Growth and migration markers of rat C6 glioma cells identified by serial analysis of gene expression

Tumors derived from rat C6 cell implants into rat brain exhibit similar morphological characteristics and degree of vascularization to human glioblastomas. To establish a molecular basis for C6 gliosarcoma malignancy, we have constructed a molecular profile of the most abundantly expressed genes, using serial analysis of gene expression (SAGE). Sequence tags (1168) representing 738 individual transcripts were collected and tag-to-gene mapping was carried out using the UniGene data set for rat. Differentially expressed C6 transcripts were identified by comparison of tags collected for C6 cells with a similar number (1002) of tags from a rat primary astrocyte library. Genes found to be expressed at increased levels in C6 cells are associated with cell surface interactions, migration, or metastasis formation and proliferation. These include the receptor for hyaluronan-mediated motility (RHAMM), S-100 related protein 42A, galectin I, preproenkephalin, osteopontin, autocrine motility factor, alpha-tubulin, ad1 antigen, and cofilin. In addition, a tag with no database match probably representing a previously uncharacterized transcript was differentially expressed in C6 cells. Transcripts showing reduced expression in C6 cells relative to astrocytes included the extracellular matrix glycoprotein osteonectin/SPARC (secreted protein, acidic, rich in cysteine), actin-binding proteins thymosins beta-4 and beta-10, the cysteine protease inhibitor cystatin C, the actin-gelling protein SM22/transgelin, and ferritin-H. SAGE results were confirmed by Northern blot for all transcripts tested, reaffirming the value of the SAGE technique for expression profiling in cancer biology.

Conformations of nicotinamide adenine dinucleotide (NAD(+)) in various environments

Enzymes bind NAD(+) in extended conformations and yet NAD(+) exists in aqueous solution as a compact, folded molecule. Thus, NAD(+) conformation is environment dependent. In an attempt to investigate the effects of environmental changes on the conformation of NAD(+), a series of molecular dynamics simulations in different solvents was performed. The solvents investigated (water, DMSO, methanol and chloroform) represented changes in relative permittivity and hydrophobic character. The simulations predicted folded conformations of NAD(+) to be more stable in water, DMSO and methanol. In contrast, extended conformations of NAD(+) were observed to be more stable in chloroform. Furthermore, the extended conformations observed in chloroform were similar to conformations of NAD(+) bound to enzymes. In particular, a large separation between the aromatic rings and a strong interaction between the pyrophosphate and nicotinamide groups were observed. The implications of these observations for the recognition of NAD(+) by enzymes is discussed. It is argued that a hydrophobic environment is important for stabilizing unfolded conformations of NAD(+).

Neurology in the National Gallery

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Nocturnal oxygenation and prognosis in Duchenne muscular dystrophy

REM-related oxygen desaturation occurs in advanced Duchenne muscular dystrophy (DMD) and might be an independent predictor of disease progression. We have followed 18 patients for 10 yr after an initial respiratory sleep study or until death or onset of nasal ventilation. We measured baseline spirometry, blood gas tensions, maximal respiratory pressures, and body mass index. In 11 cases, VC was recorded serially. Median survival was 50 (range, 13 to 89) mo from initial study and unrelated to age at time of study, BMI, or mouth pressures but correlated with PaCO2 (r = -0.72, p < 0.005, n = 17), minimal nocturnal SaO2 (r = 0.62, p < 0.007, n = 18) and VC (r = 0. 65, p < 0.005, n = 17). Cox regression analysis showed a VC of less than 1 L at the time of study to be the best single predictor of subsequent survival. The only measure associated with age of death was the age at which the VC fell below 1 L (r = 0.79, p < 0.004). These data suggest measurement of PaCO2 or serial assessment of VC should be studied further as valid methods of assessing prognosis in DMD.

Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation

The dielectrically consistent reference interaction site model (DRISM) integral equation theory is applied to determine the potential of mean force (PMF) for an alanine tetramer. A stochastic dynamics simulation of the alanine tetramer using this PMF is then compared with an explicit water molecular dynamics simulation. In addition, comparison is also done with simulations using other solvent models like the extended reference interaction site model (XRISM) theory, constant dielectric and linear distance-dependent dielectric models. The results show that the DRISM method offers a fairly accurate and computationally inexpensive alternative to explicit water simulations for studies on small peptides.

Single-grain 40Ar-39Ar ages of glauconies: implications for the geologic time scale and global sea level variations

The mineral series glaucony supplies 40% of the absolute-age database for the geologic time scale of the last 250 million years. However, glauconies have long been suspected of giving young potassium-argon ages on bulk samples. Laser-probe argon-argon dating shows that glaucony populations comprise grains with a wide range of ages, suggesting a period of genesis several times longer ( approximately 5 million years) than previously thought. An estimate of the age of their enclosing sediments (and therefore of time scale boundaries) is given by the oldest nonrelict grains in the glaucony populations, whereas the formation times of the younger grains appear to be modulated by global sea level.

Cough responsiveness in neurogenic dysphagia

OBJECTIVES

In neurogenic dysphagia a good cough is important for airway protection. If triggering of cough, or its effectiveness, is impaired this might result in an increased aspiration risk. Capsaicin, an agent which induces cough through sensory nerve stimulation, was used to test cough sensitivity in groups of patients with and without neurogenic dysphagia.

METHODS

On the basis of swallowing speed (ml/s) in a validated water test 28 alert neurological inpatients (16 women, aged 22-71 years) were classified into 13 with abnormal and 15 with normal swallowing (median swallowing speed 23% and 99%, median volume/swallow 43% and 106% of that predicted for age and sex respectively: p<0.001). Capsaicin nebulised on air in saline was inhaled via a low resistance valve using a mouthpiece and noseclip. Up to seven incremental concentrations of capsaicin ranging from 0.07-20.0 x 10(-4) mol/l were each inhaled for up to a minute. A pneumotachograph connected to the expiratory limb gave a paper recording of expiratory air flow. Coughs were recorded as high flow expirations of short duration. Capsaicin concentrations at first cough (threshold) were recorded; concentrations at frequencies of 10 and 20 coughs/minute were interpolated from the dose-response curve.

RESULTS

Cough threshold tended to be lower in those with abnormal swallowing (non-significant): the (log) concentration of capsaicin producing 10 or 20 coughs/ minute also tended to be lower (p=0.12 and 0.07 respectively) in those with abnormal swallowing.

CONCLUSION

Contrary to expectation, these results suggest that cough responsiveness is enhanced in alert patients with neurogenic dysphagia even after allowing for diagnostic category, the possible presence of a bulbar upper motor neuron lesion, or voluntary respiratory capacity. It is concluded that these patients with neurogenic dysphagia do not have a reduced sensitivity of cough triggering.

Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, Nlac-P

Recent advances in the experimentally determined structures and dynamics of the domains within LacI provide a rare context for evaluating dynamics calculations. A 1500-ps trajectory was simulated for a variant of the LacI DNA-binding domain, which consists of the first three helices in LacI and the hinge helix of the homologous PurR. Order parameters derived from dynamics simulations are compared to those obtained for the LacI DNA-binding domain with 15N relaxation NMR spectroscopy (Slijper et al., 1997. Biochemistry. 36:249-254). The MD simulations suggest that the unstructured loop between helices II and III does not exist in a discrete state under the conditions of no salt and neutral pH, but occupies a continuum of states between the DNA-bound and free structures. Simulations also indicate that the unstructured region between helix III and the hinge helix is very mobile, rendering motions of the hinge helix essentially independent of the rest of the protein. Finally, the alpha-helical hydrogen bonds in the hinge helix are broken after 1250 ps, perhaps as a prelude to helix unfolding.

High-quality nutritional interventions reduce costs

Numerous clinical studies have documented improved clinical outcomes and cost savings when patients at risk for malnutrition receive high-quality nutritional care. A survey of 19 hospitals found that patients who received high-quality nutritional care averaged 12.2 days in the hospital. Patients who received medium nutritional care averaged 14.0 days in the hospital. Patients who received low-quality nutritional care were hospitalized an average of 14.4 days. The survey further revealed that only 7.5 percent of patients at risk for malnutrition actually received the type of nutritional care that was associated with the shortest average length of stay. If all patients in the at-risk population had received high-quality nutritional care, the estimated net savings potential would have been $1,064 per patient. Financial managers can determine the financial consequences of clinical nutritional policies and practices from information and analytical tools that are readily available.

A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins

A simple method is presented for projecting the conformation of extended secondary structure elements of peptides and proteins that extend over four C alpha atoms onto a simple two-dimensional surface. A new set of two degrees of freedom is defined, a pseudodihedral involving four sequential C alpha atoms, as well as the triple scalar product for the vectors describing the orientation of the three intervening peptide groups. The method provides a reduction in dimensionality, from the usual combination of multiple phi,psi pairs to a single pair, yielding valuable information concerning the structure and dynamics of these important elements. The new two-dimensional surface is explored by reference to 63 selected protein crystal structures together with a comparison of model built peptides representing the common secondary structural elements. Dynamical aspects on this new surface are examined using a molecular dynamics trajectory of Basic Pancreatic Trypsin Inhibitor.