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Biology

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Selected Works

2007

Articles 1 - 21 of 21

Full-Text Articles in Life Sciences

Microarray-Based Method For Detection Of Unknown Genetic Modifications, Torstein Tengs Dec 2007

Microarray-Based Method For Detection Of Unknown Genetic Modifications, Torstein Tengs

Dr. Torstein Tengs

Background

Due to the increased use of genetic modifications in crop improvement, there is a need to develop effective methods for the detection of both known and unknown transgene constructs in plants. We have developed a strategy for detection and characterization of unknown genetic modifications and we present a proof of concept for this method using Arabidopsis thaliana and Oryza sativa (rice). The approach relies on direct hybridization of total genomic DNA to high density microarrays designed to have probes tiled throughout a set of reference sequences.

Results

We show that by using arrays with 25 basepair probes covering both …

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Cerebrospinal Fluid And Serum Biomarkers Of Cerebral Malaria Mortality In Ghanaian Children, Winston A. Anderson Oct 2007

Cerebrospinal Fluid And Serum Biomarkers Of Cerebral Malaria Mortality In Ghanaian Children, Winston A. Anderson

Winston Anderson

Plasmodium falciparum can cause a diffuse encephalopathy known as cerebral malaria (CM), a major contributor to malaria associated mortality. Despite treatment, mortality due to CM can be as high as 30% while 10% of survivors of the disease may experience short- and long-term neurological complications. The pathogenesis of CM and other forms of severe malaria is multi-factorial and appear to involve cytokine and chemokine homeostasis, inflammation and vascular injury/repair. Identification of prognostic markers that can predict CM severity will enable development of better intervention.
Postmortem serum and cerebrospinal fluid (CSF) samples were obtained within 2-4 hours of death in Ghanaian …

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Atplai Is An Acyl Hydrolase Involved In Basal Jasmonic Acid Production And Arabidopsis Resistance To Botrytis Cinerea, Xuemin Wang, Wenyu Yang, Shivakumar P. Devaiah, Xiangqing Pan, Giorgis Isaac, Ruth Welti Jun 2007

Atplai Is An Acyl Hydrolase Involved In Basal Jasmonic Acid Production And Arabidopsis Resistance To Botrytis Cinerea, Xuemin Wang, Wenyu Yang, Shivakumar P. Devaiah, Xiangqing Pan, Giorgis Isaac, Ruth Welti

Xuemin (Sam) Wang

Intracellular phospholipase A2 (PLA2) plays an important role in regulating oxylipin biosynthesis in mammals, but the molecular and biochemical nature of intracellular PLA2 is not well understood in plants. Arabidopsis thaliana gene At1g61850 (AtPLAI) encodes a 140-kDa protein that is most similar to mammalian calcium-independent PLA2, and additionally contains leucine-rich repeats and Armadillo repeats. AtPLAI hydrolyzes phospholipids at both the sn-1 and sn-2 positions, but prefers galactolipids to phospholipids as substrates. Profiling of lipid species altered in response to the necrotrophic fungus Botrytis cinerea revealed decreases in the levels of phosphatidylglycerol and digalactosyldiacylglycerol, suggesting that hydrolysis of plastidic polar lipids …

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Depleted Carbon Monoxide In Fragment C Of The Jupiter-Family Comet 73p/Schwassmann-Wachmann 3, M. A. Disanti, W. M. Anderson, G. L. Villanueva, B. P. Bonev, K. Magee-Sauer, E. L. Gibb, M. J. Mumma May 2007

Depleted Carbon Monoxide In Fragment C Of The Jupiter-Family Comet 73p/Schwassmann-Wachmann 3, M. A. Disanti, W. M. Anderson, G. L. Villanueva, B. P. Bonev, K. Magee-Sauer, E. L. Gibb, M. J. Mumma

Erika Gibb

Carbon monoxide emission was targeted in fragment C of the recently split Jupiter-family comet 73P/Schwassmann-Wachmann 3 during its 2006 apparition, using the Cryogenic Echelle Spectrograph (CSHELL) at the NASA IRTF on Mauna Kea, Hawaii. Simultaneous sounding with H2O near 4.65 μm revealed highly depleted CO, consistent with a mixing ratio of 0.5% ± 0.13%. Along with depleted CH3OH but nearly normal HCN, this may indicate that this comet formed in the inner giant planets' region or, alternatively, that it formed relatively late, after significant clearing of the protosolar nebula.

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Using Math In Cell Biology: A Tale Of Two Channel Types, Borbala Mazzag Mar 2007

Using Math In Cell Biology: A Tale Of Two Channel Types, Borbala Mazzag

Borbala Mazzag

No abstract provided.

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The Carnegie Protein Trap Library: A Versatile Tool For Drosophila Developmental Studies, Anna K. Allen Feb 2007

The Carnegie Protein Trap Library: A Versatile Tool For Drosophila Developmental Studies, Anna K. Allen

Anna Allen

Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600-900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were …

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Correction: African American Mitochondrial Dnas Often Match Mtdnas Found In Multiple African Ethnic Groups, Bert Ely, Jamie L. Wilson, Fatimah Linda Collier Jackson, Bruce A. Jackson Feb 2007

Correction: African American Mitochondrial Dnas Often Match Mtdnas Found In Multiple African Ethnic Groups, Bert Ely, Jamie L. Wilson, Fatimah Linda Collier Jackson, Bruce A. Jackson

Fatimah Linda Collier Jackson

After the publication of this work [1], we became aware that AFDIL data set used to construct our database of sub-Saharan mtDNA sequences had been mislabelled, and in fact, did not contain Sierra Leone mtDNA sequences. We have obtained the correct Sierra Leone data set from AFDIL, reconstructed the database using the new file, and reanalyzed all of the data. The size of our database was reduced from 3725 to 3717 since the new Sierra Leone data set contained 109 sequences instead of 117 in the
mislabelled data set. The swapping of data sets resulted in a cascade of minor …

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Esa And Environmental Justice, George Middendorf, Charles Nilon Feb 2007

Esa And Environmental Justice, George Middendorf, Charles Nilon

George Middendorf

No abstract provided.

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Dna Extraction From Resting Eggs Of The Clam Shrimp Eulimnadia Texana (Branchiopoda : Spinicaudata : Limnadiidae), R. Joel Duff, Chiara Benvenuto, Traci L. Branch, Stephen C. Weeks Jan 2007

Dna Extraction From Resting Eggs Of The Clam Shrimp Eulimnadia Texana (Branchiopoda : Spinicaudata : Limnadiidae), R. Joel Duff, Chiara Benvenuto, Traci L. Branch, Stephen C. Weeks

R. Joel Duff

Large branchiopod crustaceans inhabiting ephemeral ponds are well adapted to their highly unpredictable habitat with a life cycle that includes a short-lived adult stage and a long-lived, desiccation-resistant egg stage. One well studied large branchiopod is the clam shrimp Eulimnadia texana, an androdioecious species with populations comprised of males and self-compatible hermaphrodites. Likely due to the harsh environments in which the eggs are found, e.g., dry areas with high heat and high irradiation, extraction of DNA from individual eggs for genetic analyses can be problematic. Here we report a number of modifications that we have tested allowing for increased efficiency …

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Plant And Pollinator Diversity In Northern Arizona, Warren Abrahamson, L.E. Stevens, T.L. Griswold, O. Messenger, T.J. Ayers Dec 2006

Plant And Pollinator Diversity In Northern Arizona, Warren Abrahamson, L.E. Stevens, T.L. Griswold, O. Messenger, T.J. Ayers

Warren G. Abrahamson, II

No abstract provided.

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Leaf Traits And Leaf Life Spans Of Two Xeric-Adapted Palmettos, Warren Abrahamson Dec 2006

Leaf Traits And Leaf Life Spans Of Two Xeric-Adapted Palmettos, Warren Abrahamson

Warren G. Abrahamson, II

Plants of nutrient-poor, arid environments often have leaf traits that include small size, sclerophylly, long life span, low nutrient concentration, and low photosynthetic rate. Hence, the success of two large-leaved palmettos in peninsular Florida’s seasonally xeric, nutrient-impoverished uplands seems anomalous, given that their leaves are orders of magnitude larger than the leaves of co-occurring species. An examination of leaf traits and leaf life spans across four vegetative associations differing in available light using a 16-yr data set showed that leaves of Serenoa repens and Sabal etonia had low rates of leaf production coupled with long leaf life spans reaching 3.5 …

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Computational Modeling Of Calcium Dynamics Near Heterogeneous Release Sites, Borbala Mazzag, Zachary Cooper, Michael Greenwood Dec 2006

Computational Modeling Of Calcium Dynamics Near Heterogeneous Release Sites, Borbala Mazzag, Zachary Cooper, Michael Greenwood

Borbala Mazzag

Background: Calcium is known to play an important role in many physiological
processes, such as egg fertilization and heart muscle functions.
Several recent theoretical studies ([4], [1]) investigated calcium dynamics
near so-called release sites – clusters of calcium-regulated channels on
the intracellular calcium stores. Interest in the synchronized openings of
channels within a release site has increased because these openings are
thought to be the building blocks of global calcium events.
Methods: We conduct computational studies of the effect of heterogeneity
in the make-up of the release site on the resulting calcium dynamics.
We introduce heterogeneity into the model of …

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Review Of The Nearctic Gallwasp Species Of The Genus Bassettia Ashmead, 1887, With Description Of New Species (Hymenoptera: Cynipidae: Cynipini), Warren G. Abrahamson Ii, G. Melika Dec 2006

Review Of The Nearctic Gallwasp Species Of The Genus Bassettia Ashmead, 1887, With Description Of New Species (Hymenoptera: Cynipidae: Cynipini), Warren G. Abrahamson Ii, G. Melika

Warren G. Abrahamson, II

No abstract provided.

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Force-Induced Unfolding Of Fibronectin In The Extracellular Matrix Of Living Cells, M. L. Smith, D. Gourdon, W. C. Little, Kristopher E. Kubow, R. A. Eguiluz, S. Luna-Morris, V. Vogel Dec 2006

Force-Induced Unfolding Of Fibronectin In The Extracellular Matrix Of Living Cells, M. L. Smith, D. Gourdon, W. C. Little, Kristopher E. Kubow, R. A. Eguiluz, S. Luna-Morris, V. Vogel

Kristopher E Kubow

No abstract provided.

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Rapid Characterization Of The Fatty Acyl Composition Of Complex Lipids By Collision-Induced Dissociation Time-Of-Flight Mass Spectrometry, Xuemin Wang, Steven Wynn Esch, Pamela Tamura, Alexis A. Sparks, Mary R. Roth, Shivakumar P. Devaiah, Ernst Heinz, Todd D. Williams, Ruth Welti Dec 2006

Rapid Characterization Of The Fatty Acyl Composition Of Complex Lipids By Collision-Induced Dissociation Time-Of-Flight Mass Spectrometry, Xuemin Wang, Steven Wynn Esch, Pamela Tamura, Alexis A. Sparks, Mary R. Roth, Shivakumar P. Devaiah, Ernst Heinz, Todd D. Williams, Ruth Welti

Xuemin (Sam) Wang

Profiling of leaf extracts from mutants of Arabidopsis with defects in lipid desaturation demonstrates the utility of collision-induced dissociation time-of-flight mass spectrometry (CID-TOF MS) for screening biological samples for fatty acid compositional alterations. CID-TOF MS uses the collision cell of a quadrupole time-of-flight mass spectrometer to simultaneously fragment all of the ions produced by an ionization source. Electrospray ionization CID-TOF MS in the negative mode can be used to analyze fatty acyl anions derived from complex lipids as well as free fatty acids. Although acyl anion yield is shown to be a function of the lipid class and the position …

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Augmenting The Lobster Catch: Oyster Aquaculture In Modified Lobster Traps, Joseph Buttner Dec 2006

Augmenting The Lobster Catch: Oyster Aquaculture In Modified Lobster Traps, Joseph Buttner

Joseph Buttner

Capture fisheries globally are imperiled with many tra-ditional stocks fully or over-exploited (Schiermeler 2002, FAO 2004, NMFS 2003). Regulations that restrict commer-cial harvest and entry into fisheries are growing and have reached a point where the livelihood and lifestyle of many fishers have been compromised. An important fishing voca-tion and tradition is threatened. If explored and implemented in a manner that provides comfort and confidence in commercial fishers, aquaculture can serve as a conduit and alternative option to keep fisher-men on the water, working in an environment and pursuing a vocation consistent with their experience and preference. Perhaps the best …

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In The Heat Of The Law, It's Not Just Steam: Geothermal Resources And The Impact On Thermophile Biodiversity, Donald J. Kochan, Tiffany Grant Dec 2006

In The Heat Of The Law, It's Not Just Steam: Geothermal Resources And The Impact On Thermophile Biodiversity, Donald J. Kochan, Tiffany Grant

Donald J. Kochan

Significant research has been conducted into the utilization of geothermal resources as a ‘green’ energy source. However, minimal research has been conducted into geothermal resource utilization and depletion impacts on thermophile biodiversity. Thermophiles are organisms which have adapted over millions of year to extreme temperature and chemical compositions and exist in hot springs and other geothermal resources. Their ability to withstand high temperatures makes them invaluable to scientific and medical research. Current federal and California case law classify geothermal resources as a mineral, not a water resource. Acquisition of rights to develop a geothermal resource owned or reserved by the …

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Does Direct Optimization Produce More Accurate Alignments And Topologies? Poy Vs. Clustalw+Paup*, T. Heath Ogden Dec 2006

Does Direct Optimization Produce More Accurate Alignments And Topologies? Poy Vs. Clustalw+Paup*, T. Heath Ogden

T. Heath Ogden

Direct optimization frameworks for simultaneously estimating alignments and phylogenies have recently been developed. One such method, implemented in the program POY, is becoming more common for analyses of variable length sequences (e.g., analyses using ribosomal genes) and for combined evidence analyses (morphology + multiple genes). Simulation of sequences containing insertion and deletion events was performed in order to directly compare a widely used method of multiple sequence alignment (ClustalW) and subsequent parsimony analysis in PAUP* with direct optimization via POY. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (clocklike, non-clocklike, and ultrametric). Alignment accuracy …

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How Should Gaps Be Treated In Parsimony? A Comparison Of Approaches Using Simulation, T. Heath Ogden Dec 2006

How Should Gaps Be Treated In Parsimony? A Comparison Of Approaches Using Simulation, T. Heath Ogden

T. Heath Ogden

Simulation with indels was used to produce alignments where true site homologies in DNA sequences were known; the gaps from these datasets were removed and the sequences were then aligned to produce hypothesized alignments. Both alignments were then analyzed under three widely used methods of treating gaps during tree reconstruction under the maximum parsimony principle. With the true alignments, for many cases (82%), there was no diVerence in topological accuracy for the diVerent methods of gap coding. However, in cases where a diVerence was present, coding gaps as a Wfth state character or as separate presence/absence characters outperformed treating gaps …

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Diatom Biodiversity And Distribution On Wetwalls In Great Smoky Mountains National Park, Rex L. Lowe, Paula Furey, Jennifer A. Ress, Jeffrey R. Johansen Dec 2006

Diatom Biodiversity And Distribution On Wetwalls In Great Smoky Mountains National Park, Rex L. Lowe, Paula Furey, Jennifer A. Ress, Jeffrey R. Johansen

Paula Furey

No abstract provided.

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New Algal Species Records For The Great Smoky Mountains National Park, U.S.A., With An Annotated Checklist Of All Reported Algal Species For The Park, Jeffrey R. Johansen, Rex L. Lowe, Susan Carty, Karolina Fucikova, Catherine E. Olsen, Margaret H. Fitzpatrick, Jennifer A. Ress, Paula Furey Dec 2006

New Algal Species Records For The Great Smoky Mountains National Park, U.S.A., With An Annotated Checklist Of All Reported Algal Species For The Park, Jeffrey R. Johansen, Rex L. Lowe, Susan Carty, Karolina Fucikova, Catherine E. Olsen, Margaret H. Fitzpatrick, Jennifer A. Ress, Paula Furey

Paula Furey

No abstract provided.

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