Tissue-simulating Phantoms for Assessing Potential Near-infrared Fluorescence Imaging Applications in Breast Cancer Surgery

Inaccuracies in intraoperative tumor localization and evaluation of surgical margin status result in suboptimal outcome of breast-conserving surgery (BCS). Optical imaging, in particular near-infrared fluorescence (NIRF) imaging, might reduce the frequency of positive surgical margins following BCS by providing the surgeon with a tool for pre- and intraoperative tumor localization in real-time. In the current study, the potential of NIRF-guided BCS is evaluated using tissue-simulating breast phantoms for reasons of standardization and training purposes.Breast phantoms with optical characteristics comparable to those of normal breast tissue were used to simulate breast conserving surgery. Tumor-simulating inclusions containing the fluorescent dye indocyanine green (ICG) were incorporated in the phantoms at predefined locations and imaged for pre- and intraoperative tumor localization, real-time NIRF-guided tumor resection, NIRF-guided evaluation on the extent of surgery, and postoperative assessment of surgical margins. A customized NIRF camera was used as a clinical prototype for imaging purposes.Breast phantoms containing tumor-simulating inclusions offer a simple, inexpensive, and versatile tool to simulate and evaluate intraoperative tumor imaging. The gelatinous phantoms have elastic properties similar to human tissue and can be cut using conventional surgical instruments. Moreover, the phantoms contain hemoglobin and intralipid for mimicking absorption and scattering of photons, respectively, creating uniform optical properties similar to human breast tissue. The main drawback of NIRF imaging is the limited penetration depth of photons when propagating through tissue, which hinders (noninvasive) imaging of deep-seated tumors with epi-illumination strategies.     

Folding Pathways of the Tetrahymena Ribozyme

Like many structured RNAs, the Tetrahymena group I intron ribozyme folds through multiple pathways and intermediates. Under standard conditions in vitro, a small fraction reaches the native state (N) with k_obs ≈ 0.6 min^− 1, while the remainder forms a long-lived misfolded conformation (M) thought to differ in topology. These alternative outcomes reflect a pathway that branches late in folding, after disruption of a trapped intermediate (I_trap). Here we use catalytic activity to probe the folding transitions from I_trap to the native and misfolded states. We show that mutations predicted to weaken the core helix P3 do not increase the rate of folding from I_trap but they increase the fraction that reaches the native state rather than forming the misfolded state. Thus, P3 is disrupted during folding to the native state but not to the misfolded state, and P3 disruption occurs after the rate-limiting step. Interestingly, P3-strengthening mutants also increase native folding. Additional experiments show that these mutants are rapidly committed to folding to the native state, although they reach the native state with approximately the same rate constant as the wild-type ribozyme (~ 1 min^− 1). Thus, the P3-strengthening mutants populate a distinct pathway that includes at least one intermediate but avoids the M state, most likely because P3 and the correct topology are formed early. Our results highlight multiple pathways in RNA folding and illustrate how kinetic competitions between rapid events can have long-lasting effects because the “choice” is enforced by energy barriers that grow larger as folding progresses.     

Prenatal developmental toxicity evaluation of 2',3'-dideoxyinosine (ddI) and 2',3'-didehydro-3'-deoxythymidine (d4T) co-administered to Swiss Albino (CD-1) mice

BACKGROUND: In pregnant women, antiretroviral drugs improve maternal health and reduce vertical transmission of human immunodeficiency virus to the infant. However, few nonclinical studies have examined the potential for adverse drug interactions. METHODS: On gestational days (GD) 6-16, mice were dosed with vehicle, ddI (360, 1440, or 2,880 mg/kg/day, p.o.), d4T (60, 240, or 480), or ddI/d4T combinations (360/60, 1,440/240, or 2,880/480). Daily doses were divided into two equal parts that were administered >or=6-hr apart. Body weight, clinical signs, and feed consumption were monitored. Pregnancies (22-24/group) were confirmed at necropsy. Maternal liver and gravid uterine weights (GUW), uterine implants (resorption, live or dead fetus), fetal body weight, gender, and morphologic anomalies (external, visceral, skeletal) were recorded. RESULTS: Maternal body weight, clinical signs, and GUW were unaffected. Maternal weight change corrected for GUW was greater than controls at 60 and 480 d4T. Relative feed consumption during treatment was increased relative to controls at 1,440 and 2,880 ddI and 2,880/480 ddI/d4T. Relative maternal liver weight was elevated above controls at 240 and 480 d4T and 2,880/480 ddI/d4T, and above the constituent dose of ddI at 1,440/240 and 2,880/480 ddI/d4T. Liver weight was not affected by ddI and there was no significant drug interaction. Prenatal mortality and morphologic anomalies were not increased. Fetal body weight showed only a decreasing trend for ddI/d4T, no effect for ddI or d4T, and no statistically significant drug interaction. CONCLUSIONS: In pregnant mice, ddI/d4T combinations were not associated with well-defined developmental toxicity or adverse drug interactions.     

Interactive effects of predators and a pesticide on aquatic communities

Chemical contaminants are ubiquitous in nature and a major goal of ecologists has been to understand and predict their impacts on natural communities. While direct toxic effects can be garnered from single‐species laboratory studies, the full suite of possible effects can only be observed when organisms are embedded within a community. In this study, we manipulated the concentration of malathion (a broad‐spectrum insecticide) to determine the impacts on aquatic communities containing phytoplankton, periphyton, and 27 species of animals (16 zooplankton, 5 snails, 3 tadpoles and 3 predatory insects). Using relatively low concentrations (0.13 to 0.46 mg l^?1), we found important direct (and interactive) effects of predators and malathion on the food web as well as a number of apparent density‐ and trait‐mediated indirect effects. Malathion initiated an indirect effect by decreasing zooplankton diversity and abundance, which propagated an increase in phytoplankton, a decrease in periphyton, and a subsequent decrease in the growth of leopard frog tadpoles. There also was an apparent trait‐mediated indirect effect whereby increased amounts of the pesticide reduced predation rates on amphibians without affecting the survival of the primary amphibian predator (larval Anax dragonflies). In contrast, snail survival and growth was unaffected by the pesticide but there were strong, species‐specific effects from their primary predator (adult Belostoma water bugs). This is one of few studies to examine the impacts of malathion on aquatic communities across a range of concentrations, despite the fact that it is currently the most commonly applied insecticide in the United States, it is applied around the world, and it can be legally directly sprayed over aquatic habitats to control the mosquitoes that carry malaria and West Nile virus. Our results suggest several mechanisms by which a wide variety of pesticides with similar modes of action might impact aquatic communities.     

A Dual-Purpose Protein Ligand for Effective Therapy and Sensitive Diagnosis of Anthrax

This article reports the design of a bivalent protein ligand with dual use in therapy and diagnosis of anthrax caused by Bacillus anthracis. The ligand specifically binds to PA and thereby blocks the intracellular delivery of LF and EF toxins that, respectively, cause cell lysis and edema. The ligand is a chimeric scaffold with two PA-binding domains (called VWA) linked to an IgG-Fc frame. Molecular modeling and binding measurements reveal that the VWA-Fc dimer binds to PA with high affinity (K (D) = 0.2 nM). An in vitro bio-luminescence assay shows that VWA-Fc (at nanomolar concentration) protects mouse macrophages from lysis by PA/LF. In vivo studies demonstrate that VWA-Fc at low doses ( approximately 50 mug/animal) are able to rescue animals from lethal doses of PA/LF and B. anthracis spores. Finally, VWA-Fc is utilized as the capture molecule in the sensitive (down to 30 picomolar) detection of PA using surface plasmon resonance.     

Fine needle aspiration biopsy of primary renal synovial sarcoma. A case report

BACKGROUND: Primary renal synovial sarcoma is a relatively recently described and characterized neoplasm, formerly designated embryonal sarcoma of the kidney, and has not been diagnosed before by fine needle aspiration biopsy cytology. We describe the cytologic features of a malignant biphasic neoplasm of the kidney that was subsequently diagnosed at nephrectomy and confirmed with molecular genetic analysis as a biphasic renal synovial sarcoma. CASE: A 38-year-old male presented with acute abdominal pain. Computed tomography (CT) demonstrated a 4.7-cm mass in the left kidney. No soft tissue or extrarenal masses were identified. A CT-guided fine needle aspiration biopsy revealed a malignant biphasic tumor characterized by minimally atypical tubular epithelium, immature spindle cells and foci of coagulative tumor necrosis. At nephrectomy, a necrotic, pseudo-encapsulated synovial sarcoma of the upper pole of the left kidney was identified and was additionally evaluated with immunohistochemistry and molecular genetic studies. The case is unique since biphasic synovial sarcomas have yet to be reported to occur in the kidney and fine needle aspiration biopsy findings of this renal neoplasm have never been reported to our knowledge. CONCLUSION: Synovial sarcoma should be a diagnostic consideration particularly in a young adult with a malignant spindle cell neoplasm of the kidney. The list of differential diagnoses should include sarcomatoid renal cell carcinoma, sarcomatoid transitional cell carcinoma of the renal pelvis, angiomyolipoma and monophasic or biphasic synovial sarcoma.     

Aspects of direct phasing in femtosecond nanocrystallography

X-ray free-electron laser diffraction patterns from protein nanocrystals provide information on the diffracted amplitudes between the Bragg reflections, offering the possibility of direct phase retrieval without the use of ancillary experimental data. Proposals for implementing direct phase retrieval are reviewed. These approaches are limited by the signal-to-noise levels in the data and the presence of different and incomplete unit cells in the nanocrystals. The effects of low signal to noise can be ameliorated by appropriate selection of the intensity data samples that are used. The effects of incomplete unit cells may be small in some cases, and a unique solution is likely if there are four or fewer molecular orientations in the unit cell.     

Oral transmissibility of prion disease is enhanced by binding to soil particles

Soil may serve as an environmental reservoir for prion infectivity and contribute to the horizontal transmission of prion diseases (transmissible spongiform encephalopathies [TSEs]) of sheep, deer, and elk. TSE infectivity can persist in soil for years, and we previously demonstrated that the disease-associated form of the prion protein binds to soil particles and prions adsorbed to the common soil mineral montmorillonite (Mte) retain infectivity following intracerebral inoculation. Here, we assess the oral infectivity of Mte- and soil-bound prions. We establish that prions bound to Mte are orally bioavailable, and that, unexpectedly, binding to Mte significantly enhances disease penetrance and reduces the incubation period relative to unbound agent. Cox proportional hazards modeling revealed that across the doses of TSE agent tested, Mte increased the effective infectious titer by a factor of 680 relative to unbound agent. Oral exposure to Mte-associated prions led to TSE development in experimental animals even at doses too low to produce clinical symptoms in the absence of the mineral. We tested the oral infectivity of prions bound to three whole soils differing in texture, mineralogy, and organic carbon content and found soil-bound prions to be orally infectious. Two of the three soils increased oral transmission of disease, and the infectivity of agent bound to the third organic carbon-rich soil was equivalent to that of unbound agent. Enhanced transmissibility of soil-bound prions may explain the environmental spread of some TSEs despite the presumably low levels shed into the environment. Association of prions with inorganic microparticles represents a novel means by which their oral transmission is enhanced relative to unbound agent.     

Breeding cycle of the Southern Bald Ibis,Geronticus calvus

Kopij, G., Kok, O.B. & Nuttall, R.J. 2000. Breeding cycle of the Southern Bald lbis, Geronticus calvus. Ostrich 71(3&4): 393-399. The breeding cycle of the Southern Bald lbis, Geronticus calvus, was studied at a colony in the eastern Free State. Birds were paired before breeding commenced and nest bulding began regularly two weeks before the first eggs were laid. Nesting material was collected chiefly by the male. Incubation statted with the first egg and lasted 26-32 days. Both sexes incubated, the female usually in the morning, the male around noon, and both sexes in the afternoon. Hatching is asynchronous with intervals between eggs ranging from one to four days. Bothe parents participate in rearing the young; the female broods more often, while the male brings the bulk of the food for the nestlings that were fed 3-4 times a day. Strong competition for food between nestlings was recorded. Nestlings remain in nests for at least 35 days.     

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011

This report details the outcome of the 1st International Earth Microbiome Project Conference. The 2-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on the 14th-15th June 2011, and was hosted by BGI (formally the Beijing Genomics Institute). The conference was arranged as a formal launch for the Earth Microbiome Project, to highlight some of the exciting research projects, results of the preliminary pilot studies, and to provide a discussion forum for the types of technology and experimental approaches that will come to define the standard operating procedures of this project.