Showing papers by "University of Arizona published in 2002"

Salt and drought stress signal transduction in plants

Abstract: Salt and drought stress signal transduction consists of ionic and osmotic homeostasis signaling pathways, detoxification (i.e., damage control and repair) response pathways, and pathways for growth regulation. The ionic aspect of salt stress is signaled via the SOS pathway where a calcium-responsive SOS3-SOS2 protein kinase complex controls the expression and activity of ion transporters such as SOS1. Osmotic stress activates several protein kinases including mitogen-activated kinases, which may mediate osmotic homeostasis and/or detoxification responses. A number of phospholipid systems are activated by osmotic stress, generating a diverse array of messenger molecules, some of which may function upstream of the osmotic stress-activated protein kinases. Abscisic acid biosynthesis is regulated by osmotic stress at multiple steps. Both ABA-dependent and -independent osmotic stress signaling first modify constitutively expressed transcription factors, leading to the expression of early response transcriptional activators, which then activate downstream stress tolerance effector genes.

The Use of Molecular Profiling to Predict Survival after Chemotherapy for Diffuse Large-B-Cell Lymphoma

Abstract: Background The survival of patients with diffuse large-B-cell lymphoma after chemotherapy is influenced by molecular features of the tumors. We used the gene-expression profiles of these lymphomas to develop a molecular predictor of survival. Methods Biopsy samples of diffuse large-B-cell lymphoma from 240 patients were examined for gene expression with the use of DNA microarrays and analyzed for genomic abnormalities. Subgroups with distinctive gene-expression profiles were defined on the basis of hierarchical clustering. A molecular predictor of risk was constructed with the use of genes with expression patterns that were associated with survival in a preliminary group of 160 patients and was then tested in a validation group of 80 patients. The accuracy of this predictor was compared with that of the international prognostic index. Results Three gene-expression subgroups — germinal-center B-cell–like, activated B-cell–like, and type 3 diffuse large-B-cell lymphoma — were identified. Two common oncogeni...

Performance-effective and low-complexity task scheduling for heterogeneous computing

Abstract: Efficient application scheduling is critical for achieving high performance in heterogeneous computing environments. The application scheduling problem has been shown to be NP-complete in general cases as well as in several restricted cases. Because of its key importance, this problem has been extensively studied and various algorithms have been proposed in the literature which are mainly for systems with homogeneous processors. Although there are a few algorithms in the literature for heterogeneous processors, they usually require significantly high scheduling costs and they may not deliver good quality schedules with lower costs. In this paper, we present two novel scheduling algorithms for a bounded number of heterogeneous processors with an objective to simultaneously meet high performance and fast scheduling time, which are called the Heterogeneous Earliest-Finish-Time (HEFT) algorithm and the Critical-Path-on-a-Processor (CPOP) algorithm. The HEFT algorithm selects the task with the highest upward rank value at each step and assigns the selected task to the processor, which minimizes its earliest finish time with an insertion-based approach. On the other hand, the CPOP algorithm uses the summation of upward and downward rank values for prioritizing tasks. Another difference is in the processor selection phase, which schedules the critical tasks onto the processor that minimizes the total execution time of the critical tasks. In order to provide a robust and unbiased comparison with the related work, a parametric graph generator was designed to generate weighted directed acyclic graphs with various characteristics. The comparison study, based on both randomly generated graphs and the graphs of some real applications, shows that our scheduling algorithms significantly surpass previous approaches in terms of both quality and cost of schedules, which are mainly presented with schedule length ratio, speedup, frequency of best results, and average scheduling time metrics.

Detailed structural decomposition of galaxy images

Abstract: We present a two-dimensional fitting algorithm (GALFIT) designed to extract structural components from galaxy images, with emphasis on closely modeling light profiles of spatially well-resolved, nearby galaxies observed with the Hubble Space Telescope. Our algorithm improves on previous techniques in two areas: by being able to simultaneously fit a galaxy with an arbitrary number of components and with optimization in computation speed, suited for working on large galaxy images. We use two-dimensional models such as the "Nuker" law, the Sersic (de Vaucouleurs) profile, an exponential disk, and Gaussian or Moffat functions. The azimuthal shapes are generalized ellipses that can fit disky and boxy components. Some potential applications of our program include: standard modeling of global galaxy profiles; extracting bars, stellar disks, double nuclei, and compact nuclear sources; and measuring absolute dust extinction or surface brightness fluctuations after removing the galaxy model. When examined in detail, we find that even simple looking galaxies generally require at least three components to be modeled accurately, rather than the one or two components more often employed. Many galaxies with complex isophotes, ellipticity changes, and position angle twists can be modeled accurately in two dimensions. We illustrate this by way of 11 case studies, which include regular and barred spiral galaxies, highly disky lenticular galaxies, and elliptical galaxies displaying various levels of complexities. A useful extension of this algorithm is to accurately extract nuclear point sources in galaxies. We compare two-dimensional and one-dimensional extraction techniques on simulated images of galaxies having nuclear slopes with different degrees of cuspiness, and we then illustrate the application of the program to several examples of nearby galaxies with weak nuclei.

Sloan digital sky survey: Early data release

Abstract: The Sloan Digital Sky Survey (SDSS) is an imaging and spectroscopic survey that will eventually cover approximately one-quarter of the celestial sphere and collect spectra of ≈106 galaxies, 100,000 quasars, 30,000 stars, and 30,000 serendipity targets. In 2001 June, the SDSS released to the general astronomical community its early data release, roughly 462 deg2 of imaging data including almost 14 million detected objects and 54,008 follow-up spectra. The imaging data were collected in drift-scan mode in five bandpasses (u, g, r, i, and z); our 95% completeness limits for stars are 22.0, 22.2, 22.2, 21.3, and 20.5, respectively. The photometric calibration is reproducible to 5%, 3%, 3%, 3%, and 5%, respectively. The spectra are flux- and wavelength-calibrated, with 4096 pixels from 3800 to 9200 A at R ≈ 1800. We present the means by which these data are distributed to the astronomical community, descriptions of the hardware used to obtain the data, the software used for processing the data, the measured quantities for each observed object, and an overview of the properties of this data set.

Cell Signaling during Cold, Drought, and Salt Stress

Abstract: Low temperature, drought, and high salinity are common stress conditions that adversely affect plant growth and crop production. The cellular and molecular responses of plants to environmental stress have been studied intensively ([Thomashow, 1999][1]; [Hasegawa et al., 2000][2]). Understanding the

Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription.

Abstract: The nuclease hypersensitivity element III1 upstream of the P1 promoter of c-MYC controls 85–90% of the transcriptional activation of this gene. We have demonstrated that the purine-rich strand of the DNA in this region can form two different intramolecular G-quadruplex structures, only one of which seems to be biologically relevant. This biologically relevant structure is the kinetically favored chair-form G-quadruplex, which is destabilized when mutated with a single G → A transition, resulting in a 3-fold increase in basal transcriptional activity of the c-MYC promoter. The cationic porphyrin TMPyP4, which has been shown to stabilize this G-quadruplex structure, is able to suppress further c-MYC transcriptional activation. These results provide compelling evidence that a specific G-quadruplex structure formed in the c-MYC promoter region functions as a transcriptional repressor element. Furthermore, we establish the principle that c-MYC transcription can be controlled by ligand-mediated G-quadruplex stabilization.

American Cancer Society Guidelines on Nutrition and Physical Activity for Cancer Prevention: Reducing the Risk of Cancer with Healthy Food Choices and Physical Activity

Abstract: The American Cancer Society (ACS) publishes Nutrition and Physical Activity Guidelines to serve as a foundation for its communication, policy, and community strategies and ultimately, to affect dietary and physical activity patterns among Americans. These Guidelines, published every 5 years, are developed by a national panel of experts in cancer research, prevention, epidemiology, public health, and policy, and as such, they represent the most current scientific evidence related to dietary and activity patterns and cancer risk. The ACS Guidelines include recommendations for individual choices regarding diet and physical activity patterns, but those choices occur within a community context that either facilitates or interferes with healthy behaviors. Community efforts are essential to create a social environment that promotes healthy food choices and physical activity. Therefore, this committee presents one key recommendation for community action to accompany the four recommendations for individual choices to reduce cancer risk. This recommendation for community action recognizes that a supportive social environment is indispensable if individuals at all levels of society are to have genuine opportunities to choose healthy behaviors. The ACS Guidelines are consistent with guidelines from the American Heart Association and the American Diabetes Association for the prevention of coronary heart disease and diabetes, as well as for general health promotion, as defined by the Department of Health and Human Services' 2005 Dietary Guidelines for Americans.

Spectroscopic Target Selection in the Sloan Digital Sky Survey: The Main Galaxy Sample

Abstract: We describe the algorithm that selects the main sample of galaxies for spectroscopy in the Sloan Digital Sky Survey (SDSS) from the photometric data obtained by the imaging survey. Galaxy photometric properties are measured using the Petrosian magnitude system, which measures flux in apertures determined by the shape of the surface brightness profile. The metric aperture used is essentially independent of cosmological surface brightness dimming, foreground extinction, sky brightness, and the galaxy central surface brightness. The main galaxy sample consists of galaxies with r-band Petrosian magnitudes r ≤ 17.77 and r-band Petrosian half-light surface brightnesses μ50 ≤ 24.5 mag arcsec-2. These cuts select about 90 galaxy targets per square degree, with a median redshift of 0.104. We carry out a number of tests to show that (1) our star-galaxy separation criterion is effective at eliminating nearly all stellar contamination while removing almost no genuine galaxies, (2) the fraction of galaxies eliminated by our surface brightness cut is very small (~0.1%), (3) the completeness of the sample is high, exceeding 99%, and (4) the reproducibility of target selection based on repeated imaging scans is consistent with the expected random photometric errors. The main cause of incompleteness is blending with saturated stars, which becomes more significant for brighter, larger galaxies. The SDSS spectra are of high enough signal-to-noise ratio (S/N > 4 per pixel) that essentially all targeted galaxies (99.9%) yield a reliable redshift (i.e., with statistical error less than 30 km s-1). About 6% of galaxies that satisfy the selection criteria are not observed because they have a companion closer than the 55'' minimum separation of spectroscopic fibers, but these galaxies can be accounted for in statistical analyses of clustering or galaxy properties. The uniformity and completeness of the galaxy sample make it ideal for studies of large-scale structure and the characteristics of the galaxy population in the local universe.

A Long-Term Hydrologically Based Dataset of Land Surface Fluxes and States for the Conterminous United States*

Abstract: A frequently encountered difficulty in assessing model-predicted land–atmosphere exchanges of moisture and energy is the absence of comprehensive observations to which model predictions can be compared at the spatial and temporal resolutions at which the models operate. Various methods have been used to evaluate the land surface schemes in coupled models, including comparisons of model-predicted evapotranspiration with values derived from atmospheric water balances, comparison of model-predicted energy and radiative fluxes with tower measurements during periods of intensive observations, comparison of model-predicted runoff with observed streamflow, and comparison of model predictions of soil moisture with spatial averages of point observations. While these approaches have provided useful model diagnostic information, the observation-based products used in the comparisons typically are inconsistent with the model variables with which they are compared—for example, observations are for points or a...

DNA and its associated processes as targets for cancer therapy

Abstract: DNA is the molecular target for many of the drugs that are used in cancer therapeutics, and is viewed as a non-specific target of cytotoxic agents. Although this is true for traditional chemotherapeutics, other agents that were discovered more recently have shown enhanced efficacy. Furthermore, a new generation of agents that target DNA-associated processes are anticipated to be far more specific and effective. How have these agents evolved, and what are their molecular targets?

Predictors of sleep-disordered breathing in community-dwelling adults: the Sleep Heart Health Study.

Abstract: Background Sleep-disordered breathing (SDB) is common, but largely undiagnosed in the general population. Information on demographic patterns of SDB occurrence and its predictive factors in the general population is needed to target high-risk groups that may benefit from diagnosis. Methods The sample comprised 5615 community-dwelling men and women aged between 40 and 98 years who were enrolled in the Sleep Heart Health Study. Data were collected by questionnaire, clinical examinations, and in-home polysomnography. Sleep-disordered breathing status was based on the average number of apnea and hypopnea episodes per hour of sleep (apnea-hypopnea index [AHI]). We used multiple logistic regression modeling to estimate cross-sectional associations of selected participant characteristics with SDB defined by an AHI of 15 or greater. Results Male sex, age, body mass index, neck girth, snoring, and repeated breathing pause frequency were independent, significant correlates of an AHI of 15 or greater. People reporting habitual snoring, loud snoring, and frequent breathing pauses were 3 to 4 times more likely to have an AHI of 15 or greater vs an AHI less than 15, but there were weaker associations for other factors with an AHI of 15 or greater. The odds ratios (95% confidence interval) for an AHI of 15 or greater vs an AHI less than 15 were 1.6 and 1.5, respectively, for 1-SD increments in body mass index and neck girth. As age increased, the magnitude of associations for SDB and body habitus, snoring, and breathing pauses decreased. Conclusions A significant proportion of occult SDB in the general population would be missed if screening or case finding were based solely on increased body habitus or male sex. Breathing pauses and obesity may be particularly insensitive for identifying SDB in older people. A better understanding of predictive factors for SDB, particularly in older adults, is needed.

Organic semiconductors: A theoretical characterization of the basic parameters governing charge transport

Abstract: Organic semiconductors based on π-conjugated oligomers and polymers constitute the active elements in new generations of plastic (opto)electronic devices. The performance of these devices depends largely on the efficiency of the charge-transport processes; at the microscopic level, one of the major parameters governing the transport properties is the amplitude of the electronic transfer integrals between adjacent oligomer or polymer chains. Here, quantum-chemical calculations are performed on model systems to address the way transfer integrals between adjacent chains are affected by the nature and relative positions of the interacting units. Compounds under investigation include oligothienylenes, hexabenzocoronene, oligoacenes, and perylene. It is shown that the amplitude of the transfer integrals is extremely sensitive to the molecular packing. Interestingly, in contrast to conventional wisdom, specific arrangements can lead to electron mobilities that are larger than hole mobilities, which is, for instance, the case of perylene.

The putative plasma membrane Na(+)/H(+) antiporter SOS1 controls long-distance Na(+) transport in plants.

Abstract: The salt tolerance locus SOS1 from Arabidopsis has been shown to encode a putative plasma membrane Na(+)/H(+) antiporter. In this study, we examined the tissue-specific pattern of gene expression as well as the Na(+) transport activity and subcellular localization of SOS1. When expressed in a yeast mutant deficient in endogenous Na(+) transporters, SOS1 was able to reduce Na(+) accumulation and improve salt tolerance of the mutant cells. Confocal imaging of a SOS1-green fluorescent protein fusion protein in transgenic Arabidopsis plants indicated that SOS1 is localized in the plasma membrane. Analysis of SOS1 promoter-beta-glucuronidase transgenic Arabidopsis plants revealed preferential expression of SOS1 in epidermal cells at the root tip and in parenchyma cells at the xylem/symplast boundary of roots, stems, and leaves. Under mild salt stress (25 mM NaCl), sos1 mutant shoot accumulated less Na(+) than did the wild-type shoot. However, under severe salt stress (100 mM NaCl), sos1 mutant plants accumulated more Na(+) than did the wild type. There also was greater Na(+) content in the xylem sap of sos1 mutant plants exposed to 100 mM NaCl. These results suggest that SOS1 is critical for controlling long-distance Na(+) transport from root to shoot. We present a model in which SOS1 functions in retrieving Na(+) from the xylem stream under severe salt stress, whereas under mild salt stress it may function in loading Na(+) into the xylem.

Vitamin D Receptor As an Intestinal Bile Acid Sensor

Abstract: The vitamin D receptor (VDR) mediates the effects of the calcemic hormone 1alpha,25-dihydroxyvitamin D3 [1,25(OH)2D3]. We show that VDR also functions as a receptor for the secondary bile acid lithocholic acid (LCA), which is hepatotoxic and a potential enteric carcinogen. VDR is an order of magnitude more sensitive to LCA and its metabolites than are other nuclear receptors. Activation of VDR by LCA or vitamin D induced expression in vivo of CYP3A, a cytochrome P450 enzyme that detoxifies LCA in the liver and intestine. These studies offer a mechanism that may explain the proposed protective effects of vitamin D and its receptor against colon cancer.

Regulation of SOS1, a plasma membrane Na+/H+ exchanger in Arabidopsis thaliana, by SOS2 and SOS3

Abstract: Maintaining low levels of sodium ions in the cell cytosol is critical for plant growth and development. Biochemical studies suggest that Na(+)/H(+) exchangers in the plasma membrane of plant cells contribute to cellular sodium homeostasis by transporting sodium ions out of the cell; however, these exchangers have not been identified at the molecular level. Genetic analysis has linked components of the salt overly sensitive pathway (SOS1-3) to salt tolerance in Arabidopsis thaliana. The predicted SOS1 protein sequence and comparisons of sodium ion accumulation in wild-type and sos1 plants suggest that SOS1 is involved directly in the transport of sodium ions across the plasma membrane. To demonstrate the transport capability of SOS1, we studied Na(+)/H(+)-exchange activity in wild-type and sos plants using highly purified plasma membrane vesicles. The results showed that plasma membrane Na(+)/H(+)-exchange activity was present in wild-type plants treated with 250 mM NaCl, but this transport activity was reduced by 80% in similarly treated sos1 plants. In vitro addition of activated SOS2 protein (a protein kinase) increased Na(+)/H(+)-exchange activity in salt-treated wild-type plants 2-fold relative to transport without added protein. However, the addition of activated SOS2 did not have any stimulatory effect on the exchange activity in sos1 plants. Although vesicles of sos2 and sos3 plants had reduced plasma membrane Na(+)/H(+)-exchange activity, transport activity in both increased with the addition of activated SOS2 protein. These results demonstrate that SOS1 contributes to plasma membrane Na(+)/H(+) exchange and that SOS2 and SOS3 regulate SOS1 transport activity.

Ecological restoration of southwestern ponderosa pine ecosystems: a broad perspective

Abstract: The purpose of this paper is to promote a broad and flexible perspective on ecological restoration of Southwestern (U.S.) ponderosa pine forests. Ponderosa pine forests in the region have been radically altered by Euro-American land uses, including livestock grazing, fire suppression, and logging. Dense thickets of young trees now abound, old- growth and biodiversity have declined, and human and ecological communities are in- creasingly vulnerable to destructive crown fires. A consensus has emerged that it is urgent to restore more natural conditions to these forests. Efforts to restore Southwestern forests will require extensive projects employing varying combinations of young-tree thinning and reintroduction of low-intensity fires. Treatments must be flexible enough to recognize and accommodate: high levels of natural heterogeneity; dynamic ecosystems; wildlife and other biodiversity considerations; scientific uncertainty; and the challenges of on-the-ground im- plementation. Ecological restoration should reset ecosystem trends toward an envelope of ''natural variability,'' including the reestablishment of natural processes. Reconstructed historic reference conditions are best used as general guides rather than rigid restoration prescriptions. In the long term, the best way to align forest conditions to track ongoing climate changes is to restore fire, which naturally correlates with current climate. Some stands need substantial structural manipulation (thinning) before fire can safely be reintro- duced. In other areas, such as large wilderness and roadless areas, fire alone may suffice as the main tool of ecological restoration, recreating the natural interaction of structure and process. Impatience, overreaction to crown fire risks, extractive economics, or hubris could lead to widespread application of highly intrusive treatments that may further damage forest ecosystems. Investments in research and monitoring of restoration treatments are essential to refine restoration methods. We support the development and implementation of a diverse range of scientifically viable restoration approaches in these forests, suggest principles for ecologically sound restoration that immediately reduce crown fire risk and incrementally return natural variability and resilience to Southwestern forests, and present ecological perspectives on several forest restoration approaches.

Distribution of Hydrogen in the Near-Surface of Mars: Evidence for Subsurface Ice Deposits

Abstract: Using the Gamma-Ray Spectrometer on the Mars Odyssey, we have identified two regions near the poles that are enriched in hydrogen. The data indicate the presence of a subsurface layer enriched in hydrogen overlain by a hydrogen-poor layer. The thickness of the upper layer decreases with decreasing distance to the pole, ranging from a column density of about 150 grams per square centimeter at -42 degrees latitude to about 40 grams per square centimeter at -77 degrees. The hydrogen-rich regions correlate with regions of predicted ice stability. We suggest that the host of the hydrogen in the subsurface layer is ice, which constitutes 35 +/- 15% of the layer by weight.

Molecular and genetic aspects of plant responses to osmotic stress

Abstract: Drought, high salinity and freezing impose osmotic stress on plants. Plants respond to the stress in part by modulating gene expression, which eventually leads to the restoration of cellular homeostasis, detoxification of toxins and recovery of growth. The signal transduction pathways mediating these adaptations can be dissected by combining forward and reverse genetic approaches with molecular, biochemical and physiological studies. Arabidopsis is a useful genetic model system for this purpose and its relatives including the halophyte Thellungiella halophila, can serve as valuable complementary genetic model systems.

Pictorial Illustrations Still Improve Students' Learning From Text

Abstract: Research conducted primarily during the 1970s and 1980s supported the assertion that carefully constructed text illustrations generally enhance learners' performance on a variety of text-dependent cognitive outcomes. Research conducted throughout the 1990s still strongly supports that assertion. The more recent research has extended pictures-in-text conclusions to alternative media and technological formats and has begun to explore more systematically the “whys,” “whens,” and “for whoms” of picture facilitation, in addition to the “whethers” and “how muchs.” Consideration is given here to both more and less conventional types of textbook illustration, with several “tenets for teachers” provided in relation to each type.

Toward maintaining the genome: DNA damage and replication checkpoints.

Abstract: DNA checkpoints play a significant role in cancer pathology, perhaps most notably in maintaining genome stability. This review summarizes the genetic and molecular mechanisms of checkpoint activation in response to DNA damage. The major checkpoint proteins common to all eukaryotes are identified and discussed, together with how the checkpoint proteins interact to induce arrest within each cell cycle phase. Also discussed are the molecular signals that activate checkpoint responses, including single-strand DNA, double-strand breaks, and aberrant replication forks. We address the connection between checkpoint proteins and damage repair mechanisms, how cells recover from an arrest response, and additional roles that checkpoint proteins play in DNA metabolism. Finally, the connection between checkpoint gene mutation and genomic instability is considered.

A Single P450 Allele Associated with Insecticide Resistance in Drosophila

Abstract: Insecticide resistance is one of the most widespread genetic changes caused by human activity, but we still understand little about the origins and spread of resistant alleles in global populations of insects. Here, via microarray analysis of all P450s in Drosophila melanogaster, we show that DDT-R, a gene conferring resistance to DDT, is associated with overtranscription of a single cytochrome P450 gene, Cyp6g1. Transgenic analysis of Cyp6g1 shows that overtranscription of this gene alone is both necessary and sufficient for resistance. Resistance and up-regulation in Drosophila populations are associated with a single Cyp6g1 allele that has spread globally. This allele is characterized by the insertion of an Accord transposable element into the 5' end of the Cyp6g1 gene.

Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.

Abstract: Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing of the S. oneidensis genome, which consists of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and a 161,613-base pair plasmid with 173 CDSs. We identified the first Shewanella lambda-like phage, providing a potential tool for further genome engineering. Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S. oneidensis, and a novel periplasmic [Fe] hydrogenase, which are integral members of the electron transport system. This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion-reducing capabilities.

Watermarking, tamper-proofing, and obfuscation - tools for software protection

Abstract: We identify three types of attack on the intellectual property contained in software and three corresponding technical defenses. A defense against reverse engineering is obfuscation, a process that renders software unintelligible but still functional. A defense against software piracy is watermarking, a process that makes it possible to determine the origin of software. A defense against tampering is tamper-proofing, so that unauthorized modifications to software (for example, to remove a watermark) will result in nonfunctional code. We briefly survey the available technology for each type of defense.