Hydrogen bonding of nucleotide base pairs: Application of the PM3 method

The ability of the pm3 semiempirical quantum mechanical method to reproduce hydrogen bonding in nucleotide base pairs was assessed. Results of pm3 calculations on the nucleotides 2′-deoxyadenosine 5′-monophosphate (pdA), 2′-deoxyguanosine 5′-monophosphate (pdG), 2′-deoxycytidine 5′-monophosphate (pdC), and 2′-deoxythymidine 5′-monophosphate (pdT) and the base pairs pdA–pdT, pdG–pdC, and pdG(syn)–pdC are presented and discussed. The pm3 method is the first of the parameterized nddo quantum mechanical models with any ability to reproduce hydrogen bonding between nucleotide base pairs. Intermolecular hydrogen bond lengths between nucleotides displaying Watson–Crick base pairing are 0.1–0.2 Å less than experimental results. Nucleotide bond distances, bond angles, and torsion angles about the glycosyl bond (χ), the C4′C5′ bond (γ), and the C5′O5′ bond (β) agree with experimental results. There are many possible conformations of nucleotides. pm3 calculations reveal that many of the most stable conformations are stabilized by intramolecular CHO hydrogen bonds. These interactions disrupt the usual sugar puckering. The stacking interactions of a dT–pdA duplex are examined at different levels of gradient optimization. The intramolecular hydrogen bonds found in the nucleotide base pairs disappear in the duplex, as a result of the additional constraints on the phosphate group when part of a DNA backbone. Sugar puckering is reproduced by the pm3 method for the four bases in the dT–pdA duplex. pm3 underestimates the attractive stacking interactions of base pairs in a B-DNA helical conformation. The performance of the pm3 method implemented in SPARTAN is contrasted with that implemented in MOPAC. At present, accurate ab initio calculations are too timeconsuming to be of practical use, and molecular mechanics methods cannot be used to determine quantum mechanical properties such as reaction-path calculations, transition-state structures, and activation energies. The pm3 method should be used with extreme caution for examination of small DNA systems. Future parameterizations of semiempirical methods should incorporate base stacking interactions into the parameterization data set to enhance the ability of these methods.

In Vitro and In Vivo Imaging Characteristics Assessment of Polymeric Coils Compared with Standard Platinum Coils for the Treatment of Intracranial Aneurysms

BACKGROUND AND PURPOSE:Conventional platinum coils cause imaging artifacts that reduce imaging quality and therefore impair imaging interpretation on intraprocedural or noninvasive follow-up imaging. The purpose of this study was to evaluate imaging characteristics and artifact production of polymeric coils compared with standard platinum coils in vitro and in vivo.MATERIALS AND METHODS:Polymeric coils and standard platinum coils were evaluated in vitro with the use of 2 identical silicon aneurysm models coiled with a packing attenuation of 20% each. DSA, flat panel CT, CT, and MR imaging were performed. In vivo evaluation of imaging characteristics of polymeric coils was performed in experimentally created rabbit carotid bifurcation aneurysms. DSA, CT/CTA, and MR imaging were performed after endovascular treatment of the aneurysms. Images were evaluated regarding visibility of individual coils, coil mass, artifact production, and visibility of residual flow within the aneurysm.RESULTS:Overall, in vitro and in vivo imaging showed relevantly reduced artifact production of polymeric coils in all imaging modalities compared with standard platinum coils. Image quality of CT and MR imaging was improved with the use of polymeric coils, which permitted enhanced depiction of individual coil loops and residual aneurysm lumen as well as the peri-aneurysmal area. Remarkably, CT images demonstrated considerably improved image quality with only minor artifacts compared with standard coils. On DSA, polymeric coils showed transparency and allowed visualization of superimposed vessel structures.CONCLUSIONS:This initial experimental study showed improved imaging quality with the use of polymeric coils compared with standard platinum coils in all imaging modalities. This might be advantageous for improved intraprocedural imaging for the detection of complications and posttreatment noninvasive follow-up imaging.

Three-dimensional vision enhances task performance independently of the surgical method

Within the next few years, the medical industry will launch increasingly affordable three-dimensional (3D) vision systems for the operating room (OR). This study aimed to evaluate the effect of two-dimensional (2D) and 3D visualization on surgical skills and task performance.

Membrane microdialysis: Evaluation of a new method to assess splanchnic tissue metabolism

OBJECTIVE: Measuring peritoneal lactate concentrations could be useful for detecting splanchnic hypoperfusion. The aims of this study were to evaluate the properties of a new membrane-based microdialyzer in vitro and to assess the ability of the dialyzer to detect a clinically relevant decrease in splanchnic blood flow in vivo. DESIGN: A membrane-based microdialyzer was first validated in vitro. The same device was tested afterward in a randomized, controlled animal experiment. SETTING: University experimental research laboratory. SUBJECTS: Twenty-four Landrace pigs of both genders. INTERVENTIONS: In vitro: Membrane microdialyzers were kept in warmed sodium lactate baths with lactate concentrations between 2 and 8 mmol/L for 10-120 mins, and microdialysis lactate concentrations were measured repeatedly (210 measurements). In vivo: An extracorporeal shunt with blood reservoir and roller pump was inserted between the proximal and distal abdominal aorta, and a microdialyzer was inserted intraperitoneally. In 12 animals, total splanchnic blood flow (measured by transit time ultrasound) was reduced by a median 43% (range, 13% to 72%) by activating the shunt; 12 animals served as controls. MEASUREMENTS AND MAIN RESULTS: In vitro: The fractional lactate recovery was 0.59 (0.32-0.83) after 60 mins and 0.82 (0.71-0.87) after 90 mins, with no further increase thereafter. At 60 and 90 mins, the fractional recovery was independent of the lactate concentration. In vivo: Abdominal blood flow reduction resulted in an increase in peritoneal microdialysis lactate concentration from 1.7 (0.3-3.8) mmol/L to 2.8 (1.3-6.2) mmol/L (p = .006). At the same time, mesenteric venous-arterial lactate gradient increased from 0.1 (-0.2-0.8) mmol/L to 0.3 (-0.3 -1.8) mmol/L (p = .032), and mesenteric venous-arterial Pco2 gradients increased from 12 (8-19) torr to 21 (11-54) torr (p = .005). CONCLUSIONS: Peritoneal membrane microdialysis provides a method for the assessment of splanchnic ischemia, with potential for clinical application.

Distribution of amyloid precursor protein and amyloid-beta immunoreactivity in DBA/2J glaucomatous mouse retinas

PURPOSE: Evidence suggests that altered metabolism of amyloid precursor protein (APP) may play a role in the pathophysiology of retinal ganglion cell (RGC) death in the etiology of glaucoma. The authors sought to determine the distribution of APP and amyloid-beta (Abeta) in DBA/2J glaucomatous mouse retinas. METHODS: The retinas of 3- and 15-month-old DBA/2J mice and C57/BL-6 mice (control group) were fixed with 4% paraformaldehyde and processed for immunohistochemistry. Antibodies used included a polyclonal antibody to the C terminus of Abeta 40 and a polyclonal antibody to the APP ectodomain. Immunohistochemically stained tissue was graded using light microscopy. Distribution and semiquantitative expression of APP and Abeta in young and old glaucomatous and normal retinas were determined and compared. RESULTS: Strong APP and Abeta immunoreactivity was found in the RGC layer, optic nerve, and pia/dura of old DBA/2J retinas, with considerably higher intensity found in the old compared with the young DBA/2J mice. In contrast to glaucomatous mice, the control group did not show any notable age-related difference. CONCLUSIONS: Disruption of the homeostatic properties of secreted APP with consecutive Abeta cytotoxicity might be a contributing factor of ganglion cell loss in glaucomatous mouse retinas.

Observation and identification of metabolites emerging during postmortem decomposition of brain tissue by means of in situ 1H-magnetic resonance spectroscopy

Postmortem decomposition of brain tissue was investigated by (1)H-magnetic resonance spectroscopy (MRS) in a sheep head model and selected human cases. Aiming at the eventual estimation of postmortem intervals in forensic medicine, this study focuses on the characterization and identification of newly observed metabolites. In situ single-voxel (1)H-MRS at 1.5 T was complemented by multidimensional homo- and heteronuclear high-resolution NMR spectroscopy of an extract of sheep brain tissue. The inclusion of spectra of model solutions in the program LC Model confirmed the assignments in situ. The first postmortem phase was characterized mainly by changes in the concentrations of metabolites usually observed in vivo and by the appearance of previously reported decay products. About 3 days postmortem, new metabolites, including free trimethylammonium, propionate, butyrate, and iso-butyrate, started to appear in situ. Since the observed metabolites and the time course is comparable in sheep and human brain tissue, the model system seems to be appropriate.

Effects of elevated atmospheric CO2 and O3 on wood density, antomical proerties and decomposition of Northern Hardwoods

Anthropogenic activities continue to drive atmospheric CO2 and O3 concentrations to levels higher than during the pre-industrial era. Accumulating evidence indicates that both elevated CO2 and elevated O3 could modify the quantity and biochemistry of woody plant biomass. Anatomical properties of woody plants are largely influenced by the activity of the cambium and the growth characteristics of wood cells, which are in turn influenced by a range of environmental factors. Hence, alterations in the concentrations of atmospheric CO2 and / or O3 could also impact wood anatomical properties. Many fungi derive their metabolic resources for growth from plant litter, including woody tissue, and therefore modifications in the quantity, biochemistry and anatomical properties of woody plants in response to elevated CO2 and / or O3 could impact the community of wood-decaying fungi and rates of wood decomposition. Consequently carbon and nutrient cycling and productivity of terrestrial ecosystem could also be impacted. Alterations in wood structure and biochemistry of woody plants could also impact wood density and subsequently impact wood quality. This dissertation examined the long term effects of elevated CO2 and / or O3 on wood anatomical properties, wood density, wood-decaying fungi and wood decomposition of northern hardwood tree species at the Aspen Free-Air CO2 and O3 Enrichment (Aspen FACE) project, near Rhinelander, WI, USA. Anatomical properties of wood varied significantly with species and aspen genotypes and radial position within the stem. Elevated CO2 did not have significant effects on wood anatomical properties in trembling aspen, paper birch or sugar maple, except for marginally increasing (P < 0.1) the number of vessels per square millimeter. Elevated O3 marginally or significantly altered vessel lumen diameter, cell wall area and vessel lumen area proportions depending on species and radial position. In line with the modifications in the anatomical properties, elevated CO2 and O3, alone, significantly modified wood density but effects were species and / or genotype specific. However, the effects of elevated CO2 and O3, alone, on wood anatomical properties and density were ameliorated when in combination. Wood species had a much greater impact on the wood-decaying fungal community and initial wood decomposition rate than did growth or decomposition of wood in elevated CO2 and / or O3. Polyporales, Agaricales, and Russulales were the dominant orders of fungi isolated. Based on the current results, future higher levels of CO2 and O3 may have moderate effects on wood quality of northern hardwoods, but for utilization purposes these may not be considered significant. However, wood-decaying fungal community composition and decomposition of northern hardwoods may be altered via shifts in species and / or genotype composition under future higher levels of CO2 and O3.

Validation of a new method for determination of cup orientation in THA

Our goal was to validate accuracy, consistency, and reproducibility/reliability of a new method for determining cup orientation in total hip arthroplasty (THA). This method allows matching the 3D-model from CT images or slices with the projected pelvis on an anteroposterior pelvic radiograph using a fully automated registration procedure. Cup orientation (inclination and anteversion) is calculated relative to the anterior pelvic plane, corrected for individual malposition of the pelvis during radiograph acquisition. Measurements on blinded and randomized radiographs of 80 cadaver and 327 patient hips were investigated. The method showed a mean accuracy of 0.7 +/- 1.7 degrees (-3.7 degrees to 4.0 degrees) for inclination and 1.2 +/- 2.4 degrees (-5.3 degrees to 5.6 degrees) for anteversion in the cadaver trials and 1.7 +/- 1.7 degrees (-4.6 degrees to 5.5 degrees) for inclination and 0.9 +/- 2.8 degrees (-5.2 degrees to 5.7 degrees) for anteversion in the clinical data when compared to CT-based measurements. No systematic errors in accuracy were detected with the Bland-Altman analysis. The software consistency and the reproducibility/reliability were very good. This software is an accurate, consistent, reliable, and reproducible method to measure cup orientation in THA using a sophisticated 2D/3D-matching technique. Its robust and accurate matching algorithm can be expanded to statistical models.