Purification of oligonucleotides by high affinity, low molecular weight displacers

High affinity, low molecular weight anionic displacers were successfully employed for the purification of antisense oligonucleotides. Several important structural characteristics were identified that contribute to the affinity of low molecular weight displacers to a hydrophilized polystyrene divinyl benzene anion exchanger. Sulfonic acid groups were found to possess higher affinity than carboxylic acid and phosphate functionalities, and nonspecific interactions (particularly hydrophobic interactions) were shown to play a major role in the retention process on this stationary phase material. Using this information, two high affinity, low molecular weight displacers were identified. These molecules are relatively inexpensive organic dyes that possess multiple sulfonic acid moieties, as well as aromatic functionalities, which increase nonspecific interactions with the stationary phase. These high affinity displacers, which can be readily detected, were then employed to displace several strongly retained antisense oligonucleotides that could not be displaced by previously established low molecular weight displacers. The displacement process resulted in very high purities of the antisense oligonucleotides. The results presented in this paper are significant in that they demonstrate that low molecular weight displacers for ion-exchange chromatography can possess equal to or greater affinities than their higher molecular weight counterparts, when nonspecific interactions with the stationary phase are exploited. In addition, the results illustrate the high resolutions possible with displacement chromatography and demonstrate an attractive technology for the process scale purification of oligonucleotides.

Binding interactions of vancomycin tracers with a bacterial cell wall peptidoglycan analogue

Binding interactions between several vancomycin tracers and (N,N'-diacetyl)KDADA in solution were evaluated in a competition format using a surface plasmon resonance instrument. Tracers derivatized from the carboxy terminus or the N-vancosaminyl sugar moiety of vancomycin bind the peptide with an affinity similar to that of underivatized vancomycin. In contrast, N-methylleucyl derivatized vancomycin tracers bind the peptide with a reduced affinity relative to vancomycin.

Use of advanced breast biopsy instrumentation while performing stereotactic breast biopsies: review of 150 consecutive biopsies

BACKGROUND

Stereotactic breast biopsies are being performed in the United States with increasing frequency. Advanced breast biopsy instrumentation (ABBI) is a recent addition to the list of available stereotactic breast biopsy devices (eg, fine-needle aspiration, automated needle cores, and vacuum-assisted devices). Indications for the ABBI procedure in the management of patients with nonpalpable mammographic lesions have not been established.

STUDY DESIGN

Prospectively collected data on 150 patients biopsied with the ABBI procedure were reviewed.

RESULTS

From April 1996 to May 1997, 150 patients with indeterminate or suspicious nonpalpable mammographic lesions were biopsied using the ABBI technique. Complications were minor. One patient (0.6%) required a repeat biopsy because of insufficient tissue and one patient had repeat excision to confirm the diagnosis of atypical ductal hyperplasia. Cancer was diagnosed in 26%. Followup mammograms were obtained in 94% of the patients. Lesions were missed in three patients (2%), none of whom were later found to have cancer. One patient (0.6%) required a repeat ABBI biopsy for postbiopsy architectural distortion. Postprocedure mammographic scarring was otherwise minimal and was noted in only 16% of the patients. Of the 111 patients with benign diagnoses, 67 were seen for clinical followup; 98% had good cosmetic outcomes and were satisfied with the ABBI technique.

CONCLUSIONS

The ABBI technique is a safe, reliable stereotactic breast biopsy technique that is well accepted by patients. The sensitivity and specificity of ABBI biopsy for the diagnosis of carcinoma in this series were each 100% for the 142 patients returning for followup. Indications for the technique are similar to those for traditional needle localization excisional breast biopsies.

Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: pre-steady-state kinetic studies

Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase (DMAPP-tRNA transferase) catalyzes the first step in the biosynthesis of the hypermodified A37 residue in tRNAs that read codons beginning with uridine. The mechanism of the enzyme-catalyzed reaction was studied by isotope trapping, pre-steady-state rapid quench, and single turnover experiments. Isotope trapping indicated that the enzyme.tRNA complex is catalytically competent, whereas the enzyme.DMAPP complex is not. The results are consistent with an ordered sequential mechanism for substrate binding where tRNA binds first. The association and dissociation rate constants for the enzyme.tRNA binary complex are 1. 15+/-0.33x10(7) M(-1) s(-1) and 0.06+/-0.01 s(-1), respectively. Addition of DMAPP gives an enzyme.tRNA.DMAPP ternary complex in rapid equilibrium with the binary complex and DMAPP. Rapid quench studies yielded a linear profile (k(cat)=0.36+/-0.01 s(-1)) with no evidence for buildup of enzyme-bound product. Product release from DMAPP-tRNA transferase is therefore not rate-limiting. The Michaelis constant for tRNA and the equilibrium dissociation constant for DMAPP calculated from the individual rate constants determined here are consistent with values obtained from a steady-state kinetic analysis.

Evaluation of chemiluminescent estradiol conjugates by using a surface plasmon resonance detector

A series of chemiluminescent 17beta-estradiol probes were synthesized. Relative equilibrium dissociation constants (K(D)) for the interaction of an anti-E(2) Fab fragment for the probes in solution were evaluated using a single E(2)-analog biosensor surface on a BIAcore surface plasmon resonance instrument. The results show the antibody fragment binds all chemiluminescent conjugates tested with high affinity showing only minor preferences for site of substitution (C6 versus C7), stereochemistry (alpha versus beta), or linker moiety.

Application of surface plasmon resonance toward studies of low-molecular-weight antigen-antibody binding interactions

Methods for studying low-molecular-weight antigen-antibody binding interactions using surface plasmon resonance detection are presented. The experimental parameters most relevant to studies of low-molecular-weight antigen-antibody binding interactions are discussed. Direct kinetic analysis of the binding interactions is most informative, providing both apparent association and dissociation rate constants from which equilibrium constants can be calculated. Equilibrium analysis, including steady-state and solution affinity studies, offers an alternative approach to direct kinetic analysis when knowledge of the individual kinetic rate constants is not required or difficult to determine. The various methods are illustrated by studies of an anti-T(4) Fab fragment binding interaction with several thyroxine analogs. The methods utilized were dependent on the affinity of the interaction. The high-affinity anti-T(4) Fab fragment/l-T(4) binding interaction was evaluated using direct kinetic analysis. An intermediate affinity anti-T(4) Fab fragment/l-T(3) binding interaction was evaluated using a combination of direct kinetic analysis, steady-state analysis, and solution affinity analysis. The relatively weak anti-T(4) Fab fragment/l-T(2) binding interaction was evaluated using steady-state and solution affinity analysis protocols. Several thyroxine tracers that could not be immobilized to a biosensor surface were also evaluated via the solution affinity format. In cases where a given binding interaction was examined using multiple methods the results were comparable.

Renal artery angioplasty and stent placement: predictors of a favorable outcome

BACKGROUND

Renal artery stenosis is a common disorder and is an established cause of hypertension and renal insufficiency. Although treatment with renal artery stents has been shown to improve blood pressure and renal function for some patients, the patient population most likely to benefit is unknown. The current study was designed to determine which factors are predictive of improved blood pressure and renal function when patients with renal artery stenosis are treated with renal artery angioplasty and stent placement.

METHODS

In a prospective evaluation 127 consecutively enrolled patients with renal artery stenosis in 171 vessels were treated with angioplasty and intravascular stents. Blood pressure and serum creatinine concentration were measured before stent placement and during the follow-up period.

RESULTS

The mean length of the follow-up period was 15 +/- 14 months. Mean systolic blood pressure improved among patients with hypertension (from 177 +/- 26 mm Hg before stent placement to 151 +/- 24 mm Hg 6 months after stent placement (P <.001). The greatest improvement occurred among those with the highest baseline systolic blood pressure. This beneficial effect on blood pressure was sustained for 3 years. Sex, age, diastolic blood pressure, number of vessels into which stents were placed, serum creatinine concentration, presence of bilateral disease, race, and severity of stenosis were not predictive of improved blood pressure. Mean creatinine concentration was not significantly changed for the group as a whole. A significant decrease in serum creatinine concentration occurred among 43% of patients with baseline renal insufficiency. None of the examined variables was predictive of improvement.

CONCLUSIONS

Renal artery angioplasty and stent placement produced a significantly greater reduction in systolic blood pressure among patients with the highest baseline systolic blood pressure. Other examined variables were not predictive of a significant improvement in blood pressure. No examined variable was predictive of improved renal function. We concluded that management of renal artery stenosis with renal artery angioplasty and stent placement is most likely to result in significant improvement in systolic blood pressure among patients with the highest baseline systolic blood pressure.

Colloid cyst in ectopic thyroid gland

A five year old girl presented with a mid-line neck swelling. At operation, a multiloculated cyst was excised with a portion of hyoid bone and a suprahyoid gelatinous tract extending into the base of the tongue. Histology revealed a benign colloid cyst with associated thyroid tissue. Post-operative investigations indicated severe hypothyroidism. The cystic nature of the lesion was misleading at operation and pre-operative thyroid ultrasonography (US) is recommended for all patients with suspected thyroglossal tract cysts (TGC).

Comparison of risk of conductive hearing loss among three ethnic groups of Arctic audiology patients

The purpose of the study was to investigate the relative contributions of age, gender, ethnic background, and a history of middle ear disease on the amount of conductive hearing impairment among native and non-native audiology patients in the Canadian North. A second goal of the study was to determine risk factors for conductive hearing loss in the patients studied. Three ethnic groups were represented among the 3,094 patients: Inuit, American Indian, and non-native. Loglinear and logit statistical models were applied, and these data were best explained by a 3-way interaction of history of middle ear disease, ethnic group, and hearing loss, and the 2-way interaction of age and hearing loss. The Inuit appear to be at higher risk for conductive hearing impairment than the other ethnic groups. Conductive hearing loss also appears to increase as age increases through the teenage years for all the patients regardless of ethnic group membership. Preschoolers were at the lowest risk for conductive hearing loss. The trend for the amount of hearing impairment to increase throughout childhood suggests that children living in the Arctic may manifest a unique and more serious form of the disease not often observed in audiology patients who are Caucasian in southern Canada or the United States or that they may be exposed to additional risk factors.

Synthesis of a chemiluminescent acridinium hydroxylamine (AHA) for the direct detection of abasic sites in DNA

[structure: see text] The synthesis of a chemiluminescent acridinium hydroxylamine (AHA) for the direct detection of abasic sites in damaged nucleic acids is described. The reagent reacts readily with abasic sites of damaged calf thymus DNA generated in a time-dependent manner under acid/heat depurination conditions. Preliminary results indicate the sensitivity of the direct chemiluminescent detection format is approximately 0.1 abasic sites detected per 10(6) nucleotides using as little as 200 ng of DNA.

Computational blood flow modeling based on in vivo measurements

Study of the relationship between hemodynamics and atherogenesis requires accurate three-dimensional descriptions of in vivo arterial geometries. Common methods for obtaining such geometries include in vivo medical imaging and postmortem preparations (vessel casts, pressure-fixed vessels). We sought to determine the relative accuracy of these methods. The aorto-iliac (A/I) region of six rabbits was imaged in vivo using contrast-enhanced magnetic resonance imaging (MRI). After sacrifice, the geometry of the A/I region was preserved via vascular casts in four animals, and ex situ pressure fixation (while preserving dimensions) in the remaining two animals. The MR images and postmortem preparations were used to build computer representations of the A/I bifurcations, which were then used as input for computational blood flow analyses. Substantial differences were seen between MRI-based models and postmortem preparations. Bifurcation angles were consistently larger in postmortem specimens, and vessel dimensions were consistently smaller in pressure-fixed specimens. In vivo MRI-based models underpredicted aortic dimensions immediately proximal to the bifurcation, causing appreciable variation in the aorto-iliac parent/child area ratio. This had an important effect on wall shear stress and separation patterns on the "hips" of the bifurcation, with mean wall shear stress differences ranging from 15% to 35%, depending on the model. The above results, as well as consideration of known and probable sources of error, suggests that in vivo MRI best replicates overall vessel geometry (vessel paths and bifurcation angle). However, vascular casting seems to better capture detailed vessel cross-sectional dimensions and shape. It is important to accurately characterize the local aorto-iliac area ratio when studying in vivo bifurcation hemodynamics.

Effect of transradial access on quality of life and cost of cardiac catheterization: A randomized comparison

BACKGROUND

Transradial access is a recently developed alternative for diagnostic cardiac catheterization. Its effects on quality of life after the procedure, patient preference, and cost are unknown.

METHODS AND RESULTS

We performed a randomized single-center trial in which 99 patients underwent transfemoral and 101 underwent transradial diagnostic cardiac catheterization. Quality of life was measured with the SF-36 and visual analog scales at baseline, 1 day, and 1 week. Patients were examined at 1 day and at 1 week after for complications. Costs were measured prospectively. One patient in the femoral group and 2 in the radial group crossed over to the alternative access site. There were no major access site complications. One patient in the transfemoral group had a minor stroke. Transradial catheterization significantly reduced median length of stay (3.6 vs 10.4 hours, P <.0001). Over the first day after the procedure, measures of bodily pain, back pain, and walking ability favored the transradial group (P <.05 for all comparisons). Over the week after the procedure, changes in role limitations caused by physical health, bodily pain, and back pain favored the transradial group (P <.05 for all comparisons). There was a strong patient preference for transradial catheterization as well (P <. 0001). Transradial catheterization led to significant reductions in bed, pharmacy, and total hospital costs ($2010 vs $2299, P <.0001).

CONCLUSIONS

Among patients undergoing diagnostic cardiac catheterization, transradial access leads to improved quality of life after the procedure, is strongly preferred by patients, and reduces hospital costs.

Investigations into self-association of vancomycin covalent dimers using surface plasmon resonance technology

Covalent dimers of vancomycin linked through the vancosamine sugar moieties of the glycopeptide antibiotic have been synthesized in one step in 67-69% yield. The propensity for self-association of these and related vancomycin covalent dimers is evaluated using surface plasmon resonance technology.

A numerical study of blood flow patterns in anatomically realistic and simplified end-to-side anastomoses

PURPOSE

Recently, some numerical and experimental studies of blood flow in large arteries have attempted to accurately replicate in vivo arterial geometries, while others have utilized simplified models. The objective of this study was to determine how much an anatomically realistic geometry can be simplified without the loss of significant hemodynamic information.

METHOD

A human femoral-popliteal bypass graft was used to reconstruct an anatomically faithful finite element model of an end-to-side anastomosis. Nonideal geometric features of the model were removed in sequential steps to produce a series of successively simplified models. Blood flow patterns were numerically computed for each geometry, and the flow and wall shear stress fields were analyzed to determine the significance of each level of geometric simplification.

RESULTS

The removal of small local surface features and out-of-plane curvature did not significantly change the flow and wall shear stress distributions in the end-to-side anastomosis. Local changes in arterial caliber played a more significant role, depending upon the location and extent of the change. The graft-to-host artery diameter ratio was found to be a strong determinant of wall shear stress patterns in regions that are typically associated with disease processes.

CONCLUSIONS

For the specific case of an end-to-side anastomosis, simplified models provide sufficient information for comparing hemodynamics with qualitative or averaged disease locations, provided the "primary" geometric features are well replicated. The ratio of the graft-to-host artery diameter was shown to be the most important geometric feature. "Secondary" geometric features such as local arterial caliber changes, out-of-plane curvature, and small-scale surface topology are less important determinants of the wall shear stress patterns. However, if patient-specific disease information is available for the same arterial geometry, accurate replication of both primary and secondary geometric features is likely required.

Chitinases from uncultured marine microorganisms

Our understanding of the degradation of organic matter will benefit from a greater appreciation for the genes encoding enzymes involved in the hydrolysis of biopolymers such as chitin, one of the most abundant polymers in nature. To isolate representative and abundant chitinase genes from uncultivated marine bacteria, we constructed libraries of genomic DNA isolated from coastal and estuarine waters. The libraries were screened for genes encoding proteins that hydrolyze a fluorogenic analogue of chitin, 4-methylumbelliferyl beta-D-N,N'-diacetylchitobioside (MUF-diNAG). The abundance of clones capable of MUF-diNAG hydrolysis was higher in the library constructed with DNA from the estuary than in that constructed with DNA from coastal waters, although the abundance of positive clones was also dependent on the method used to screen the library. Plaque assays revealed nine MUF-diNAG-positive clones of 75,000 screened for the estuarine sample and two clones of 750,000 for the coastal sample. A microtiter plate assay revealed approximately 1 positive clone for every 500 clones screened in the coastal library. The number of clones detected with the plaque assay was consistent with estimates of the portion of culturable bacteria that degrade chitin. Our results suggest that culture-dependent methods do not greatly underestimate the portion of marine bacterial communities capable of chitin degradation.

Chemoenzymatic synthesis of 3'-O-(carboxyalkyl)fluorescein labels

A general and versatile method is described for the synthesis of fluorescent labels. Coupling of the 3'-phenol of fluorescein methyl ester with hydroxyalkyl benzyl esters, followed by benzyl ester hydrolysis, provided a series of fluorescein carboxyalkyl ethers. Use of the Mitsunobu reaction allowed for the introduction of linkers of different lengths onto the 3'-phenol of fluorescein. Chemoenzymatic benzyl ester hydrolysis was achieved with LPL-80 lipase, providing pH-independent labels useful for the preparation of fluorescent conjugates.

Flake density of steam-processed sorghum grain alters performance and sites of digestibility by growing-finishing steers

The effect of several flake densities (FD) of steam-processed sorghum grain on performance, and site and extent of nutrient digestibilities by steers fed growing and finishing diets was determined. The effectiveness of common laboratory methods of starch availability (enzymatic hydrolysis or gelatinization) to provide target specifications for quality control of steam-flaked grains was also measured. In vitro starch availability of the processed grains increased (P < .05) linearly in response to decreased FD. Flake density was more highly correlated with enzymatic measures than with percentage gelatinization (R2 = .87 to .93 vs .36). Using 140 crossbred beef steers (181 kg initial weight), feedlot performance was determined for 112 d with a growing diet (50% grain), followed by 119 d with a finishing diet (78% grain). Each FD treatment (412, 360, 309, and 257 g/L or 32, 28, 24, and 20 lb/bu) was randomly assigned to five pens of seven steers each. Intake of DM by steers decreased linearly (P < .05) as FD decreased (7 and 13%, respectively, for growing and finishing diets). Decreasing FD reduced linearly (P < .05) ADG in the finishing phase and for the entire 231-d trial. With the growing diet only, feed efficiency and estimated diet NEm and NEg responses to decreasing FD were curvilinear (P < .05), with the 360 g/L (28 lb/bu) flake being most efficient. Electrical energy requirements for processing increased linearly (P < .05) as FD decreased. Using four multi-cannulated crossbred steers (275 kg), starch digestibility increased linearly (P < .05) in the rumen (82 to 91%) and total tract (98.2 to 99.2%) as FD decreased. Digestibilities within the small (74%) and large intestines (62%) were not altered by FD. Decreasing FD increased (P < .05) total CP digestibility, but did not consistently alter fiber digestibility or DE content of the diets. In conclusion, enzymatic laboratory methods to evaluate starch availability in processed grains can be used satisfactorily to establish FD criteria for quality control of the steam-flaking process. The greatest improvements in efficiency, estimated diet NE, and starch and protein digestibilities usually occurred when FD was decreased from 412 to 360 g/L (32 to 28 lb/bu). Based on these measures and processing costs, the optimal FD was 360 g/L (28 lb/bu).

Structure-binding relationships for the interaction between a vancomycin monoclonal antibody Fab fragment and a library of vancomycin analogues and tracers

A series of vancomycin analogues and tracers were synthesized, and their binding interactions with an anti-vancomycin Fab fragment were evaluated under mass transport limiting conditions using surface plasmon resonance detection. Differences observed in binding interactions were utilized to define the vancomycin structural elements critical for antibody recognition. Major structural regions of vancomycin shown to play an important role in anti-vancomycin Fab fragment recognition include two sugar moieties and one chlorinated phenyl ring. The N-methylleucyl residue, the carboxy terminal residue, and residues in the peptide-binding region of vancomycin have minimal impact on the anti-vancomycin Fab fragment/vancomycin binding interaction. The selection of an antibody with such binding properties plays a critical role in the development of a vancomycin immunoassay that employs stable calibrators and controls.

Accuracy of computational hemodynamics in complex arterial geometries reconstructed from magnetic resonance imaging

PURPOSE

Combining computational blood flow modeling with three-dimensional medical imaging provides a new approach for studying links between hemodynamic factors and arterial disease. Although this provides patient-specific hemodynamic information, it is subject to several potential errors. This study quantifies some of these errors and identifies optimal reconstruction methodologies.

METHODS

A carotid artery bifurcation phantom of known geometry was imaged using a commercial magnetic resonance (MR) imager. Three-dimensional models were reconstructed from the images using several reconstruction techniques, and steady and unsteady blood flow simulations were performed. The carotid bifurcation from a healthy, human volunteer was then imaged in vivo, and geometric models were reconstructed.

RESULTS

Reconstructed models of the phantom showed good agreement with the gold standard geometry, with a mean error of approximately 15% between the computed wall shear stress fields. Reconstructed models of the in vivo carotid bifurcation were unacceptably noisy, unless lumenal profile smoothing and approximating surface splines were used.

CONCLUSIONS

All reconstruction methods gave acceptable results for the phantom model, but in vivo models appear to require smoothing. If proper attention is paid to smoothing and geometric fidelity issues, models reconstructed from MR images appear to be suitable for use in computational studies of in vivo hemodynamics.