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This chapter provides a guide to analyzing gene function using DNA microarrays. First, I discuss the design and interpretation of experiments where gene expression levels in mutant and wild-type strains are compared. I then provide a detailed description of the protocols for isolating mRNA from yeast cells, converting the RNA into dye-labeled cDNA, and hybridizing these samples to a microarray. Finally, I discuss methods for washing, scanning, and analyzing the arrays. Emphasis is placed on describing approaches and techniques that help to minimize the artifacts and noise that so often plague microarray data.

Evolution of resistance by pests can reduce the efficacy oftransgenic crops that produce insecticidal toxins from the bacterium Bacillus thuringiensis Berliner (Bt). In conjunction with refuges of non-Bt host plants, fitness costs can delay the evolution of resistance. Furthermore, fitness costs often vary with ecological conditions, suggesting that agricultural landscapes can be manipulated to magnify fitness costs and thereby prolong the efficacy of Bt crops. In the current study, we tested the effects of four species of entomopathogenic nematodes (Steinernematidae and Heterorhabditidae) on the magnitude and dominance of fitness costs of resistance to Bt toxin CrylAc in pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae). For more than a decade, field populations of pink bollworm in the United States have remained susceptible to Bt cotton Gossypium hirsutum L. producing CrylAc; however, we used laboratory strains that had a mixture of susceptible and resistant individuals. In laboratory experiments, dominant fitness costs were imposed by the nematode Steinernema riobrave Cabanillas, Poinar, and Raulston but no fitness costs were imposed by Steinernema carpocapsae Weiser, Steinernema sp. (ML18 strain), or Heterorhabditis sonorensis Stock, Rivera-Orduño, and Flores-Lara. In computer simulations, evolution of resistance to Cry1Ac by pink bollworm was substantially delayed by treating some non-Bt cotton refuge fields with nematodes that imposed a dominant fitness cost, similar to the cost observed in laboratory experiments with S. riobrave. Based on the results here and in related studies, we conclude that entomopathogenic nematodes could bolster insect resistance management, but the success of this approach will depend on selecting the appropriate species of nematode and environment, as fitness costs were magnified by only two of five species evaluated and also depended on environmental factors.

BACKGROUND:
Characterizing the spatial patterns of gene flow from transgenic crops is challenging, making it difficult to design containment strategies for markets that regulate the adventitious presence of transgenes. Insecticidal Bacillus thuringiensis (Bt) cotton is planted on millions of hectares annually and is a potential source of transgene flow.

METHODOLOGY/PRINCIPAL FINDINGS:
Here we monitored 15 non-Bt cotton (Gossypium hirsutum, L.) seed production fields (some transgenic for herbicide resistance, some not) for gene flow of the Bt cotton cry1Ac transgene. We investigated seed-mediated gene flow, which yields adventitious Bt cotton plants, and pollen-mediated gene flow, which generates outcrossed seeds. A spatially-explicit statistical analysis was used to quantify the effects of nearby Bt and non-Bt cotton fields at various spatial scales, along with the effects of pollinator abundance and adventitious Bt plants in fields, on pollen-mediated gene flow. Adventitious Bt cotton plants, resulting from seed bags and planting error, comprised over 15% of plants sampled from the edges of three seed production fields. In contrast, pollen-mediated gene flow affected less than 1% of the seed sampled from field edges. Variation in outcrossing was better explained by the area of Bt cotton fields within 750 m of the seed production fields than by the area of Bt cotton within larger or smaller spatial scales. Variation in outcrossing was also positively associated with the abundance of honey bees.

CONCLUSIONS/SIGNIFICANCE:
A comparison of statistical methods showed that our spatially-explicit analysis was more powerful for understanding the effects of surrounding fields than customary models based on distance. Given the low rates of pollen-mediated gene flow observed in this study, we conclude that careful planting and screening of seeds could be more important than field spacing for limiting gene flow.

Genetically engineered crops that produce insecticidal toxins from Bacillus thuringiensis (Bt) are grown widely for pest control. However, insect adaptation can reduce the toxins' efficacy. The predominant strategy for delaying pest resistance to Bt crops requires refuges of non-Bt host plants to provide susceptible insects to mate with resistant insects. Variable farmer compliance is one of the limitations of this approach. Here we report the benefits of an alternative strategy where sterile insects are released to mate with resistant insects and refuges are scarce or absent. Computer simulations show that this approach works in principle against pests with recessive or dominant inheritance of resistance. During a large-scale, four-year field deployment of this strategy in Arizona, resistance of pink bollworm (Pectinophora gossypiella) to Bt cotton did not increase. A multitactic eradication program that included the release of sterile moths reduced pink bollworm abundance by >99%, while eliminating insecticide sprays against this key invasive pest.

1. Negative interspecific interactions, such as resource competition or reproductive interference, can lead to the displacement of species (species exclusion). 2. Here, we investigated the effect of life history, mating behaviour and adaptation to insecticides on species exclusion between cryptic whitefly species that make up the Bemisia tabaci species complex. We conducted population cage experiments independently in China, Australia, the United States and Israel to observe patterns of species exclusion between an invasive species commonly referred to as the B biotype and three other species commonly known as biotypes ZHJ1, AN and Q. 3. Although experimental conditions and species varied between regions, we were able to predict the observed patterns of exclusion in each region using a stochastic model that incorporated data on development time, mating behaviour and resistance to insecticides. 4. Between-species variation in mating behaviour was a more significant factor affecting species exclusion than variation in development time. Specifically, the ability of B to copulate more effectively than other species resulted in a faster rate of population increase for B, as well as a reduced rate of population growth for other species, leading to species exclusion. The greater ability of B to evolve resistance to insecticides also contributed to exclusion of other species in some cases. 5. Results indicate that an integrative analysis of the consequences of variation in life-history traits, mating behaviours and adaption to insecticides could provide a robust framework for predicting species exclusion following whitefly invasions.

Current gated radiation therapy starts with simulation 4DCT images of a patient with lung cancer. We propose a method to confirm the phase of 4DCT for planning and setup position at the time of treatment. An intensity-based rigid algorithm was developed in this work to register an orthogonal set of on-board projection X-ray images with each phase of the 4DCT. Multiple DRRs for one of ten 4DCT phases are first generated and the correlation coefficient (CC) between the projection X-ray image and each DRR is computed. The maximum value of CC for the phase is found via a simulated annealing optimization process. The whole process repeats for all ten phases. The 4DCT phase that has the highest CC is identified as the breathing phase of the X-ray. The phase verification process is validated by a moving phantom study. Thus, the method may be used to independently confirm the correspondence between the gating phase at the times of 4DCT simulation and radiotherapy delivery. When the intended X-ray phase and actual gating phase are consistent, the registration of the DRRs and the projection images may also yield the values of patient shifts for treatment setup. This method could serve as the 4D analog of the conventional setup film as it provides both verification of the specific phase at the time of treatment and isocenter positioning shifts for treatment delivery.

Elucidating the mechanisms by which honey bees process pollen vs. protein supplements are important in the generation of artificial diets needed to sustain managed honeybees. We measured the effects of diet on protein concentration, hypopharyngeal gland development and virus titers in worker honey bees fed either pollen, a protein supplement (MegaBee), or a protein-free diet of sugar syrup. Workers consumed more pollen than protein supplement, but protein amounts and size of hypopharyngeal gland acini did not differ between the two feeding treatments. Bees fed sugar syrup alone had lower protein concentrations and smaller hypopharyngeal glands compared with the other feeding treatments especially as the bees aged. Deformed wing virus was detected in workers at the start of a trial. The virus concentrations increased as bees aged and were highest in those fed sugar syrup and lowest in bees fed pollen. Overall results suggest a connection between diet, protein levels and immune response and indicate that colony losses might be reduced by alleviating protein stress through supplemental feeding.

We report integration of an InAs quantum well micro-Hall magnetic sensor with microfluidics and real-time detection of moving superparamagnetic beads. Beads moving within and around the Hall cross area result in positive and negative Hall voltage signals respectively. Relative magnitudes and polarities of the signals measured for a random distribution of immobilized beads over the sensor are in good agreement with calculated values and explain consistently the shape of the dynamic signal.

Understanding the influence of total body fat mass (TBFM) on bone during the peri-pubertal years is critical for the development of future interventions aimed at improving bone strength and reducing fracture risk. Thus, we evaluated the relationship of TBFM to volumetric bone mineral density (vBMD), geometry, and strength at metaphyseal and diaphyseal sites of the femur and tibia of young girls. Data from 396 girls aged 8-13 years from the "Jump-In: Building Better Bones" study were analyzed. Bone parameters were assessed using peripheral quantitative computed tomography (pQCT) at the 4% and 20% distal femur and 4% and 66% distal tibia of the non-dominant leg. Bone parameters at the 4% sites included trabecular vBMD, periosteal circumference, and bone strength index (BSI), while at the 20% femur and 66% tibia, parameters included cortical vBMD, periosteal circumference, and strength-strain index (SSI). Multiple linear regression analyses were used to assess associations between bone parameters and TBFM, controlling for muscle cross-sectional area (MCSA). Regression analyses were then repeated with maturity, bone length, physical activity, and ethnicity as additional covariates. Analysis of covariance (ANCOVA) was used to compare bone parameters among tertiles of TBFM. In regression models with TBFM and MCSA, associations between TBFM and bone parameters at all sites were not significant. TBFM explained very little variance in all bone parameters (0.2-2.3%). In contrast, MCSA was strongly related (p<0.001) to all bone parameters, except cortical vBMD. The addition of maturity, bone length, physical activity, and ethnicity did not alter the relationship between TBFM and bone parameters. With bone parameters expressed relative to total body mass, ANCOVA showed that all outcomes were significantly (p<0.001) greater in the lowest compared to the middle and highest tertiles of TBFM. Although TBFM is correlated with femur and tibia vBMD, periosteal circumference, and strength in young girls, this relationship is significantly attenuated after adjustment for MCSA. Nevertheless, girls with higher TBFM relative to body mass have markedly diminished vBMD, geometry, and bone strength at metaphyseal and diaphyseal sites of the femur and tibia.

OBJECTIVES:
To prospectively examine the relationship between anemia and incident fractures of the hip, spine, and all skeletal sites in women from diverse racial and ethnic backgrounds enrolled in the Women's Health Initiative (WHI) Observational Study and Clinical Trials.

DESIGN:
Prospective cohort study.

SETTING:
Forty WHI clinical centers across the United States.

PARTICIPANTS:
Postmenopausal women (n=160,080), mean age 63.2±7.2, were recruited and followed for an average of 7.8 years.

MEASUREMENTS:
Anemia was defined as hemoglobin levels at baseline less than 12 g/dL. All fractures were self-reported. Trained physicians further confirmed hip fractures using medical records.

RESULTS:
Eight thousand seven hundred thirty-nine of the participants (5.5%) were anemic. The age-adjusted incidence rate of hip fractures per 10,000 person-years was 21.4 in women with anemia and 15.0 in women without anemia; higher incidence rates for spine and all fractures were also observed in anemic women. After multiple covariates were included in the Cox proportional hazards models, significantly greater fracture risk associated with anemia still existed, as demonstrated by hazard ratios of fractures associated with anemia of 1.38 (95% confidence interval (CI)=1.13-1.68) for hip, 1.30 (95% CI=1.09-1.55) for spine, and 1.07 (95% CI=1.01-1.14) for all types. No significant racial or ethnic difference was found in these relationships.

CONCLUSION:
A significantly greater fracture risk was observed in multiethnic postmenopausal women with anemia. Given the high prevalence of anemia in the elderly population, it is important to better understand the relationship and mechanisms linking anemia to fracture risk.

The chemopreventive and antitumor properties of perillyl alcohol (POH) that were studied preclinically indicate that topical POH inhibits both UVB-induced murine skin carcinogenesis (squamous cell tumor models) and 7,12-dimethylbenz(a)anthracene-induced murine melanoma (transgenic models involving tyrosinase-driven Ras). A previous phase 1 clinical trial in participants with normal-appearing skin showed that topical POH cream was well tolerated at a dose of 0.76% (w/w). Here, we performed a 3-month, double-blind, randomized, placebo-controlled phase 2a trial of two different doses of topical POH in individuals with sun-damaged skin. Participants applied POH cream twice daily to each dorsal forearm. Baseline and end-of-study biopsies were taken from each participant to evaluate whether the topical application of POH was effective in reversing actinic damage as evidenced by normalization of quantitative skin histopathologic scores and change in nuclear chromatin pattern as measured by karyometric analysis. There was a borderline reduction in the histopathologic score of the lower-dose POH group compared with the placebo (P = 0.1), but this was not observed in the high-dose group. However, in the high-dose group, a statistically significant reduction in the proportion of nuclei deviating from normal was observed by the use of karyometric analysis (P < 0.01). There was no statistical significance shown in the lower-dose group. No changes were observed in p53 expression, cellular proliferation (by proliferating cell nuclear antigen expression), or apoptosis in either treatment group compared with the placebo group. These results suggest that whereas our karyometric analyses can detect a modest effect of POH in sun-damaged skin, improved delivery into the epidermis may be necessary.

Evaporative deposition from a sessile drop is a simple and appealing way to deposit materials on a surface. In this work, we deposit living, motile colloidal particles (bacteria) on mica from drops of aqueous solution. We show for the first time that it is possible to produce a continuous variation in the deposition pattern from ring deposits to cellular pattern deposits by incremental changes in surface wettability which we achieve by timed exposure of the mica surface to the atmosphere. We show that it is possible to change the contact angle of the drop from less than 5 degrees to near 20 degrees by choice of atmospheric exposure time. This controls the extent of drop spreading, which in turn determines the architecture of the deposition pattern.

We present a Green's function-based perturbative approach to solving nonlinear reaction-diffusion problems in networks of endothelial cells. We focus on a single component (Ca2+), piecewise nonlinear model of endoplasmic calcium dynamics and trans-membrane diffusion. The decoupling between nonlinear reaction dynamics and the linear diffusion enables the calculation of the diffusion part of the Green's function for network of cells with nontrivial topologies. We verify analytically and then numerically that our approach leads to the known transition from propagation of calcium front to failure of propagation when the diffusion rate is varied relative to the reaction rates. We then derive the Green's function for a semi-infinite chain of cells with various boundary conditions. We show that the calcium dynamics of cells in the vicinity of the end of the semi-infinite chain is strongly dependent on the boundary conditions. The behavior of the semi-infinite chain with absorbing boundary conditions, a simple model of a multicellular structure with an end in contact with the extracellular matrix, suggests behavioral differentiation between cells at the end and cells embedded within the chain.

Signal conduction between endothelial cells along the walls of vessels appears to play an important role in circulatory function. A recently developed approach to calculate analytically the spectrum of propagating compositional waves in models of multicellular architectures is extended to study putative signal conduction dynamics across networks of endothelial cells. Here, compositional waves originate from negative feedback loops, such as between Ca2+ and inositol triphosphate (IP3) in endothelial cells, and are shaped by their connection topologies. We consider models of networks constituted of a main chain of endothelial cells and multiple side chains. The resulting transmission spectra encode information concerning the position and size of the side branches in the form of gaps. This observation suggests that endothelial cell networks may be able to "communicate" information regarding long-range order in their architecture.

In this study we report crystallization of Taxol in pure water, aqueous solutions containing tubulin proteins and tubulin-containing agarose gels. We show that crystallization of Taxol in tubulin-free aqueous solutions occurs by the formation of sheaf-like crystals, while in the presence of tubulin Taxol crystallizes in the form of spherulites. Whereas sheaves are characteristic for crystals formed by homogeneous nucleation, the spherical symmetry of the Taxol crystal formed in the presence of tubulin suggests they result from heterogeneous nucleation. To explain the formation of tubulin-Taxol nuclei we suggest a new, secondary Taxol-binding site within the tubulin heterodimer. Contrary to the known binding site, where the Taxol molecule is almost completely buried in the protein, the Taxol molecule in the secondary binding site is partially exposed to the solution and may serve as a bridge, connecting other Taxol molecules. Results presented in this work are important for in vivo and in vitro microtubule studies due to the possibility of mistaking these Taxol spherulites for microtubule asters, moreover a novel variable is proposed in the study of cells treated with Taxol for cancer treatment via sequestration of tubulin.

Previous work showed that retaining residual ovarian tissue protects young mice from accelerated bone loss following ovarian failure. The present study was designed to determine whether this protection is also present in aged animals. Aged (9-12 months) C57BL/6Hsd female mice were divided into: CON (vehicle), VCD (160 mg/kg; 15d), or OVX (ovariectomized). Lumbar BMD was monitored by DXA and μCT used to assess vertebral microarchitecture. BMD was not different between VCD and CON at any time point but was lower (P < .05) than baseline, starting 1 month after ovarian failure in VCD and OVX mice. Following μCT analysis there were no differences between CON and VCD, but OVX mice had lower bone volume fraction, trabecular thickness, and a trend for decreased connectivity density. These findings provide evidence that retention of residual ovarian tissue may protect aged follicle-depleted mice from accelerated bone loss to a lesser extent than that observed in young mice.

Extracts prepared from turmeric (Curcuma longa L., [Zingiberaceae]) containing bioactive phenolic curcuminoids were evaluated for bone-protective effects in a hypogonadal rat model of postmenopausal osteoporosis. Three-month female Sprague-Dawley rats were ovariectomized (OVX) and treated with a chemically complex turmeric fraction (41% curcuminoids by weight) or a curcuminoid-enriched turmeric fraction (94% curcuminoids by weight), both dosed at 60 mg/kg 3x per week, or vehicle alone. Effects of two months of treatment on OVX-induced bone loss were followed prospectively by serial assessment of bone mineral density (BMD) of the distal femur using dual-energy X-ray absorptiometry (DXA), while treatment effects on trabecular bone microarchitecture were assessed at two months by microcomputerized tomography (microCT). Chemically complex turmeric did not prevent bone loss, however, the curcuminoid-enriched turmeric prevented up to 50% of OVX-induced loss of trabecular bone and also preserved the number and connectedness of the strut-like trabeculae. These results suggest that turmeric may have bone-protective effects but that extract composition is a critical factor.

Turmeric (Curcuma longa L., Zingiberaceae) rhizomes contain two classes of secondary metabolites, curcuminoids and the less well-studied essential oils. Having previously identified potent anti-arthritic effects of the curcuminoids in turmeric extracts in an animal model of rheumatoid arthritis (RA), studies were undertaken to determine whether the turmeric essential oils (TEO) were also joint protective using the same experimental model. Crude or refined TEO extracts dramatically inhibited joint swelling (90-100% inhibition) in female rats with streptococcal cell wall (SCW)-induced arthritis when extracts were administered via intraperitoneal injection to maximize uniform delivery. However, this anti-arthritic effect was accompanied by significant morbidity and mortality. Oral administration of a 20-fold higher dose TEO was nontoxic, but only mildly joint-protective (20% inhibition). These results do not support the isolated use of TEO for arthritis treatment but, instead, identify potential safety concerns in vertebrates exposed to TEO.

Invasive species may be released from consumption by their native herbivores in novel habitats and thereby experience higher fitness relative to native species. However, few studies have examined release from herbivory as a mechanism of invasion in oceanic island systems, which have experienced particularly high loss of native species due to the invasion of non-native animal and plant species. We surveyed putative defensive traits and leaf damage rates in 19 pairs of taxonomically related invasive and native species in Hawaii, representing a broad taxonomic diversity. Leaf damage by insects and pathogens was monitored in both wet and dry seasons. We found that native species had higher leaf damage rates than invasive species, but only during the dry season. However, damage rates across native and invasive species averaged only 2% of leaf area. Native species generally displayed high levels of structural defense (leaf toughness and leaf thickness, but not leaf trichome density) while native and invasive species displayed similar levels of chemical defenses (total phenolics). A defense index, which integrated all putative defense traits, was significantly higher for native species, suggesting that native species may allocate fewer resources to growth and reproduction than do invasive species. Thus, our data support the idea that invasive species allocate fewer resources to defense traits, allowing them to outperform native species through increased growth and reproduction. While strong impacts of herbivores on invasion are not supported by the low damage rates we observed on mature plants, population-level studies that monitor how herbivores influence recruitment, mortality, and competitive outcomes are needed to accurately address how herbivores influence invasion in Hawaii.

Entamoeba histolytica is the etiological agent of amoebiasis, the second cause of global morbidity and mortality due to parasitic diseases in humans. In approximately 1% of the cases, amoebas penetrate the intestinal mucosa and spread to other organs, producing extra-intestinal lesions, among which amoebic liver abscess (ALA) is the most common. To study ALA, in vivo and in vitro models are used. However, animal models may pose ethical issues, and are time-consuming and costly; and cell cultures represent isolated cellular lineages. The present study reports the infection of precision-cut hamster liver slices with Entamoeba histolytica trophozoites. The infection time-course, including tissue damage, parallels findings previously reported in the animal model. At the same time amoebic virulence factors were detected in the infected slices. This new model to study ALA is simple and reproducible, and employs less than 1/3 of the hamsters required for in vivo analyses.

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