Ellen Tarr | Midwestern University (original) (raw)

Papers by Ellen Tarr

MOESM1 of Establishing a reference array for the CS-αβ superfamily of defensive peptides

Additional file 1: Figure S1. Alignment of CS-αβ superfamily sequences with reference array. Alig... more Additional file 1: Figure S1. Alignment of CS-αβ superfamily sequences with reference array. Alignment to a ten-cysteine reference array based on the cysteines forming the CSH motif (C3–C8, C4–C9) and the third bond completing the CS-αβ fold (C2–C6). The GXC of the γ-core is usually at C6, except for mytilins (C7). A filled square indicates presence of the indicated cysteine and numbers in unfilled blocks represent the number of intervening amino acids. Sequences are grouped based on the basic cysteine patterns observed and within these by major taxonomic group (listed in column A). Additional cysteines at the N or C-terminus of the conserved array are represented by additional filled boxes. Additional cysteines within the conserved array are represented as “C.” Major taxonomic groups are color-coded: Annelida (dark rose), Arachnida (light orange), Bacteria (black), Bivalvia (light blue), Cnidaria (light grey), Crustacea (peach), Echinodermata (pink), Fungi (light green), Gastropoda (blue), Hexapoda (orange), Myriapoda (dark orange), Nematoda (lavender), Onychophora (light purple), Plantae (green), Platyhelminthes (light rose), Porifera (dark grey), and Tardigrada (yellow).

Neuron, 2001

chanical and noxious stimuli into electrical signals (Caterina and Julius, 1999; Lewin and Stucky... more chanical and noxious stimuli into electrical signals (Caterina and Julius, 1999; Lewin and Stucky, 2000). Earlier studies suggested that the receptors for many of these stimuli are ion channels (French, 1992; Hamill and McBride, 1996).

Nature, 2002

All cell lines were obtained from the American Tissue Culture Collection or the Coriell Institute... more All cell lines were obtained from the American Tissue Culture Collection or the Coriell Institute apart from ATLD1 and ATLD3 cells (a gift from J. Petrini), ATM cells (a gift from Y. Shiloh and J. Engelhardt), and cells with mutant ligase IV (180BRM; a gift from H. Wang and G. Iliakis). To complement cells, the complementary DNAs for Mre11 and NBS1 were amplified by PCR and cloned under control of the CMV promoter in a modified version of the pCLNC retrovirus vector 27. Retroviruses were generated by transfecting gag/pol packaging cell lines, together with a plasmid expressing the VSV-G envelope protein. ATLD or NBS cells were infected with retrovirus supernatants and selected in 900 mg ml 21 G418. We assessed expression of Mre11 and NBS1 by immunoblotting and used pools of resistant clones for complementation experiments. The mre11-3 mutant contains the HD129/130LV mutation generated by site-directed mutagenesis using QuickChange (Stratagene). Antibodies We visualized viral replication centres by staining for DBP with either a mouse monoclonal antibody (B6-8) or rabbit polyclonal antisera. Antibodies were purchased from Novus (NBS1, ATM), Genetex (Mre11-12D7, Rad50-13B3), Santa Cruz (haemagglutinin A (HA), Ku86, DNA-PKcs, NBS1-S343) and Roche (BrdU). Antisera to E4orf6, pTP, PML, RPA70 and DBP were gifts from P. Branton, J. Schaack, T. Sternsdorf, T. Melendy, A. Levine and P. van der Vliet, respectively. All secondary antibodies were from Jackson Laboratories. Viruses, infections, PFGE and western blotting The E4 mutant viruses have been described 8,11 and were propagated and titred by plaque assays on W162, a Vero-derived E4-complementing cell line 28. Wild-type Ad type 5 (Ad5) and dl110 were propagated in human 293 cells. We purified all viruses by two sequential rounds of ultracentrifugation in CsCl gradients and stored them in 40% glycerol at 220 8C. HeLa cells were infected with a multiplicity of infection (MOI) of 25 plaqueforming units (p.f.u.) per cell and collected at the indicated hour post-infection (h.p.i.). Other cell lines were infected with MOIs of 25-100 and collected between 48 and 72 h.p.i. We carried out PFGE essentially as described 5,6 and included l DNA size markers. Western blotting was done as described 20 .

Nematode antimicrobial peptides

DOAJ (DOAJ: Directory of Open Access Journals), Jun 1, 2012

Project Core Anonymous Survey Synopsis of Results

Project Core was an anonymous web-based survey of persons reporting paranormal experiences. Parti... more Project Core was an anonymous web-based survey of persons reporting paranormal experiences. Participants answered a battery of descriptive autobiographical questions and provided narrative accounts of their experiences. The request for accounts was open ended leaving participants entirely free to select and describe in their own words the experience(s) they deemed both significant and paranormal. (See appendix.) The survey was open for a period of one year and yielded a total of 210 responses, 206 of which were examined critically. The overall range of experiences reported was broad with some participants revealing encounters in several event categories. We compared attributes of the self-selected participant group and elements extracted from their paranormal experience reports for potential interrelationships. Our effort suggests several avenues for future hypothesis‐driven investigations. In general, the medical status of experiencers has received scant consideration from investig...

The Hess Deep Rift Valley exposes a young ( 1 Ma) section of lower oceanic crust generated at the... more The Hess Deep Rift Valley exposes a young ( 1 Ma) section of lower oceanic crust generated at the East Pacific Rise (EPR). The drillers recovered 154 m of plutonic rocks from Hole 894G. The mineralogy and textures of these rocks suggest that they represent the roof of a magma chamber. These high-level gabbros, olivine-gabbros, and gabbronorites are slightly hydrated (average LOI = 0.75%, N = 27) and crosscut by a few olivine basaltic dikes. The dikes were altered under greenschist facies conditions, and the gabbros were amphibolitized. Most of the gabbros have Sr-isotopic ratios that range from 0.70247 to 0.70309, indicative of low water-rock ratios (<l), with a circulating fluid having a 87 Sr/ 86 Sr ratio calculated at 0.7032. The δ' 8 O values of the gabbros range from 2.2 to 6.5 and are generally much lower (average δ l8 θ = 4.8, N = 31) than the mantle reference value (5.7 ± 0.2), whereas olivine basalts do not show any I8 O depletion. The δ 18 θ values of clinopyroxenes are often anomalously low (5.1-5.3). Clinopyroxene-plagioclase fractionation values reach 1.5 and reveal strong isotopic disequilibrium attributed to high-temperature isotopic exchange with a discrete aqueous fluid. Clinopyroxenes with δ 18 θ 5 contain minute Mg-rich amphibole lamellae (1-5 mm) that represent a very early stage of high-temperature alteration before altering totally into amphibole. Except for a few samples with isotopic compositions that were reequilibrated at low temperatures (<200°C), the gabbros contain low-δ 18 θ Plagioclase (δ' 8 O = 3-5) that recrystallized at high temperatures (400°-600°C) without exchanging major cations (An-,,^). The Hess Deep gabbros record mechanisms of isotopic exchanges governed by percolation of fluids along grain boundaries and self-diffusion of oxygen through Plagioclase without involving macroscopic brittle deformation. These water-rock interactions produced a sequence of low-18 O oceanic rocks early in the spreading history of the EPR that can be compared with the gabbro sequence of the Oman ophiolite.

Project Core, Ellen's Commentary

Review of "Novel North American Hominins, Next Generation Sequencing of Three Whole Genomes and Associated Studies," Ketchum et al., 2012

Background: Plant resistance (R) gene products recognize pathogen effector molecules. Many R gene... more Background: Plant resistance (R) gene products recognize pathogen effector molecules. Many R genes code for proteins containing nucleotide binding site (NBS) and C-terminal leucine-rich repeat (LRR) domains. NBS-LRR proteins can be divided into two groups, TIR-NBS-LRR and non-TIR-NBS-LRR, based on the structure of the N-terminal domain. Although both classes are clearly present in gymnosperms and eudicots, only non-TIR sequences have been found consistently in monocots. Since most studies in monocots have been limited to agriculturally important grasses, it is difficult to draw conclusions. The purpose of our study was to look for evidence of these sequences in additional monocot orders. Findings: Using degenerate PCR, we amplified NBS sequences from four monocot species (C. blanda, D. marginata, S. trifasciata, and Spathiphyllum sp.), a gymnosperm (C. revoluta) and a eudicot (C. canephora). We successfully amplified TIR-NBS-LRR sequences from dicot and gymnosperm DNA, but not from monocot DNA. Using databases, we obtained NBS sequences from additional monocots, magnoliids and basal angiosperms. TIR-type sequences were not present in monocot or magnoliid sequences, but were present in the basal angiosperms. Phylogenetic analysis supported a single TIR clade and multiple non-TIR clades. Conclusion: We were unable to find monocot TIR-NBS-LRR sequences by PCR amplification or database searches. In contrast to previous studies, our results represent five monocot orders (Poales, Zingiberales, Arecales, Asparagales, and Alismatales). Our results establish the presence of TIR-NBS-LRR sequences in basal angiosperms and suggest that although these sequences were present in early land plants, they have been reduced significantly in monocots and magnoliids.

Journal of nematology, 2017

Caenorhabditis elegans responds to infections by upregulating specific antimicrobial peptides. Th... more Caenorhabditis elegans responds to infections by upregulating specific antimicrobial peptides. The caenacin-2 (cnc-2) gene is consistently upregulated in C. elegans by infection with the filamentous fungus Drechmeria coniospora, but there have been no direct studies of the CNC-2 peptide's in vivo or in vitro role in defending the nematode against this pathogen. We compared infection of wild-type and cnc-2 knockout nematode strains with four potential pathogens: D. coniospora, Candida albicans, Staphylococcus aureus, and Bacillus subtilis. There was no significant difference in survival between strains for any of the pathogens or on the maintenance strain of Escherichia coli. While we were unable to demonstrate definitively that CNC-2 is integral to fungal defenses in C. elegans, we identified possible explanations for these results as well as future work that is needed to investigate CNC-2's potential as a new antifungal treatment.

{"__content__"=>"An Investigation of the Potential Antifungal Properties of CNC-2 in .", "i"=>{"__content__"=>"Caenorhabditis elegans"}}

Journal of nematology, 2017

responds to infections by upregulating specific antimicrobial peptides. The caenacin-2 () gene is... more responds to infections by upregulating specific antimicrobial peptides. The caenacin-2 () gene is consistently upregulated in by infection with the filamentous fungus , but there have been no direct studies of the CNC-2 peptide's in vivo or in vitro role in defending the nematode against this pathogen. We compared infection of wild-type and knockout nematode strains with four potential pathogens: , , , and . There was no significant difference in survival between strains for any of the pathogens or on the maintenance strain of . While we were unable to demonstrate definitively that CNC-2 is integral to fungal defenses in , we identified possible explanations for these results as well as future work that is needed to investigate CNC-2's potential as a new antifungal treatment.

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Journal of Visualized Experiments

BMC research notes, Jan 18, 2016

Background: "Invertebrate defensins" belong to the cysteine-stabilized alpha-beta (CS-αβ), also k... more Background: "Invertebrate defensins" belong to the cysteine-stabilized alpha-beta (CS-αβ), also known as the scorpion toxin-like, superfamily. Some other peptides belonging to this superfamily of defensive peptides are indistinguishable from "defensins, " but have been assigned other names, making it unclear what, if any, criteria must be met to qualify as an "invertebrate defensin. " In addition, there are other groups of defensins in invertebrates and vertebrates that are considered to be evolutionarily unrelated to those in the CS-αβ superfamily. This complicates analyses and discussions of this peptide group. This paper investigates the criteria for classifying a peptide as an invertebrate defensin, suggests a reference cysteine array that may be helpful in discussing peptides in this superfamily, and proposes that the superfamily (rather than the name "defensin") is the appropriate context for studying the evolution of invertebrate defensins with the CS-αβ fold. Methods: CS-αβ superfamily sequences were identified from previous literature and BLAST searches of public databases. Sequences were retrieved from databases, and the relevant motifs were identified and used to create a conceptual alignment to a ten-cysteine reference array. Amino acid sequences were aligned in MEGA6 with manual adjustments to ensure accurate alignment of cysteines. Phylogenetic analyses were performed in MEGA6 (maximum likelihood) and MrBayes (Bayesian). Results: Across invertebrate taxa, the term "defensin" is not consistently applied based on number of cysteines, cysteine spacing pattern, spectrum of antimicrobial activity, or phylogenetic relationship. The analyses failed to reveal any criteria that unify "invertebrate defensins" and differentiate them from other defensive peptides in the CS-αβ superfamily. Sequences from various groups within the CS-αβ superfamily of defensive peptides can be described by a ten-cysteine reference array that aligns their defining structural motifs. Conclusions: The proposed ten-cysteine reference array can be used in addition to current nomenclature to compare sequences in the CS-αβ superfamily and clarify their features relative to one another. This will facilitate analysis and discussion of "invertebrate defensins" in an appropriate evolutionary context, rather than relying on nomenclature.

Molecular and biochemical parasitology, 2004

Nematode sperm utilize a crawling motility based on polymerization--depolymerization of a nematod... more Nematode sperm utilize a crawling motility based on polymerization--depolymerization of a nematode-specific cytoskeletal molecule-major sperm protein (MSP). While several proteins that interact with and regulate MSP filament formation have been identified using in vitro approaches, it is likely that additional molecules participate in vivo in the regulation of MSP cytoskeletal dynamics. By comparing EST data generated from an Ascaris suum testis germinal zone cDNA library with EST data from other tissue- and stage-specific A. suum cDNA libraries and with expression profile data from Caenorhabditis elegans, 42 genes were selected with exclusive or enhanced expression in male germ line cells. In addition to 11 protein kinases and seven protein phosphatases, 10 genes encoding proteins with protein-protein interaction domains were identified. These potential cytoskeletal modifiers included five novel MSP-domain proteins (As-MDPs). All five As-mdps were highly expressed in male germ line...

MSP domain proteins

Trends in Parasitology, 2005

The major sperm protein (MSP) has attracted interest because of its ability to mediate actin-like... more The major sperm protein (MSP) has attracted interest because of its ability to mediate actin-like ameboid motility in nematode sperm, despite a lack of sequence or structural similarity to actin. The basic immunoglobulin-like organization of MSP defines a structural domain found in proteins from many eukaryotic species. Within the context of MSP domain proteins (MDPs), evidence suggests that this structure functions as a protein-protein interaction domain and a signaling element. In this article, we describe the current status of knowledge about the MDP family of proteins, outline their structure and phylogeny, and discuss potential roles of MDPs in the biology of parasitic nematodes.

Proceedings of the National Academy of Sciences, 1999

The epithelial Na ؉ channel (ENaC) is composed of three homologous subunits: ␣, ␤ and ␥. We used ... more The epithelial Na ؉ channel (ENaC) is composed of three homologous subunits: ␣, ␤ and ␥. We used gene targeting to disrupt the ␤ subunit gene of ENaC in mice. The ␤ENaC-deficient mice showed normal prenatal development but died within 2 days after birth, most likely of hyperkalemia. In the ؊͞؊ mice, we found an increased urine Na ؉ concentration despite hyponatremia and a decreased urine K ؉ concentration despite hyperkalemia. Moreover, serum aldosterone levels were increased. In contrast to ␣ENaC-deficient mice, which die because of defective lung liquid clearance, neonatal ␤ENaC deficient mice did not die of respiratory failure and showed only a small increase in wet lung weight that had little, if any, adverse physiologic consequence. The results indicate that, in vivo, the ␤ subunit is required for ENaC function in the renal collecting duct, but, in contrast to the ␣ subunit, the ␤ subunit is not required for the transition from a liquid-filled to an air-filled lung. The phenotype of the ␤ENaC-deficient mice is similar to that of humans with pseudohypoaldosteronism type 1 and may provide a useful model to study the pathogenesis and treatment of this disorder.

Molecular and Biochemical Parasitology, 2005

Nematode sperm utilize a crawling motility based on a nematode sperm-specific cytoskeletal protei... more Nematode sperm utilize a crawling motility based on a nematode sperm-specific cytoskeletal protein called the major sperm protein (MSP). Although MSP has no similarity to actin in sequence or structure, the motility mediated by these two proteins is nearly indistinguishable at a phenotypic level. As with the traditional actin cytoskeleton, the central component of MSP-based motility (MSP) interacts with accessory proteins that regulate polymerization and depolymerization and play a key role in cell motility. A bioinformatics approach has led to the identification of proteins with enhanced expression in the Ascaris suum male germ line, including five new proteins each containing an MSP domain. One of these MSP domain proteins (As-MDP-1) contains an MSP domain in the C-terminus and a N-terminal extension rich in prolines and alanines. The 15.6 kDa As-MDP-1 was shown to be >90% identical at the amino acid level to members of a small family of Ascaris proteins that have been shown to bind to the MSP cytoskeleton and to negatively regulate MSP fiber growth. Further, it was demonstrated that As-MDP-1 is the smallest member of the MFP1 triplet of negative regulators of MSP cytoskeleton formation. Antibodies were used to detect the presence of As-MDP-1 along the entire length of the MSP fibers suggesting that As-MDP-1 binds directly to the higher order forms of MSP. This protein has orthologues in other nematode species, is present in Ascaris in at least six allelic forms, and is likely to form multimers.

Molecular and Biochemical Parasitology, 2002

The protozoan Leishmania chagasi expresses a surface metalloprotease, GP63, whose abundance incre... more The protozoan Leishmania chagasi expresses a surface metalloprotease, GP63, whose abundance increases 14-fold as parasites grow from logarithmic to stationary phase. L. chagasi GP63 is encoded by three classes of MSP genes that are differentially expressed during parasite growth. Using metabolic labeling and immunoprecipitation, we found L. chagasi GP63 first appeared as a 66-kDa band that was replaced by a 63-kDa protein. This pattern also occurred in transfected L. donovani harboring detectable products of only one MSP gene, suggesting a precursor Á/product relationship. The half-life of GP63 increased from 29 h in logarithmic phase to /72 h in stationary phase promastigotes. GP63 loss from the cell was complemented by the appearance of a 63-kDa GP63 in extracellular medium in both membrane-associated and-free forms. Calculations suggested that the long and lengthening T 1/2 of cell-associated GP63 accounts in part for its progressive accumulation in the cell during promastigote growth. The current findings add yet another level of complexity to post-transcriptionally regulated expression of an abundant surface molecule in a trypanosomatid protozoan.

Gene, 2001

Macrophage migration inhibitory factor (MIF) from vertebrate species is a molecule that exerts a ... more Macrophage migration inhibitory factor (MIF) from vertebrate species is a molecule that exerts a wide-range of effects in inflammatory responses, cell activation and cell differentiation. Several species of parasitic nematodes have been shown to express genes encoding orthologues of the mammalian MIF that appear to play a key role in immune evasion by modifying the activity of host cells. In addition, MIF accumulates in nematode somatic cells where its role has not yet been defined. In order to identify the role that MIF plays in the cell biology of nematodes, we have characterized the members of the mif gene family in the free-living species Caenorhabditis elegans. Unlike the single mif gene found in humans and mice, C. elegans expresses four distinct mif genes: Ce-mif-1, Ce-mif-2, Ce-mif-3 and Ce-mif-4. The Ce-MIF proteins are between 15-30% identical to each other, 34-38% identical to the MIFs from the parasitic nematode Brugia malayi, and 22-35% identical to mammalian MIFs. The transcription of Ce-mif-2 and Ce-mif-3, but not Ce-mif-1, was upregulated .100-fold compared to L2 levels when the worms entered the dauer stage. The transcription levels of Ce-mif-2 and Ce-mif-3 fell to near baseline a few hours after exit from dauer. Ce-MIF/GFP transgenic animals and immunostaining were used to demonstrate that the main sites of MIF production are in the hypodermis, body wall muscles and in the nuclei of developing embryos. The results suggest a role for C. elegans MIF in cellular maintenance during periods of adverse conditions that lead to developmental arrest.

Developmental & Comparative Immunology, 2012

Several groups of antimicrobial effector molecules have been identified in nematodes, but most st... more Several groups of antimicrobial effector molecules have been identified in nematodes, but most studies have been limited to Caenorhabditis elegans and, to a lesser extent, Ascaris suum. Although these two species are not closely related, they are not representative of overall nematode diversity. This study utilized available sequence information to investigate whether four groups of antimicrobial effectors (defensinlike antibacterial factors [ABFs], cecropins, saposin domain-containing proteins, and lysozymes) are components of an archetypal nematode immune system or more narrowly restricted. Saposin domaincontaining proteins (caenopores in C. elegans) and lysozymes were widely distributed and found in most taxa, but likely have digestive as well as defensive functions. ABFs were widely distributed in fewer taxa, suggesting selective loss in some lineages. In contrast, cecropins were identified in only three related species, suggesting acquisition of this effector molecule in their common ancestor.

MOESM1 of Establishing a reference array for the CS-αβ superfamily of defensive peptides

Additional file 1: Figure S1. Alignment of CS-αβ superfamily sequences with reference array. Alig... more Additional file 1: Figure S1. Alignment of CS-αβ superfamily sequences with reference array. Alignment to a ten-cysteine reference array based on the cysteines forming the CSH motif (C3–C8, C4–C9) and the third bond completing the CS-αβ fold (C2–C6). The GXC of the γ-core is usually at C6, except for mytilins (C7). A filled square indicates presence of the indicated cysteine and numbers in unfilled blocks represent the number of intervening amino acids. Sequences are grouped based on the basic cysteine patterns observed and within these by major taxonomic group (listed in column A). Additional cysteines at the N or C-terminus of the conserved array are represented by additional filled boxes. Additional cysteines within the conserved array are represented as “C.” Major taxonomic groups are color-coded: Annelida (dark rose), Arachnida (light orange), Bacteria (black), Bivalvia (light blue), Cnidaria (light grey), Crustacea (peach), Echinodermata (pink), Fungi (light green), Gastropoda (blue), Hexapoda (orange), Myriapoda (dark orange), Nematoda (lavender), Onychophora (light purple), Plantae (green), Platyhelminthes (light rose), Porifera (dark grey), and Tardigrada (yellow).

Neuron, 2001

chanical and noxious stimuli into electrical signals (Caterina and Julius, 1999; Lewin and Stucky... more chanical and noxious stimuli into electrical signals (Caterina and Julius, 1999; Lewin and Stucky, 2000). Earlier studies suggested that the receptors for many of these stimuli are ion channels (French, 1992; Hamill and McBride, 1996).

Nature, 2002

All cell lines were obtained from the American Tissue Culture Collection or the Coriell Institute... more All cell lines were obtained from the American Tissue Culture Collection or the Coriell Institute apart from ATLD1 and ATLD3 cells (a gift from J. Petrini), ATM cells (a gift from Y. Shiloh and J. Engelhardt), and cells with mutant ligase IV (180BRM; a gift from H. Wang and G. Iliakis). To complement cells, the complementary DNAs for Mre11 and NBS1 were amplified by PCR and cloned under control of the CMV promoter in a modified version of the pCLNC retrovirus vector 27. Retroviruses were generated by transfecting gag/pol packaging cell lines, together with a plasmid expressing the VSV-G envelope protein. ATLD or NBS cells were infected with retrovirus supernatants and selected in 900 mg ml 21 G418. We assessed expression of Mre11 and NBS1 by immunoblotting and used pools of resistant clones for complementation experiments. The mre11-3 mutant contains the HD129/130LV mutation generated by site-directed mutagenesis using QuickChange (Stratagene). Antibodies We visualized viral replication centres by staining for DBP with either a mouse monoclonal antibody (B6-8) or rabbit polyclonal antisera. Antibodies were purchased from Novus (NBS1, ATM), Genetex (Mre11-12D7, Rad50-13B3), Santa Cruz (haemagglutinin A (HA), Ku86, DNA-PKcs, NBS1-S343) and Roche (BrdU). Antisera to E4orf6, pTP, PML, RPA70 and DBP were gifts from P. Branton, J. Schaack, T. Sternsdorf, T. Melendy, A. Levine and P. van der Vliet, respectively. All secondary antibodies were from Jackson Laboratories. Viruses, infections, PFGE and western blotting The E4 mutant viruses have been described 8,11 and were propagated and titred by plaque assays on W162, a Vero-derived E4-complementing cell line 28. Wild-type Ad type 5 (Ad5) and dl110 were propagated in human 293 cells. We purified all viruses by two sequential rounds of ultracentrifugation in CsCl gradients and stored them in 40% glycerol at 220 8C. HeLa cells were infected with a multiplicity of infection (MOI) of 25 plaqueforming units (p.f.u.) per cell and collected at the indicated hour post-infection (h.p.i.). Other cell lines were infected with MOIs of 25-100 and collected between 48 and 72 h.p.i. We carried out PFGE essentially as described 5,6 and included l DNA size markers. Western blotting was done as described 20 .

Nematode antimicrobial peptides

DOAJ (DOAJ: Directory of Open Access Journals), Jun 1, 2012

Project Core Anonymous Survey Synopsis of Results

Project Core was an anonymous web-based survey of persons reporting paranormal experiences. Parti... more Project Core was an anonymous web-based survey of persons reporting paranormal experiences. Participants answered a battery of descriptive autobiographical questions and provided narrative accounts of their experiences. The request for accounts was open ended leaving participants entirely free to select and describe in their own words the experience(s) they deemed both significant and paranormal. (See appendix.) The survey was open for a period of one year and yielded a total of 210 responses, 206 of which were examined critically. The overall range of experiences reported was broad with some participants revealing encounters in several event categories. We compared attributes of the self-selected participant group and elements extracted from their paranormal experience reports for potential interrelationships. Our effort suggests several avenues for future hypothesis‐driven investigations. In general, the medical status of experiencers has received scant consideration from investig...

The Hess Deep Rift Valley exposes a young ( 1 Ma) section of lower oceanic crust generated at the... more The Hess Deep Rift Valley exposes a young ( 1 Ma) section of lower oceanic crust generated at the East Pacific Rise (EPR). The drillers recovered 154 m of plutonic rocks from Hole 894G. The mineralogy and textures of these rocks suggest that they represent the roof of a magma chamber. These high-level gabbros, olivine-gabbros, and gabbronorites are slightly hydrated (average LOI = 0.75%, N = 27) and crosscut by a few olivine basaltic dikes. The dikes were altered under greenschist facies conditions, and the gabbros were amphibolitized. Most of the gabbros have Sr-isotopic ratios that range from 0.70247 to 0.70309, indicative of low water-rock ratios (<l), with a circulating fluid having a 87 Sr/ 86 Sr ratio calculated at 0.7032. The δ' 8 O values of the gabbros range from 2.2 to 6.5 and are generally much lower (average δ l8 θ = 4.8, N = 31) than the mantle reference value (5.7 ± 0.2), whereas olivine basalts do not show any I8 O depletion. The δ 18 θ values of clinopyroxenes are often anomalously low (5.1-5.3). Clinopyroxene-plagioclase fractionation values reach 1.5 and reveal strong isotopic disequilibrium attributed to high-temperature isotopic exchange with a discrete aqueous fluid. Clinopyroxenes with δ 18 θ 5 contain minute Mg-rich amphibole lamellae (1-5 mm) that represent a very early stage of high-temperature alteration before altering totally into amphibole. Except for a few samples with isotopic compositions that were reequilibrated at low temperatures (<200°C), the gabbros contain low-δ 18 θ Plagioclase (δ' 8 O = 3-5) that recrystallized at high temperatures (400°-600°C) without exchanging major cations (An-,,^). The Hess Deep gabbros record mechanisms of isotopic exchanges governed by percolation of fluids along grain boundaries and self-diffusion of oxygen through Plagioclase without involving macroscopic brittle deformation. These water-rock interactions produced a sequence of low-18 O oceanic rocks early in the spreading history of the EPR that can be compared with the gabbro sequence of the Oman ophiolite.

Project Core, Ellen's Commentary

Review of "Novel North American Hominins, Next Generation Sequencing of Three Whole Genomes and Associated Studies," Ketchum et al., 2012

Background: Plant resistance (R) gene products recognize pathogen effector molecules. Many R gene... more Background: Plant resistance (R) gene products recognize pathogen effector molecules. Many R genes code for proteins containing nucleotide binding site (NBS) and C-terminal leucine-rich repeat (LRR) domains. NBS-LRR proteins can be divided into two groups, TIR-NBS-LRR and non-TIR-NBS-LRR, based on the structure of the N-terminal domain. Although both classes are clearly present in gymnosperms and eudicots, only non-TIR sequences have been found consistently in monocots. Since most studies in monocots have been limited to agriculturally important grasses, it is difficult to draw conclusions. The purpose of our study was to look for evidence of these sequences in additional monocot orders. Findings: Using degenerate PCR, we amplified NBS sequences from four monocot species (C. blanda, D. marginata, S. trifasciata, and Spathiphyllum sp.), a gymnosperm (C. revoluta) and a eudicot (C. canephora). We successfully amplified TIR-NBS-LRR sequences from dicot and gymnosperm DNA, but not from monocot DNA. Using databases, we obtained NBS sequences from additional monocots, magnoliids and basal angiosperms. TIR-type sequences were not present in monocot or magnoliid sequences, but were present in the basal angiosperms. Phylogenetic analysis supported a single TIR clade and multiple non-TIR clades. Conclusion: We were unable to find monocot TIR-NBS-LRR sequences by PCR amplification or database searches. In contrast to previous studies, our results represent five monocot orders (Poales, Zingiberales, Arecales, Asparagales, and Alismatales). Our results establish the presence of TIR-NBS-LRR sequences in basal angiosperms and suggest that although these sequences were present in early land plants, they have been reduced significantly in monocots and magnoliids.

Journal of nematology, 2017

Caenorhabditis elegans responds to infections by upregulating specific antimicrobial peptides. Th... more Caenorhabditis elegans responds to infections by upregulating specific antimicrobial peptides. The caenacin-2 (cnc-2) gene is consistently upregulated in C. elegans by infection with the filamentous fungus Drechmeria coniospora, but there have been no direct studies of the CNC-2 peptide's in vivo or in vitro role in defending the nematode against this pathogen. We compared infection of wild-type and cnc-2 knockout nematode strains with four potential pathogens: D. coniospora, Candida albicans, Staphylococcus aureus, and Bacillus subtilis. There was no significant difference in survival between strains for any of the pathogens or on the maintenance strain of Escherichia coli. While we were unable to demonstrate definitively that CNC-2 is integral to fungal defenses in C. elegans, we identified possible explanations for these results as well as future work that is needed to investigate CNC-2's potential as a new antifungal treatment.

{"__content__"=>"An Investigation of the Potential Antifungal Properties of CNC-2 in .", "i"=>{"__content__"=>"Caenorhabditis elegans"}}

Journal of nematology, 2017

responds to infections by upregulating specific antimicrobial peptides. The caenacin-2 () gene is... more responds to infections by upregulating specific antimicrobial peptides. The caenacin-2 () gene is consistently upregulated in by infection with the filamentous fungus , but there have been no direct studies of the CNC-2 peptide's in vivo or in vitro role in defending the nematode against this pathogen. We compared infection of wild-type and knockout nematode strains with four potential pathogens: , , , and . There was no significant difference in survival between strains for any of the pathogens or on the maintenance strain of . While we were unable to demonstrate definitively that CNC-2 is integral to fungal defenses in , we identified possible explanations for these results as well as future work that is needed to investigate CNC-2's potential as a new antifungal treatment.

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Journal of Visualized Experiments

BMC research notes, Jan 18, 2016

Background: "Invertebrate defensins" belong to the cysteine-stabilized alpha-beta (CS-αβ), also k... more Background: "Invertebrate defensins" belong to the cysteine-stabilized alpha-beta (CS-αβ), also known as the scorpion toxin-like, superfamily. Some other peptides belonging to this superfamily of defensive peptides are indistinguishable from "defensins, " but have been assigned other names, making it unclear what, if any, criteria must be met to qualify as an "invertebrate defensin. " In addition, there are other groups of defensins in invertebrates and vertebrates that are considered to be evolutionarily unrelated to those in the CS-αβ superfamily. This complicates analyses and discussions of this peptide group. This paper investigates the criteria for classifying a peptide as an invertebrate defensin, suggests a reference cysteine array that may be helpful in discussing peptides in this superfamily, and proposes that the superfamily (rather than the name "defensin") is the appropriate context for studying the evolution of invertebrate defensins with the CS-αβ fold. Methods: CS-αβ superfamily sequences were identified from previous literature and BLAST searches of public databases. Sequences were retrieved from databases, and the relevant motifs were identified and used to create a conceptual alignment to a ten-cysteine reference array. Amino acid sequences were aligned in MEGA6 with manual adjustments to ensure accurate alignment of cysteines. Phylogenetic analyses were performed in MEGA6 (maximum likelihood) and MrBayes (Bayesian). Results: Across invertebrate taxa, the term "defensin" is not consistently applied based on number of cysteines, cysteine spacing pattern, spectrum of antimicrobial activity, or phylogenetic relationship. The analyses failed to reveal any criteria that unify "invertebrate defensins" and differentiate them from other defensive peptides in the CS-αβ superfamily. Sequences from various groups within the CS-αβ superfamily of defensive peptides can be described by a ten-cysteine reference array that aligns their defining structural motifs. Conclusions: The proposed ten-cysteine reference array can be used in addition to current nomenclature to compare sequences in the CS-αβ superfamily and clarify their features relative to one another. This will facilitate analysis and discussion of "invertebrate defensins" in an appropriate evolutionary context, rather than relying on nomenclature.

Molecular and biochemical parasitology, 2004

Nematode sperm utilize a crawling motility based on polymerization--depolymerization of a nematod... more Nematode sperm utilize a crawling motility based on polymerization--depolymerization of a nematode-specific cytoskeletal molecule-major sperm protein (MSP). While several proteins that interact with and regulate MSP filament formation have been identified using in vitro approaches, it is likely that additional molecules participate in vivo in the regulation of MSP cytoskeletal dynamics. By comparing EST data generated from an Ascaris suum testis germinal zone cDNA library with EST data from other tissue- and stage-specific A. suum cDNA libraries and with expression profile data from Caenorhabditis elegans, 42 genes were selected with exclusive or enhanced expression in male germ line cells. In addition to 11 protein kinases and seven protein phosphatases, 10 genes encoding proteins with protein-protein interaction domains were identified. These potential cytoskeletal modifiers included five novel MSP-domain proteins (As-MDPs). All five As-mdps were highly expressed in male germ line...

MSP domain proteins

Trends in Parasitology, 2005

The major sperm protein (MSP) has attracted interest because of its ability to mediate actin-like... more The major sperm protein (MSP) has attracted interest because of its ability to mediate actin-like ameboid motility in nematode sperm, despite a lack of sequence or structural similarity to actin. The basic immunoglobulin-like organization of MSP defines a structural domain found in proteins from many eukaryotic species. Within the context of MSP domain proteins (MDPs), evidence suggests that this structure functions as a protein-protein interaction domain and a signaling element. In this article, we describe the current status of knowledge about the MDP family of proteins, outline their structure and phylogeny, and discuss potential roles of MDPs in the biology of parasitic nematodes.

Proceedings of the National Academy of Sciences, 1999

The epithelial Na ؉ channel (ENaC) is composed of three homologous subunits: ␣, ␤ and ␥. We used ... more The epithelial Na ؉ channel (ENaC) is composed of three homologous subunits: ␣, ␤ and ␥. We used gene targeting to disrupt the ␤ subunit gene of ENaC in mice. The ␤ENaC-deficient mice showed normal prenatal development but died within 2 days after birth, most likely of hyperkalemia. In the ؊͞؊ mice, we found an increased urine Na ؉ concentration despite hyponatremia and a decreased urine K ؉ concentration despite hyperkalemia. Moreover, serum aldosterone levels were increased. In contrast to ␣ENaC-deficient mice, which die because of defective lung liquid clearance, neonatal ␤ENaC deficient mice did not die of respiratory failure and showed only a small increase in wet lung weight that had little, if any, adverse physiologic consequence. The results indicate that, in vivo, the ␤ subunit is required for ENaC function in the renal collecting duct, but, in contrast to the ␣ subunit, the ␤ subunit is not required for the transition from a liquid-filled to an air-filled lung. The phenotype of the ␤ENaC-deficient mice is similar to that of humans with pseudohypoaldosteronism type 1 and may provide a useful model to study the pathogenesis and treatment of this disorder.

Molecular and Biochemical Parasitology, 2005

Nematode sperm utilize a crawling motility based on a nematode sperm-specific cytoskeletal protei... more Nematode sperm utilize a crawling motility based on a nematode sperm-specific cytoskeletal protein called the major sperm protein (MSP). Although MSP has no similarity to actin in sequence or structure, the motility mediated by these two proteins is nearly indistinguishable at a phenotypic level. As with the traditional actin cytoskeleton, the central component of MSP-based motility (MSP) interacts with accessory proteins that regulate polymerization and depolymerization and play a key role in cell motility. A bioinformatics approach has led to the identification of proteins with enhanced expression in the Ascaris suum male germ line, including five new proteins each containing an MSP domain. One of these MSP domain proteins (As-MDP-1) contains an MSP domain in the C-terminus and a N-terminal extension rich in prolines and alanines. The 15.6 kDa As-MDP-1 was shown to be >90% identical at the amino acid level to members of a small family of Ascaris proteins that have been shown to bind to the MSP cytoskeleton and to negatively regulate MSP fiber growth. Further, it was demonstrated that As-MDP-1 is the smallest member of the MFP1 triplet of negative regulators of MSP cytoskeleton formation. Antibodies were used to detect the presence of As-MDP-1 along the entire length of the MSP fibers suggesting that As-MDP-1 binds directly to the higher order forms of MSP. This protein has orthologues in other nematode species, is present in Ascaris in at least six allelic forms, and is likely to form multimers.

Molecular and Biochemical Parasitology, 2002

The protozoan Leishmania chagasi expresses a surface metalloprotease, GP63, whose abundance incre... more The protozoan Leishmania chagasi expresses a surface metalloprotease, GP63, whose abundance increases 14-fold as parasites grow from logarithmic to stationary phase. L. chagasi GP63 is encoded by three classes of MSP genes that are differentially expressed during parasite growth. Using metabolic labeling and immunoprecipitation, we found L. chagasi GP63 first appeared as a 66-kDa band that was replaced by a 63-kDa protein. This pattern also occurred in transfected L. donovani harboring detectable products of only one MSP gene, suggesting a precursor Á/product relationship. The half-life of GP63 increased from 29 h in logarithmic phase to /72 h in stationary phase promastigotes. GP63 loss from the cell was complemented by the appearance of a 63-kDa GP63 in extracellular medium in both membrane-associated and-free forms. Calculations suggested that the long and lengthening T 1/2 of cell-associated GP63 accounts in part for its progressive accumulation in the cell during promastigote growth. The current findings add yet another level of complexity to post-transcriptionally regulated expression of an abundant surface molecule in a trypanosomatid protozoan.

Gene, 2001

Macrophage migration inhibitory factor (MIF) from vertebrate species is a molecule that exerts a ... more Macrophage migration inhibitory factor (MIF) from vertebrate species is a molecule that exerts a wide-range of effects in inflammatory responses, cell activation and cell differentiation. Several species of parasitic nematodes have been shown to express genes encoding orthologues of the mammalian MIF that appear to play a key role in immune evasion by modifying the activity of host cells. In addition, MIF accumulates in nematode somatic cells where its role has not yet been defined. In order to identify the role that MIF plays in the cell biology of nematodes, we have characterized the members of the mif gene family in the free-living species Caenorhabditis elegans. Unlike the single mif gene found in humans and mice, C. elegans expresses four distinct mif genes: Ce-mif-1, Ce-mif-2, Ce-mif-3 and Ce-mif-4. The Ce-MIF proteins are between 15-30% identical to each other, 34-38% identical to the MIFs from the parasitic nematode Brugia malayi, and 22-35% identical to mammalian MIFs. The transcription of Ce-mif-2 and Ce-mif-3, but not Ce-mif-1, was upregulated .100-fold compared to L2 levels when the worms entered the dauer stage. The transcription levels of Ce-mif-2 and Ce-mif-3 fell to near baseline a few hours after exit from dauer. Ce-MIF/GFP transgenic animals and immunostaining were used to demonstrate that the main sites of MIF production are in the hypodermis, body wall muscles and in the nuclei of developing embryos. The results suggest a role for C. elegans MIF in cellular maintenance during periods of adverse conditions that lead to developmental arrest.

Developmental & Comparative Immunology, 2012

Several groups of antimicrobial effector molecules have been identified in nematodes, but most st... more Several groups of antimicrobial effector molecules have been identified in nematodes, but most studies have been limited to Caenorhabditis elegans and, to a lesser extent, Ascaris suum. Although these two species are not closely related, they are not representative of overall nematode diversity. This study utilized available sequence information to investigate whether four groups of antimicrobial effectors (defensinlike antibacterial factors [ABFs], cecropins, saposin domain-containing proteins, and lysozymes) are components of an archetypal nematode immune system or more narrowly restricted. Saposin domaincontaining proteins (caenopores in C. elegans) and lysozymes were widely distributed and found in most taxa, but likely have digestive as well as defensive functions. ABFs were widely distributed in fewer taxa, suggesting selective loss in some lineages. In contrast, cecropins were identified in only three related species, suggesting acquisition of this effector molecule in their common ancestor.