Toward single-molecule optical mapping of the epigenome

The past decade has seen an explosive growth in the utilization of single-molecule techniques for the study of complex systems. The ability to resolve phenomena otherwise masked by ensemble averaging has made these approaches especially attractive for the study of biological systems, where stochastic events lead to inherent inhomogeneity at the population level. The complex composition of the genome has made it an ideal system to study at the single-molecule level, and methods aimed at resolving genetic information from long, individual, genomic DNA molecules have been in use for the last 30 years. These methods, and particularly optical-based mapping of DNA, have been instrumental in highlighting genomic variation and contributed significantly to the assembly of many genomes including the human genome. Nanotechnology and nanoscopy have been a strong driving force for advancing genomic mapping approaches, allowing both better manipulation of DNA on the nanoscale and enhanced optical resolving power for analysis of genomic information. During the past few years, these developments have been adopted also for epigenetic studies. The common principle for these studies is the use of advanced optical microscopy for the detection of fluorescently labeled epigenetic marks on long, extended DNA molecules. Here we will discuss recent single-molecule studies for the mapping of chromatin composition and epigenetic DNA modifications, such as DNA methylation.

Microfluidic laminate-based phantom for diffusion tensor-magnetic resonance imaging (DT-MRI)

This paper reports fabrication of a magnetic resonance imaging (MRI) phantom created by stacking of multiple thin polydimethylsiloxane (PDMS) layers. PDMS is spin coated on SU-8 molds to obtain the desired layer thickness and imprints of the microchannel patterns that define the phantom geometry. This paper also identifies the unique challenges related to the fabrication and assembly of multiple thin layers and reports for the first time assembly of a large number of thin laminates of this nature. Use of photolithography techniques allows us to create a wide range of phantom geometries. The target dimensions of the phantoms reported here are (i) a stack of 30 thin PDMS layers of 10 µm thickness (ii) curved 5 µm × 5 µm microchannels with 8.7 µm spacing, and (iii) straight 5 µm × 5 µm microchannels with 3.6 µm spacing. SEM scans of the assembled phantoms show open microchannels and a monolithic cross-section with no visible interface between PDMS layers. Based on the results of diffusion tensor magnetic resonance imaging (DT-MRI) scan, the anisotropic diffusion of water molecules due to the physical restriction of the microchannels was detected, which means that the phantom can be used to calibrate and optimize MRI instrumentation.

NK/T-cell lymphoma in a renal transplant recipient and review of literature

T-cell lymphomas, particularly NK/T-cell lymphomas are rare post transplantation malignancies. Only a few cases have been described. These tumors behave aggressively and the outcome is poor. We present here a case of NK/T-cell lymphoma who presented to us with an orbital swelling 9 years after renal transplantation, along with the review of literature. To the best of our knowledge, this is the first case of NK/T-cell lymphoma post-renal transplantation reported from India.

Lighting up individual DNA binding proteins with quantum dots

The ability to determine the precise loci and occupancy of DNA-binding proteins is instrumental to our understanding of cellular processes like gene expression and regulation. We propose a single-molecule approach for the direct visualization of proteins bound to their template DNA. Fluorescent quantum dots (QD) are used to label proteins bound to DNA, allowing multicolor, nanometer-resolution localization. Protein-DNA complexes are linearly extended and imaged to determine the precise location of the protein binding sites. The method is demonstrated by detecting individual QD-labeled T7-RNA polymerases on the T7 bacteriophage genome. This work demonstrates the potential of this approach to precisely read protein binding position or, alternatively, "write" such information on extended DNA with QDs via sequence-specific molecular recognition.

Operational feasibility of establishing community reporting systems

BACKGROUND

In developing countries the absence ofa credible disease surveillance system results in an inappropriate response to an outbreak. Since a functioning and responsive disease surveillance system cannot be provided immediately, some interim surveillance system for early detection of outbreaks is needed to institute a prompt response. This operational research study was conducted to assess the feasibility of establishing community reporting systems involving women self-help groups and members of Panchayati raj institutions through syndromic surveillance at the community level.

METHODS

Reporting was initiated from 8 villages in 4 gram panchayats of Begunia block of Khurda district in Orissa during May and June 2005. Members of women self-help groups and Panchayati raj institutions were trained on structured reporting guidelines. In congruence with the state disease surveillance system, weekly reporting was started for comparison where feasible.

RESULTS

Completeness of reporting was better achieved by women self-help groups (91.6%) than members of Panchayati raj institutions (66.6%). Data capture was more complete as compared with the existing disease surveillance system. Illnesses among women were better captured and greater ownership of the public health service was noted.

CONCLUSION

Establishing community reporting systems using women self-help groups and members of Panchayat raj institutions for disease surveillance in India is a feasible option.

Infections associated with ventricular assist devices: epidemiology and effect on prognosis after transplantation

BACKGROUND

Ventricular assist devices (VADs) can be used as a bridge to orthotopic heart transplantation (OHT) in people with severe congestive heart failure. Although they can be inserted for an indefinite time period (unlike balloon pumps), they do carry a substantial risk of infection. We studied the epidemiology, microbiology, and consequences of infection in patients with VADs who ultimately had cardiac transplantation.

METHODS

Records of VAD-supported patients at our institution between January 1995 and January 2005 were identified by ICD-9 code. Infection was classified as driveline infection, pocket infection, mediastinitis, or VAD endocarditis in increasing severity of illness.

RESULTS

Of 73 patients identified by ICD-9 code, 60 had charts available for review. Of these 60, 72% had a VAD infection: 13 had VAD endocarditis; 3, mediastinitis; 25, pocket infection; and 29, driveline infection. The only association of infection (43 patients, 72%) and demography or underlying disease was that of endocarditis with older age (median age 59 vs. 53 years; P=0.02) and diabetes mellitus (13 patients, 30%; risk ratio 3.4; P=0.01). The duration of VAD support was longer in infected patients (median 125 days) vs. uninfected ones (25 days). Median survival measured from the time of VAD placement (although also true from the time of transplantation) was shorter in patients with VAD endocarditis (120 days) and pocket infection (350 days) vs. no infection (>2400 days) with a significant P=0.017 for endocarditis. Four patients had infections after transplantation that were caused by the same organism as their VAD infection. The predominant pathogens in VAD infection were Staphylococcus and Enterococcus spp.

CONCLUSION

VAD use as a bridge to cardiac transplantation is associated with a large number of device-related infections. Patients with infected VADs, on average, wait longer for transplantation than patients with uninfected VADs, and patients with VAD endocarditis have a shorter survival than patients with no VAD infection or simple driveline infection.

Problem-based learning: Is anatomy a casualty?

INTRODUCTION

The teaching of medical anatomy is changing. Medical schools worldwide are moving away from dissection and lectures to a more integrated course, where basic science and clinical skills are taught simultaneously. Medical students on these integrated courses have reported a lack of confidence in their basic science knowledge, especially concerning anatomy. Our aim was to perform a randomised controlled trial (RCT) to compare anatomical knowledge of two groups of second-year medical students, the first group taught on a traditional course, the second on an integrated course.

MATERIALS AND METHODS

Testing was done using a Questionnaire in a "True/False" format. There were 80 students in each group. There was no penalty for an incorrect answer. The test was performed under examination conditions. Papers were marked under blind conditions. Results were analysed using a Student's t test analysis.

RESULTS

Those students taught on a traditional course exhibited a significantly higher level of basic anatomical knowledge (p<0.001) than those taught on an integrated course. The students taught on an integrated course showed a much greater range of results.

CONCLUSIONS

Students taught on a traditional course have a higher level of anatomical knowledge than those taught on an integrated course. Our results differ from previous studies done in Europe which show no difference between the courses.

Infective endocarditis following orthotopic heart transplantation: 10 cases and a review of the literature

BACKGROUND

Infective endocarditis is a known complication of cardiac transplantation. However, published information has been limited to case reports and small case series.

METHODS

Cardiac transplantation has been performed at Temple University Hospital since 1983. We identified transplant patients with ICD-9 codes for endocarditis or bacteremia. A diagnosis of endocarditis required fulfillment of the Duke criteria and presence of a vegetation. Clinical and microbiologic data were collected. Demographic and survival information were compared with heart transplant recipients without endocarditis. We reviewed all previously published cases using a MEDLINE search.

RESULTS

Ten of 659 heart transplant recipients had endocarditis (1.5%, 187 cases per 100,000 person years). Mitral and tricuspid valves were involved predominantly. No patient had aortic valve infection. Patients with tricuspid valve infection had a greater median number of endomyocardial biopsies (n=23) than those with mitral valve infection (n=9, P=0.10). The major pathogens were Staphylococcus aureus (4 cases) and Aspergillus fumigatus (3 cases). Factors associated with S. aureus infection were new hemodialysis catheters, cellulitis, and a contaminated donor organ. All patients with A. fumigatus had antecedent cytomegalovirus viremia and disseminated fungal infection, including endophthalmitis. Endocarditis-related mortality was 80%. Median survival after transplant was 1.4 years in patients with endocarditis, compared with 9.3 years in other heart transplant recipients (P<0.001).

CONCLUSIONS

Endocarditis is substantially more common in heart transplant recipients than in general populations. Frequent central venous catheter access and multiple endomyocardial biopsies appear to predispose to infection. Aspergillus is a common pathogen and endocarditis follows infection elsewhere. The prognosis of post-cardiac transplant endocarditis is poor.