Use of spectral vegetation indices derived from airborne hyperspectral imagery for detection of European corn borer infestation in Iowa corn plots

Eleven spectral vegetation indices that emphasize foliar plant pigments were calculated using airborne hyperspectral imagery and evaluated in 2004 and 2005 for their ability to detect experimental plots of corn manually inoculated with Ostrinia nubilalis (Hübner) neonate larvae. Manual inoculations were timed to simulate infestation of corn, Zea mays L., by first and second flights of adult O. nubilalis. The ability of spectral vegetation indices to detect O. nubilalis-inoculated plots improved as the growing season progressed, with multiple spectral vegetation indices able to identify infested plots in late August and early September. Our findings also indicate that for detecting O. nubilalis-related plant stress in corn, spectral vegetation indices targeting carotenoid and anthocyanin pigments are not as effective as those targeting chlorophyll. Analysis of image data suggests that feeding and stem boring by O. nubilalis larvae may increase the rate of plant senescence causing detectable differences in plant biomass and vigor when compared with control plots. Further, we identified an approximate time frame of 5-6 wk postinoculation, when spectral differences of manually inoculated "second" generation O. nubilalis plots seem to peak.     

Effects of drill cuttings on biogeochemical fluxes and macrobenthos of marine sediments

Experimental work was performed on drill cuttings sampled from off-shore drilling operations. The cuttings contained remnants of two different types of drilling muds: a water-ilmenite based mud and an olefin-barite based mud. In a pilot experiment, a gradient of up to 65 mm thick layers of water-ilmenite based cuttings were added to 78 cm² core samples. In another set-up, 3 mm layers of water-ilmenite and olefin-barite based cuttings were added to replicate 1000 cm² box-core samples with natural benthic communities transferred from the Oslofjord, S.E. Norway. Boxes with no addition and addition of 3 mm “clean” sediment were used for control. Increased consumption of oxygen and nitrate indicated the presence of degradable organic phases in both mud systems. The release of silicate showed a general decrease with increasing thickness of the cuttings layer, but maximum rates in the 3.1 mm treatment indicated increased bioturbation at low and moderate doses. The initial (field) composition of the macrobenthic communities was maintained throughout the 3 months experimental period, and at community level, no significant difference was observed between the four treatments at the end of the exposure period. However, after grouping the treatments into “clean” (untreated control and 3 mm clean sediment) and “cuttings” (3 mm water-ilmenite and 3 mm olefin-barite based cuttings), multivariate statistical analyses revealed a significant difference in community composition between clean and cuttings treatments, and three taxa showed significantly reduced abundances in the cuttings treatments. Chemical toxicity of mud components is assumed to be small, and the observed effect was more likely a result of physical properties such as the size or shape of cuttings particles.     

Influence of aging on the in vivo properties of human patellar tendon

Tendons are important for optimal muscle force transfer to bone and play a key role in functional ability. Changes in tendon properties with aging could contribute to declines in physical function commonly associated with aging. We investigated the in vivo mechanical properties of the patellar tendon in 37 men and women [11 young (27 +/- 1 yr) and 26 old (65 +/- 1 yr)] using ultrasonography and magnetic resonance imaging (MRI). Patella displacement relative to the tibia was monitored with ultrasonography during ramped isometric contractions of the knee extensors, and MRI was used to determine tendon cross-sectional area (CSA) and signal intensity. At peak force, patellar tendon deformation, stress, and strain were 13 (P = 0.05), 19, and 12% less in old compared with young (P < 0.05). Additionally, deformation, stiffness, stress, CSA, and length were 18, 35, 41, 28, and 11% greater (P < 0.05), respectively, in men compared with women. After normalization of mechanical properties to a common force, no age differences were apparent; however, stress and strain were 26 and 22% higher, respectively, in women compared with men (P < 0.05). CSA and signal intensity decreased 12 and 24%, respectively, with aging (P < 0.05) in the midregion of the tendon. These data suggest that differences in patellar tendon in vivo mechanical properties with aging are more related to force output rather than an age effect. In contrast, the decrease in signal intensity indirectly suggests that the internal milieu of the tendon is altered with aging; however, the physiological and functional consequence of this finding requires further study.     

Protozoal digestion of coat-defective Bacillus subtilis spores produces "rinds" composed of insoluble coat protein

The Bacillus subtilis spore coat is a multilayer, proteinaceous structure that consists of more than 50 proteins. Located on the surface of the spore, the coat provides resistance to potentially toxic molecules as well as to predation by the protozoan Tetrahymena thermophila. When coat-defective spores are fed to Tetrahymena, the spores are readily digested. However, a residue termed a "rind" that looks like coat material remains. As observed with a phase-contrast microscope, the rinds are spherical or hemispherical structures that appear to be devoid of internal contents. Atomic force microscopy and chemical analyses showed that (i) the rinds are composed of insoluble protein largely derived from both outer and inner spore coat layers, (ii) the amorphous layer of the outer coat is largely responsible for providing spore resistance to protozoal digestion, and (iii) the rinds and intact spores do not contain significant levels of silicon.     

Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels

Microbial enumeration, 16S rRNA gene clone libraries, and chemical analysis were used to evaluate the in situ biological reduction and immobilization of uranium(VI) in a long-term experiment (more than 2 years) conducted at a highly uranium-contaminated site (up to 60 mg/liter and 800 mg/kg solids) of the U.S. Department of Energy in Oak Ridge, TN. Bioreduction was achieved by conditioning groundwater above ground and then stimulating growth of denitrifying, Fe(III)-reducing, and sulfate-reducing bacteria in situ through weekly injection of ethanol into the subsurface. After nearly 2 years of intermittent injection of ethanol, aqueous U levels fell below the U.S. Environmental Protection Agency maximum contaminant level for drinking water and groundwater (<30 microg/liter or 0.126 microM). Sediment microbial communities from the treatment zone were compared with those from a control well without biostimulation. Most-probable-number estimations indicated that microorganisms implicated in bioremediation accumulated in the sediments of the treatment zone but were either absent or in very low numbers in an untreated control area. Organisms belonging to genera known to include U(VI) reducers were detected, including Desulfovibrio, Geobacter, Anaeromyxobacter, Desulfosporosinus, and Acidovorax spp. The predominant sulfate-reducing bacterial species were Desulfovibrio spp., while the iron reducers were represented by Ferribacterium spp. and Geothrix spp. Diversity-based clustering revealed differences between treated and untreated zones and also within samples of the treated area. Spatial differences in community structure within the treatment zone were likely related to the hydraulic pathway and to electron donor metabolism during biostimulation.     

Molecular cloning, characterization and regulation of two different NADH-glutamate synthase cDNAs in bean nodules

NADH-dependent glutamate synthase (NADH-GOGAT) is a key enzyme in primary ammonia assimilation in Phaseolus vulgaris nodules. Two different types of cDNA clones of PvNADH-GOGAT were isolated from the nodule cDNA libraries. The full-length cDNA clones of PvNADH-GOGAT-I (7.4 kb) and PvNADH-GOGAT-II (7.0 kb), which displayed an 83% homology between them, were isolated using cDNA library screening, 'cDNA library walking' and RT-PCR amplification. Southern analysis employing specific 5' cDNA probes derived from PvNADH-GOGAT-I and PvNADH-GOGAT-II indicated the existence of a single copy of each gene in the bean genome. Both these proteins contain ∼100 amino acid sequences theoretically addressing each isoenzyme to different subcellular compartments. RT-PCR analysis indicated that PvNADH-GOGAT-II expression is higher than PvNADH-GOGAT-I during nodule development. Expression analysis by RT-PCR also revealed that both of these genes are differentially regulated by sucrose. On the other hand, the expression of PvNADH-GOGAT-I , but not PvNADH-GOGAT-II, was inhibited with nitrogen compounds. In situ hybridization and promoter expression analyses demonstrated that the NADH-GOGAT-I and -II genes are differentially expressed in bean root and nodule tissues. In silico analyses of the NADH-GOGAT promoters revealed the presence of potential cis elements in them that could mediate differential tissue-specific, and sugar and amino acid responsive expression of these genes.     

Developmentally acquired PKA localisation in mouse oocytes and embryos

Localisation of Protein Kinase A (PKA) by A-Kinase Anchoring Proteins (AKAPs) is known to coordinate localised signalling complexes that target cAMP-mediated signalling to specific cellular sub-domains. The cAMP PKA signalling pathway is implicated in both meiotic arrest and meiotic resumption, thus spatio-temporal changes in PKA localisation during development may determine the oocytes response to changes in cAMP. In this study we aim to establish whether changes in PKA localisation occur during oocyte and early embryo development.Using fluorescently-labelled PKA constructs we show that in meiotically incompetent oocytes PKA is distributed throughout the cytoplasm and shows no punctuate localisation. As meiotic competence is acquired, PKA associates with mitochondria. Immature germinal vesicle (GV) stage oocytes show an aggregation of PKA around the GV and PKA remains co-localised with mitochondria throughout oocyte maturation. After fertilisation, the punctuate, mitochondrial distribution was lost, such that by the 2-cell stage there was no evidence of PKA localisation. RT-PCR and Western blotting revealed two candidate AKAPs that are known to be targeted to mitochondria, AKAP1 and D-AKAP2. In summary these data show a dynamic regulation of PKA localisation during oocyte and early embryo development.     

Nonparametric variance estimation in the analysis of microarray data: a measurement error approach

We investigate the effects of measurement error on the estimationof nonparametric variance functions. We show that either ignoringmeasurement error or direct application of the simulation extrapolation,SIMEX, method leads to inconsistent estimators. Nevertheless,the direct SIMEX method can reduce bias relative to a naiveestimator. We further propose a permutation SIMEX method thatleads to consistent estimators in theory. The performance ofboth the SIMEX methods depends on approximations to the exactextrapolants. Simulations show that both the SIMEX methods performbetter than ignoring measurement error. The methodology is illustratedusing microarray data from colon cancer patients.     

Joint modelling of paired sparse functional data using principal components

We propose a modelling framework to study the relationship betweentwo paired longitudinally observed variables. The data for eachvariable are viewed as smooth curves measured at discrete time-pointsplus random errors. While the curves for each variable are summarizedusing a few important principal components, the associationof the two longitudinal variables is modelled through the associationof the principal component scores. We use penalized splinesto model the mean curves and the principal component curves,and cast the proposed model into a mixed-effects model frameworkfor model fitting, prediction and inference. The proposed methodcan be applied in the difficult case in which the measurementtimes are irregular and sparse and may differ widely acrossindividuals. Use of functional principal components enhancesmodel interpretation and improves statistical and numericalstability of the parameter estimates.