The mutational landscape of head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, and frequently lethal malignancy. To uncover its mutational spectrum, we analyzed whole-exome sequencing data from 74 tumor-normal pairs. The majority exhibited a mutational profile consistent with tobacco exposure; human papillomavirus was detectable by sequencing DNA from infected tumors. In addition to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), our analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbored mutations in genes that regulate squamous differentiation (for example, NOTCH1, IRF6, and TP63), implicating its dysregulation as a major driver of HNSCC carcinogenesis. More generally, the results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms.     

Characterization of polyphenolics in the seed coat of Black Jamapa bean (Phaseolus vulgaris L.)

The common bean contains phytochemicals, including phenolic compounds, which can provide health benefits to the consumer. Our objective was to characterize the polyphenolic compounds present in the seed coat of Black Jamapa bean and to test fractionation methods that permit the recovery of polyphenolics in their naturally occurring forms. A 100% methanol extract from seed coats was subjected to different chromatographic fractionation methods. Analysis by HPLC-MS revealed that a better separation of phytochemicals was achieved using direct silica gel fractionation, which allowed more accurate identification of compounds, especially of the flavonols. Anthocyanins, flavanol monomers, and heterogeneous flavanol oligomers up to hexamers were detected. To our knowledge, this is the first time that myricetin glycoside and proanthocyanidin oligomers containing (epi)-gallocatechin have been reported in the black bean. The fractionation methods used in this study produced large quantities of natural mixtures of flavonoids suitable for testing bioactivity and phytochemical interactions.     

A comparison of genetic relationship measures in strawberry (Fragaria × ananassa Duch.) based on AFLPs, RAPDs, and pedigree data

Nineteen of the major strawberry (Fragaria × ananassa Duch.) cultivars grown in the UnitedStates and Canada were examined for AFLP markerpolymorphisms. For the AFLP reactions, the EcoRI-ACC primer was used in combination with fourMseI primers (MseI-CAC, MseI-CAG,MseI-CAT, or MseI-CTT). Each set ofprimers produced 46–66 scorable fragments ranging insize between 50 and 500 bp. The polymorphic fragmentsproduced from each set of primers were more thansufficient to distinguish among all the cultivars,demonstrating the usefulness of AFLP markers forcultivar identification. Similarity coefficients werecalculated based on data from 228 AFLP markers anddata from 15 previously characterized RAPD markers. The RAPD markers had been specifically selected forfingerprinting purposes because they succesfullydistinguish 41 strawberry cultivars, including the 19cultivars analyzed in this study. Separatedendrograms were constructed based on analysis of theAFLP and RAPD marker data using a neighbor-joiningalgorithm. The dendrograms were compared and found tobe very different. Correlations between similaritycoefficients calculated from AFLP marker data,similarity coefficients calculated from RAPD markerdata, and coefficients of coancestry calculated frompedigree information were evaluated. Interestingly,a better correlation with the coefficients ofcoancestry was observed with the RAPD marker data thanwith the AFLP marker data.     

Evaluating innovative technologies for multistage fish growth processes: Case study of an eel (Anguilla anguilla L.) farm

A new method for evaluating innovative technologies for multistage fish growth processes was developed. An earlier economic model was adapted to meet the real-world requirements of a commercial eel (Anguilla anguilla L.) farm. The economic benefits of different innovative technologies at the farm level were evaluated where the technology included multiple production alternatives at various intensities and several growth stages. Data were gathered into “bio-economic” tables that take into account the biological parameters of each production alternative and the costs related to its development and implementation. The adjusted data were then divided into groups of production alternatives and feasible combinations of alternatives for each of three growth stages were evaluated to determine the best technology for the overall growth process. A computer program enabled us to enumerate all potential innovative technologies, collect information on biological parameters and costs by growth stage, and compare additional profit expected after implementation of each innovation. Results reveal the most profitable innovative technologies by growth stage for the 5-year eel culture. Comparison of the 10 best technologies shows that combining the alternatives with the best biological parameters for each growth stage does not necessarily result in the maximum additional profit for the farm.     

Biosynthesis and characterization of 14C-enriched flavonoid fractions from plant cell suspension cultures

A range of radiolabeled anthocyanins, proanthocyanidins, and other flavonoids were accumulated by cell suspension cultures of two plant species, ohelo (Vaccinium pahalae) and grape (a Vitis hybrid, Bailey Alicant A), after providing uniformly labeled [(14)C]sucrose to the medium. Approximately 15% of administered label was recovered in a series of flavonoid-rich fractions varying in composition. Anthocyanins, and monomers to oligomers of proanthocyanidins, were labeled effectively and characterized from both species. Most of the proanthocyanidin oligomers were based on the flavan-3-ols (+)-catechin and (-)-epicatechin. Cyanidin and peonidin glycosides were the dominant forms of anthocyanins in both species. Whereas the predominant form of flavonoids identified from ohelo cell cultures was proanthocyanidins, grape cell cultures produced mostly anthocyanins. The labeled phytochemicals were produced for use in subsequent in vivo animal feeding studies to gauge their bioavailability and accumulation in target organs.     

In vivo prediction of extracellular and intracellular water in cattle and sheep using thiocyanate and urea

Two experiments were conducted in cattle and sheep to determine the earliest time for thiocyanate equilibration with extracellular water. In Exp. 1, nine animals were infused to determine marker concentrations and sampling times. In Exp. 2, five steers were infused and then exsanguinated for tissue analyses. Thiocyanate equilibrated 22 to 31 min after infusion with a pool size equivalent to expected extracellular water. Plasma thiocyanate half-life averaged 29 h. Tissue concentrations 24 or 48 h after thiocyanate infusion were 20 to 24% of those observed in plasma for heart muscle and kidney and 6 to 8% in liver and skeletal muscle. A procedure is proposed for the in vivo estimation of empty body water (urea dilution), extracellular water (thiocyanate dilution) and, by difference, intracellular water in cattle and sheep, requiring only three blood samples, an initial sample and two samples taken 12 and 28 min after intravenous infusion of a urea-thiocyanate solution.     

Mixed Ehrlichia canis, Hepatozoon canis, and presumptive Anaplasma phagocytophilum infection in a dog

A 5-month-old, female, mongrel dog was admitted to the Clinic of Companion Animal Medicine, Aristotle University of Thessaloniki, Greece, with depression, anorexia, fever, peripheral lymphadenopathy, splenomegaly, oculonasal discharge, nonregenerative anemia, and mild thrombocytopenia. Cytology of Giemsa-stained buffy coat, bone marrow, and lymph node aspiration smears revealed numerous morulae in mononuclear leukocytes and in neutrophils, and Hepatozoon canis gamonts in neutrophils. The dog was seropositive to Ehrlichia canis (immunofluorescence assay [IFA]) and Hepatozoon canis (ELISA) but not to Anaplasma phagocytophilum (IFA). A nested polymerase chain reaction performed on bone marrow aspirates was positive for E canis. This method was not applied for the detection of A phagocytophilum. Treatment with doxycycline and imidocarb dipropionate resulted in both clinical and parasitologic cure. This is the first reported case of a mixed infection with E canis, H canis, and presumptive A phagocytophilum. The findings emphasize the value of cytology in offering a quick and inexpensive diagnosis in mixed tick-borne infections of dogs.