The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research.

Model organism research is essential for discovering the mechanisms of human diseases by defining biologically meaningful gene to disease relationships. The Rat Genome Database (RGD, ( https://rgd.mcw.edu )) is a cross-species knowledgebase and the premier online resource for rat genetic and physiologic data. This rich resource is enhanced by the inclusion and integration of comparative data for human and mouse, as well as other human disease models including chinchilla, dog, bonobo, pig, 13-lined ground squirrel, green monkey, and naked mole-rat. Functional information has been added to records via the assignment of annotations based on sequence similarity to human, rat, and mouse genes. RGD has also imported well-supported cross-species data from external resources. To enable use of these data, RGD has developed a robust infrastructure of standardized ontologies, data formats, and disease- and species-centric portals, complemented with a suite of innovative tools for discovery and analysis. Using examples of single-gene and polygenic human diseases, we illustrate how data from multiple species can help to identify or confirm a gene as involved in a disease and to identify model organisms that can be studied to understand the pathophysiology of a gene or pathway. The ultimate aim of this report is to demonstrate the utility of RGD not only as the core resource for the rat research community but also as a source of bioinformatic tools to support a wider audience, empowering the search for appropriate models for human afflictions.

An unusual muscle of the wrist with potential compression of the ulnar nerve.

During routine cadaveric dissection of the upper extremity an unusual muscle was discovered arising from the tendon of the flexor carpi ulnaris and inserting into the muscle belly of the flexor digiti minimi. The muscle's course was superficial to the ulnar nerve and artery in Guyon's canal. We review the literature regarding such muscle variations and discuss the potential for compression of the ulnar nerve by such muscles.

Monoclonal antibodies against EGFRvIII are tumor specific and react with breast and lung carcinomas and malignant gliomas.

Despite molecular biological advances in understanding human cancers, translation into therapy has been less forthcoming; targeting neoplastic cells still requires that tumor-specific markers, preferably those on the cell surface, be identified. The epidermal growth factor receptor (EGFR) exists in a deletion-mutant form, EGFRvIII, which has been identified by genetic and immunological means in a subset of gliomas and non-small cell lung carcinomas. Specific polyvalent antisera to the extracellular portion of the variant were readily induced, but immunization using a synthetic linear peptide representing the unique EGFRvIII primary sequence has been unsuccessful in mice or macaques. We report here five specific monoclonal antibodies (mAbs) developed through long-term immunization protocols using the EGFRvIII-specific synthetic peptide and the intact variant in different formats that maintained secondary and tertiary conformation. These mAbs identify the EGFRvIII on the cell surface with relatively high affinity (KA range, 0.13 to 2.5 x 10(9) M-1) by live cell Scatchard analysis. These mAbs are specific for EGFRvIII as determined by RIA, ELISA, Western blot, analytical flow cytometry, autophosphorylation, and immunohistochemistry. Isolating specific mAbs enabled us to analyze normal and neoplastic human tissue and establish that EGFRvIII is truly tumor specific for subsets of breast carcinomas and for previously reported non-small cell lung carcinomas and gliomas. Also, this receptor is not expressed by any normal human tissues thus far examined, including elements of the peripheral, central nervous, and lymphoid systems. With mAbs, we identified a higher incidence of EGFRvIII positivity in gliomas than previously described and identified an EGFRvIII-positive subset of breast tumors; also, we observed that the EGFRvIII epitope is not expressed in normal tissues, and we demonstrated the localizing and therapeutic potential of the mAbs for tumors expressing this epitope. Our observations strongly warrant development of this mAb-antigen system as therapy for breast, lung, and central nervous system tumors.

Crystal structure of the histone acetyltransferase Hpa2: A tetrameric member of the Gcn5-related N-acetyltransferase superfamily.

We report the crystal structure of the yeast protein Hpa2 in complex with acetyl coenzyme A (AcCoA) at 2.4 A resolution and without cofactor at 2.9 A resolution. Hpa2 is a member of the Gcn5-related N-acetyltransferase (GNAT) superfamily, a family of enzymes with diverse substrates including histones, other proteins, arylalkylamines and aminoglycosides. In vitro, Hpa2 is able to acetylate specific lysine residues of histones H3 and H4 with a preference for Lys14 of histone H3. Hpa2 forms a stable dimer in solution and forms a tetramer upon binding AcCoA. The crystal structure reveals that the Hpa2 tetramer is stabilized by base-pair interactions between the adenine moieties of the bound AcCoA molecules. These base-pairs represent a novel method of stabilizing an oligomeric protein structure. Comparison of the structure of Hpa2 with those of other GNAT superfamily members illustrates a remarkably conserved fold of the catalytic domain of the GNAT family even though members of this family share low levels of sequence homology. This comparison has allowed us to better define the borders of the four sequence motifs that characterize the GNAT family, including a motif that is not discernable in histone acetyltransferases by sequence comparison alone. We discuss implications of the Hpa2 structure for the catalytic mechanism of the GNAT enzymes and the opportunity for multiple histone tail modification created by the tetrameric Hpa2 structure.

An activity pacing scale for the chronic pain coping inventory: development in a sample of patients with fibromyalgia syndrome.

Patients with fibromyalgia syndrome (FS) experience a decreased ability to participate in both vocational and avocational activities. Although many treatment programs advocate activity pacing techniques, 'pacing' is a poorly understood concept for which there are no available measures. The present study describes a brief six-item pacing scale that can be administered as part of the Chronic Pain Coping Inventory (CPCI). Preliminary data indicate that this scale is a valid, reliable index of the pacing construct that is associated with physical impairment in patients with FS and is unrelated to simple task persistence.

Synthesis and antiviral properties of 5-(2-substituted vinyl)-6-aza-2'-deoxyuridines.

The following 5-(2-substituted vinyl)-6-aza-2'-deoxyuridines were synthesized: (E)-5-(2-bromovinyl) (2) (6-aza-BVDU), 5-(2-bromo-2-fluorovinyl) (a mixture of E and Z isomers) (3), (E)-5-(2-chlorovinyl) (4), (E)-5-[2-(methylthio)vinyl] (5), 5-(2,2-dibromovinyl) (6), and 5-(3-furyl) (7). The synthesis of 2-6 utilized Wittig-type reactions on 5-formyl-1-(2'-deoxy-3', 5'-di-O-p-toluoyl-beta-D-erythro-pentofuranosyl)-6-azauracil (16). 6-Aza-BVDU (and its alpha-anomer) was also synthesized from (E)-5-(2-bromovinyl)-6-azauracil (12) by using standard deoxyribosidation methodology. Compound 7 was prepared from 5-(3-furyl)-6-azauracil (33) via a ribosidation/deoxygenation sequence. An attempt to prepare the corresponding 5-(2,2-difluorovinyl) analogue afforded instead a mixture of the 5-[(2,2-difluoro-2-methoxy)ethyl] and 5-(2,2,2-trifluoroethyl) derivatives 29 and 30. Compounds 2-7, 29, and 30 were tested for in vitro activity against herpes simplex virus types 1 and 2 (HSV-1, HSV-2). 6-Aza-BVDU (2) exhibited ID50s of 8 micrograms/mL vs. HSV-1 and 190 micrograms/mL vs. HSV-2. BVDU (1) had ID50s of 0.015 and 1.6 micrograms/mL against HSV-1 and HSV-2, respectively. Compound 4 showed a similar profile of activity, but the other analogues were either weakly active or inactive.

Resolution of experimental pneumothorax in rabbits by oxygen therapy.

The treatment of asymptomatic patients with small pneumothoraces (ie, less than 20% by volume) has included observation, tube thoracostomy, and operation. When observation is used, the anticipated expansion of the lung has been estimated to be 1.25% of the lung volume daily. This study was designed to evaluate the use of inhaled oxygen as a method to accelerate the resolution of a pneumothorax in a rabbit model. Experimental pneumothoraces were created in 23 white New Zealand rabbits. Group 1 (9 rabbits) were placed in a cage with room air and group 2 (11 rabbits) were placed in a cage with high oxygen concentration. Three rabbits died before completion of the study. Serial chest roentgenograms were performed until the pneumothoraces resolved. The majority of rabbits treated with oxygen had resolution of their pneumothoraces by 36 hours, whereas the majority of rabbits treated with room air did not show complete resolution before 48 hours. Biopsies showed no evidence of damage secondary to oxygen treatment. Oxygen treatment was found to be significantly better in the early resolution of pneumothoraces when compared with room air. This establishes an alternative treatment for some pneumothoraces that are small and asymptomatic.

An analysis of employer evaluations of workers with mental retardation.

A critical component of supported competitive employment is the provision of long-term consumer assessment and systematic follow-along services. To date, there is a paucity of information that describes or validates the process of ongoing consumer assessment. In this article, written employer evaluations of workers with mental retardation were analyzed regarding their relationship to employment retention. Three factors were identified which related to employment retention: (a) workers' attendance, (b) punctuality patterns, and (c) consistency in task performance. These findings are discussed in light of their implications for curriculum design and habilitation efforts for persons with mental retardation.

Benefit-cost analysis of supported competitive employment for persons with mental retardation.

A review of the literature on unemployment rates among adults with mental retardation is presented and the societal impact of the number of adults with mental retardation who remain unemployed is discussed. The supported competitive employment model is presented as illustrative of a habilitation program allowing greater monetary returns to society than traditional adult service programs. A benefit-cost analysis of our supported competitive employment program, occurring during the period from 1978 to 1986, is presented from two perspectives: that of the consumer (i.e., the adult with severe disabilities) and that of the taxpayer. Results of the benefit-cost analysis indicate that supported competitive employment is a financially prosperous venture from both perspectives. That is, from the consumers' perspective, for every $1.00 relinquished in taxes, supplemental security income (SSI), and forgone workshop earnings, $1.97 was received in increased income; the net benefit per year was $3,894 consumer. From the taxpayers' perspective, for every $1.00 expended for the funding of supported competitive employment programs and in lost tax revenues realized by the provision of targeted jobs tax credits, $1.87 was accumulated in benefits; the net yearly benefit to the taxpayer was $4,063 per consumer. The authors conclude that supported competitive employment is a financially profitable venture for both consumers and taxpayers.

Optimization of exposure parameters for cone beam computed tomography sialography.

OBJECTIVES: The assessment of image quality is a crucial step in the development of a new imaging protocol. Having proposed and reported on a preliminary protocol for sialography using cone beam CT (CBCT), the purpose of this study was to further optimize this protocol by maximizing the image signal difference-to-noise ratio (SDNR) and to relate these new data to previously published dosimetric data for CBCT sialography. METHODS: An imaging phantom was constructed using samples with different concentrations of iodine and a water-immersed mandible. The CB MercuRay (Hitachi Medical Systems, Tokyo, Japan) was used to image the phantom using different peak kilovoltage (kVp) and milliamperage (mA) settings. SDNR was then calculated using the raw images based on mean pixel values (MPV) measured in selected regions of interest (ROI). Finally, a figure of merit (FOM) was calculated to examine the trade-off between image SDNR and effective radiation dose. RESULTS: The SDNR demonstrated an expected increase as the kVp increased from 60 to 120. Also, images made with the higher mA setting (15) had greater SDNR. The iodine concentration also influenced the image quality such that SDNR increased with increased amounts of iodine. The calculated FOM was greatest for the technique using 80 kVp, with equivalent results for 10 mA and 15 mA. CONCLUSION: An optimized protocol for CBCT sialography using CB MercuRay entails a 6 inch field of view with 80 kVp and 10 mA.

A silver-alginate-coated dressing to reduce peripherally inserted central catheter (PICC) infections in NICU patients: a pilot randomized controlled trial.

OBJECTIVE: Our aim was to evaluate the safety of a silver-alginate-containing dressing to reduce peripherally inserted central catheter (PICC) infections in neonatal intensive care unit (NICU) patients. STUDY DESIGN: Patients were randomized 3:1 to receive a patch containing silver, alginate and maltodextrin or standard of care. Patches were placed under the regular transparent retention dressing at the PICC exit site at insertion and were replaced with every dressing change at least every 2 weeks until PICC discontinuation. All study infants were monitored for adverse skin reactions. RESULT: A total of 100 infants were followed up for 1922 person-days, including 75 subjects with 89 PICCs who received the patch. The median birth weight (1330 g) and median gestational age (30 weeks) was lower in the patch group when compared with the controls (P=0.001 and 0.005, respectively). Study patients received the patch with their PICC at a median age of 5 days; the patch stayed in place for a median of 13 days. We noted no adverse skin reactions and found no evidence that the patch alters the microbiology of PICC-associated infections. CONCLUSION: This pilot trial suggests that silver-alginate-coated dressings are skin safe and their inclusion in future trials aimed at reduction of PICC-associated bloodstream infections in the NICU should be considered.

Cytoskeletal damage during myocardial ischemia: changes in vinculin immunofluorescence staining during total in vitro ischemia in canine heart.

The role of cytoskeletal damage in the disruption of the plasma membrane observed during myocardial ischemia has been studied using antibodies to vinculin to identify changes in the distribution of this membrane associated cytoskeletal protein. Vinculin is a component of the cytoskeletal attachment complex between the plasma membrane and the Z-line of the underlying myofibrils. The effects of varying periods of total ischemia on the localization of vinculin were assessed by immunofluorescence and evidence of membrane disruption was evaluated by electron microscopy. Thin tissue slices prepared from the ischemic tissue were incubated in oxygenated Krebs-Ringer phosphate buffer at 37 degrees C to assess inulin permeability, ultrastructure, and any changes in the distribution of vinculin associated with incubation. The previously reported costameric pattern of vinculin staining was observed in longitudinal sections of control myocardium, myocardium subjected to 60 minutes of total ischemia, and myocardium subjected to 60 minutes of ischemia followed by 60 minutes of incubation in oxygenated media. Electron microscopy and inulin permeability measurements confirmed that plasma membrane integrity was preserved under these conditions. However, when the duration of total ischemia was extended to 120 minutes or longer, there was a progressive loss of vinculin staining along the lateral margin of myocytes. This change correlates with the appearance of subsarcolemmal blebs and breaks in the plasma membranes observed by electron microscopy and confirmed by the increase in inulin permeability observed in tissue slices.(ABSTRACT TRUNCATED AT 250 WORDS)

Prolonged depletion of ATP because of delayed repletion of the adenine nucleotide pool following reversible myocardial ischemic injury in dogs.

Sixty-five percent of the ATP and 50% of the total adenine nucleotide (sigma Ad) pool is lost from the subendocardial myocardium after 15 min of severe ischemia induced by circumflex artery occlusion in open-chest dogs (12). In the present experiment, we assessed the effects of various periods of arterial reflow following 15 min of ischemic injury on resynthesis of ATP and sigma Ad. The circumflex artery was occluded for 15 min and reperfused for 20 or 60 min or 24 or 96 hr. The mean ATP after 15 min of ischemia was reduced 62% from 5.42 +/- 0.33 to 2.08 +/- 0.21 mumol/g; and the total nucleotide content was reduced by 50%. ATP content recovered slightly during the first 20 min of reperfusion but remained markedly depressed for at least 24 hr because of the initial depletion of adenine nucleotides and because minimal salvage of de novo repletion occurred in the injured muscle during this time period. By 4 days, ATP and total adenine nucleotides were still slightly depressed but had recovered to 88% and 91% of control. Electrolyte changes and an increased inulin-diffusible space, which are characteristic of irreversibly injured myocardium, reperfused for 20 or 60 min, were not observed. Also, tissue necrosis was absent in the hearts reperfused for 24 or 96 hr. These observations indicate that the marked depression of ATP and adenine nucleotides and the slow recovery of these metabolites occurred in myocardium that nevertheless was reversibly injured in terms of cellular viability.

Atmospheric transmittance of an absorbing gas. 3: A computationally fast and accurate transmittance model for absorbing gases with variable mixing ratios.

Atmospheric transmittance models for absorbing gases with constant mixing ratios were described in the two preceding papers of this series. In this paper a method for calculating atmospheric transmittances for absorbing gases with variable mixing ratios is described. Because the model uses only arithmetic operations, it is computationally fast as well as accurate. Details of the computational algorithm are given, including the calculation of the expansion coefficients. In a test of eleven independent profiles, the resulting transmittances agreed with line-by-line calculations in an rms sense to within 0.0090 in the worst case and to within 0.0018 in all other cases. This paper also includes a discussion for computing transmittances when several gases absorb in the same spectral interval. These three papers provide a complete treatment for modeling transmittances in inhomogeneous atmospheres.

Volume regulation and plasma membrane injury in aerobic, anaerobic, and ischemic myocardium in vitro. Effects of osmotic cell swelling on plasma membrane integrity.

The relationship between cell swelling and plasma membrane disruption has been evaluated in thin myocardial slices incubated in oxygenated or anoxic Krebs-Ringer phosphate media. Electron microscopy and measurements of inulin-diffusible space were used to monitor plasma membrane integrity. Inulin is excluded from the intracellular space of intact cells; therefore, an increase in tissue inulin content is an excellent marker of loss of plasma membrane integrity. Cell volume was increased during exposure of aerobic slices to hypotonic media, but the inulin-diffusible space was not increased and electron micrographs showed no detectable plasma membrane alterations. Likewise, during prolonged anoxic isotonic incubation, no evidence of plasma membrane damage was observed. Incubation in anoxic hypotonic media for 60 minutes resulted in a larger increase in cell volume than under aerobic conditions, but plasma membrane integrity was maintained. Extended anoxic hypotonic incubation (300 minutes) produced no further change in tissue water, but the inulin-diffusible space was increased and electron micrographs revealed breaks in the plasma membranes primarily in association with large subsarcolemmal blebs. Likewise, myocardial slices incubated in isotonic anoxic media for 240 minutes and hypotonic anoxic media for 60 minutes had an increased inulin-diffusible space and the ultrastructural appearance was similar. This ultrastructural appearance is indistinguishable from that observed in myocytes lethally injured by ischemia. Measurements of tissue osmolarity during total ischemia showed that osmotically induced cell swelling could occur in ischemic myocardium prior to the onset of plasma membrane disruption. Our results indicate that cell swelling per se is incapable of rupturing plasma membranes; however, after prolonged periods of energy deficiency, the plasma membrane or its cytoskeletal scaffold become injured, which allows the membrane to rupture if the cell is swollen, as might occur during ischemia or reperfusion.

Four brief periods of myocardial ischemia cause no cumulative ATP loss or necrosis.

The effect of repetitive periods of coronary occlusion on myocardial adenine nucleotides, lactate, and infarct size was studied. In one series of dogs, the circumflex artery was occluded for one, two, or four 10-min episodes, each separated by 20 min of reperfusion. Hearts were excised and sampled for metabolic assays after one or more periods of ischemia before or after reperfusion. One 10-min period of ischemia caused a 61% loss of ATP and 41% loss of adenine nucleotides from the most severely ischemic subendocardial zone. Reperfusion resulted in rapid restoration of the adenylate charge but in only slight repletion of the adenine nucleotide pool. However, two or even four 10-min periods of ischemia caused no further adenine nucleotide loss. In contrast, 40 min of continuous coronary occlusion caused an 87% depletion of ATP and 67% of the adenine nucleotide pool from the same subendocardial region. Collateral blood flow was similar during all occlusions, but lactate accumulation was less during later occlusions. In a second series of experiments, myocardial necrosis was quantitated 4 days after four 10-min periods of ischemia. Necrosis was observed in only one of six dogs and, in this dog, was only 1.5% of the anatomic area at risk. Thus intermittent reperfusion prevents cumulative metabolic deficits and myocardial ischemic cell death, perhaps by restoring the capacity for high-energy phosphate (HEP) production and/or washing out deleterious catabolites. A first episode of ischemia also slows HEP utilization in subsequent episodes.

Comparison of the effect of ischaemia and anoxia on the sarcolemma of the dog heart.

Contraction-band necrosis, a striking morphologic lesion, is common to many types of myocardial injury including the calcium paradox and ischaemic injury with reperfusion. This lesion is characterized by explosive swelling, massive calcium overload, and severe disruption of the myofibrils due to the formation of contraction bands. The studies reviewed in this paper provide evidence that in ischaemia and reperfusion, these changes are preceded by sarcolemmal injury that occurs during the period of ischaemia. Sarcolemmal injury was evaluated by electron microscopy and by measurements of inulin diffusible space (IDS) in thin slices of myocardium incubated in vitro. Reversibly injured ischaemic myocytes have ultrastructurally intact plasma membranes which are impermeable to inulin. Longer durations of ischaemia, sufficient to produce contraction-band necrosis during reperfusion, result in fragmentation of plasma membranes during the ischaemic intervals, and the IDS is markedly increased during subsequent incubation. Thus ultrastructural evidence of membrane damage is present early in ischaemia and is associated temporally with the increased IDS. The role of anoxia, per se, in inducing membrane damage was investigated in tissue slices incubated at 37 degrees C in crystalloidal media gassed with nitrogen. Anoxic slices produced lactate and lost ATP and adenine nucleotides, but cell volume and the IDS were not significantly increased for at least five hours (twice the time required for severe membrane damage to develop in total ischaemia) and the plasmalemma remained intact by electron microscopy. Thus, despite depletion of high energy phosphates, membrane damage, detectable by alterations in IDS or ultrastructure, occurs much more slowly during anoxia alone than during ischaemia. These results suggest that anoxia, per se, may not be the cause of membrane damage in ischaemia.

Effect of reversible ischemia on the activity of the mitochondrial ATPase: relationship to ischemic preconditioning.

The mitochondrial ATPase enzyme accounts for roughly 35-50% of the overall energy demand that leads to ATP depletion under conditions of severe myocardial ischemia. In larger mammalian hearts, this energy squandering action of the ATPase is modulated by an endogenous inhibitor protein. The present studies were undertaken to characterize the time course of inhibition of the mitochondrial ATPase in canine myocardium under conditions of severe regional ischemia in vivo. In addition, we determined if the energy sparing effects of ischemic preconditioning (PC) can be explained by persistent inhibition of the mitochondrial ATPase enzyme. The circumflex coronary artery was ligated for 1.5 min (n = 4), 5 min (n = 6), or 15 min (n = 5). In a separate group (n = 7), hearts were preconditioned by four 5-min periods of ischemia each followed by 5 min of reperfusion. Sub-mitochondrial particles were prepared from the sub-endocardial zone of the ischemic and non-ischemic regions and were assayed for oligomycin-sensitive ATPase activity. ATPase activity was reduced to about 79% at 1.5 min and to approximately 55% at 5 and 15 min of ischemia, relative to non-ischemic tissue from the same heart. The rate of HEP utilization slowed concurrently with the development of ATPase inhibition. In preconditioned myocardium, ATPase activity was not significantly different from control myocardium from the same heart. We conclude that the early inhibition of the mitochondrial ATPase activity slows the utilization of high energy phosphate and thereby serves as an important endogenous cardioprotective mechanism. Nevertheless, altered activity of the ATPase is not the explanation of the energy sparing effect of ischemic preconditioning.