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School of Biological Sciences

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College of Sciences

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Center for the Study of Systems Biology

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Publication Search Results

Now showing 1 - 10 of 214

Gene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells

(Georgia Institute of Technology, 2009-12-29) Bowen, Nathan J. ; Walker, L. DeEtte ; Matyunina, Lilya V. ; Logani, Sanjay ; Totten, Kimberly A. ; Benigno, Benedict B. ; McDonald, John F.

Background Accumulating evidence suggests that somatic stem cells undergo mutagenic transformation into cancer initiating cells. The serous subtype of ovarian adenocarcinoma in humans has been hypothesized to arise from at least two possible classes of progenitor cells: the ovarian surface epithelia (OSE) and/or an as yet undefined class of progenitor cells residing in the distal end of the fallopian tube. Methods Comparative gene expression profiling analyses were carried out on OSE removed from the surface of normal human ovaries and ovarian cancer epithelial cells (CEPI) isolated by laser capture micro-dissection (LCM) from human serous papillary ovarian adenocarcinomas. The results of the gene expression analyses were randomly confirmed in paraffin embedded tissues from ovarian adenocarcinoma of serous subtype and non-neoplastic ovarian tissues using immunohistochemistry. Differentially expressed genes were analyzed using gene ontology, molecular pathway, and gene set enrichment analysis algorithms. Results Consistent with multipotent capacity, genes in pathways previously associated with adult stem cell maintenance are highly expressed in ovarian surface epithelia and are not expressed or expressed at very low levels in serous ovarian adenocarcinoma. Among the over 2000 genes that are significantly differentially expressed, a number of pathways and novel pathway interactions are identified that may contribute to ovarian adenocarcinoma development.
Nanoparticle-mediated r-depression in the rotifer Brachionus manjavacas

(Georgia Institute of Technology, 2009-12) Hicks, Daniel

Nanotechnology research promises novel and practical applications of well-characterized materials. However, responsible development of the nanotechnology industry necessitates proactive research into the ecological responses of communities to the presence of nano-scale materials. I attempt to discern if and how the presence of inert nanoparticles at varying concentrations and size affects the fitness of populations of Brachionus manjavacas (Rotifera). Feeding fluorescently labeled 50 nm latex microspheres to rotifers produced dramatic fluorescence distributed throughout the females and their eggs. Fluorescent intensity was distinct from background epifluorescence exhibited by B. manjavacas, and increased with concentration, availability of food, and duration of exposure. Transfer of exposed maternal females and F1 offspring into nanoparticle-free environments demonstrated that these nanoparticles were rapidly cleared from the animals, and that the offspring suffered no significant effects from parental exposure. However, the population growth rate was depressed 50% in rotifer cultures exposed to 0.30 ug/mL of 50 nm particles, and 89% in cultures with nanoparticle concentrations of 1.14 ìg/mL. Nanoparticles of identical composition but of larger diameter (up to 3000 nm, comparable to algae cells, a natural food source), caused no reduction in population growth rate. These larger particles remained confined in the gut, implicating nanoparticle size as a critical factor in bioactivity. Causes of growth rate depression include, but are not limited to, a marked decrease in feeding behavior. Mode of entry is suspected to be either epithelial digestive-tract phagocytosis or introduction through cellular pores.
Competition for biotic resources and coexistence in variable environments

(Georgia Institute of Technology, 2009-12-01) Jiang, Lin
Mechanisms and implications of sodium loss in sweat during exercise in the heat for patients with cystic fibrosis and healthy individuals

(Georgia Institute of Technology, 2009-11-17) Brown, Mary Beth

Our aim was to understand mechanisms responsible for excessive electrolyte loss in the sweat gland and the potential impact on fluid balance during exercise in heat stress conditions. Human physiological testing under exercise/heat stress and immunofluorescence staining of sweat glands from skin biopsies were compared between healthy individuals (with normal and high sweat sodium chloride concentration, [NaCl]) and with cystic fibrosis patients (CF), who exhibit excessively salty sweat due to a defect of Cl- channel cystic fibrosis transmembrane conductance regulator (CFTR). Three novel findings are presented. First, excessively salty sweat may be associated with reduced expression of CFTR in the sweat gland reabsorptive duct of healthy individuals in addition to in those with CF; however, although a link to a CF gene mutation in healthy individuals with high sweat [NaCl] was not demonstrated, the possibility of an undetected CFTR mutation or polymorphism remains to be investigated as an underlying mechanism. Two, CF and healthy individuals with excessively salty sweat respond to moderate dehydration (3% body weight loss during exercise) with an attenuated rise in serum osmolality, greater relative loss in plasma volume, but similar perceived thirst compared to healthy individuals with "normal" sweat [NaCl]. However, individuals with CF respond to rehydration with hypotonic beverage by drinking less ad libitum in response to reduced serum [NaCl], suggesting that thirst-guided fluid replacement may be more appropriate for this population rather than restoring 100% of sweat loss following dehydration as is often recommended in healthy individuals.
Development of an assay for fatty acyl-CoAs using liquid chromatography-electrospray ionization-tandem mass spectrometry and its application to the stable isotope labeling and quantitation of sphingolipid metabolism

(Georgia Institute of Technology, 2009-11-16) Haynes, Christopher Allen

Fatty acyl-Coenzyme As are metabolites of lipid anabolism and catabolism. A method was developed for their quantitation in extracts of cultured mammalian cells using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Palmitoyl-CoA (C16:0-CoA) is utilized for de novo sphingolipid biosynthesis catalyzed by serine palmitoyltransferase (SPT), which condenses palmitoyl-CoA and serine to form 3-ketosphinganine. After reduction to form sphinganine (Sa), dihydroceramide synthase (CerS) can N-acylate the Sa using a second fatty acyl-CoA molecule, forming dihydroceramide (DHCer). The CerS enzyme family utilizes different acyl chain lengths of fatty acyl-CoAs in an isoform-specific manner, resulting in DHCer with N-acyl chains ranging from C16 to C26 [and even longer] in mammalian tissues. DHCer is trans-4,5-desaturated to yield ceramide, which is further metabolized by the addition of moieties at the 1-O-position, forming sphingomyelin (SM) and ceramide monohexose (CMH). The rates of fatty acyl-CoA and sphingolipid biosynthesis were determined using stable isotope-labeling and LC-ESI-MS/MS analysis of the analyte isotopologues and isotopomers. Isotopic labeling of palmitoyl-CoA with [U-13C]-palmitate in HEK293 and RAW264.7 cells was robust and rapid (~ 60% labeling of the metabolite pool in 3 hr). Isotopic labeling of sphingolipids indicated utilization of [M + 16]-palmitoyl-CoA by SPT and CerS isoforms in both cell types. Metabolic flux modeling was applied to the data for [U-13C]-palmitate activation to [M + 16]-palmitoyl-CoA and its subsequent utilization in de novo sphingolipid biosynthesis, and this analysis indicated rapid turn-over rates for palmitoyl-CoA and ceramide in both cell types. Palmitate treatment of cultured cells alters their metabolic status and gene expression, therefore labeling of palmitoyl-CoA by treatment with [1-13C]-acetate was employed. A distribution of mass-shifted palmitoyl-CoA species (isotopologues) is observed based on the number of incorporations of [1-13C]-acetate during de novo biosynthesis, requiring computational analysis to derive two parameters: the isotopic enrichment of the precursor pool, and the fraction of palmitoyl-CoA that was biosynthesized during the experiment. Previous reports by others describe mass isotopomer distribution analysis (MIDA) and isotopomer spectral analysis (ISA) for this purpose, and both calculation approaches indicated concurrent results. In summary, the quantitation of fatty acyl-CoAs and their isotopic enrichment during stable isotope-labeling studies of lipid metabolism can provide data that significantly change the interpretation of analyte quantitation in these experiments, as demonstrated here for investigations of de novo sphingolipid biosynthesis.
A Threading-Based Method for the Prediction of DNABinding Proteins with Application to the Human GenomeProteins with Application to the Human Genome

(Georgia Institute of Technology, 2009-11-13) Gao, Mu ; Skolnick, Jeffrey

Diverse mechanisms for DNA-protein recognition have been elucidated in numerous atomic complex structures from various protein families. These structural data provide an invaluable knowledge base not only for understanding DNA protein interactions, but also for developing specialized methods that predict the DNA-binding function from protein structure. While such methods are useful, a major limitation is that they require an experimental structure of the target as input. To overcome this obstacle, we develop a threading-based method, DNA-Binding-Domain-Threader (DBD-Threader, for the prediction of DNA-binding domains and associated DNA-binding protein residues. Our method, which uses a template library composed of DNA-protein complex structures, requires only the target protein’s sequence. In our approach,fold similarity and DNA-binding propensity are employed as two functional discriminating properties. In benchmark tests on 179 DNA-binding and 3,797 non-DNA-binding proteins, using templates whose sequence identity is less than 30% to the target, DBD-Threader achieves a sensitivity/precision of 56%/86%. This performance is considerably better than the standard sequence comparison method PSI-BLAST and is comparable to DBD-Hunter, which requires an experimental structure as input. Moreover, for over 70% of predicted DNA-binding domains, the backbone Root Mean Square Deviations (RMSDs) of the top-ranked structural models are within 6.5 A°of their experimental structures, with their associated DNA binding sites identified at satisfactory accuracy. Additionally, DBD-Threader correctly assigned the SCOP superfamily for most predicted domains. To demonstrate that DBD-Threader is useful for automatic function annotation on a large-scale, DBD-Threader was applied to 18,631 protein sequences from the human genome; 1,654 proteins are predicted to have DNA-binding function. Comparison with existing Gene Ontology (GO) annotations suggests that ,30% of our predictions are new. Finally, we present some interesting predictions in detail. In particular, it is estimated that 20% of classic zinc finger domains play a functional role not related to direct DNA-binding.
Transactivation of Beta 2 Adrenergic Receptor by Bradykinin type 2 Receptor via heterodimerization

(Georgia Institute of Technology, 2009-11-10) Vincent, Karla Kristine

Although a long standing convention maintained that G Protein Coupled Receptors (GPCRs) exist in the plasma membrane solely as monomers, substantial work over the last two decades has demonstrated that these ubiquitous receptors can and in many cases, preferentially, exist as homodimers, heterodimers, or higher order oligomers. Often, two GPCRs of the same class heterodimerize; it is less common for two GPCRs of different signaling pathways to interact. The work presented here studied the physical and functional interaction of two GPCRs from discrete classes, the Beta 2 Adrenergic Receptor (β2AR), a Gαs-coupled receptor, and Bradykinin type 2 Receptor (Bk2R), a Gαq coupled receptor. These data show that Bk2R and β2AR are physically coupled when heterologously expressed in Xenopus oocytes, and in pheochromocytoma (PC12) cells and in freshly isolated murine ventricular myocytes, two systems that endogenously express these receptors. This physical coupling led to functional consequences in heterologous and endogenous expression systems, as Bk2R was able to transactivate β2AR signaling via its direct interaction with the receptor. Furthermore, coexpression of Bk2R shifted the dose response curve of β2AR for its selective agonist rightward in Xenopus oocyte electrophysiology experiments, suggesting the presence of Bk2R negatively affected β2AR native pharmacology. Up to thirty minutes of either bradykinin (BK) or isoproterenol exposure did not change the relative amount of Bk2R/β2AR heterodimer in PC12 cells, a rat adrenal medulla tumor cell line that endogenously expresses these receptors. Despite the obvious signaling consequences, the Bk2R/β2AR heterodimer accounted for only 10% of the total β2AR protein detected and 20% of the total Bk2R protein detected. When other Bk2R-specific ligands were also tested to examine the extent of β2AR transactivation, our data showed that both Lys-des-Arg-Bradykinin, a Bk2R partial agonist and NPC 567, a Bk2R antagonist, transactivated β2AR to the same extent as BK. Taken together, our data provide a novel mode of receptor regulation and signaling via Bk2R/β2AR heterodimerization. Because a large percentage of therapeutics target GPCRs, a greater understanding of how a GPCR heterodimer functions could be beneficial for targeting new drugs and refining existing drugs. Understanding the Bk2R/β2AR heterodimer provides a new perspective on the myriad of fucntional consequences that occur when a GPCR is activated.
Different Effects of Species Diversity on Temporal Stability in Single‐Trophic and Multitrophic Communities

(Georgia Institute of Technology, 2009-11) Jiang, Lin ; Pu, Zhichao

The question of how species diversity affects ecological stability has long interested ecologists and yet remains largely unresolved. Historically, attempts to answer this question have been hampered by the presence of multiple potentially confounding stability concepts, confusion over responses at different levels of ecological organization, discrepancy between theoretical predictions, and, particularly, the paucity of empirical studies. Here we used meta‐analyses to synthesize results of empirical studies published primarily in the past 2 decades on the relationship between species diversity and temporal stability. We show that the overall effect of increasing diversity was positive for community‐level temporal stability but neutral for population‐level temporal stability. There were, however, striking differences in the diversity‐stability relationship between single‐ and multitrophic systems, with diversity stabilizing both population and community dynamics in multitrophic but not single‐trophic communities. These patterns were broadly equivalent across experimental and observational studies as well as across terrestrial and aquatic studies. We discuss possible mechanisms for population stability to increase with diversity in multitrophic systems and for diversity to influence community‐level stability in general. Overall, our results indicate that diversity can affect temporal stability, but the effects may critically depend on trophic complexity.
AAV recombineering with single strand oligonucleotides

(Georgia Institute of Technology, 2009-11) Hirsch, Matthew L. ; Storici, Francesca ; Li, Chengwen ; Choi, Vivian W. ; Samulski, R. Jude

Adeno-associated virus (AAV) transduction initiates a signaling cascade that culminates in a transient DNA damage response. During this time, host DNA repair proteins convert the linear single-strand AAV genomes to double-strand circular monomers and concatemers in processes stimulated by the AAV inverted terminal repeats (ITRs). As the orientation of AAV genome concatemerization appears unbiased, the likelihood of concatemerization in a desired orientation is low (less than 1 in 6). Using a novel recombineering method, Oligo-Assisted AAV Genome Recombination (OAGR), this work demonstrates the ability to direct concatemerization specifically to a desired orientation in human cells. This was achieved by a singlestrand DNA oligonucleotide (oligo) displaying homology to distinct AAV genomes capable of forming an intermolecular bridge for recombination. This DNA repair process results in concatemers with genomic junctions corresponding to the sequence of oligo homology. Furthermore, OAGR was restricted to single-strand, not duplexed, AAV genomes suggestive of replication-dependent recombination. Consistent with this process, OAGR demonstrated oligo polarity biases in all tested configurations except when a portion of the oligo targeted the ITR. This approach, in addition to being useful for the elucidation of intermolecular homologous recombination, may find eventual relevance for AAV mediated large gene therapy.
Biology and ecology of newly discovered diazotrophs in the open ocean

(Georgia Institute of Technology, 2009-10-30) Montoya, Joseph P. ; Zehr, Jon