Li-Fraumeni syndrome (LFS) is a highly penetrant, autosomal dominant, human familial cancer predisposition. Although a key role for the tumor suppressor p53 has been implicated in LFS, the genetic and cellular mechanisms underpinning this disease remain unknown. Therefore, modeling LFS in a vertebrate system that is accessible to both large-scale genetic screens and in vivo cell biological studies will facilitate the in vivo dissection of disease mechanisms, help identify candidate genes, and spur the discovery of therapeutic compounds. Here, we describe a forward genetic screen in zebrafish embryos that was used to identify LFS candidate genes, which yielded a p53 mutant (p53(I166T)) that as an adult develops tumors, predominantly sarcomas, with 100% penetrance. As in humans with LFS, tumors arise in heterozygotes and display loss of heterozygosity (LOH). This report of LOH indicates that Knudson's two-hit hypothesis, a hallmark of human autosomal dominant cancer syndromes, can be modeled in zebrafish. Furthermore, as with some LFS mutations, the zebrafish p53(I166T) allele is a loss-of-function allele with dominant-negative activity in vivo. Additionally, we demonstrate that the p53 regulatory pathway, including Mdm2 regulation, is evolutionarily conserved in zebrafish, providing a bona fide biological context in which to systematically uncover novel modifier genes and therapeutic agents for human LFS.

CONTEXT: Despite the recognition of the follicular variant of papillary carcinoma of the thyroid (FVPTC) for over 50 years, reproducibility of this diagnostic category has remained poor. Architectural features have been of variable utility as some FVPTC seem encapsulated, whereas others are multifocal and may be confused with nodular hyperplasia. Nuclear features are important for diagnosis of FVPTC, but some authors have discounted the utility of nuclear grooves and inclusions. More recently, BRAF and HBME-1 (Human Bone Marrow Endothelial Cell-1) have been suggested as markers for FVPTC. OBJECTIVE: To investigate the frequency of BRAF mutations and HBME-1 immunopositivity, in a series of FVPTCs in which the diagnosis was established by 100% consensus among a panel of 6 surgical pathologists. DESIGN: Twenty-eight specimens with an original diagnosis of FVPTC and 10 cases with other diagnoses were obtained from the surgical pathology files of the University of Utah School of Medicine. All specimens were independently reviewed by 6 surgical pathologists. Tissue blocks were analyzed for BRAF exon 15 mutations and HMBE-1 expression. RESULTS: Complete agreement among pathologists for the diagnosis of FVPTC was obtained in 28.6%(8/28) of cases originally diagnosed as FVPTC. Mutations in BRAF exon 15 were found in 25%(2/8) of cases with a 100% consensus diagnosis of FVPTC and 32%(6/19) of cases unanimously diagnosed as a type of papillary carcinoma (classic or follicular variant). HBME-1 was expressed in 87.5%(7/8) of lesions with a 100% consensus diagnosis of FVPTC and 84.2%(16/19) of lesions with a unanimous diagnosis of a type of papillary carcinoma of the thyroid (classic or follicular variant). CONCLUSIONS: Interobserver agreement for the diagnosis of FVPTC is poor and testing for the BRAF mutation is only marginally helpful because a minority of FVPTCs possess the mutation. HBME-1 expression when coupled with a BRAF mutation, results in 100% specificity but low sensitivity for the presence of papillary carcinoma of the thyroid including the follicular variant.

Lentivirus infections including HIV and feline immunodeficiency virus (FIV) cause neurovirulence, which is largely mediated by innate immunity. To investigate the interactions between neurovirulence and repeated conditioning by innate immune activation, models of lentivirus infection were exposed to LPS. Gene expression in HIV-infected (HIV+) and control (HIV-) patient brains was compared by real time RT-PCR and immunocytochemistry. Supernatants from mock and HIV-infected monocyte-derived macrophages exposed to LPS were applied to human neurons. FIV-infected (FIV+) and control (FIV-) animals were exposed repeatedly to LPS postinfection together with concurrent neurobehavioral testing, viral load, and host gene analyses. Brains from HIV+ individuals exhibited induction of CD3epsilon, CXCL10, and granzyme A expression (p < 0.05). Supernatants from HIV+ monocyte-derived macrophages induced CXCL10 expression in neurons, which was diminished by IL-10 treatment (p < 0.05). LPS-exposed FIV+ animals demonstrated lower plasma and brain viral loads (p < 0.05). Neuronal CXCL10 expression was increased in FIV+ animals but was suppressed by LPS exposure, together with reduced brain CD3epsilon and granzyme A expression (p < 0.05). In conjunction with preserved NeuN-positive neuronal counts in parietal cortex (p < 0.05), FIV+ animals exposed to LPS also showed less severe neurobehavioral deficits (p < 0.05). Repeated LPS exposures suppressed CXCL10 in the brain and ensuing T cell infiltration with a concomitant reduction in neurovirulence. Thus, innate immune chronic conditioning exerted beneficial effects on neurovirulence through suppression of a specific chemotactic factor, CXCL10, mediated by IL-10, leading to reduced leukocyte infiltration and release of neurotoxic factors.

Composite pheochromocytoma is a rare adrenal tumor composed of ordinary pheochromocytoma and other components, most frequently neuroblastic elements. Little is known about its biologic potential, therefore creating a clinical dilemma on diagnosis. This study investigates the clinical characteristics and N-myc amplification status of 4 cases of composite pheochromocytoma and compares them with selected cases of ordinary pheochromocytoma and neuroblastoma. The age range of the patients with composite pheochromocytoma was 15 to 40 years with an equal M/F ratio, including 2 patients with syndromes. None of these composite pheochromocytomas demonstrated N-myc amplification, none recurred, and there were no deaths. Of the classic pheochromocytomas, none demonstrated N-myc amplification, 2 recurred, and there were no deaths. Of the neuroblastomas, 5 (50%) of 10 showed significant N-myc amplification, and there were 4 known recurrences and 5 known deaths. These findings suggest that composite pheochromocytoma may be regarded as a histologic variant of classic pheochromocytoma.

Upland peat soils represent a large terrestrial carbon store and as such have the potential to be either an ongoing net sink of carbon or a significant net source of carbon. In the UK many upland peats are managed for a range of purposes but these purposes have rarely included carbon stewardship. However, there is now an opportunity to consider whether management practices could be altered to enhance storage of carbon in upland peats. Further, there are now voluntary and regulated carbon trading schemes operational throughout Europe that mean stored carbon, if verified, could have an economic and tradeable value. This means that new income streams could become available for upland management. The 'Sustainable Uplands' RELU project has developed a model for calculating carbon fluxes from peat soils that covers all carbon uptake and release pathways (e.g. fluvial and gaseous pathways). The model has been developed so that the impact of common management options within UK upland peats can be considered. The model was run for a decade from 1997-2006 and applied to an area of 550km(2) of upland peat soils in the Peak District. The study estimates that the region is presently a net sink of -62ktonnes CO(2) equivalent at an average export of -136tonnes CO(2) equivalent/km(2)/yr. If management interventions were targeted across the area the total sink could increase to -160ktonnes CO(2)/yr at an average export of -219tonnes CO(2) equivalent/km(2)/yr. However, not all interventions resulted in a benefit; some resulted in increased losses of CO(2) equivalents. Given present costs of peatland restoration and value of carbon offsets, the study suggests that 51% of those areas, where a carbon benefit was estimated by modelling for targeted action of management interventions, would show a profit from carbon offsetting within 30years. However, this percentage is very dependent upon the price of carbon used.

Rice is a commonly consumed food staple for many Asian and Pacific cultures thus, nutrient enrichment of rice has the potential to increase nutrient intakes for these populations. The objective of this study was to determine the levels of enrichment nutrients (ie, thiamin, niacin, iron, and folic acid) in white rice found in Guam, Saipan (Commonwealth of the Northern Mariana Islands), and Oahu (Hawaii). The proportion of white rice that was labeled "enriched" varied by type, bag size, and location. Most long-grain rice was labeled as enriched and most medium-grain rice was not. Bags of either type weighing >10 lb were seldom labeled as enriched in Hawaii or Saipan. Samples of various types of rice were collected on these three islands (n=19; 12 of which were labeled as enriched) and analyzed for their content of enrichment nutrients. Rice that was labeled as enriched in Hawaii and Guam seldom met the minimum enrichment standards for the United States. For comparison, three samples of enriched rice from California were also analyzed, and all met the enrichment standards. Food and nutrition professionals who are planning or evaluating diets of these Pacific island populations cannot assume that rice is enriched.

In recent years there has been a dramatic increase in artificial drain-blocking in world peatlands. The UK blanket peatlands have been severely drained over the past few decades but now drains are being blocked in an attempt to improve peatland environments. The drain-blocking has been a disparate process with limited knowledge transfer between organisations and within organisations operating in different geographic areas. Consequently, there has been no compilation of techniques used and their effectiveness. During this study thirty-two drain-blocked sites were surveyed and all the key stakeholders interviewed. Drain-blocking using peat turf was preferred by practitioners and was also the most cost-effective method. Peat turves were successful except on steep slopes, in areas of severe erosion, in very wet or very dry locations, or if the mineral substrate was exposed. A drain-blocking best practice guide is offered by this paper, providing information on the most suitable methods for blocking peatland drains under different circumstances. Additional considerations are provided for practitioners to ensure peatland drain-blocking is as successful as possible.

Environmental change caused by urban development, possibly augmented by climate change, may result in accelerated decay of in situ archaeological resources. Damage may be related to changes in hydrological processes. Such archaeological resources have to be considered in environmental planning. In this paper we highlight the need for improved hydrological data from urban archaeological sites using the case study of the City of York, UK, arguably one of the most well studied and well preserved urban archaeological environments globally. We suggest that the quality of hydrological data collected during routine surveys and experimental work must be improved and standardised in order for us to produce reliable archaeological risk models for urban sites.

OBJECTIVE: A mutation of B-type RAF kinase (B-RAF) represents the most common genetic alteration in papillary thyroid cancer (PTC), possibly signifying a more aggressive biology. Fine needle aspiration (FNA) represents the most useful initial diagnostic tool of thyroid nodules. Molecular analysis of the mutation status of B-RAF in thyroid nodule FNAs may provide guidance for treatment planning. STUDY DESIGN: Cross-sectional study. SUBJECTS AND METHODS: A retrospective chart review was undertaken for clinically relevant data of papillary thyroid cancer (PTC), follicular variant of PTC (FV-PTC), and nonmalignant goiters. After blinded pathologic review, histologic and cytologic samples were analyzed by LightCycler PCR (LCPCR) with allele-specific fluorescent probe melting curve analysis (FMCA) for the V600E mutation of B-RAF. RESULTS: Of the 45 patient samples analyzed, B-RAF mutation was found to be significantly higher in papillary carcinomas when compared to follicular variant of papillary thyroid carcinomas (55.6% vs 14.3%, P = 0.05). Pathologic B-RAF mutational status significantly correlated with cytologic B-RAF mutational status (P < 0.0001), cytologic interpretation (P = 0.012), and histologic diagnosis (P = 0.011). CONCLUSIONS: Determination of B-RAF V600E mutation of thyroid nodule FNAs by LCPCR may be a useful tool to guide treatment planning. These data support investigating the utility of this molecular marker in a prospective manner.

Background. Use of self-obtained vaginal specimens processed by nucleic acid amplification tests (NAATs) has significantly increased the utilization of nontraditional locations for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) screening programs. One important emerging source of such venues includes home self-sample kits available via the Internet. The objective of our study was to evaluate the performance of three commercially available NAATs: Becton-Dickinson ProbeTec(TM) SDA, Gen-Probe(R) APTIMA(R) Combo2 TMA, and Roche Amplicor(R) PCR for the detection of CT and NG from vaginal samples obtained via an Internet-based screening program. Methods. From July 2004 to August 2005, 500 self-collected vaginal swabs were tested for CT and NG using all three NAATs. Another 500 samples were collected between August 2005 and November 2007 and tested by ProbeTec and Combo2; PCR testing was discontinued due to low specificity for NG. All tests were conducted according to manufacturers' procedures; the gold standard for an infected CT or NG patient was defined as >/=2 positive NAATs. Results. Of the first 500 swabs submitted, 46 were CT infected (9.2%), 5 NG infected (1.0%), and 3 of these were co-infected (0.6%). All CT and NG Combo2 positive/ProbeTec negative samples were confirmed as true positives by an alternative NAAT. For CT, ProbeTec, Combo2, and PCR had sensitivities of 82.6%, 100% and 100%, with specificities of 100%, 100% and 99.3%, respectively. For NG, ProbeTec, Combo2, and PCR had sensitivities of 80%, 100% and 100%, with specificities of 100%, 100% and 98.8%, respectively. Of the total 1000 swabs submitted, 92 were CT infected (9.2%), 15 NG infected (1.5%), and 7 of these were co-infected (0.7%). There were no ProbeTec positive/Combo2 negative samples. For CT, ProbeTec and Combo2 had sensitivities of 81.5% and 100%, with specificities of 100% and 100%, respectively. For NG, ProbeTec and Combo2 had sensitivities of 80% and 100%, with specificities of 100% and 100%, respectively. Overall, ProbeTec had 17 CT false negative results (1.7%) and 3 NG false negative results (0.3%), while Combo2 had none. Our results were consistent with the sensitivities and specificities stated by the manufacturers. Conclusions: NAAT assays perform well for detection of chlamydia and gonorrhea using self-obtained vaginal swabs shipped in a dry state to a laboratory.