A vertically stacked, polymer, microfluidic point mutation analyzer: rapid high accuracy detection of low-abundance K-ras mutations

Recognition of point mutations in the K-ras gene can be used for the clinical management of several types of cancers. Unfortunately, several assay and hardware concerns must be addressed to allow users not well trained in performing molecular analyses the opportunity to undertake these measurements. To provide for a larger user base for these types of molecular assays, a vertically stacked microfluidic analyzer with a modular architecture and process automation was developed. The analyzer employs a primary polymerase chain reaction (PCR) coupled to an allele-specific ligase detection reaction (LDR). Each functional device, including continuous flow thermal reactors for the PCR and LDR, passive micromixers, and ExoSAP-IT purification, was designed and tested. Individual devices were fabricated in polycarbonate using hot embossing and were assembled using adhesive bonding for system assembly. The system produced LDR products from a DNA sample in approximately 1 h, an 80% reduction in time compared with conventional benchtop instrumentation. Purifying the post-PCR products with the ExoSAP-IT enzyme led to optimized LDR performance, minimizing false-positive signals and producing reliable results. Mutant alleles in genomic DNA were quantified to the level of 0.25 ng of mutant DNA in 50 ng of wild-type DNA for a 25-μl sample, equivalent to DNA from 42 mutant cells.     

Leaf litter inputs reinforce islands of nitrogen fertility in a lowland tropical forest

The role of lowland tropical forest tree communities in shaping soil nutrient cycling has been challenging to elucidate in the face of high species diversity. Previously, we showed that differences in tree species composition and canopy foliar nitrogen (N) concentrations correlated with differences in soil N availability in a mature Costa Rican rainforest. Here, we investigate potential mechanisms explaining this correlation. We used imaging spectroscopy to identify study plots containing 10–20 canopy trees with either high or low mean canopy N relative to the landscape mean. Plots were restricted to an uplifted terrace with relatively uniform parent material and climate. In order to assess whether canopy and soil N could be linked by litterfall inputs, we tracked litter production in the plots and measured rates of litter decay and the carbon and N content of leaf litter and leaf litter leachate. We also compared the abundance of putative N fixing trees and rates of free-living N fixation as well as soil pH, texture, cation exchange capacity, and topographic curvature to assess whether biological N fixation and/or soil properties could account for differences in soil N that were, in turn, imprinted on the canopy. We found no evidence of differences in legume communities, free-living N fixation, or abiotic properties. However, soils beneath high canopy N assemblages received ~ 60% more N via leaf litterfall due to variability in litter N content between plot types. The correlation of N in canopy leaves, leaf litter, and soil suggests that, under similar abiotic conditions, litterfall-mediated feedbacks can help maintain soil N differences among tropical tree assemblages in this diverse tropical forest.

     

Major role for mRNA binding and restructuring in sRNA recruitment by Hfq

Bacterial small RNAs (sRNAs) modulate gene expression by base-pairing with target mRNAs. Many sRNAs require the Sm-like RNA binding protein Hfq as a cofactor. Well-characterized interactions between DsrA sRNA and the rpoS mRNA leader were used to understand how Hfq stimulates sRNA pairing with target mRNAs. DsrA annealing stimulates expression of rpoS by disrupting a secondary structure in the rpoS leader, which otherwise prevents translation. Both RNAs bind Hfq with similar affinity but interact with opposite faces of the Hfq hexamer. Using mutations that block interactions between two of the three components, we demonstrate that Hfq binding to a functionally critical (AAN)(4) motif in rpoS mRNA rescues DsrA binding to a hyperstable rpoS mutant. We also show that Hfq cannot stably bridge the RNAs. Persistent ternary complexes only form when the two RNAs are complementary. Thus, Hfq mainly acts by binding and restructuring the rpoS mRNA. However, Hfq binding to DsrA is needed for maximum annealing in vitro, indicating that transient interactions with both RNAs contribute to the regulatory mechanism.     

Nanostructure shape effects on response of plasmonic aptamer sensors

A localized surface plasmon resonance (LSPR) sensor surface was fabricated by the deposition of gold nanorods on a glass substrate and subsequent immobilization of the DNA aptamer, which specifically bind to thrombin. This LSPR aptamer sensor showed a response of 6‐nm λ_max shift for protein binding with the detection limit of at least 10 pM, indicating one of the highest sensitivities achieved for thrombin detection by optical extinction LSPR. We also tested the LSPR sensor fabricated using gold bipyramid, which showed higher refractive index sensitivity than the gold nanorods, but the overall response of gold bipyramid sensor appears to be 25% less than that of the gold nanorod substrate, despite the approximately twofold higher refractive index sensitivity. XPS analysis showed that this is due to the low surface density of aptamers on the gold bipyramid compared with gold nanorods. The low surface density of the aptamers on the gold bipyramid surface may be due to the effect of shape of the nanostructure on the kinetics of aptamer monolayer formation. The small size of aptamers relative to other bioreceptors is the key to achieving high sensitivity by biosensors on the basis of LSPR, demonstrated here for protein binding. The generality of aptamer sensors for protein detection using gold nanorod and gold nanobipyramid substrates is anticipated to have a large impact in the important development of sensors toward biomarkers, environmental toxins, and warfare agents. Copyright © 2013 John Wiley & Sons, Ltd.     

Modest Gaseous Nitrogen Losses Point to Conservative Nitrogen Cycling in a Lowland Tropical Forest Watershed

Primary tropical rainforests are generally considered to be relatively nitrogen (N) rich, with characteristically large hydrologic and gaseous losses of inorganic N. However, emerging evidence suggests that some tropical ecosystems can exhibit tight N cycling, with low biologically available losses. In this study, we combined isotopic data with a well-characterized watershed N mass balance to close the N budget and characterize gaseous N losses at the ecosystem scale in a lowland tropical rainforest on the Osa Peninsula in southwestern Costa Rica. We measured δ¹⁵N and δ¹⁸O of nitrate (NO₃ ^?) in precipitation, surface, shallow and deep soil lysimeters and stream water biweekly for 1 year. Enrichment of both isotopes indicates that denitrification occurs predominantly as NO₃ ^? moves from surface soil down to 15 cm depth or laterally to stream water, with little further processing in deeper soil. Two different isotopic modeling approaches suggested that the gaseous fraction comprises 14 or 32% of total N loss (2.7 or 7.5 kg N ha^?1 y^?1), though estimates are sensitive to selection of isotopic fractionation values. Gas loss estimates using the mass balance approach (3.2 kg N ha^?1 y^?1) fall within this range and include N₂O losses of 0.9 kg N ha^?1 y^?1. Overall, gaseous and soluble hydrologic N losses comprise a modest proportion (~ 25%) of the total N inputs to this ecosystem. By contrast, relatively large, episodic hydrologic losses of non-biologically available particulate N balance the majority of N inputs and may contribute to maintaining conservative N cycling in this lowland tropical forest. Similar patterns of N cycling may occur in other tropical forests with similar state factor combinations—high rainfall, steep topography, relatively fertile soils—such as the western arc of the Amazon Basin and much of IndoMalaysia, but this hypothesis remains untested.     

The identification and characterization of hydrazinyl urea-based antibacterial agents through combinatorial chemistry

An effort to identify novel inhibitors of peptidoglycan synthesis with antibacterial activity resulted in the discovery of a series of biaryl urea-based antibacterial agents through isolation of a by-product from a mixture-based combinatorial library of semi-carbazones and subsequent parallel synthesis efforts. The compounds were shown to possess broad spectrum antibacterial activity against gram-positive drug resistant pathogens, and showed apparent specificity for disruption of the bacterial cell wall biosynthesis pathway.     

Synthesis and in vitro evaluation of human FP-receptor selective prostaglandin analogues

The in vitro evaluation of a series of saturated prostaglandins revealed that compounds with omega chain aromatic rings retain nanomolar potency for the human prostaglandin F receptor (hFP receptor), exemplified by compound 8. In contrast, the double bonds are required for activity in the series with an acyclic omega chain as in PGF2alpha.     

A quantitative real‐time PCR assay for identification and enumeration of the occasionally co‐occurring ichthyotoxic Pseudochattonella farcimen and P. verruculosa (Dictyochophyceae) and analysis of variation in gene copy numbers during the growth phase of single and mixed cultures

The ichthyotoxic genus Pseudochattonella forms recurrent extensive blooms in coastal waters in Japan, New Zealand and Northern Europe. It comprises of two morphologically similar species, P. verruculosa and P. farcimen, which complicates visual species identification and enumeration of live and fixed material. Primers designed previously could not quantitatively distinguish species in mixed assemblages. To address this issue we developed two primer sets: one revealed itself to be genus specific for Pseudochattonella and the other species‐specific for P. verruculosa. By subtracting cell estimates for P. verruculosa from combined results we could calculate cell numbers for P. farcimen. This approach has overcome the challenges posed by the very limited sequence availability and low gene variability between the two species. The qPCR assay was extensively tested for specificity, efficiency and sensitivity over an entire growth cycle in both single and mixed assemblages. Comparison of cell abundance estimates obtained by qPCR assay and microscopy showed no statistically significant difference until stationary and death phases. The assay was also tested on environmental samples collected during a small Pseudochattonella bloom in Denmark in March–April 2015. It was impossible to distinguish P. farcimen and P. verruculosa by light microscopy but qPCR showed both species were present. The two methods provided nearly identical cell numbers but the assay provided discrimination and enumeration of both species.     

Chromosome aberrations in individuals occupationally exposed to ethylene oxide, and in a large control population

Chromosome aberration frequencies in 61 employees potentially exposed to ethylene oxide (ETO) were compared with those in unexposed control groups. We studied 3 worksites with differing historical ambient levels of ETO. Within worksites, groups were classified as high potential exposed, low potential exposed, or controls. Further control groups including an off-site community control group were added to give a total of 304 control individuals. Blood samples were drawn several times over a 24-month period. Aberrations were analyzed in 100 cells per sample after culture for 48-51 h. Worksites I, II and III respectively represented increasing levels of potential ETO exposure. At worksites I and II, no consistent differences in aberration frequencies were found among groups. At worksite III aberration frequencies in potentially exposed individuals were significantly increased compared with controls. The frequencies of cells with aberrations were 5.6% for the 2 individuals in the high potential exposure category and 2.6% for 23 persons in the low potential exposure group. The overall frequency of cells with aberrations in the matched control individuals was 1.4%. In the total control group of 304 individuals we found significant increases in aberrations associated with smoking and with increasing age. We have also reported previously an association between sister-chromatid exchange (SCE) frequency and ETO exposure (Stolley et al., 1984). When aberration frequencies were compared with levels of SCEs there was only a weak overall association. The correlation was found in potentially exposed but not in control groups, and for any individual, one observation could not be used to predict the other.