Methods for Investigating DNA Accessibility with Single Nucleosomes

Nucleosomes are the fundamental organizing unit of all eukaryotic genomes. Understanding how proteins gain access to DNA-binding sites located within nucleosomes is important for understanding DNA processing including transcription, replication, and repair. Single-molecule total internal reflection fluorescence (smTIRF) microscopy measurements can provide key insight into how proteins gain and maintain access to DNA sites within nucleosomes. Here, we describe methods for smTIRF experiments including the preparation of fluorophore-labeled nucleosomes, the smTIRF system, data acquisition, analysis, and controls. These methods are presented for investigating transcription factor binding within nucleosomes. However, they are applicable for investigating the binding of any site-specific DNA-binding protein within nucleosomes.

Estimation of bias with the single-zone assumption in measurement of residential air exchange using the perfluorocarbon tracer gas method

Residential air exchange rates (AERs) are vital in understanding the temporal and spatial drivers of indoor air quality (IAQ). Several methods to quantify AERs have been used in IAQ research, often with the assumption that the home is a single, well-mixed air zone. Since 2005, Health Canada has conducted IAQ studies across Canada in which AERs were measured using the perfluorocarbon tracer (PFT) gas method. Emitters and detectors of a single PFT gas were placed on the main floor to estimate a single-zone AER (AER(1z)). In three of these studies, a second set of emitters and detectors were deployed in the basement or second floor in approximately 10% of homes for a two-zone AER estimate (AER(2z)). In total, 287 daily pairs of AER(2z) and AER(1z) estimates were made from 35 homes across three cities. In 87% of the cases, AER(2z) was higher than AER(1z). Overall, the AER(1z) estimates underestimated AER(2z) by approximately 16% (IQR: 5-32%). This underestimate occurred in all cities and seasons and varied in magnitude seasonally, between homes, and daily, indicating that when measuring residential air exchange using a single PFT gas, the assumption of a single well-mixed air zone very likely results in an under prediction of the AER.

PRACTICAL IMPLICATIONS

The results of this study suggest that the long-standing assumption that a home represents a single well-mixed air zone may result in a substantial negative bias in air exchange estimates. Indoor air quality professionals should take this finding into consideration when developing study designs or making decisions related to the recommendation and installation of residential ventilation systems.

Spinal subarachnoid hematoma resulting from lumbar myelography

We describe a rare complication of myelography. A subarachnoid filling defect was apparent on the postmyelographic CT but not on conventional myelography. MR imaging performed later showed a spinal subarachnoid hematoma (SSAH), extending from L3 to L5. Lumbar puncture may rarely be a cause for SSAH and is more common in patients with coagulopathy. Significant back pain, paresis, radiculopathy, and even altered consciousness or meningeal signs may herald an SSAH.

Experimental feline Lyme borreliosis as a model for testing Borrelia burgdorferi vaccines

The feline model investigated establishes that domestic cats may act as an animal model for evaluating the pathogenesis of Lyme borreliosis. Specifically this feline model demonstrates: First, that animals seroconvert following either needle injection of, or arthropod delivery of, Borrelia burgdorferi. Clinical findings obtained are consistent with those observed in human Lyme disease; histopathological observations are also consistent with those observed in human Lyme disease. Therefore, cats may also be used as a representative animal model for measuring immune protection against Lyme borreliosis. Specifically we are exploring the protective capacity of Borrelia burgdorferi antigenic compounds in cats, namely OspA, OspB, OspC, heat shock proteins, flagellar antigens and various protective immunological combinations.

Percutaneous transluminal aortic angioplasty: techniques and results

Percutaneous transluminal angioplasty of the infrarenal abdominal aorta has been reported by a few authors. In the present series, aortic stenoses in 32 patients were treated with various percutaneous angioplasty techniques. Isolated aortic stenoses and primary aortic stenoses extending into the iliac arteries were successfully dilated. The initial success rate was 100%, without evidence of rupture, thrombosis, dissection, or distal embolization. In only three of the 28 patients who returned for follow-up did symptoms recur or noninvasive vascular laboratory indexes deteriorate (mean follow-up, 25 months). Percutaneous transluminal aortic angioplasty has proved safe and efficacious in the treatment of atherosclerotic aortic stenoses.

Image-directed percutaneous biopsies with a biopsy gun

Core tissue for histologic study is believed by many pathologists to be more diagnostic than material from needle aspiration. Recently, a biopsy "gun" has been introduced, which simplifies core biopsies. With this device, 182 biopsies of multiple anatomic sites were performed with ultrasonic, computed tomographic, and fluoroscopic guidance and 18-gauge needles. High-quality histopathologic specimens were obtained in 177 of the biopsies, and diagnostic target tissue was obtained in 167. Only three significant complications occurred: one bleeding complication that required transfusion and two cases of pneumothorax that necessitated placement of chest tubes. The biopsy gun eliminated the disjointed movements of conventional "skinny" needle biopsies, and none of the samples demonstrated significant "crush" artifact or obscuring blood, problems that are commonly associated with manual biopsy techniques. Patient discomfort was decreased with this system compared with that of manual biopsies, and the total procedure time was reduced. Because of these distinct advantages, the authors now use the biopsy gun exclusively for all percutaneous biopsies and recommend that other institutions consider the use of this biopsy method.

Symptomatic vascular malformations: ethanol embolotherapy

Absolute ethanol was used to perform nine transcatheter embolizations and 21 direct percutaneous puncture embolizations in eight patients with unresectable vascular malformations. Six patients had arteriovenous malformations and two patients had hemangiomas. Four of these patients had undergone unsuccessful surgery, and the other four were not considered candidates for operation. All large complex symptomatic vascular malformations (SVMs) required multiple embolizations that were staged procedures. Ethanol embolotherapy, performed according to strict techniques, has proved efficacious in the management of SVMs.

Adaptation of the bard prostate biopsy gun for CT-guided abdominal biopsies

The Bard prostate biopsy gun under ultrasonic guidance provides consistent, high quality prostatic core samples for histopathologic diagnosis. This device can be adapted for biopsy of abdominal organs using computed tomographic guidance. We demonstrate how these technical modifications can be made. Having used this modified device in conjunction with the 18-gauge prostate biopsy needle in 25 patients, we have had excellent results and no complications.

Fatigue fracture of the femoral neck after total knee arthroplasty a case report

Prolonged immobility predisposes to a multitude of medical problems. In the rheumatoid patient, immobility contributes to a preexisting problem of osteoporosis. Our patient with longstanding rheumatoid arthritis underwent total knee arthroplasty and subsequently developed a fatigue fracture of the ipsilateral femoral neck. To our knowledge, this is the first such case to be reported in a patient with rheumatoid arthritis.

Chronic granulomatous disease with gastric antral narrowing

Marked narrowing of the gastric antrum produced vomiting in a boy with chronic granulomatous disease; the antral stenosis resolved after five months of medical management. A review of the seven previously reported cases indicates that this uncommon lesion may be self-limited and should be given an exhaustive trial of nonsurgical therapy, in view of the high morbidity of surgery in these children. Antibiotics may speed resolution.