuropathic Pain in the Rat
Authors: Bennett Gary J. , Chung Jin Mo , Honore Marie , Seltzer Ze'ev 
Published: June 2004

AbstractThere are now three models of neuropathic pain in the rat that are in widespread use: the chronic constriction injury, the partial sciatic ligation model, and the spinal nerve ligation model. The procedures to create these models and the behavioral assays used to quantify the resulting abnormal pain sensations are described in this unit.
Place Preference Test in Rodents
Authors: Roux Sylvain , Froger Christelle , Porsolt Roger D. , Valverde Olga , Maldonado Rafael 
Published: June 2004

AbstractConditioned place preference is a behavioral model currently used to measure the rewarding properties induced by the administration of a drug. In this paradigm, the rewarding properties of a compound are associated with the particular characteristics of a given environment. Due to the recent availability of multiple lines of genetically modified mice, this unit includes procedures for testing place preference in both rats and mice.
Transfection by Electroporation
Authors: Potter Huntington 
Published: June 2004

AbstractElectroporation‐‐the use of high‐voltage electric shocks to introduce DNA into cells‐‐can be used with most cell types,yields a high frequency of both stable transformation and transient gene expression,and,because it requires fewer steps,can be easier than alternate techniques. In this unit,the basic protocol describes the electroporation of mammalian cells and an alternate protocol outlines modifications for preparation and transfection of plant protoplasts.
Purification and Concentration of DNA from Aqueous Solutions
Authors: Moore David 
Published: June 2004

AbstractThis unit presents basic procedures for manipulating solutions of single‐ or double‐stranded DNA through purification and concentration steps. These techniques are useful when proteins or solute molecules need to be removed from aqueous solutions, or when DNA solutions need to be concentrated for reasons of convenience. The , using phenol extraction and ethanol (or isopropanol) precipitation, is appropriate for the purification of DNA from small volumes (<0.4 ml) at concentrations lower than 1 mg/ml. Three support protocols outline methods to buffer the phenol used in extractions, concentrate DNA using butanol, and extract residual organic solvents with ether. An alternative to these methods is nucleic acid purification using glass beads and this is also presented. These protocols may also be used for purifying RNA. The final two alternate protocols provide modifications to the basic protocol that are used for concentrating RNA and extracting and precipitating DNA from larger volumes and from dilute solutions, and for removing low‐molecular‐weight oligonucleotides and triphosphates.
Preparation of an Iodinated Radioligand
Authors: True C. Diane 
Published: June 2004

AbstractRadioactive tracers are useful for receptor measurement and for radioimmunoassays because of the ease with which radioactive ligands are detected. Typical receptor measurement methods include whole tissue receptor assays, autoradiography, and cell and membrane binding assays. The isotopes most commonly used in receptor measurement studies are tritium, carbon‐14, and iodine‐125, with the choice of isotope most often based on the specific activity required and the sensitivity and type of detection system available. Its high specific activity and easy detection make I‐125 ideal for labeling large peptides and proteins. While the short half‐life (60 days) of iodine requires frequent replacement with freshly iodinated compounds, this is also an advantage, as unused portions of radioligand can be held for decay and disposed of as nonradioactive waste. This unit describes the iodination of proteins or peptides using the 125I‐labeled Bolton Hunter reagent, a convenient, easy‐to‐use, nonoxidizing labeling reagent.
Internet Resources for Genomic, Bioinformatics, and Medical Genetics Information
Authors: Phillips Tamara J. , Belknap J.K. , Hitzemann R.J. , Buck K.J. , Cunningham C.L. , Crabbe J.C. 
Published: June 2004

AbstractInternet Resources for Genomic, Bioinformatics, and Medical Genetics Information (Tamara J. Phillips, Veterans Affairs Medical Center, Portland, Oregon). Many diseases are influenced by multiple genetic and environmental factors. Identifying the genes contributing to the probability of developing such diseases poses an extraordinary challenge because each gene may have a small influence. Further, in the presence of other influential genes and environmental factors, the impact of a single gene may be amplified. Many approaches are being taken to address the challenge presented by complex trait genetics, and data are being amassed at an alarming rate. Access to these data is crucial for coordination of efforts and avoidance of unnecessary duplication of research. This appendix describes some of the resources available on the World Wide Web that provide genetic and genomic data, tools for analyzing genome data, information on funding opportunities, and information about ethical, legal and social issues associated with the genetic analysis of disease traits.
Synthesis of N2‐Substituted Deoxyguanosine Nucleosides from 2‐Fluoro‐6‐O‐(Trimethylsilylethyl)‐2′‐Deoxyinosine
Authors: Harris Thomas M. , Harris Constance M. 
Published: June 2004

AbstractSyntheses of N2‐substituted nucleosides have been studied for many years, primarily with ribonucleosides. However, the primary route to these compounds requires acidic conditions that are too vigorous for the acid‐labile deoxyribonucleosides. The current strategy takes advantage of methods for low‐temperature, nonaqueous diazotization of ribosides in organic solvents using t‐butyl nitrate as the diazotizing agent and HF/pyridine as the fluoride source for the preaparation of a 2‐fluoro‐2?‐deoxyinosine derivative that can be used to synthesize N2‐substituted deoxyguanosine.
Synthesis, Characterization, and Application of Substituted Pyrazolopyrimidine Nucleosides
Authors: Dempcy Robert O. , Podyminogin Mikhail A. , Reed Michael W. 
Published: June 2004

AbstractThis unit describes, in detail, the preparation of 3‐aminopropyl‐substituted pyrazolo[3,4‐d]pyrimidine analogs of the purines deoxyadenosine (dA) and deoxyguanosine (dG). Phosphoramidite reagents of these so‐called aminopropyl‐PPA and ‐PPG nucleosides (AP‐PPA and AP‐PPG, respectively) allow introduction of amino linkers into internal positions of synthetic DNA strands. Synthesis of suitably protected AP‐PPA and AP‐PPG phosphoramidites are described. The stepwise alkynylation, hydrogenation, selective protection, and phosphoramidite synthesis is similar for both the PPA and PPG analogs. To demonstrate the application of these reagents, a protocol is given in which a simple DNA strand is synthesized and conjugated to a lipophilic activated ester (dabcyl‐SE) to form a stable amide linkage. Utility of this chemistry for preparing internally modified DNA conjugates is discussed.
Nucleobase Protection of Deoxyribo‐ and Ribonucleosides
Authors: Iyer Radhakrishnan P. 
Published: June 2004

AbstractProtecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, prevent irreversible nucleobase modifications that may occur in the presence of alkylating or condensing reagents that are commonly used in nucleoside protection and oligonucleotide synthesis. This unit reviews these protecting groups, and also identifies protecting groups for the exocyclic amino function of cytosine, adenine, and guanine. The unit also explores recent trends in nucleobase protection that permit reliable oligonucleotide synthesis and removal of N‐protecting groups under very mild conditions.
Protection of 2′‐Hydroxy Functions of Ribonucleosides
Authors: Reese Colin B. 
Published: June 2004

AbstractThe main purpose of this article is to discuss 2′‐protection in the context of effective oligoribonucleotide synthesis. Emphasis is placed on the 2′‐protecting groups of choice in the synthesis of oligo‐and polyribonucleotides, and the requirements that a protective group must satisfy to become the 2′‐hydroxyl‐protecting group of choice. Finally, the unit discusses the issue of 2′‐O‐acyl and 2′‐O‐silyl group migration to the 3′‐hydroxy function of ribonucleosides during protection, along with the consequences of the conditions used for their removal on the stability of internucleotide linkages.
2′‐Hydroxyl‐Protecting Groups that are Either Photochemically Labile or Sensitive to Fluoride Ions
Authors: Miller Tod J. , Schwartz Miriam E. , Gough Geoffrey R. 
Published: June 2004

AbstractProtected ribonucleotide monomers are more difficult to obtain than their 2′‐deoxy counterparts because of the need to protect the 2′‐hydroxy function. This unit describes the stepwise preparation of suitably 2′‐protected ribonucleosides using two protecting groups: 2‐nitrobenzyloxymethyl (NBOM) and tert‐butyldimethylsilyl (TBDMS). In addition, details are given for protecting the 5′‐hydroxyl and the nucleobase, yielding nucleosides that are easily converted to phosphoramidite or H‐phosphonate derivatives for automated oligoribonucleotide synthesis.
Preparation of 5′‐Silyl‐2′‐Orthoester Ribonucleosides for Use in Oligoribonucleotide Synthesis
Authors: Scaringe Stephen A. , Kitchen David , Kaiser Robert J. , Marshall William S. 
Published: June 2004

AbstractThe recent discovery that small interfering RNAs (siRNAs) induce gene suppression in mammalian cells has sparked tremendous interest in using siRNA‐based assays and high‐throughput screens to study gene function. As a result, research programs at leading academic and commercial institutions have become a substantial and rapidly growing market for synthetic RNA. Important considerations in synthesizing RNA for biological gene function studies are sequence integrity, purity, scalability, and resistance to nucleases; ease of chemical modification, deprotection, and handling; and cost. Of the well‐established RNA synthesis methods, 2′‐ACE chemistry is the only one that meets all of these criteria. 2′‐ACE technology employs a unique class of silyl ethers to protect the 5′‐hydroxyl, in combination with an acid‐labile orthoester protecting group on the 2′‐hydroxyl (2′‐ACE). 2′‐ACE‐protected phosphoramidite monomers are joined using standard solid‐phase technology to achieve RNA synthesis at efficiencies rivaling those for DNA. This unit describes the synthesis of standard 5′‐silyl‐2′‐ACE‐protected phosphoramidites.
Chemical Synthesis of RNA Sequences with 2′‐O‐[(Triisopropylsilyl)oxy]methyl‐protected Ribonucleoside Phosphoramidites
Authors: Pitsch Stefan , Weiss Patrick A. 
Published: June 2004

AbstractThe [(triisopropylsilyl)oxy]methyl (TOM) group is a useful protecting group for the 2′‐OH of ribonucleosides to be used for oligoribonucleotide synthesis by the phosphoramidite method. It is completely stable to all reaction conditions applied during assembly and the first deprotection step. It does not interfere with the coupling reaction and leads to very good coupling yields under DNA‐coupling conditions. The final cleavage occurs quantitatively without concomitant destruction of the RNA product. This unit describes the synthesis of TOM‐phosphoramidites from 2′‐O‐TOM‐5′‐O‐dimethoxytrityl‐N‐acetyl ribonucleosides, oligoribonucleotide assembly on an automated DNA synthesizer, and subsequent deprotection. Preparation of the TOM‐protected ribonucleosides is presented elsewhere in the series.
3‐(N‐tert‐Butylcarboxamido)‐1‐propyl and 4‐Oxopentyl Groups for Phosphate/Thiophosphate Protection in Oligodeoxyribonucleotide Synthesis
Authors: Wilk Andrzej , Chmielewski Marcin K. , Grajkowski Andrzej , Beaucage Serge L. , Phillips Lawrence R. 
Published: June 2004

AbstractThis unit provides procedures for the preparation of deoxyribonucleoside phosphoramidites and appropriate phosphordiamidite precursors with P(III) protecting groups different than the standard 2‐cyanoethyl group. Specifically, these phosphoramidites are functionalized with the 3‐(N‐tert‐butylcarboxamido)‐1‐propyl or 4‐oxopentyl groups. The usefulness of these novel deoxyribonucleoside phosphoramidites in the solid‐phase synthesis of a 20‐mer DNA oligonucleotide and its phosphorothioated analog is demonstrated. It is also shown that removal of the 3‐(N‐tert‐butylcarboxamido)‐1‐propyl phosphate/thiophosphate‐protecting group from these oligonucleotides is rapidly effected under thermolytic conditions at neutral pH, whereas the 4‐oxopentyl group is preferably removed by treatment with pressurized ammonia gas or concentrated ammonium hydroxide at ambient temperature. These detailed methods constitute an economical and alkylation‐free approach to large‐scale preparations of therapeutic oligonucleotides.
3′‐Modified Oligonucleotides and their Conjugates
Authors: Lyttle Matthew H. 
Published: June 2004

AbstractSolid‐phase synthesis of 3′‐aminoalkyl, 3′‐thioalkyl, and 3′‐polyethyleneglycol are described. The first two are important as specific points of attachment for a large variety of reporter groups; the latter is important because of its increased cell membrane permeability, which aids in the development of antisense drugs. These protocols cover details of the synthetic organic chemistry needed to make each solid support, as well as DNA synthesis, workup, characterization, and conjugation.
Modification of the 5′ Terminus of Oligodeoxyribonucleotides for Conjugation with Ligands
Authors: Asseline Ulysse , Thuong Nguyen T. 
Published: June 2004

AbstractLigands can be introduced at the 5′ terminus of an oligonucleotide by adding a linker to the ligand and modifying the 5′ terminus of the oligonucleotide. These are then reacted to give the ligand‐oligonucleotide conjugate. This unit describes the addition of carboxylated and aminoalkylated linkers, and phosphorothioate, phosphate, and masked thiol groups to the 5′ terminus of an oligonucleotide. The addition of linkers to ligands and the final reaction that produces the ligand‐conjugated oligonucleotide are described elsewhere in the series. This approach is particularly useful when there is a limited amount of ligand available, when the ligand is sensitive to chemical conditions required for oligonucleotide deprotection, or when the ligand is weakly soluble in solvents required for phosphoramidite‐ or H‐phosphonate‐mediated oligonucleotide synthesis.
Solid‐Phase Synthesis of 2′‐Deoxy‐2′‐fluoro‐ β‐D‐Oligoarabinonucleotides (2′F‐ANA) and Their Phosphorothioate Derivatives
Authors: Viazovkina Ekaterina , Mangos Maria M. , Elzagheid Mohamed I. , Damha Masad J. 
Published: June 2004

AbstractThis unit describes the chemical synthesis of 2'‐deoxy‐2'‐fluoro‐b‐D‐oligoarabinonucleotides (2'F‐ANA), both with phosphodiester and phosphorothioate linkages. The protocols described herein include araF phosphoramidite preparation, assembly on DNA synthesizers, and final deprotection and purification of oligonucleotides.