BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies

The tricarboxylate reagent benzene-1,3,5-triacetic acid (BTA) was used to attach 5′-aminated DNA primers and templates on an aminosilanized glass surface for subsequent generation of DNA colonies by in situ solid-phase amplification. We have characterized the derivatized surfaces for the chemical attachment of oligonucleotides and evaluate the properties relevant for the amplification process: surface density, thermal stability towards thermocycling, functionalization reproducibility and storage stability. The derivatization process, first developed for glass slides, was then adapted to microfabricated glass channels containing integrated fluidic connections. This implementation resulted in an important reduction of reaction times, consumption of reagents and process automation. Innovative analytical methods for the characterization of attached DNA were developed for assessing the surface immobilized DNA content after amplification. The results obtained showed that the BTA chemistry is compatible and suitable for forming highly dense arrays of DNA colonies with optimal surface coverage of about 10 million colonies/cm² from the amplification of initial single-template DNA molecules immobilized. We also demonstrate that the dsDNA colonies generated can be quantitatively processed in situ by restriction enzymes digestion. DNA colonies generated using the BTA reagent can be used for further sequence analysis in an unprecedented parallel fashion for low-cost genomic studies.     

Characterization of the γδ T cell response to acute leukemia

Background: Previous work from our center has suggested a correlation between increased donor-derived Vδ1+ γδ T cells and long-term relapse-free survival following bone marrow transplantation for leukemia. Questions remain, however, as to whether this observation can be explained by a γδ T cell-based immune response against primary leukemia. Methods: We examined γδ T cell receptor (TCR) phenotype, cell proliferation, and cytolytic activity following culture with irradiated primary leukemia blasts from a haploidentical first-degree relative. Subsequently, we also studied the γδ TCR phenotype and complimentarity determining region 3 (CDR3) cDNA sequences from 17 newly diagnosed leukemia patients. Results: In 17/28 (61%) of in vitro cultures, γδ T cells proliferated in culture with primary blasts. Vδ1+ T cells were proportionally increased in all cultures and were the predominant cell population in 6/17. In the 7 cultures where cytotoxicity could be assessed, 6 (86%) showed some degree of cytotoxicity to the primary leukemia. Vδ1+ T cells were also the predominant γδ T cell subtype in pre-treatment leukemia patients principally due to loss of Vδ2+ T cells rather than expansion of Vδ1+ cells. The Vδ1 CDR3-region cDNA sequence from these patients revealed exclusive use of the Jδ1 constant region and sequence conservation in 4/11 patients. Conclusions: γδ T cells exhibit an in vitro response to primary leukemia blasts that is manifested by proliferation, an increased proportion of Vδ1+ T cells, and cytotoxicity to the primary leukemia blasts. The Vδ1+ T cell population is also predominant in newly diagnosed leukemia patients likely due to a loss of circulating Vδ2+ T cells. A small proportion of newly diagnosed patients showed Vδ1 CDR3 region similarity. These findings suggest a role for γδ T cells in the immune response to leukemia.Paul F. Meeh and Michelle King are contributed equally to this work.     

Homer Wheelon, M.D., physiologist, artist, and poet: origins of the tailpieces in journals of the American Physiological Society

Since 1953, illustrations have been inserted as "tailpieces" at the ends of articles in The American Journal of Physiology and The Journal of Applied Physiology. The drawings were made by Homer Wheelon, a member of the American Physiological Society from 1919 until his death in 1960. Forty-five years after his death, Wheelon is unknown, but he contributed 32 publications to the medical literature and trained J. Earl Thomas, an important 20th century gastrointestinal physiologist. Wheelon was born into poverty in 1883 to itinerant Methodist preachers, circumstances that guided his education and career choices. Throughout his life, Wheelon exhibited a fondness and talent for art and photography and an unusual breadth of intellectual interests and knowledge. Wheelon received a bachelor's degree from the University of Washington, then studied at the University of Oregon, Northwestern University, and St. Louis University. Earning his M.D. from St. Louis University and assuming a faculty position there, Wheelon and his graduate student, Thomas, conducted widely recognized gastrointestinal research. Returning to Seattle in 1921, Wheelon became a highly respected physician and hospital administrator, but he also found time to indulge his interest in visual art and poetry. In 1933, inspired by observing a rabbit being used in a pregnancy test, Wheelon began to write and illustrate an epic, 322-page poem, Rabbit No. 202, illustrations from which became the journals' tailpieces. The present study traces Wheelon's personal life and scientific career in an attempt to understand this complex man and the origins of his unusual poem and its drawings.     

Oleanane-type triterpenes of Embelia schimperi leaves

An investigation of an ethyl acetate extract of Embelia schimperi leaves has led to the isolation of 10 oleanane-type triterpenes characterized as 3beta,16alpha-di-O-acetyl-13beta, 28-epoxyoleanane (1), 3beta-acetyl-16-oxo-13beta, 28-epoxyoleanane (2), 3beta-acetyl-16alpha-hydroxy-13beta, 28-epoxyoleanane (3), 3beta-acetyl-16alpha-hydroxyoleanane-13beta, 28-olide (4), 3beta-acetyl-28-hydroxy-16-oxo-12-oleanene (5), 3beta, 28-di-O-acetyl-16alpha-hydroxy-12-oleanene (6), 3beta-acetyl-11alpha, 28-dihydroxy-16-oxo-12-oleanene (7), 3beta, 11alpha, 16alpha, 28-tetrahydroxy-12-oleanene (8), 3beta-acetyl-16alpha, 28alpha-dihydroxy-13beta, 28-oxydooleanane (9) and 3beta, 28alpha-dihydroxy-16-oxo-13beta, 28-oxydooleanane (10). The known compounds isolated from the same extract included 3beta, 16alpha-dihydroxy-13beta, 28-epoxyoleanane (protoprimulagenin A) (11), 3beta-hydroxy-16-oxo-13beta, 28-epoxyoxyoleanane (aegicerin) (12), 3, 16-dioxo-13beta, 28-epoxyoleanane (embilionone) (13), 3beta, 28-dihydroxy-16-oxo-12-oleanene (schimperinone) (14), taraxerone (15), taraxerol (16) and stigmasterol (17). Structure elucidations were carried out spectroscopically.     

Metabolism of thioamides by Ralstonia pickettii TA

Information on bacterial thioamide metabolism has focused on transformation of the antituberculosis drug ethionamide and related compounds by Mycobacterium tuberculosis. To study this metabolism more generally, a bacterium that grew using thioacetamide as the sole nitrogen source was isolated via enrichment culture. The bacterium was identified as Ralstonia pickettii and designated strain TA. Cells grown on thioacetamide also transformed other thioamide compounds. Transformation of the thioamides tested was dependent on oxygen. During thioamide degradation, sulfur was detected in the medium at the oxidation level of sulfite, further suggesting an oxygenase mechanism. R. pickettii TA did not grow on thiobenzamide as a nitrogen source, but resting cells converted thiobenzamide to benzamide, with thiobenzamide S-oxide and benzonitrile detected as intermediates. Thioacetamide S-oxide was detected as an intermediate during thioacetamide degradation, but the only accumulating metabolite of thioacetamide was identified as 3,5-dimethyl-1,2,4-thiadiazole, a compound shown to derive from spontaneous reaction of thioacetamide and oxygenated thioacetamide species. This dead-end metabolite accounted for only ca. 12% of the metabolized thioacetamide. Neither acetonitrile nor acetamide was detected during thioacetamide degradation, but R. pickettii grew on both compounds as nitrogen and carbon sources. It is proposed that R. pickettii TA degrades thioamides via a mechanism involving consecutive oxygenations of the thioamide sulfur atom.     

Purification and characterization of TrzF: biuret hydrolysis by allophanate hydrolase supports growth

TrzF, the allophanate hydrolase from Enterobacter cloacae strain 99, was cloned, overexpressed in the presence of a chaperone protein, and purified to homogeneity. Native TrzF had a subunit molecular weight of 65,401 and a subunit stoichiometry of alpha(2) and did not contain significant levels of metals. TrzF showed time-dependent inhibition by phenyl phosphorodiamidate and is a member of the amidase signature protein family. TrzF was highly active in the hydrolysis of allophanate but was not active with urea, despite having been previously considered a urea amidolyase. TrzF showed lower activity with malonamate, malonamide, and biuret. The allophanate hydrolase from Pseudomonas sp. strain ADP, AtzF, was also shown to hydrolyze biuret slowly. Since biuret and allophanate are consecutive metabolites in cyanuric acid metabolism, the low level of biuret hydrolase activity can have physiological significance. A recombinant Escherichia coli strain containing atzD, encoding cyanuric acid hydrolase that produces biuret, and atzF grew slowly on cyanuric acid as a source of nitrogen. The amount of growth produced was consistent with the liberation of 3 mol of ammonia from cyanuric acid. In vitro, TrzF was shown to hydrolyze biuret to liberate 3 mol of ammonia. The biuret hydrolyzing activity of TrzF might also be physiologically relevant in native strains. E. cloacae strain 99 grows on cyanuric acid with a significant accumulation of biuret.     

Karyology of a Marine Non-Motile Dinoflagellate, Pyrocystis lunula

Dinoflagellates have a unique and interesting intracellular architecture such as permanently condensed chromosomes throughout the cell cycle. However the study of dinoflagellate chromosomes is not amendable because of the unusually higher number of chromosomes and problems in sample preparation. The species of Pyrocystis spend most of their life cycle as vegetative cyst forms and have been used as experimental organisms for bioluminescence and circadian rhythms. Here, we documented the content of DNA in different life stages and the chromosome karyology in a marine non-motile dinoflagellate Pyrocystis lunula, through light and fluorescent microscopy, serial ultra-thin sectioning, and three dimension (3D) modeling. The DNA content doubles during DNA synthesis and in the end of the cell division two separate daughter cells have the approximately same fluorescent values for the mother cells. Using serial ultra-thin sectioning and 3D modeling, we report the first ultrastructural karyogram. The cells chosen were at the end of karyokinesis. A total of 98 chromosomes were counted and assigned to 49 pairs. In this species, DNA synthesis appears to occur before, or during asexual division and P. lunula lives a diplontic life cycle.     

Validation of a randomization procedure to assess animal habitat preferences: microhabitat use of tiger sharks in a seagrass ecosystem

1. Tiger sharks Galeocerdo cuvier are important predators in a variety of nearshore communities, including the seagrass ecosystem of Shark Bay, Western Australia. Because tiger sharks are known to influence spatial distributions of multiple prey species, it is important to understand how they use habitats at a variety of spatial scales. We used a combination of catch rates and acoustic tracking to determine tiger shark microhabitat use in Shark Bay. 2. Comparing habitat-use data from tracking against the null hypothesis of no habitat preference is hindered in Shark Bay, as elsewhere, by the difficulty of defining expected habitat use given random movement. We used randomization procedures to generate expected habitat use in the absence of habitat preference and expected habitat use differences among groups (e.g. males and females). We tested the performance of these protocols using simulated data sets with known habitat preferences. 3. The technique correctly classified sets of simulated tracks as displaying a preference or not and was a conservative test for differences in habitat preferences between subgroups of tracks (e.g. males vs. females). 4. Sharks preferred shallow habitats over deep ones, and preferred shallow edge microhabitats over shallow interior ones. The use of shallow edges likely increases encounter rates with potential prey and may have profound consequences for the dynamics of Shark Bay's seagrass ecosystem through indirect effects transmitted by grazers that are common prey of tiger sharks. 5. Females showed a greater tendency to use shallow edge microhabitats than did males; this pattern was not detected by traditional analysis techniques. 6. The randomization procedures presented here are applicable to many field studies that use tracking by allowing researchers both to determine overall habitat preferences and to identify differences in habitat use between groups within their sample.     

Mutant analysis of the Shal (Kv4) voltage-gated fast transient K+ channel in Caenorhabditis elegans

Shal (Kv4) alpha-subunits are the most conserved among the family of voltage-gated potassium channels. Previous work has shown that the Shal potassium channel subfamily underlies the predominant fast transient outward current in Drosophila neurons (Tsunoda, S., and Salkoff, L. (1995) J. Neurosci. 15, 1741-1754) and the fast transient outward current in mouse heart muscle (Guo, W., Jung, W. E., Marionneau, C., Aimond, F., Xu, H., Yamada, K. A., Schwarz, T. L., Demolombe, S., and Nerbonne, J. M. (2005) Circ. Res. 97, 1342-1350). We show that Shal channels also play a role as the predominant transient outward current in Caenorhabditis elegans muscle. Green fluorescent protein promoter experiments also revealed SHL-1 expression in a subset of neurons as well as in C. elegans body wall muscle and in male-specific diagonal muscles. The shl-1 (ok1168) null mutant removed all fast transient outward current from muscle cells. SHL-1 currents strongly resembled Shal currents in other species except that they were active in a more depolarized voltage range. We also determined that the remaining delayed-rectifier current in cultured myocytes was carried by the Shaker ortholog SHK-1. In shl-1 (ok1168) mutants there was a significant compensatory increase in the SHK-1 current. Male shl-1 (ok1168) animals exhibited reduced mating efficiency resulting from an apparent difficulty in locating the hermaphrodite vulva. SHL-1 channels are apparently important in fine-tuning complex behaviors, such as mating, that play a crucial role in the survival and propagation of the species.     

Principal component analysis and artificial neural network analysis of oral tissue fluorescence spectra: classification of normal premalignant and malignant pathological conditions

Pulsed laser-induced autofluorescence spectroscopic studies of pathologically certified normal, premalignant, and malignant oral tissues were carried out at 325 nm excitation. The spectral analysis and classification for discrimination among normal, premalignant, and malignant conditions were performed using principal component analysis (PCA) and artificial neural network (ANN) separately on the same set of spectral data. In case of PCA, spectral residuals, Mahalanobis distance, and scores of factors were used for discrimination among normal, premalignant, and malignant cases. In ANN, parameters like mean, spectral residual, standard deviation, and total energy were used to train the network. The ANN used in this study is a classical multiplayer feed-forward type with a back-propagation algorithm for the training of the network. The specificity and sensitivity were determined in both classification schemes. In the case of PCA, they are 100 and 92.9%, respectively, whereas for ANN they are 100 and 96.5% for the data set considered.