Scholarly Works, Biological Sciences
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- Aberrant early growth of individual trigeminal sensory and motor axons in a series of mouse genetic models of 22q11.2 deletion syndromeMotahari, Zahra; Maynard, Thomas M.; Popratiloff, Anastas; Moody, Sally A.; LaMantia, Anthony-Samuel (2020-09-15)We identified divergent modes of initial axon growth that prefigure disrupted differentiation of the trigeminal nerve (CN V), a cranial nerve essential for suckling, feeding and swallowing (S/F/S), a key innate behavior compromised in multiple genetic developmental disorders including DiGeorge/22q11.2 Deletion Syndrome (22q11.2 DS). We combined rapid in vivo labeling of single CN V axons in LgDel(+/-) mouse embryos, a genomically accurate 22q11.2DS model, and 3D imaging to identify and quantify phenotypes that could not be resolved using existing methods. We assessed these phenotypes in three 22q11.2-related genotypes to determine whether individual CN V motor and sensory axons wander, branch and sprout aberrantly in register with altered anterior-posterior hindbrain patterning and gross morphological disruption of CN V seen in LgDel(+/-). In the additional 22q11.2-related genotypes: Tbx1(+/-), Ranbp1(+/-), Ranbp1(+/-) and LgDel(+/-):Raldh2(+/-); axon phenotypes are seen when hindbrain patterning and CN V gross morphology is altered, but not when it is normal or restored toward WT. This disordered growth of CN V sensory and motor axons, whose appropriate targeting is critical for optimal S/F/S, may be an early, critical determinant of imprecise innervation leading to inefficient oropharyngeal function associated with 22q11.2 deletion from birth onward.
- Absence of Mycobacterium intracellulare and Presence of Mycobacterium chimaera in Household Water and Biofilm Samples of Patients in the United States with Mycobacterium avium Complex Respiratory DiseaseWallace, Richard J. Jr.; Iakhiaeva, Elena; Williams, Myra D.; Brown-Elliott, Barbara A.; Vasireddy, Sruthi; Vasireddy, Ravikiran; Lande, Leah; Peterson, Donald D.; Sawicki, Janet; Kwait, Rebecca; Tichenor, Wellington S.; Turenne, Christine; Falkinham, Joseph O. III (American Society for Microbiology, 2013-03-27)Recent studies have shown that respiratory isolates from pulmonary disease patients and household water/biofilm isolates of Mycobacterium avium could be matched by DNA fingerprinting. To determine if this is true for Mycobacterium intracellulare, household water sources for 36 patients with Mycobacterium avium complex (MAC) lung disease were evaluated. MAC household water isolates from three published studies that included 37 additional MAC respiratory disease patients were also evaluated. Species identification was done initially using nonsequencing methods with confirmation by internal transcribed spacer (ITS) and/or partial 16S rRNA gene sequencing. M. intracellulare was identified by nonsequencing methods in 54 respiratory cultures and 41 household water/biofilm samples. By ITS sequencing, 49 (90.7%) respiratory isolates were M. intracellulare and 4 (7.4%) were Mycobacterium chimaera. In contrast, 30 (73%) household water samples were M. chimaera, 8 (20%) were other MAC X species (i.e., isolates positive with a MAC probe but negative with species-specific M. avium and M. intracellulare probes), and 3 (7%) were M. avium; none were M. intracellulare. In comparison, M. avium was recovered from 141 water/biofilm samples. These results indicate that M. intracellulare lung disease in the United States is acquired from environmental sources other than household water. Nonsequencing methods for identification of nontuberculous mycobacteria (including those of the MAC) might fail to distinguish closely related species (such as M. intracellulare and M. chimaera). This is the first report of M. chimaera recovery from household water. The study underscores the importance of taxonomy and distinguishing the many species and subspecies of the MAC.
- Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental AspectsCornish-Bowden, Athel; Rasnick, David; Heng, Henry H.; Horne, Steven; Abdallah, Batoul; Liu, Guo; Ye, Christine J.; Bloomfield, Mathew; Vincent, Mark D.; Aldaz, C. M.; Karlsson, Jenny; Valind, Anders; Jansson, Caroline; Gisselsson, David; Graves, Jennifer A. M.; Stepanenko, Aleksei A.; Andreieva, Svitlana V.; Korets, Kateryna V.; Mykytenko, Dmytro O.; Huleyuk, Nataliya L.; Baklaushev, Vladimir P.; Kovaleva, Oksana A.; Chekhonin, Vladimir P.; Vassetzky, Yegor S.; Avdieiev, Stanislav S.; Bakker, Bjorn; Taudt, Aaron S.; Belderbos, Mirjam E.; Porubsky, David; Spierings, Diana C. J.; de Jong, Tristan V.; Halsema, Nancy; Kazemier, Hinke G.; Hoekstra-Wakker, Karina; Bradley, Allan; de Bont, Eveline S. J. M.; van den Berg, Anke; Guryev, Victor; Lansdorp, Peter M.; Tatché, Maria C.; Foijer, Floris; Liehr, Thomas; Baudoin, Nicolaas C.; Nicholson, Joshua M.; Soto, Kimberly; Quintanilla, Isabel; Camps, Jordi; Cimini, Daniela; Dürrbaum, M.; Donnelly, N.; Passerini, V.; Kruse, C.; Habermann, B.; Storchová, Z.; Mandrioli, Daniele; Belpoggi, Fiorella; Silbergeld, Ellen K.; Perry, Melissa J.; Skotheim, Rolf I.; Løvf, Marthe; Johannessen, Bjarne; Hoff, Andreas M.; Zhao, Sen; SveeStrømme, Jonas M.; Sveen, Anita; Lothe, Ragnhild A.; Hehlmann, R.; Voskanyan, A.; Fabarius, A.; Böcking, Alfred; Biesterfeld, Stefan; Berynskyy, Leonid; Börgermann, Christof; Engers, Rainer; Dietz, Josef; Fritz, A.; Sehgal, N.; Vecerova, J.; Stojkovicz, B.; Ding, H.; Page, N.; Tye, C.; Bhattacharya, S.; Xu, J.; Stein, G.; Stein, J.; Berezney, R.; Gong, Xue; Grasedieck, Sarah; Swoboda, Julian; Rücker, Frank G.; Bullinger, Lars; Pollack, Jonathan R.; Roumelioti, Fani-Marlen; Chiourea, Maria; Raftopoulou, Christina; Gagos, Sarantis; Duesberg, Peter; Bloomfield, Mathew; Hwang, Sunyoung; Gustafsson, Hans T.; O’Sullivan, Ciara; Acevedo-Colina, Aracelli; Huang, Xinhe; Klose, Christian; Schevchenko, Andrej; Dickson, Robert C.; Cavaliere, Paola; Dephoure, Noah; Torres, Eduardo M.; Stampfer, Martha R.; Vrba, Lukas; LaBarge, Mark A.; Futscher, Bernard; Garbe, James C.; Trinh, Andrew L.; Zhou, Yi-Hong; Digman, Michelle (2017-06-22)
- Abundance and Size Distribution of Particulate Matter Fractions Near a Caribbean Bank Barrier ReefSimmons, George M. Jr. (Inter-Research, 1979)Recent research indicates that corals have the ability to occupy several trophic levels and that particulate matter (PM) appears to play a major role in meeting their daily energy requirements. A study was undertaken to determine the amount and size distribution of PM near a bank barrier reef off the West Indies Laboratory on St. Croix, U.S.V.I. Size distributions were determined by filtration through selected sieves and filters ranging between 250 and 0.45 μm. Results showed that PM was greater in back-reef than fore-reef areas and greater during day than night hours. The PM collected on the smallest filters (0.45μm) remained constant during both sampling periods and could potentially supply 60 % of the daily energy requirements for corals. Inclusion of the PM on the next size filter (8.0 μm) would more than account for their daily energy requirements. The mean PM abundance found in this study (1.1 mg 1^-1) is the same as that reported at another Caribbean laboratory in the West Indies.
- Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profilesHighnam, Gareth; Franck, Christopher T.; Martin, Andy; Stephens, Calvin; Puthige, Ashwin; Mittelman, David (Oxford University Press, 2013-01)Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping microsatellite repeats called RepeatSeq, which uses Bayesian model selection guided by an empirically derived error model that incorporates sequence and read properties. Next, we apply RepeatSeq to high-coverage genomes from the 1000 Genomes Project to evaluate performance and accuracy. The software uses common formats, such as VCF, for compatibility with existing genome analysis pipelines. Source code and binaries are available at http://github.com/adaptivegenome/repeatseq.
- Actin Filament Attachments for Sustained Motility In Vitro Are Maintained by Filament BundlingHu, Xiaohua; Kuhn, Jeffrey R. (PLOS, 2012-02-16)We reconstructed cellular motility in vitro from individual proteins to investigate how actin filaments are organized at the leading edge. Using total internal reflection fluorescence microscopy of actin filaments, we tested how profilin, Arp2/3, and capping protein (CP) function together to propel thin glass nanofibers or beads coated with N-WASP WCA domains. Thin nanofibers produced wide comet tails that showed more structural variation in actin filament organization than did bead substrates. During sustained motility, physiological concentrations of Mg2+ generated actin filament bundles that processively attached to the nanofiber. Reduction of total Mg2+ abolished particle motility and actin attachment to the particle surface without affecting actin polymerization, Arp2/3 nucleation, or filament capping. Analysis of similar motility of microspheres showed that loss of filament bundling did not affect actin shell formation or symmetry breaking but eliminated sustained attachments between the comet tail and the particle surface. Addition of Mg2+, Lys-Lys2+, or fascin restored both comet tail attachment and sustained particle motility in low Mg2+ buffers. TIRF microscopic analysis of filaments captured by WCA-coated beads in the absence of Arp2/3, profilin, and CP showed that filament bundling by polycation or fascin addition increased barbed end capture by WCA domains. We propose a model in which CP directs barbed ends toward the leading edge and polycation-induced filament bundling sustains processive barbed end attachment to the leading edge.
- Activity of bacteria isolated from bats against Pseudogymnoascus destructans in ChinaLi, Zhongle; Li, Aoqiang; Hoyt, Joseph R.; Dai, Wentao; Leng, Haixia; Li, Yanfei; Li, Wei; Liu, Sen; Jin, Longru; Sun, Keping; Feng, Jiang (2021-02)White-nose syndrome, a disease that is caused by the psychrophilic fungus Pseudogymnoascus destructans, has threatened several North America bat species with extinction. Recent studies have shown that East Asian bats are infected with P. destructans but show greatly reduced infections. While several factors have been found to contribute to these reduced infections, the role of specific microbes in limiting P. destructans growth remains unexplored. We isolated three bacterial strains with the ability to inhibit P. destructans, namely, Pseudomonas yamanorum GZD14026, Pseudomonas brenneri XRD11711 and Pseudomonas fragi GZD14479, from bats in China. Pseudomonas yamanorum, with the highest inhibition score, was selected to extract antifungal active substance. Combining mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy analyses, we identified the active compound inhibiting P. destructans as phenazine-1-carboxylic acid (PCA), and the minimal inhibitory concentration (MIC) was 50.12 mu g ml(-1). Whole genome sequencing also revealed the existence of PCA biosynthesis gene clusters. Gas chromatography-mass spectrometry (GC-MS) analysis identified volatile organic compounds. The results indicated that 10 ppm octanoic acid, 100 ppm 3-tert-butyl-4-hydroxyanisole (isoprenol) and 100 ppm 3-methyl-3-buten-1-ol (BHA) inhibited the growth of P. destructans. These results support that bacteria may play a role in limiting the growth of P. destructans on bats.
- Acyl-Homoserine Lactone Recognition and Response Hindering the Quorum-Sensing Regulator EsaRSchu, Daniel J.; Scruggs, Jessica M.; Geissenger, Jared S.; Michel, Katherine G.; Stevens, Ann M. (Public Library of Science, 2014-09-19)During quorum sensing in the plant pathogen Pantoea stewartii subsp. stewartii, EsaI, an acyl-homoserine lactone (AHL) synthase, and the transcription factor EsaR coordinately control capsular polysaccharide production. The capsule is expressed only at high cell density when AHL levels are high, leading to inactivation of EsaR. In lieu of detailed structural information, the precise mechanism whereby EsaR recognizes AHL and is hindered by it, in a response opposite to that of most other LuxR homologues, remains unresolved. Hence, a random mutagenesis genetic approach was designed to isolate EsaR* variants that are immune to the effects of AHL. Error-prone PCR was used to generate the desired mutants, which were subsequently screened for their ability to repress transcription in the presence of AHL. Following sequencing, site-directed mutagenesis was used to generate all possible mutations of interest as single, rather than multiple amino acid substitutions. Eight individual amino acids playing a critical role in the AHL-insensitive phenotype have been identified. The ability of EsaR* variants to bind AHL and the effect of individual substitutions on the overall conformation of the protein were examined through in vitro assays. Six EsaR* variants had a decreased ability to bind AHL. Fluorescence anisotropy was used to examine the relative DNA binding affinity of the final two EsaR* variants, which retained some AHL binding capability but remained unresponsive to it, perhaps due to an inability of the N-terminal domain to transduce information to the C-terminal domain.
- Adapting to Symptoms of Global Warming Rather Than Addressing the CauseCairns, John Jr. (Virginia Tech, 2006)In recent years, global warming has been ignored and scientists producing evidence supporting this hypothesis have been denigrated and even investigated. However, as irrefutable evidence showing that global warming was a reality mounted, the message shifted to global warming may be occurring, but it is not caused by human activity. Now the message is shifting again, and humankind I been told to adapt to global warming instead of making an effort to reverse it.
- Adaptive radiation along a deeply conserved genetic line of least resistance in Anolis lizardsMcGlothlin, Joel W.; Kobiela, Megan E.; Wright, Helen V.; Mahler, Luke D.; Kolbe, Jason K.; Losos, Jonathan B.; Brodie, Edmund D. III (Wiley, 2018)On microevolutionary timescales, adaptive evolution depends upon both natural selection and the underlying genetic architecture of traits under selection, which may constrain evolutionary outcomes. Whether such genetic constraints shape phenotypic diversity over macroevolutionary timescales is more controversial, however. One key prediction is that genetic constraints should bias the early stages of species divergence along “genetic lines of least resistance” defined by the genetic (co)variance matrix, G. This bias is expected to erode over time as species means and G matrices diverge, allowing phenotypes to evolve away from the major axis of variation. We tested for evidence of this signal in West Indian Anolis lizards, an iconic example of adaptive radiation. We found that the major axis of morphological evolution was well aligned with a major axis of genetic variance shared by all species despite separation times of 20–40 million years, suggesting that divergence occurred along a conserved genetic line of least resistance. Further, this signal persisted even as G itself evolved, apparently because the largest evolutionary changes in G were themselves aligned with the line of genetic least resistance. Our results demonstrate that the signature of genetic constraint may persist over much longer timescales than previously appreciated, even in the presence of evolving genetic architecture. This pattern may have arisen either because pervasive constraints have biased the course of adaptive evolution or because the G matrix itself has been shaped by selection to conform to the adaptive landscape.
- The adhesion function of the sodium channel beta subunit (beta 1) contributes to cardiac action potential propagationVeeraraghavan, Rengasayee; Hoeker, Gregory S.; Alvarez-Laviada, Anita; Hoagland, Daniel T.; Wan, Xiaoping; King, D. Ryan; Sanchez-Alonso, Jose; Chen, Chunling; Jourdan, L. Jane; Isom, Lori L.; Deschenes, Isabelle; Smith, James W.; Gorelik, Julia; Poelzing, Steven; Gourdie, Robert G. (2018-08-14)Computational modeling indicates that cardiac conduction may involve ephaptic coupling - intercellular communication involving electrochemical signaling across narrow extracellular clefts between cardiomyocytes. We hypothesized that beta 1(SCN1B) - mediated adhesion scaffolds trans-activating Na(V)1.5 (SCN5A) channels within narrow (<30 nm) perinexal clefts adjacent to gap junctions (GJs), facilitating ephaptic coupling. Super-resolution imaging indicated preferential beta 1 localization at the perinexus, where it co-locates with Na(V)1.5. Smart patch clamp (SPC) indicated greater sodium current density (I-Na) at perinexi, relative to non-junctional sites. A novel, rationally designed peptide, beta adp1, potently and selectively inhibited beta 1-mediated adhesion, in electric cell-substrate impedance sensing studies. beta adp1 significantly widened perinexi in guinea pig ventricles, and selectively reduced perinexal I-Na, but not whole cell I-Na, in myocyte monolayers. In optical mapping studies, beta adp1 precipitated arrhythmogenic conduction slowing. In summary, beta 1-mediated adhesion at the perinexus facilitates action potential propagation between cardiomyocytes, and may represent a novel target for anti-arrhythmic therapies.
- Advancing lake and reservoir water quality management with near-term, iterative ecological forecastingCarey, Cayelan C.; Woelmer, Whitney M.; Lofton, Mary E.; Figueiredo, Renato J.; Bookout, Bethany J.; Corrigan, Rachel S.; Daneshmand, Vahid; Hounshell, Alexandria G.; Howard, Dexter W.; Lewis, Abigail S. L.; McClure, Ryan P.; Wander, Heather L.; Ward, Nicole K.; Thomas, R. Quinn (2021-01-18)Near-term, iterative ecological forecasts with quantified uncertainty have great potential for improving lake and reservoir management. For example, if managers received a forecast indicating a high likelihood of impending impairment, they could make decisions today to prevent or mitigate poor water quality in the future. Increasing the number of automated, real-time freshwater forecasts used for management requires integrating interdisciplinary expertise to develop a framework that seamlessly links data, models, and cyberinfrastructure, as well as collaborations with managers to ensure that forecasts are embedded into decision-making workflows. The goal of this study is to advance the implementation of near-term, iterative ecological forecasts for freshwater management. We first provide an overview of FLARE (Forecasting Lake And Reservoir Ecosystems), a forecasting framework we developed and applied to a drinking water reservoir to assist water quality management, as a potential open-source option for interested users. We used FLARE to develop scenario forecasts simulating different water quality interventions to inform manager decision-making. Second, we share lessons learned from our experience developing and running FLARE over 2 years to inform other forecasting projects. We specifically focus on how to develop, implement, and maintain a forecasting system used for active management. Our goal is to break down the barriers to forecasting for freshwater researchers, with the aim of improving lake and reservoir management globally.
- An aeroponic culture system for the study of root herbivory on Arabidopsis thalianaVaughan, Martha M.; Tholl, Dorothea; Tokuhisa, James G. (Biomed Central, 2011-03-10)Background Plant defense against herbivory has been studied primarily in aerial tissues. However, complex defense mechanisms have evolved in all parts of the plant to combat herbivore attack and these mechanisms are likely to differ in the aerial and subterranean environment. Research investigating defense responses belowground has been hindered by experimental difficulties associated with the accessibility and quality of root tissue and the lack of bioassays using model plants with altered defense profiles. Results We have developed an aeroponic culture system based on a calcined clay substrate that allows insect herbivores to feed on plant roots while providing easy recovery of the root tissue. The culture method was validated by a root-herbivore system developed for Arabidopsis thaliana and the herbivore Bradysia spp. (fungus gnat). Arabidopsis root mass obtained from aeroponically grown plants was comparable to that from other culture systems, and the plants were morphologically normal. Bradysia larvae caused considerable root damage resulting in reduced root biomass and water absorption. After feeding on the aeroponically grown root tissue, the larvae pupated and emerged as adults. Root damage of mature plants cultivated in aeroponic substrate was compared to that of Arabidopsis seedlings grown in potting mix. Seedlings were notably more susceptible to Bradysia feeding than mature plants and showed decreased overall growth and survival rates. Conclusions A root-herbivore system consisting of Arabidopsis thaliana and larvae of the opportunistic herbivore Bradysia spp. has been established that mimics herbivory in the rhizosphere. Bradysia infestation of Arabidopsis grown in this culture system significantly affects plant performance. The culture method will allow simple profiling and in vivo functional analysis of root defenses such as chemical defense metabolites that are released in response to belowground insect attack.
- Algal periphyton growth on nutrient-diffusing substrates: an in situ bioassayFairchild, G. Winfield; Lowe, Rex L.; Richardson, William B. (Ecological Society of America, 1985)Differences in nutrient limitation for dominant species within an algal periphyton community were determined using additions of N and P supplied by nutrient-diffusing artificial substrates. Sealed clay flowerpots were filled with 2% agar and one of nine nutrient treatments (all combinations of K2HPO4 at 0.0, 0.05, and 0.5 mol/L with NaNO3 at 0.0, 0.05, and 0.5 mol/L). The pots were submerged at 0.5 m depth in Douglas Lake, Michigan, and diffused N and P to their outer surfaces in proportion to internal concentrations. After 51 d the pots were scraped and analyzed for attached algae. Total algal biomass as chlorophyll a on the pots ranged from 0.17 - 0.02 (SE) mg/cm2 for pots without added nutrients to 15.7 - 2.0 mg/cm2 for pots with K2HPO4 at 0.05 mol/L and NaNO3 at 0.5 mol/L. chlorophyll a on pots containing just P (0.05, 0.5 mol/L) increased 6- to 10-fold over controls. The diatoms Epithemia adnata and Rhopalodia gibba and the blue-green alga Anabaena increased significantly on the P-only pots; these species are suspected of N-fixing capability. Chlorophyll a on pots containing just N (0.05 mol/L) increased 1.5- to 2-fold, though this increase was nonsignificant; Achnanthes minutissima, Gomphonema tenellum, and Cocconeis placentula showed enhanced growth on these pots. Combinations of N and P caused heavy growth of the filamentous alga Stigeoclonium tenue. Naviculoid diatoms were also most abundant on the N + P pots. Average nutrient levels in Douglas Lake during the study were: NH3, 2.02 _mol/L; NO3, 0.44 _mol/L; and PO4, 0.06 _mol/L. The low ambient concentrations of both N and P, together with results of the periphyton bioassay, indicate that the two nutrients may jointly limit overall growth, and that the form of growth limitation differs by species within the periphyton community.
- The Alternaria alternata Mycotoxin Alternariol Suppresses Lipopolysaccharide-Induced InflammationGrover, Shivani; Lawrence, Christopher B. (MDPI, 2017-07-20)The Alternaria mycotoxins alternariol (AOH) and alternariol monomethyl ether (AME) have been shown to possess genotoxic and cytotoxic properties. In this study, the ability of AOH and AME to modulate innate immunity in the human bronchial epithelial cell line (BEAS-2B) and mouse macrophage cell line (RAW264.7) were investigated. During these studies, it was discovered that AOH and to a lesser extent AME potently suppressed lipopolysaccharide (LPS)-induced innate immune responses in a dose-dependent manner. Treatment of BEAS-2B cells with AOH resulted in morphological changes including a detached pattern of growth as well as elongated arms. AOH/AME-related immune suppression and morphological changes were linked to the ability of these mycotoxins to cause cell cycle arrest at the G2/M phase. This model was also used to investigate the AOH/AME mechanism of immune suppression in relation to aryl hydrocarbon receptor (AhR). AhR was not found to be important for the immunosuppressive properties of AOH/AME, but appeared important for the low levels of cell death observed in BEAS-2B cells.
- The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic speciesDang, Ha X.; Pryor, Barry M.; Peever, Tobin L.; Lawrence, Christopher B. (2015-03-25)Background Alternaria is considered one of the most common saprophytic fungal genera on the planet. It is comprised of many species that exhibit a necrotrophic phytopathogenic lifestyle. Several species are clinically associated with allergic respiratory disorders although rarely found to cause invasive infections in humans. Finally, Alternaria spp. are among the most well known producers of diverse fungal secondary metabolites, especially toxins. Description We have recently sequenced and annotated the genomes of 25 Alternaria spp. including but not limited to many necrotrophic plant pathogens such as A. brassicicola (a pathogen of Brassicaceous crops like cabbage and canola) and A. solani (a major pathogen of Solanaceous plants like potato and tomato), and several saprophytes that cause allergy in human such as A. alternata isolates. These genomes were annotated and compared. Multiple genetic differences were found in the context of plant and human pathogenicity, notably the pro-inflammatory potential of A. alternata. The Alternaria genomes database was built to provide a public platform to access the whole genome sequences, genome annotations, and comparative genomics data of these species. Genome annotation and comparison were performed using a pipeline that integrated multiple computational and comparative genomics tools. Alternaria genome sequences together with their annotation and comparison data were ported to Ensembl database schemas using a self-developed tool (EnsImport). Collectively, data are currently hosted using a customized installation of the Ensembl genome browser platform. Conclusion Recent efforts in fungal genome sequencing have facilitated the studies of the molecular basis of fungal pathogenicity as a whole system. The Alternaria genomes database provides a comprehensive resource of genomics and comparative data of an important saprophytic and plant/human pathogenic fungal genus. The database will be updated regularly with new genomes when they become available. The Alternaria genomes database is freely available for non-profit use at http://alternaria.vbi.vt.edu .
- Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the OrchidaceaeBarthet, Michelle M.; Moukarzel, Keenan; Smith, Kayla N.; Patel, Jaimin; Hilu, Khidir W. (2015-09-29)Background The plastid maturase MatK has been implicated as a possible model for the evolutionary “missing link” between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution. Results Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history. Conclusion These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.
- Analysis of a generic model of eukaryotic cell-cycle regulationCsikasz-Nagy, A.; Battogtokh, D.; Chen, Katherine C.; Novak, Bela; Tyson, John J. (CELL PRESS, 2006-06)We propose a protein interaction network for the regulation of DNA synthesis and mitosis that emphasizes the universality of the regulatory system among eukaryotic cells. The idiosyncrasies of cell cycle regulation in particular organisms can be attributed, we claim, to specific settings of rate constants in the dynamic network of chemical reactions. The values of these rate constants are determined ultimately by the genetic makeup of an organism. To support these claims, we convert the reaction mechanism into a set of governing kinetic equations and provide parameter values (specific to budding yeast, fission yeast, frog eggs, and mammalian cells) that account for many curious features of cell cycle regulation in these organisms. Using one-parameter bifurcation diagrams, we show how overall cell growth drives progression through the cell cycle, how cell-size homeostasis can be achieved by two different strategies, and how mutations remodel bifurcation diagrams and create unusual cell-division phenotypes. The relation between gene dosage and phenotype can be summarized compactly in two-parameter bifurcation diagrams. Our approach provides a theoretical framework in which to understand both the universality and particularity of cell cycle regulation, and to construct, in modular fashion, increasingly complex models of the networks controlling cell growth and division.
- Analysis of global gene expression changes in human bronchial epithelial cells exposed to spores of the allergenic fungus, Alternaria alternataBabiceanu, Mihaela; Howard, B. A.; Rumore, A. C.; Kita, H.; Lawrence, Christopher B. (Frontiers, 2013-07-19)Exposure and sensitivity to ubiquitous airborne fungi such as Alternaria alternata have long been implicated in the development, onset, and exacerbation of chronic allergic airway disorders. This present study is the first to investigate global changes in host gene expression during the interaction of cultured human bronchial epithelial cells and live Alternaria spores. In in vitro experiments human bronchial epithelial cells (BEAS-2B) were exposed to spores or media alone for 24 h. RNA was collected from three biological replicates per treatment and was used to assess changes in gene expression patterns using Affymetrix Human Genome U133 Plus 2.0 Arrays. In cells treated with Alternaria spores compared to controls, 613 probe sets representing 460 individual genes were found differentially expressed (p <= 0.05). In this set of 460 statistically significant, differentially expressed genes, 397 genes were found to be up-regulated and 63 were down-regulated. Of these 397 up-regulated genes, 156 genes were found to be up-regulated >= 2 fold. Interestingly, none of the 63 down-regulated genes were found differentially expressed at <=-2 fold. Differentially expressed genes were identified following statistical analysis and subsequently used for pathway and network evaluation. Interestingly, many cytokine and chemokine immune response genes were up-regulated with a particular emphasis on interferon-inducible genes. Genes involved in cell death, retinoic acid signaling, and TLR3 response pathways were also significantly up-regulated. Many of the differentially up-regulated genes have been shown in other systems to be associated with innate immunity, inflammation and/or allergic airway diseases. This study now provides substantial information for further investigating specific genes and innate immune system pathways activated by Alternaria in the context of allergic airway diseases.
- Analysis of high-frequency and long-term data in undergraduate ecology classes improves quantitative literacyKlug, Jennifer L.; Carey, Cayelan C.; Richardson, David C.; Gougis, Rebekka Darner (Ecological Society of America, 2017-03)Ecologists are increasingly analyzing long-term and high-frequency sensor datasets as part of their research. As ecology becomes a more data-rich scientific discipline, the next generation of ecologists needs to develop the quantitative literacy required to effectively analyze,visualize, and interpret large datasets. We developed and assessed three modules to teach undergraduate freshwater ecology students both scientific concepts and quantitative skills needed to work with large datasets. These modules covered key ecological topics of phenology, physical mixing, and the balance between primary production and respiration, using lakes as model systems with high-frequency or long-term data. Our assessment demonstrated that participating in these modules significantly increased student comfort using spreadsheet software and their self-reported competence in performing a variety of quantitative tasks. Interestingly, students with the lowest pre-module comfort and skills achieved the biggest gains. Furthermore, students reported that participating in the modules helped them better understand the concepts presented and that they appreciated practicing quantitative skills. Our approach demonstrates that working with large datasets in ecology classrooms helps undergraduate students develop the skills and knowledge needed to help solve complex ecological problems and be more prepared for a data-intensive future.