Showing papers by "University of Georgia published in 2009"

The B73 Maize Genome: Complexity, Diversity, and Dynamics

Abstract: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

The Sorghum bicolor genome and the diversification of grasses

Abstract: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

Are there social limits to adaptation to climate change

Abstract: While there is a recognised need to adapt to changing climatic conditions, there is an emerging discourse of limits to such adaptation. Limits are traditionally analysed as a set of immutable thresholds in biological, economic or technological parameters. This paper contends that limits to adaptation are endogenous to society and hence contingent on ethics, knowledge, attitudes to risk and culture. We review insights from history, sociology and psychology of risk, economics and political science to develop four propositions concerning limits to adaptation. First, any limits to adaptation depend on the ultimate goals of adaptation underpinned by diverse values. Second, adaptation need not be limited by uncertainty around future foresight of risk. Third, social and individual factors limit adaptation action. Fourth, systematic undervaluation of loss of places and culture disguises real, experienced but subjective limits to adaptation. We conclude that these issues of values and ethics, risk, knowledge and culture construct societal limits to adaptation, but that these limits are mutable.

Market orientation, marketing capabilities, and firm performance

Abstract: Drawing on traditional resource-based theory and its recent dynamic capabilities theory extensions, we examine both the possession of a market orientation and the marketing capabilities through which resources are deployed into the marketplace as drivers of firm performance in a cross-industry sample. Our findings indicate that market orientation and marketing capabilities are complementary assets that contribute to superior firm performance. We also find that market orientation has a direct effect on firms' return on assets (ROA), and that marketing capabilities directly impact both ROA and perceived firm performance. Copyright © 2009 John Wiley & Sons, Ltd.

Polyploidy and angiosperm diversification

Abstract: Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.

PlasmoDB: a functional genomic database for malaria parasites

Abstract: PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.

Global patterns in belowground communities.

Abstract: Although belowground ecosystems have been studied extensively and soil biota play integral roles in biogeochemical processes, surprisingly we have a limited understanding of global patterns in belowground biomass and community structure. To address this critical gap, we conducted a meta-analysis of published data (> 1300 datapoints) to compare belowground plant, microbial and faunal biomass across seven of the major biomes on Earth. We also assembled data to assess biome-level patterns in belowground microbial community composition. Our analysis suggests that variation in microbial biomass is predictable across biomes, with microbial biomass carbon representing 0.6-1.1% of soil organic carbon (r(2) = 0.91) and 1-20% of total plant biomass carbon (r(2) = 0.42). Approximately 50% of total animal biomass can be found belowground and soil faunal biomass represents < 4% of microbial biomass across all biomes. The structure of belowground microbial communities is also predictable: bacterial community composition and fungal : bacterial gene ratios can be predicted reasonably well from soil pH and soil C : N ratios respectively. Together these results identify robust patterns in the structure of belowground microbial and faunal communities at broad scales which may be explained by universal mechanisms that regulate belowground biota across biomes.

Characterization of designer biochar produced at different temperatures and their effects on a loamy sand

Abstract: Biochar additions to degraded soils have the potential to improve crop yield and soil quality. We hypothesize that the biochar production process can be tailored to form designer biochars that have specific chemical characteristics matched to selective chemical and/or physical issues of a degraded soil. We produced biochars from peanut hulls, pecan shells, poultry litter, and switchgrass at temperatures ranging from 250oC to 700oC. Biochars were characterized

The Narcissism Epidemic: Living in the Age of Entitlement

Abstract: Narcissism -- a very positive and inflated view of the self -- is everywhere. It's what you have if you're a politician and you've strayed from your wife, and it's whyEfive times as many Americans undergo plastic surgery and cosmetic procedures today than did just ten years ago. It's the value that parents teach their children with song lyrics like "I am special. Look at me," the skill teenagers and young adults obsessively hone on Facebook and MySpace, and the reason high school students physically beat classmates and then broadcast their violence on YouTube for all to see. It's the message preached by prosperity gospel and the vacuous ethos spread by celebrity newsmakers. And it's what's making people depressed, lonely, and buried under piles of debt. Jean M. Twenge's influential and controversial first book, "Generation Me," generated a national debate with its trenchant depiction of the challenges twenty- and thirtysomethings face emotionally and professionally in today's world -- and the fallout these issues create for older generations as well as employers. Now, Dr. Twenge is on to a new incendiary topic that has repercussions for every age-group and class: the pernicious spread of narcissism in today's culture and its catastrophic effects. Dr. Twenge joins forces with W. Keith Campbell, Ph.D., a nationally recognized expert on narcissism, for "The Narcissism Epidemic," their eye-opening exposition of the alarming rise of narcissism -- and they show how to stop it. Every day, you encounter the real costs of narcissism: in your relationships and family, in the workplace and the economy at large, in schools that fail to teach necessary skills, in culture, and in politics. Even the world economy has been damaged by risky, unrealistic overconfidence. Filled with arresting anecdotes that illustrate the hold narcissism has on us today -- from people hiring fake paparazzi in order to experience feeling famous to college students who won't leave a professor's office until their B+ becomes an A -- "The Narcissism Epidemic" is at once a riveting window into the consequences of narcissism, a probing analysis of the culture at large, and a prescription to combat the widespread problems caused by narcissism. As a society, we have a chance to slow the epidemic of narcissism once we learn to identify it, minimize the forces that sustain and transmit it, and treat it where we find it. Drawing on their own extensive research as well as decades of other experts' studies, Drs. Twenge and Campbell show us how.

Forecasting the effects of accelerated sea‐level rise on tidal marsh ecosystem services

Abstract: We used field and laboratory measurements, geographic information systems, and simulation modeling to investigate the potential effects of accelerated sea-level rise on tidal marsh area and delivery of ecosystem ser- vices along the Georgia coast. Model simulations using the Intergovernmental Panel on Climate Change (IPCC) mean and maximum estimates of sea-level rise for the year 2100 suggest that salt marshes will decline in area by 20% and 45%, respectively. The area of tidal freshwater marshes will increase by 2% under the IPCC mean scenario, but will decline by 39% under the maximum scenario. Delivery of ecosystem services associated with productivity (macrophyte biomass) and waste treatment (nitrogen accumulation in soil, potential denitrification) will also decline. Our findings suggest that tidal marshes at the lower and upper salinity ranges, and their attendant delivery of ecosystem services, will be most affected by accelerated sea- level rise, unless geomorphic conditions (ie gradual increase in elevation) enable tidal freshwater marshes to migrate inland, or vertical accretion of salt marshes to increase, to compensate for accelerated sea-level rise.

Testing the functional significance of microbial community composition

Abstract: A critical assumption underlying terrestrial ecosystem models is that soil microbial communities, when placed in a common environment, will function in an identical manner regardless of the composition of that community. Given high species diversity in microbial communities and the ability of microbes to adapt rapidly to new conditions, this assumption of functional redundancy seems plausible. We test the assumption by comparing litter decomposition rates in experimental microcosms inoculated with distinct microbial communities. We find that rates of carbon dioxide production from litter decomposition were dependent upon the microbial inoculum, with differences in the microbial community alone accounting for substantial (;20%) variation in total carbon mineralized. Communities that shared a common history with a given foliar litter exhibited higher decomposition rates when compared to communities foreign to that habitat. Our results suggest that the implicit assumption in ecosystem models (i.e., microbial communities in the same environment are functionally equivalent) is incorrect. To predict accurately how biogeochemical processes will respond to global change may require consideration of the community composition and/or adaptation of microbial communities to past resource environments.

MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis.

Abstract: It has previously been shown that SECONDARY WALL–ASSOCIATED NAC DOMAIN PROTEIN1 (SND1) is a key transcription factor regulating secondary cell wall formation, including the biosynthesis of cellulose, xylan, and lignin. In this study, we show that two closely related SND1-regulated MYB transcription factors, MYB58 and MYB63, are transcriptional regulators specifically activating lignin biosynthetic genes during secondary wall formation in Arabidopsis thaliana. MYB58 and MYB63 are phylogenetically distinct from previously characterized MYBs shown to be associated with secondary wall formation or phenylpropanoid metabolism. Expression studies showed that MYB58 and MYB63 are specifically expressed in fibers and vessels undergoing secondary wall thickening. Dominant repression of their functions led to a reduction in secondary wall thickening and lignin content. Overexpression of MYB58 and MYB63 resulted in specific activation of lignin biosynthetic genes and concomitant ectopic deposition of lignin in cells that are normally unlignified. MYB58 was able to activate directly the expression of lignin biosynthetic genes and a secondary wall–associated laccase (LAC4) gene. Furthermore, the expression of MYB58 and MYB63 was shown to be regulated by the SND1 close homologs NST1, NST2, VND6, and VND7 and their downstream target MYB46. Together, our results indicate that MYB58 and MYB63 are specific transcriptional activators of lignin biosynthesis in the SND1-mediated transcriptional network regulating secondary wall formation.

The Toxicogenomic Multiverse: Convergent Recruitment of Proteins Into Animal Venoms

Abstract: Throughout evolution, numerous proteins have been convergently recruited into the venoms of various animals, including centipedes, cephalopods, cone snails, fish, insects (several independent venom systems), platypus, scorpions, shrews, spiders, toxicoferan reptiles (lizards and snakes), and sea anemones. The protein scaffolds utilized convergently have included AVIT/colipase/prokineticin, CAP, chitinase, cystatin, defensins, hyaluronidase, Kunitz, lectin, lipocalin, natriuretic peptide, peptidase S1, phospholipase A2, sphingomyelinase D, and SPRY. Many of these same venom protein types have also been convergently recruited for use in the hematophagous gland secretions of invertebrates (e.g., fleas, leeches, kissing bugs, mosquitoes, and ticks) and vertebrates (e.g., vampire bats). Here, we discuss a number of overarching structural, functional, and evolutionary generalities of the protein families from which these toxins have been frequently recruited and propose a revised and expanded working definition...

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

Abstract: We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

Crystalline Ultrasmooth Self-Assembled Monolayers of Alkylsilanes for Organic Field-Effect Transistors

Abstract: Crystalline self-assembled monolayers (SAMs) of organosilane compounds such as octadecyltrimethoxysilane (OTMS) and octadecyltrichlorosilane (OTCS) were deposited by a simple, spin-casting technique onto Si/SiO(2) substrates. Fabrication of the OTMS SAMs and characterization using ellipsometry, contact angle, atomic force microscopy (AFM), grazing angle attenuated total reflectance Fourier transform infrared (GATR-FTIR) spectroscopy and grazing incidence X-ray diffraction (GIXD) are described. The characterization confirms that these monolayers exhibit a well-packed crystalline phase and a remarkably high degree of smoothness. Semiconductors deposited by vapor deposition onto the crystalline OTS SAM grow in a favorable two-dimensional layered growth manner which is generally preferred morphologically for high charge carrier transport. On the OTMS SAM treated dielectric, pentacene OFETs showed hole mobilities as high as 3.0 cm(2)/V x s, while electron mobilities as high as 5.3 cm(2)/V x s were demonstrated for C(60).

Mobile Communication and Society: A Global Perspective

Abstract: Castells, M., Fernandez-Ardevol, M., Qiu, J. L., & Sey, A. (2007). Mobile communication and society: A global perspective. Cambridge, MA: The MIT Press. This theoretically hybrid, statistically sig...

Attention Modification Program in Individuals With Generalized Anxiety Disorder

Abstract: Research suggests that individuals with generalized anxiety disorder (GAD) show an attention bias for threat-relevant information. However, few studies have examined the causal role of attention bias in the maintenance of anxiety and whether modification of such biases may reduce pathological anxiety symptoms. In the present article, the authors tested the hypothesis that an 8-session attention modification program would (a) decrease attention bias to threat and (b) reduce symptoms of GAD. Participants completed a probe detection task by identifying letters (E or F) replacing one member of a pair of words. The authors trained attention by including a contingency between the location of the probe and the nonthreat word in one group (Attention Modification Program; AMP) and not in the other (attention control condition; ACC). Participants in the AMP showed change in attention bias and a decrease in anxiety, as indicated by both self-report and interviewer measures. These effects were not present in the ACC group. These results are consistent with the hypothesis that attention plays a causal role in the maintenance of GAD and suggest that altering attention mechanisms may effectively reduce anxiety.

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

Abstract: Background: Post-translational modifications of histones play important roles in maintaining normal transcription patterns by directly or indirectly affecting the structural properties of the chromatin. In plants, methylation of histone H3 lysine 4 (H3K4me) is associated with genes and required for normal plant development. Results: We have characterized the genome-wide distribution patterns of mono-, di- and trimethylation of H3K4 (H3K4me1, H3K4me2 and H3K4me3, respectively) in Arabidopsis thaliana seedlings using chromatin immunoprecipitation and high-resolution whole-genome tiling microarrays (ChIP-chip). All three types of H3K4me are found to be almost exclusively genic, and two-thirds of Arabidopsis genes contain at least one type of H3K4me. H3K4me2 and H3K4me3 accumulate predominantly in promoters and 5' genic regions, whereas H3K4me1 is distributed within transcribed regions. In addition, H3K4me3-containing genes are highly expressed with low levels of tissue specificity, but H3K4me1 or H3K4me2 may not be directly involved in transcriptional activation. Furthermore, the preferential co-localization of H3K4me3 and H3K27me3 found in mammals does not appear to occur in plants at a genome-wide level, but H3K4me2 and H3K27me3 co-localize at a higher-than-expected frequency. Finally, we found that H3K4me2/3 and DNA methylation appear to be mutually exclusive, but surprisingly, H3K4me1 is highly correlated with CG DNA methylation in the transcribed regions of genes. Conclusions: H3K4me plays widespread roles in regulating gene expression in plants. Although many aspects of the mechanisms and functions of H3K4me appear to be conserved among all three kingdoms, we observed significant differences in the relationship between H3K4me and transcription or other epigenetic pathways in plants and mammals.

A Human Telomerase Holoenzyme Protein Required for Cajal Body Localization and Telomere Synthesis

Abstract: Telomerase is a ribonucleoprotein (RNP) complex that synthesizes telomere repeats in tissue progenitor cells and cancer cells. Active human telomerase consists of at least three principal subunits, including the telomerase reverse transcriptase, the telomerase RNA (TERC), and dyskerin. Here, we identify a holoenzyme subunit, TCAB1 (telomerase Cajal body protein 1), that is notably enriched in Cajal bodies, nuclear sites of RNP processing that are important for telomerase function. TCAB1 associates with active telomerase enzyme, established telomerase components, and small Cajal body RNAs that are involved in modifying splicing RNAs. Depletion of TCAB1 by using RNA interference prevents TERC from associating with Cajal bodies, disrupts telomerase-telomere association, and abrogates telomere synthesis by telomerase. Thus, TCAB1 controls telomerase trafficking and is required for telomere synthesis in human cancer cells.

Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research

Abstract: Synthetic oligosaccharides and glycoconjugates are increasingly used as probes for biological research and as lead compounds for drug and vaccine discovery. These endeavors are, however, complicated by a lack of general methods for the routine preparation of this important class of compounds. Recent development such as one-pot multi-step protecting group manipulations, the use of unified monosaccharide building blocks, the introduction of stereoselective glycosylation protocols, and convergent strategies for oligosaccharide assembly, are beginning to address these problems. Furthermore, oligosaccharide synthesis can be facilitated by chemo-enzymatic methods, which employ a range of glycosyl transferases to modify a synthetic oligosaccharide precursor. Glycosynthases, which are mutant glycosidases, that can readily form glycosidic linkages are addressing a lack of a wide range glycosyltransferases. The power of carbohydrate chemistry is highlighted by an ability to synthesize glycoproteins.

Effects of Inquiry-Based Learning on Students' Science Literacy Skills and Confidence.

Abstract: Calls for reform in university education have prompted a movement from teacher- to student-centered course design, and included developments such as peer-teaching, problem and inquiry-based learning. In the sciences, inquiry-based learning has been widely promoted to increase literacy and skill development, but there has been little comparison to more traditional curricula. In this study, we demonstrated greater improvements in students’ science literacy and research skills using inquiry lab instruction. We also found that inquiry students gained self-confidence in scientific abilities, but traditional students’ gain was greater ‐likely indicating that the traditional curriculum promoted over-confidence. Inquiry lab students valued more authentic science exposure but acknowledged that experiencing the complexity and frustrations faced by practicing scientists was challenging, and may explain the widespread reported student resistance to inquiry curricula.

The reality of virtual schools: A review of the literature

Abstract: Virtual schooling was first employed in the mid-1990s and has become a common method of distance education used in K-12 jurisdictions. The most accepted definition of a virtual school is an entity approved by a state or governing body that offers courses through distance delivery - most commonly using the Internet. While virtual schools can be classified in different ways, the three common methods of delivery are by independent, asynchronous or synchronous means. Presently, the vast majority of virtual school students tended to be a select group of academically capable, motivated, independent learners. The benefits associated with virtual schooling are expanding educational access, providing high-quality learning opportunities, improving student outcomes and skills, allowing for educational choice, and achieving administrative efficiency. However, the research to support these conjectures is limited at best. The challenges associated with virtual schooling include the conclusion that the only students typically successful in online learning environments are those who have independent orientations towards learning, highly motivated by intrinsic sources, and have strong time management, literacy, and technology skills. These characteristics are typically associated with adult learners. This stems from the fact that research into and practice of distance education has typically been targeted to adult learners. The problem with this focus is that adults learn differently than younger learners. Researchers are calling for more research into the factors that account for K-12 student success in distance education and virtual school environments and more design research approaches than traditional comparisons of student achievement in traditional and virtual schools.

Revenue Diversification in Nonprofit Organizations: Does it Lead to Financial Stability?

Abstract: This article investigates whether revenue diversification leads to greater stability in the revenue structures of nonprofit organizations. Our findings suggest that nonprofits can indeed reduce their revenue volatility through diversification, particularly by equalizing their reliance on earned income, investments, and contributions. This positive effect of diversification on revenue stability implies that a diversified portfolio encourages more stable revenues and consequently could promote greater organizational longevity. Despite any additional complexity or crowding out, nonprofit managers may increase the financial stability of their organizations by adding additional revenue streams. However, our analysis also reveals several other important factors that contribute to nonprofit revenue stability. In particular, increasing a nonprofit organization's total expenses and fund balance reduces volatility, suggesting larger nonprofits and organizations with greater growth potential experience greater revenue stability. Finally, the results suggest nonprofits relying primarily on contributions will experience more volatility, whereas nonprofits located within urban areas will have more stable revenue structures over time.

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

Abstract: High-copy-number transposable elements comprise the majority of eukaryotic genomes where they are major contributors to gene and genome evolution. However, it remains unclear how a host genome can survive a rapid burst of hundreds or thousands of insertions because such bursts are exceedingly rare in nature and therefore difficult to observe in real time. In a previous study we reported that in a few rice strains the DNA transposon mPing was increasing its copy number by approximately 40 per plant per generation. Here we exploit the completely sequenced rice genome to determine 1,664 insertion sites using high-throughput sequencing of 24 individual rice plants and assess the impact of insertion on the expression of 710 genes by comparative microarray analysis. We find that the vast majority of transposable element insertions either upregulate or have no detectable effect on gene transcription. This modest impact reflects a surprising avoidance of exon insertions by mPing and a preference for insertion into 5' flanking sequences of genes. Furthermore, we document the generation of new regulatory networks by a subset of mPing insertions that render adjacent genes stress inducible. As such, this study provides evidence for models first proposed previously for the involvement of transposable elements and other repetitive sequences in genome restructuring and gene regulation.