145 results on '"David A. Kelly"'
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2. A distinct new species of Zosterops white‐eye from the Sulawesi region, Indonesia
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Mohammad Irham, Dewi M. Prawiradilaga, Jochen K. Menner, Darren P. O'Connell, David J. Kelly, Kangkuso Analuddin, Adi Karya, Martin Meads, Nicola M. Marples, and Frank E. Rheindt
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Animal Science and Zoology ,Ecology, Evolution, Behavior and Systematics - Published
- 2022
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3. Cryptic sexual dimorphism reveals differing selection pressures on continental islands
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Fionn Ó Marcaigh, Adi Karya, Kangkuso Analuddin, David J. Kelly, Nicola M. Marples, and Naomi Lawless
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Sexual dimorphism ,Evolutionary biology ,Size dimorphism ,Biology ,Ecology, Evolution, Behavior and Systematics ,Selection (genetic algorithm) - Published
- 2020
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4. Cover Image: Volume 25 Number 3, March 2022
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Joseph A. Tobias, Catherine Sheard, Alex L. Pigot, Adam J. M. Devenish, Jingyi Yang, Ferran Sayol, Montague H. C. Neate‐Clegg, Nico Alioravainen, Thomas L. Weeks, Robert A. Barber, Patrick A. Walkden, Hannah E. A. MacGregor, Samuel E. I. Jones, Claire Vincent, Anna G. Phillips, Nicola M. Marples, Flavia A. Montaño‐Centellas, Victor Leandro‐Silva, Santiago Claramunt, Bianca Darski, Benjamin G. Freeman, Tom P. Bregman, Christopher R. Cooney, Emma C. Hughes, Elliot J. R. Capp, Zoë K. Varley, Nicholas R. Friedman, Heiko Korntheuer, Andrea Corrales‐Vargas, Christopher H. Trisos, Brian C. Weeks, Dagmar M. Hanz, Till Töpfer, Gustavo A. Bravo, Vladimír Remeš, Larissa Nowak, Lincoln S. Carneiro, Amilkar J. Moncada R., Beata Matysioková, Daniel T. Baldassarre, Alejandra Martínez‐Salinas, Jared D. Wolfe, Philip M. Chapman, Benjamin G. Daly, Marjorie C. Sorensen, Alexander Neu, Michael A. Ford, Rebekah J. Mayhew, Luis Fabio Silveira, David J. Kelly, Nathaniel N. D. Annorbah, Henry S. Pollock, Ada M. Grabowska‐Zhang, Jay P. McEntee, Juan Carlos T. Gonzalez, Camila G. Meneses, Marcia C. Muñoz, Luke L. Powell, Gabriel A. Jamie, Thomas J. Matthews, Oscar Johnson, Guilherme R. R. Brito, Kristof Zyskowski, Ross Crates, Michael G. Harvey, Maura Jurado Zevallos, Peter A. Hosner, Tom Bradfer‐Lawrence, James M. Maley, F. Gary Stiles, Hevana S. Lima, Kaiya L. Provost, Moses Chibesa, Mmatjie Mashao, Jeffrey T. Howard, Edson Mlamba, Marcus A. H. Chua, Bicheng Li, M. Isabel Gómez, Natalia C. García, Martin Päckert, Jérôme Fuchs, Jarome R. Ali, Elizabeth P. Derryberry, Monica L. Carlson, Rolly C. Urriza, Kristin E. Brzeski, Dewi M. Prawiradilaga, Matt J. Rayner, Eliot T. Miller, Rauri C. K. Bowie, René‐Marie Lafontaine, R. Paul Scofield, Yingqiang Lou, Lankani Somarathna, Denis Lepage, Marshall Illif, Eike Lena Neuschulz, Mathias Templin, D. Matthias Dehling, Jacob C. Cooper, Olivier S. G. Pauwels, Kangkuso Analuddin, Jon Fjeldså, Nathalie Seddon, Paul R. Sweet, Fabrice A. J. DeClerck, Luciano N. Naka, Jeffrey D. Brawn, Alexandre Aleixo, Katrin Böhning‐Gaese, Carsten Rahbek, Susanne A. Fritz, Gavin H. Thomas, and Matthias Schleuning
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Ecology, Evolution, Behavior and Systematics - Published
- 2022
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5. Bloom where you are planted: Hemangioma or malignancy?
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Kimberly S. Keene, Christopher C Barnett, Kimberly Whelan, Elizabeth A. Beierle, Anh Teressa Duong, Michael H. Soike, Yoginder N. Vaid, Elizabeth Gunn, and David R. Kelly
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Male ,medicine.medical_specialty ,Vascular Malformations ,business.industry ,Vascular malformation ,Hematology ,medicine.disease ,Malignancy ,Abdominal mass ,Vascular anomaly ,Hemangioma ,Retroperitoneal tumor ,Lymphatic system ,Oncology ,Pediatrics, Perinatology and Child Health ,medicine ,Humans ,Retroperitoneal Neoplasms ,Radiology ,Toddler ,medicine.symptom ,business ,human activities - Abstract
Vascular anomalies comprise a spectrum of disorders characterized by the abnormal development or growth of blood and lymphatic vessels. These growths have unique features and diverse behaviors, mandating a multidisciplinary approach in their evaluation, diagnosis, and management. Here we describe the case of a male toddler presenting with an abdominal mass, originally treated as a metastatic retroperitoneal tumor, but subsequently felt to represent a vascular anomaly.
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- 2021
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6. Dispersal patterns in a medium‐density Irish badger population: Implications for understanding the dynamics of tuberculosis transmission
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Nicola M. Marples, Aoibheann Gaughran, Teresa MacWhite, Enda Mullen, David J. Kelly, Margaret Good, and Peter Maher
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0106 biological sciences ,Tuberculosis ,Badger ,Population ,Wildlife ,Meles ,010603 evolutionary biology ,01 natural sciences ,law.invention ,Social group ,03 medical and health sciences ,law ,lcsh:QH540-549.5 ,biology.animal ,medicine ,dispersal ,education ,Ecology, Evolution, Behavior and Systematics ,Original Research ,030304 developmental biology ,Nature and Landscape Conservation ,badger ,0303 health sciences ,education.field_of_study ,Ecology ,biology ,medicine.disease ,biology.organism_classification ,Geography ,Transmission (mechanics) ,tuberculosis ,movement ecology ,Biological dispersal ,lcsh:Ecology ,ranging behavior - Abstract
European badgers (Meles meles) are group‐living mustelids implicated in the spread of bovine tuberculosis (TB) to cattle and act as a wildlife reservoir for the disease. In badgers, only a minority of individuals disperse from their natal social group. However, dispersal may be extremely important for the spread of TB, as dispersers could act as hubs for disease transmission. We monitored a population of 139 wild badgers over 7 years in a medium‐density population (1.8 individuals/km2). GPS tracking collars were applied to 80 different individuals. Of these, we identified 25 dispersers, 14 of which were wearing collars as they dispersed. This allowed us to record the process of dispersal in much greater detail than ever before. We show that dispersal is an extremely complex process, and measurements of straight‐line distance between old and new social groups can severely underestimate how far dispersers travel. Assumptions of straight‐line travel can also underestimate direct and indirect interactions and the potential for disease transmission. For example, one female disperser which eventually settled 1.5 km from her natal territory traveled 308 km and passed through 22 different territories during dispersal. Knowledge of badgers' ranging behavior during dispersal is crucial to understanding the dynamics of TB transmission, and for designing appropriate interventions, such as vaccination., Only a minority of badgers disperse, and the process has rarely been recorded in detail. However, dispersers could act as important hubs for tuberculosis transmission. Our GPS tracking data reveal the process of dispersal in much greater detail than ever before. They show that measurements of straight‐line distance between old and new social groups severely underestimate how far dispersers travel, the potential for intraspecific interactions and the potential for disease transmission. Understanding the process of dispersal is crucial to understanding disease dynamics and designing appropriate interventions.
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- 2019
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7. Infants scan static and dynamic facial expressions differently
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Jolie R. Keemink, David J. Kelly, and Jonathan E. Prunty
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Facial expression ,media_common.quotation_subject ,Emotions ,Infant ,First year of life ,Fear ,Anger ,Disgust ,Facial Expression ,Face (geometry) ,Face ,Pediatrics, Perinatology and Child Health ,Developmental and Educational Psychology ,Visual attention ,Humans ,Emotional expression ,Emotion recognition ,Psychology ,Cognitive psychology ,media_common - Abstract
Despite being inherently dynamic phenomena, much of our understanding of how infants attend and scan facial expressions is based on static face stimuli. Here we investigate how six-, nine-, and twelve-month infants allocate their visual attention toward dynamic interactive videos of the six basic emotional expressions, and compare their responses with static images of the same stimuli. We find infants show clear differences in how they attend and scan dynamic and static expressions, looking longer toward the dynamic-face and lower-face regions. Infants across all age groups show differential interest in expressions, and show precise scanning of regions “diagnostic” for emotion recognition. These data also indicate that infants' attention toward dynamic expressions develops over the first year of life, including relative increases in interest and scanning precision toward some negative facial expressions (e.g.,\ud anger, fear, and disgust).
- Published
- 2021
8. The flavodoxin FldA activates the class Ia ribonucleotide reductase of Campylobacter jejuni
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Laura Alfs, Jordan Swann, Abdulmajeed Alqurashi, Julea N. Butt, and David J. Kelly
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Ribonucleoside Diphosphate Reductase ,Pyruvate Synthase ,Flavodoxin ,Mutant ,Flavoprotein ,Flavin group ,Biology ,Reductase ,Microbiology ,Campylobacter jejuni ,03 medical and health sciences ,Bacterial Proteins ,Ribonucleotide Reductases ,NADH, NADPH Oxidoreductases ,Molecular Biology ,Ferredoxin ,030304 developmental biology ,0303 health sciences ,Flavoproteins ,030306 microbiology ,biology.organism_classification ,Alcohol Oxidoreductases ,Ribonucleotide reductase ,Biochemistry ,biology.protein ,Oxidation-Reduction ,Gene Deletion - Abstract
Campylobacter jejuni is a microaerophilic zoonotic pathogen with an atypical respiratory Complex I that oxidizes a flavodoxin (FldA) instead of NADH. FldA is essential for viability and is reduced via pyruvate and 2-oxoglutarate oxidoreductases (POR/OOR). Here, we show that FldA can also be reduced by FqrB (Cj0559), an NADPH:FldA reductase. An fqrB deletion mutant was viable but displayed a significant growth defect. FqrB is related to flavoprotein reductases from Gram-positive bacteria that can reduce NrdI, a specialized flavodoxin that is needed for tyrosyl radical formation in NrdF, the beta subunit of class 1b-type (Mn) ribonucleotide reductase (RNR). However, C. jejuni possesses a single class Ia-type (Fe) RNR (NrdAB) that would be expected to be ferredoxin dependent. We show that CjFldA is an unusually high potential flavodoxin unrelated to NrdI, yet growth of the fqrB mutant, but not the wild-type or a complemented strain, was stimulated by low deoxyribonucleoside (dRNS) concentrations, suggesting FldA links FqrB and RNR activity. Using purified proteins, we confirmed the NrdB tyrosyl radical could be regenerated in an NADPH, FqrB, and FldA dependent manner, as evidenced by both optical and electron paramagnetic resonance (EPR) spectroscopy. Thus, FldA activates RNR in C. jejuni, partly explaining its essentiality.
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- 2021
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9. Eye Movements and Behavioural Responses to Gaze-Contingent Expressive Faces in Typically Developing Infants and Infant Siblings
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Jonathan E. Prunty, Nicky Wood, Lauren Jenner, Jolie R. Keemink, and David J. Kelly
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Male ,Eye Movements ,Autism Spectrum Disorder ,media_common.quotation_subject ,Eye contact ,Anger ,Developmental psychology ,03 medical and health sciences ,0302 clinical medicine ,Child Development ,medicine ,Humans ,0501 psychology and cognitive sciences ,Emotional expression ,Autistic Disorder ,Child ,Genetics (clinical) ,media_common ,General Neuroscience ,Siblings ,05 social sciences ,Infant ,medicine.disease ,Social relation ,Disgust ,Sadness ,Autism spectrum disorder ,Autism ,Female ,Neurology (clinical) ,Psychology ,030217 neurology & neurosurgery ,050104 developmental & child psychology - Abstract
Studies with infant siblings of children with Autism Spectrum Disorder have attempted to identify early markers for the disorder and suggest that autistic symptoms emerge between 12 and 24 months of age. Yet, a reliable first-year marker remains elusive. We propose that in order to establish first-year manifestations of this inherently social disorder, we need to develop research methods that are sufficiently socially demanding and realistically interactive. Building on Keemink et al. [2019, Developmental Psychology, 55, 1362-1371], we employed a gaze-contingent eye-tracking paradigm in which infants could interact with face stimuli. Infants could elicit emotional expressions (happiness, sadness, surprise, fear, disgust, anger) from on-screen faces by engaging in eye contact. We collected eye-tracking data and video-recorded behavioural response data from 122 (64 male, 58 female) typically developing infants and 31 infant siblings (17 male, 14 female) aged 6-, 9- and 12-months old. All infants demonstrated a significant Expression by AOI interaction (F(10, 1470) = 10.003, P
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- 2020
10. Structural basis for high-affinity adipate binding to AdpC (RPA4515), an orphan periplasmic-binding protein from the tripartite tricarboxylate transporter (TTT) family inRhodopseudomonas palustris
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David J. Kelly, S.R. Dix, Leonardo T. Rosa, and John B. Rafferty
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DNA, Bacterial ,Models, Molecular ,0301 basic medicine ,Protein Conformation ,Stereochemistry ,Adipates ,Recombinant Fusion Proteins ,education ,030106 microbiology ,Crystallography, X-Ray ,Ligands ,Biochemistry ,Substrate Specificity ,Structure-Activity Relationship ,03 medical and health sciences ,Protein structure ,Protein Domains ,Adipate ,Dicarboxylic Acids ,Amino Acid Sequence ,Molecular Biology ,Dicarboxylic Acid Transporters ,biology ,Ligand ,Chemistry ,Isothermal titration calorimetry ,Gene Expression Regulation, Bacterial ,Cell Biology ,Periplasmic space ,Membrane transport ,biology.organism_classification ,Kinetics ,Rhodopseudomonas ,Periplasmic Binding Proteins ,Rhodopseudomonas palustris ,Protein Binding - Abstract
The Tripartite Tricarboxylate Transporter (TTT) family is a poorly characterised group of prokaryotic secondary solute transport systems, which employ a periplasmic substrate binding-protein (SBP) for initial ligand recognition. The substrates of only a small number of TTT systems are known and very few SBP structures have been solved, so the mechanisms of SBP-ligand interactions in this family are not well understood. The SBP RPA4515 (AdpC) from Rhodopseudomonas palustris was found by differential scanning fluorescence and isothermal titration calorimetry to bind aliphatic dicarboxylates of a chain length of six to nine carbons, with KD values in the μM range. The highest affinity was found for the C6-dicarboxylate adipate (1,6-hexanedioate). Crystal structures of AdpC with either adipate or 2-oxoadipate bound revealed a lack of positively charged amino-acids in the binding pocket and showed that water molecules are involved in bridging hydrogen bonds to the substrate, a conserved feature in the TTT SBP family that is distinct from other types of SBP. In AdpC, both of the ligand carboxylate groups and a linear chain conformation are needed for coordination in the binding pocket. RT-PCR showed that adpC expression is upregulated by low environmental adipate concentrations, suggesting adipate is a physiologically relevant substrate but as adpC is not genetically linked to any TTT membrane transport genes, the role of AdpC may be in signalling rather than transport. Our data expands the known ligands for TTT systems and identifies a novel high-affinity binding-protein for adipate, an important industrial chemical intermediate and food additive. This article is protected by copyright. All rights reserved.
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- 2017
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11. Chasing the backup pathway for therapeutic opportunities in cancer
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Amaranth Natarajan, Gloria E. O. Borgstahl, Mona Al-Mugotir, David Lee Kelly, Carol Kolar, and Tadayoshi Bessho
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Oncology ,medicine.medical_specialty ,Backup ,business.industry ,Internal medicine ,Genetics ,medicine ,Cancer ,medicine.disease ,business ,Molecular Biology ,Biochemistry ,Biotechnology - Published
- 2020
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12. Major contribution of the type II beta carbonic anhydrase CanB (Cj0237) to the capnophilic growth phenotype ofCampylobacter jejuni
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Halah H. Al-Haideri, Michael A. White, and David J. Kelly
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0301 basic medicine ,chemistry.chemical_classification ,biology ,Carbonic anhydrase II ,Bicarbonate ,030106 microbiology ,biology.organism_classification ,Microbiology ,Campylobacter jejuni ,Pyruvate carboxylase ,03 medical and health sciences ,chemistry.chemical_compound ,Enzyme ,chemistry ,Biochemistry ,Oxaloacetic acid ,Carbonic anhydrase ,biology.protein ,Pyruvic acid ,Ecology, Evolution, Behavior and Systematics - Abstract
Campylobacter jejuni, the leading cause of human bacterial gastroenteritis, requires low environmental oxygen and high carbon dioxide for optimum growth, but the molecular basis for the carbon dioxide requirement is unclear. One factor may be inefficient conversion of gaseous CO2 to bicarbonate, the required substrate of various carboxylases. Two putative carbonic anhydrases (CAs) are encoded in the genome of C. jejuni strain NCTC 11168 (Cj0229 and Cj0237). Here, we show that the deletion of the cj0237 (canB) gene alone prevents growth in complex media at low (1% v/v) CO2 and significantly reduces the growth rate at high (5% v/v) CO2. In minimal media incubated under high CO2, the canB mutant grew on L-aspartate but not on the key C3 compounds L-serine, pyruvate and L-lactate, showing that CanB is crucial in bicarbonate provision for pyruvate carboxylase-mediated oxaloacetate synthesis. Nevertheless, purified CanB (a dimeric, anion and acetazolamide sensitive, zinc-containing type II beta-class enzyme) hydrates CO2 actively only above pH 8 and with a high Km (∼ 34 mM). At typical cytoplasmic pH values and low CO2, these kinetic properties might limit intracellular bicarbonate availability. Taken together, our data suggest CanB is a major contributor to the capnophilic growth phenotype of C. jejuni.
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- 2015
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13. TheCampylobacter jejuni RacRS system regulates fumarate utilization in a low oxygen environment
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Craig T. Parker, Anne-Xander van der Stel, Marc M. S. M. Wösten, Jos P. M. van Putten, Chris H.A. van de Lest, David J. Kelly, Linda Heijmen-van Dijk, and Andries van Mourik
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biology ,Campylobacter ,Respiratory chain ,Human pathogen ,biology.organism_classification ,medicine.disease_cause ,Microbiology ,Campylobacter jejuni ,Biochemistry ,medicine ,Gene ,Transcription factor ,Pathogen ,Ecology, Evolution, Behavior and Systematics ,Bacteria - Abstract
The natural environment of the human pathogen Campylobacter jejuni is the gastrointestinal tract of warm-blooded animals. In the gut, the availability of oxygen is limited; therefore, less efficient electron acceptors such as nitrate or fumarate are used by C. jejuni. The molecular mechanisms that regulate the activity of the highly branched respiratory chain of C. jejuni are still a mystery mainly because C. jejuni lacks homologues of transcription factors known to regulate energy metabolism in other bacteria. Here we demonstrate that dependent on the available electron acceptors the two-component system RacRS controls the production of fumarate from aspartate, as well as its transport and reduction to succinate. Transcription profiling, DNAse protection and functional assays showed that phosphorylated RacR binds to and represses at least five promoter elements located in front of genes involved in the uptake and synthesis of fumarate. The RacRS system is active in the presence of nitrate and trimethyl-amine-N-oxide under oxygen-limited conditions when fumarate is less preferred as an alternative electron acceptor. In the inactive state, RacRS allows utilization of fumarate for respiration. The unique C. jejuni RacRS regulatory system illustrates the disparate evolution of Campylobacter and aids the survival of this pathogen.
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- 2014
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14. Tetrathionate stimulated growth ofCampylobacter jejuniidentifies a new type of bi-functional tetrathionate reductase (TsdA) that is widely distributed in bacteria
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Kevin Denkmann, Yang-Wei Liu, Konrad Kosciow, Christiane Dahl, and David J. Kelly
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Tetrathionate ,chemistry.chemical_classification ,biology ,Cytochrome c ,Dehydrogenase ,biology.organism_classification ,Microbiology ,Campylobacter jejuni ,chemistry.chemical_compound ,Enzyme ,Biochemistry ,chemistry ,Intestinal mucosa ,biology.protein ,Microaerophile ,Molecular Biology ,Bacteria - Abstract
Summary Tetrathionate (S4O62−) is used by some bacteria as an electron acceptor and can be produced in the vertebrate intestinal mucosa from the oxidation of thiosulphate (S2O32−) by reactive oxygen species during inflammation. Surprisingly, growth of the microaerophilic mucosal pathogen Campylobacter jejuni under oxygen-limited conditions was stimulated by tetrathionate, although it does not possess any known type of tetrathionate reductase. Here, we identify a dihaem cytochrome c (C8j_0815; TsdA) as the enzyme responsible. Kinetic studies with purified recombinant C. jejuni TsdA showed it to be a bifunctional tetrathionate reductase/thiosulphate dehydrogenase with a high affinity for tetrathionate. A tsdA null mutant still slowly reduced, but could not grow on, tetrathionate under oxygen limitation, lacked thiosulphate-dependent respiration and failed to convert thiosulphate to tetrathionate microaerobically. A TsdA paralogue (C8j_0040), lacking the unusual His–Cys haem ligation of TsdA, had low thiosulphate dehydrogenase and tetrathionate reductase activities. Our data highlight a hitherto unrecognized capacity of C. jejuni to use tetrathionate and thiosulphate in its energy metabolism, which may promote growth in the host. Moreover, as TsdA represents a new class of tetrathionate reductase that is widely distributed among bacteria, we predict that energy conserving tetrathionate respiration is far more common than currently appreciated.
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- 2013
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15. OCT4/SOX2-independentNanogautorepression modulates heterogeneousNanoggene expression in mouse ES cells
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Violetta Karwacki-Neisius, David A. Kelly, Nicola Festuccia, Douglas Colby, Pablo Navarro, Wensheng Zhang, Rodrigo Osorno, Morag Robertson, Alessia Gagliardi, Nicholas P. Mullin, and Ian Chambers
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Regulation of gene expression ,Genetics ,Homeobox protein NANOG ,0303 health sciences ,General Immunology and Microbiology ,General Neuroscience ,Rex1 ,Cellular differentiation ,fungi ,Gene regulatory network ,Nanog Homeobox Protein ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Cell biology ,03 medical and health sciences ,0302 clinical medicine ,SOX2 ,embryonic structures ,biological phenomena, cell phenomena, and immunity ,Induced pluripotent stem cell ,Molecular Biology ,reproductive and urinary physiology ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
NANOG, OCT4 and SOX2 form the core network of transcription factors supporting embryonic stem (ES) cell self-renewal. While OCT4 and SOX2 expression is relatively uniform, ES cells fluctuate between states of high NANOG expression possessing high self-renewal efficiency, and low NANOG expression exhibiting increased differentiation propensity. NANOG, OCT4 and SOX2 are currently considered to activate transcription of each of the three genes, an architecture that cannot readily account for NANOG heterogeneity. Here, we examine the architecture of the Nanog-centred network using inducible NANOG gain- and loss-of-function approaches. Rather than activating itself, Nanog activity is autorepressive and OCT4/SOX2-independent. Moreover, the influence of Nanog on Oct4 and Sox2 expression is minimal. Using Nanog:GFP reporters, we show that Nanog autorepression is a major regulator of Nanog transcription switching. We conclude that the architecture of the pluripotency gene regulatory network encodes the capacity to generate reversible states of Nanog transcription via a Nanog-centred autorepressive loop. Therefore, cellular variability in self-renewal efficiency is an emergent property of the pluripotency gene regulatory network.
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- 2012
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16. MACROINVERTEBRATE-PRESSURE RELATIONSHIPS IN BOATABLE NEW ZEALAND RIVERS: INFLUENCE OF UNDERLYING ENVIRONMENT AND SAMPLING SUBSTRATE
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Kevin J. Collier, John R. Leathwick, Russell G. Death, David W. Kelly, Joanne E. Clapcott, Bruno O. David, and Roger G. Young
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Hydrology ,geography ,geography.geographical_feature_category ,Ecology ,fungi ,Drainage basin ,Biodiversity ,Land cover ,Vegetation ,Substrate (marine biology) ,Habitat ,Littoral zone ,Environmental Chemistry ,Environmental science ,Species richness ,General Environmental Science ,Water Science and Technology - Abstract
Responses of macroinvertebrate communities to human pressure are poorly known in large rivers compared with wadeable streams, in part because of variable substrate composition and the need to disentangle pressure responses from underlying natural environmental variation. To investigate the interaction between these factors, we sampled macroinvertebrates from the following: (i) submerged wood; (ii) littoral substrates 1.5 m) benthic habitats in eleven 6th- or 7th-order New Zealand rivers spanning a catchment vegetation land cover gradient. Cluster analysis identified primary site groupings reflecting regional environmental characteristics and secondary groupings for moderate gradient rivers reflecting the extent of catchment native vegetation cover. Low pressure sites with high levels of native vegetation had higher habitat quality and higher percentages of several Ephemeroptera and Trichoptera taxa than sites in developed catchments, whereas developed sites were more typically dominated by Diptera, Mollusca and other Trichoptera. Partial regression analysis indicated that the combination of underlying environment and human pressure accounted for 77–89% of the variation in Ephemeroptera, Trichoptera and Plecoptera taxa richness, %Diptera and %Mollusca, with human pressure explaining more variance than underlying environment for %Mollusca. Analysis of replicate deepwater and littoral samples from moderate gradient sites at the upper and lower ends of the pressure gradient indicated that total Trichoptera and Diptera richness and %Diptera responded to land use differences in these boatable river catchments. Responses to human pressure were substrate specific with the combination of littoral and deepwater substrates providing the most consistent response and yielding the highest number of taxa. These results indicate that multiple substrate sampling is required to document the biodiversity and condition of boatable river macroinvertebrate communities and that spatial variation in the underlying natural environment needs to be accounted for when interpreting pressure–response relationships. Copyright © 2012 John Wiley & Sons, Ltd.
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- 2012
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17. Quantifying relationships between land-use gradients and structural and functional indicators of stream ecological integrity
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Eric O. Goodwin, Russell G. Death, Joanne E. Clapcott, Roger G. Young, David W. Kelly, Kevin J. Collier, John R. Leathwick, and Jon S. Harding
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River ecosystem ,Land use ,Ecology ,Impervious surface ,Environmental science ,Spatial variability ,Ecosystem ,Species richness ,Water quality ,Aquatic Science ,Biotic index - Abstract
Summary 1. Modification of natural landscapes and land-use intensification are global phenomena that can result in a range of differing pressures on lotic ecosystems. We analysed national-scale databases to quantify the relationship between three land uses (indigenous vegetation, urbanisation and agriculture) and indicators of stream ecological integrity. Boosted regression tree modelling was used to test the response of 14 indicators belonging to four groups – water quality (at 578 sites), benthic invertebrates (at 2666 sites), fish (at 6858 sites) and ecosystem processes (at 156 sites). Our aims were to characterise the ecological response curves of selected functional and structural metrics in relation to three land uses, examine the environmental moderators of these relationships and quantify the relative utility of metrics as indicators of stream ecological integrity. 2. The strongest indicators of land-use effects were nitrate + nitrite, delta-15 nitrogen value (δ15N) of primary consumers and the Macroinvertebrate Community Index (a biotic index of organic pollution), while the weakest overall indicators were gross primary productivity, benthic invertebrate richness and fish richness. All indicators declined in response to removal of indigenous vegetation and urbanisation, while variable responses to agricultural intensity were observed for some indicators. 3. The response curves for several indicators suggested distinct thresholds in response to urbanisation and agriculture, specifically at 10% impervious cover and at 0.1 g m−3 nitrogen concentration, respectively. 4. Water quality and ecosystem process indicators were influenced by a combination of temperature, slope and flow variables, whereas for macroinvertebrate indicators, catchment rainfall, segment slope and temperature were significant environmental predictor variables. Downstream variables (e.g. distance to the coast) were significant in explaining residual variation in fish indicators, not surprisingly given the preponderance of diadromous fish species in New Zealand waterways. The inclusion of continuous environmental variables used to develop a stream typology improved model performance more than the inclusion of stream type alone. 5. Our results reaffirm the importance of accounting for underlying spatial variation in the environment when quantifying relationships between land use and the ecological integrity of streams. Of distinctive interest, however, were the contrasting and complementary responses of different indicators of stream integrity to land use, suggesting that multiple indicators are required to identify land-use impact thresholds, develop environmental standards and assign ecological scores for reporting purposes.
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- 2011
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18. Developing cultural differences in face processing
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David J. Kelly, Roberto Caldara, Helen Rodger, Shaoying Liu, Sebastien Miellet, and Liezhong Ge
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Facial expression ,Visual perception ,Cognitive Neuroscience ,media_common.quotation_subject ,Cultural group selection ,Eye movement ,Fixation (psychology) ,Developmental psychology ,Cultural diversity ,Perception ,Developmental and Educational Psychology ,Early childhood ,Psychology ,media_common - Abstract
Perception and eye movements are affected by culture. Adults from Eastern societies (e.g. China) display a disposition to process information holistically, whereas individuals from Western societies (e.g. Britain) process information analytically. Recently, this pattern of cultural differences has been extended to face processing. Adults from Eastern cultures fixate centrally towards the nose when learning and recognizing faces, whereas adults from Western societies spread fixations across the eye and mouth regions. Although light has been shed on how adults can fixate different areas yet achieve comparable recognition accuracy, the reason why such divergent strategies exist is less certain. Although some argue that culture shapes strategies across development, little direct evidence exists to support this claim. Additionally, it has long been claimed that face recognition in early childhood is largely reliant upon external rather than internal face features, yet recent studies have challenged this theory. To address these issues, we tested children aged 7-12 years of age from the UK and China with an old/new face recognition paradigm while simultaneously recording their eye movements. Both populations displayed patterns of fixations that were consistent with adults from their respective cultural groups, which 'strengthened' across development as qualified by a pattern classifier analysis. Altogether, these observations suggest that cultural forces may indeed be responsible for shaping eye movements from early childhood. Furthermore, fixations made by both cultural groups almost exclusively landed on internal face regions, suggesting that these features, and not external features, are universally used to achieve face recognition in childhood.
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- 2011
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19. Biological invasions and the dynamics of endemic diseases in freshwater ecosystems
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Colin R. Townsend, David W. Kelly, Rachel A. Paterson, Robert Poulin, and Daniel M. Tompkins
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Food chain ,Resistance (ecology) ,Host (biology) ,Ecology ,Introduced species ,Disease ,Aquatic Science ,Biology ,Endemism ,Freshwater ecosystem ,Invasive species - Abstract
Summary 1. Biological invasions, still occurring worldwide at an alarming rate, are widely acknowledged as threats to the integrity and functioning of ecosystems. In addition to introducing disease, biological invasions have also been linked to sudden increases in the incidence or severity of previously existing diseases. We review and illustrate the potential direct and indirect impacts of introduced species on the dynamics of endemic parasites in freshwater ecosystems. 2. Introduced species may trigger and sustain disease emergence by acting as competent hosts for endemic parasites in which infection is amplified and then ‘spilled back’ to native hosts. In contrast, if introduced species are not suitable hosts for endemic parasites but become infected anyway, they may act as sinks for parasites and thus dilute disease risk for native hosts. 3. Another mechanism by which introduced species can influence endemic parasitic diseases is by altering the relative abundance of one of the parasite’s hosts in ways that could either enhance or reduce disease transmission to other native hosts in the parasite’s life cycle. 4. Introduced species may also alter disease incidence and severity in native hosts through trait‐mediated indirect effects. For example, the introduced species could change the exposure or susceptibility of native hosts to infection by causing alterations in their behaviour or immunocompetence. Also, by directly changing physicochemical conditions and modifying environmental stressors introduced species may indirectly affect native host exposure and/or resistance to disease. 5. A survey of parasites infecting introduced freshwater fish in four distinct geographical areas revealed that use of non‐indigenous hosts by endemic parasites is widespread, mostly involving parasites transmitted via the food chain. 6. We conclude by presenting a framework, based on risk assessment, for the prediction and possible mitigation of the impact of introduced species on endemic diseases and by calling for greater recognition of the potential role of invasive species as triggers of endemic disease emergence.
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- 2011
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20. Diel variation in stream fish habitat suitability criteria: implications for instream flow assessment
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David J. Kelly, D.J. Booker, and Andrew J. H. Davey
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Ecology ,biology ,Aquatic Science ,Torrentfish ,biology.organism_classification ,Gobiomorphus breviceps ,Critical habitat ,Habitat ,Benthic zone ,Abundance (ecology) ,Gobiomorphus hubbsi ,Diel vertical migration ,Nature and Landscape Conservation - Abstract
1. Habitat suitability criteria that fail to incorporate temporal variability in habitat preferences of stream fish may mis-represent critical habitat requirements and lead to setting of inappropriate flow targets when used in instream flow assessments. Developing suitability criteria from daytime observations alone relies on the assumption that habitat preferences are constant over the diel cycle. Few studies have tested these assumptions, particularly for small-bodied, cryptic, benthic species. 2. During summer in two gravel-bed rivers, bluegill bullies (Gobiomorphus hubbsi), torrentfish (Cheimarrichthys fosteri) and upland bullies (Gobiomorphus breviceps) exhibited strong preferences with respect to water depth, velocity and substratum size. All three species underwent a diel shift in microhabitat preference for at least two of these variables. 3. Microhabitat preferences were generally weaker when fish were active at night; bluegill bullies, upland bullies and especially torrentfish were observed over a broader range of depths, velocities and substratum sizes at night than during the day. Observations of fish in a stream simulator confirmed that bluegill bullies and torrentfish showed a preference for runs at dusk and return to riffles before dawn, but habitat preferences of upland bullies remained static across the diel cycle. 4. Diel microhabitat shifts affected the assessment of flow requirements. Instream habitat analysis of the Waipara River using separate day and night suitability criteria predicted differing amounts of habitat available at a given flow, and the relationships between fish abundance, fish density and flow. The presence of diel microhabitat shifts in stream fishes suggests that instream habitat analyses will produce more effective and defensible flow recommendations when patterns of nocturnal microhabitat preferences are known and critical habitat bottlenecks can be identified. Copyright © 2011 John Wiley & Sons, Ltd.
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- 2011
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21. Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore
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Nuno Martins, Lars E.T. Jansen, Hiroshi Kimura, Vladimir Larionov, William C. Earnshaw, Mariluz Gómez Rodríguez, David A. Kelly, Hiroshi Masumoto, and Jan H. Bergmann
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Genetics ,0303 health sciences ,General Immunology and Microbiology ,biology ,Kinetochore ,General Neuroscience ,030302 biochemistry & molecular biology ,macromolecular substances ,General Biochemistry, Genetics and Molecular Biology ,Cell biology ,Chromatin ,03 medical and health sciences ,Histone H3 ,Histone ,Centromere Protein A ,Centromere ,biology.protein ,Nucleosome ,Demethylase ,Molecular Biology ,030304 developmental biology - Abstract
Kinetochores assemble on distinct 'centrochromatin' containing the histone H3 variant CENP-A and interspersed nucleosomes dimethylated on H3K4 (H3K4me2). Little is known about how the chromatin environment at active centromeres governs centromeric structure and function. Here, we report that centrochromatin resembles K4-K36 domains found in the body of some actively transcribed housekeeping genes. By tethering the lysine-specific demethylase 1 (LSD1), we specifically depleted H3K4me2, a modification thought to have a role in transcriptional memory, from the kinetochore of a synthetic human artificial chromosome (HAC). H3K4me2 depletion caused kinetochores to suffer a rapid loss of transcription of the underlying α-satellite DNA and to no longer efficiently recruit HJURP, the CENP-A chaperone. Kinetochores depleted of H3K4me2 remained functional in the short term, but were defective in incorporation of CENP-A, and were gradually inactivated. Our data provide a functional link between the centromeric chromatin, α-satellite transcription, maintenance of CENP-A levels and kinetochore stability.
- Published
- 2010
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22. The Shaping of the Face Space in Early Infancy: Becoming a Native Face Processor
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Kang Lee, Paula R. McDonald, Alan Slater, Christopher A. Longmore, Paul C. Quinn, David J. Kelly, and Olivier Pascalis
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05 social sciences ,Face (sociological concept) ,Early infancy ,Experiential learning ,050105 experimental psychology ,Preference ,Developmental psychology ,Categorization ,Face perception ,Face space ,Pediatrics, Perinatology and Child Health ,Developmental and Educational Psychology ,Perceptual narrowing ,0501 psychology and cognitive sciences ,10. No inequality ,Life-span and Life-course Studies ,Psychology ,050104 developmental & child psychology ,Cognitive psychology - Abstract
Face perception remains one of the most intensively researched areas in psychology and allied disciplines, and there has been much debate regarding the early origins and experiential determinants of face processing. This article reviews studies, the majority of which have appeared in the past decade, that discuss possible mechanisms underlying face perception at birth and document the prominent role of experience in shaping infants' face-processing abilities. In the first months of life, infants develop a preference for female and own-race faces and become better able to recognize and categorize own-race and own-species faces. This perceptual narrowing and shaping of the "face space" forms a foundation for later face expertise in childhood and adulthood and testifies to the remarkable plasticity of the developing visual system.
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- 2010
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23. Treatment of primary CNS lymphoma with high-dose methotrexate in immunocompetent pediatric patients
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Lee Hilliard, David R. Kelly, Amish C. Shah, W. Jerry Oakes, L. Burt Nabors, and Alyssa Reddy
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Oncology ,medicine.medical_specialty ,business.industry ,medicine.medical_treatment ,Primary central nervous system lymphoma ,Hematology ,Disease ,medicine.disease ,High dose methotrexate ,Radiation therapy ,Primary CNS Lymphoma ,hemic and lymphatic diseases ,Internal medicine ,Pediatrics, Perinatology and Child Health ,medicine ,Methotrexate ,business ,Anaplastic large-cell lymphoma ,Diffuse large B-cell lymphoma ,medicine.drug - Abstract
We report two cases of primary CNS lymphoma (PCNSL) treated with high-dose methotrexate. Though standard adult treatment of PCNSL incorporates whole-brain radiotherapy, the literature suggests it may be possible to delay or avoid radiotherapy and the associated increased risk of neurologic sequelae in pediatric patients. Studies in adults indicate methotrexate therapy can be effective against PCNSL and has advantages over the current standard of treatment. Both patients have no evidence of disease 9 and 7 years after treatment, suggesting high-dose methotrexate may lead to disease control in pediatric patients with PCNSL while avoiding the effects of radiotherapy. Pediatr Blood Cancer. 2010;55:1227–1230. © 2010 Wiley-Liss, Inc.
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- 2010
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24. Two respiratory enzyme systems inCampylobacter jejuniNCTC 11168 contribute to growth on<scp>l</scp>-lactate
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Marie T. Thomas, Robert K. Poole, Bruce M. Pearson, David J. Kelly, Mark Shepherd, and Arnoud H. M. van Vliet
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chemistry.chemical_classification ,Oxidase test ,biology ,Mutant ,Obligate anaerobe ,biology.organism_classification ,Microbiology ,Campylobacter jejuni ,Respiratory enzyme ,chemistry.chemical_compound ,chemistry ,Biochemistry ,Oxidoreductase ,Lactate dehydrogenase ,Ecology, Evolution, Behavior and Systematics ,Bacteria - Abstract
Campylobacter jejuni, a major food-borne intestinal pathogen, preferentially utilizes a few specific amino acids and some organic acids such as pyruvate and L- and D-lactate as carbon sources, which may be important for growth in the avian and mammalian gut. Here, we identify the enzymatic basis for C. jejuni growth on L-lactate. Despite the presence of an annotated gene for a fermentative lactate dehydrogenase (cj1167), no evidence for lactate excretion could be obtained in C. jejuni NCTC 11168, and inactivation of the cj1167 gene did not affect growth on lactate as carbon source. Instead, L-lactate utilization in C. jejuni NCTC 11168 was found to proceed via two novel NAD-independent L-LDHs; a non-flavin iron-sulfur containing three subunit membrane-associated enzyme (Cj0075c-73c), and a flavin and iron-sulfur containing membrane-associated oxidoreductase (Cj1585c). Both enzymes contribute to growth on L-lactate, as single mutants in each system grew as well as wild-type on this substrate, while a cj0075c cj1585c double mutant showed no L-lactate oxidase activity and did not utilize or grow on L-lactate; D-lactate-dependent growth was unaffected. Orthologues of Cj0075c-73c (LldEFG/LutABC) and Cj1585c (Dld-II) were recently shown to represent two novel families of L- and D-lactate oxidases; this is the first report of a bacterium where both enzymes are involved in L-lactate utilization only. The cj0075c-73c genes are located directly downstream of a putative lactate transporter gene (cj0076c, lctP), which was also shown to be specific for L-lactate. The avian and mammalian gut environment contains dense populations of obligate anaerobes that excrete lactate; our data indicate that C. jejuni is well equipped to use L- and D-lactate as both electron-donor and carbon source.
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- 2010
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25. Synergistic effects of glyphosate formulation and parasite infection on fish malformations and survival
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Colin R. Townsend, Robert Poulin, Daniel M. Tompkins, and David W. Kelly
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Ecology ,biology ,Intermediate host ,Zoology ,Aquatic animal ,Juvenile fish ,Snail ,biology.organism_classification ,Toxicology ,chemistry.chemical_compound ,chemistry ,Glyphosate ,biology.animal ,Toxicity ,Freshwater fish ,Juvenile - Abstract
Summary 1. Anthropogenic pollution and disease can cause both lethal and sub-lethal effects in aquatic species but our understanding of how these stressors interact is often not known. Contaminants can reduce host resistance to disease, but whether hosts are impacted at environmentally relevant concentrations is poorly understood. 2. We investigated the independent and combined effects of exposure to the common herbicide glyphosate and the trematode parasite Telogaster opisthorchis on survival and the development of spinal malformations in juvenile Galaxias anomalus, a New Zealand freshwater fish. We then investigated how exposure to a glyphosate concentration gradient (0AE36, 3AE6, 36 mg active ingredient (a.i.) L )1 ) affected the production and release of the infective cercarial stage of the parasite by its snail intermediate host Potamopyrgus antipodarum. 3. Survival of juvenile fish was unaffected by exposure to glyphosate alone (at an environmentally relevant concentration; 0AE36 mg a.i. L )1 ) or by T. opisthorchis infection alone. However, simultaneous exposure to infection and glyphosate significantly reduced fish survival. 4. Juvenile fish developed spinal malformations when exposed either to infections alone or to infections and glyphosate, with a trend towards greater severity of spinal malformation after exposure to both stressors. 5. All snails exposed to the highest glyphosate concentration (36 mg a.i. L )1 ) died within 24 h. Snails exposed to a moderate concentration (3AE6 mg a.i. L )1 ) produced significantly more T. opisthorchis cercariae than snails in the control group or the low concentration group (0AE36 mg a.i. L )1 ; the same concentration as in the fish experiment). 6. Synthesis and applications. This is the first study to show that parasites and glyphosate can act synergistically on aquatic vertebrates at environmentally relevant concentrations, and that glyphosate might increase the risk of disease in fish. Our results have important implications when identifying risks to aquatic communities and suggest that threshold levels of glyphosate currently set by regulatory authorities do not adequately protect freshwater systems.
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- 2010
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26. Trematode infection causes malformations and population effects in a declining New Zealand fish
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Harriet Thomas, David W. Kelly, David W. Thieltges, Robert Poulin, and Daniel M. Tompkins
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Time Factors ,Population ,Zoology ,Trematode Infections ,Disease ,Fish Diseases ,Animals ,education ,Ecology, Evolution, Behavior and Systematics ,Population Density ,education.field_of_study ,biology ,Ecology ,Incidence (epidemiology) ,Aquatic animal ,Ichthyoplankton ,biology.organism_classification ,Spine ,Disturbance (ecology) ,Osmeriformes ,Larva ,Threatened species ,Freshwater fish ,Animal Science and Zoology ,Trematoda ,New Zealand - Abstract
1. Animal malformations engender wide public and scientific concern because of associated environmental health risks. This is highlighted by increased incidence of limb malformations in amphibians associated with trematode infections and disturbance. Malformations may signal new emerging disease threats, but whether the phenomenon is broadly applicable across taxa, or has population-scale impacts, is unknown. 2. Malformations are widely reported in fish and, until now, have been attributed mainly to contaminants. We tested whether the trematode Telogaster opisthorchis caused severe malformations, leading to population effects, in Galaxias anomalus, a threatened New Zealand freshwater fish. 3. Experimental infection of larval fish caused increasing spinal malformation and mortality with infection intensity that closely matched field patterns. Field malformation frequency peaked in January (65%), before declining sharply in February (25%) and remaining low thereafter. 4. The peak occurred during a 'critical window' of larval development, with the decline coincident with a population crash, indicating that malformation was causing mortality in the field. 5. The occurrence of such critical developmental windows may explain why this mechanism of population impact has been overlooked. With global environmental stressors predicted to enhance trematode infections, our results show that parasite-induced malformation, and its population-scale impacts, could be more widespread than previously considered.
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- 2010
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27. Reduction of fumarate, mesaconate and crotonate by Mfr, a novel oxygen-regulated periplasmic reductase inCampylobacter jejuni
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David J. Kelly, Andrew Hitchcock, Stephen J. Hall, Edward Guccione, Neil Shearer, Francis Mulholland, and Arnoud H. M. van Vliet
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Operon ,Protein subunit ,Molecular Sequence Data ,Mutant ,Reductase ,Microbiology ,Campylobacter jejuni ,Bacterial Proteins ,Fumarates ,Animals ,Humans ,Amino Acid Sequence ,Ecology, Evolution, Behavior and Systematics ,chemistry.chemical_classification ,Base Sequence ,biology ,Maleates ,Gene Expression Regulation, Bacterial ,Periplasmic space ,Fumarate reductase ,biology.organism_classification ,Molecular biology ,Oxygen ,Succinate Dehydrogenase ,Protein Subunits ,Enzyme ,Biochemistry ,chemistry ,Crotonates ,Periplasm ,Oxidation-Reduction - Abstract
Summary Methylmenaquinol : fumarate reductase (Mfr) is a newly recognized type of fumarate reductase present in some e-proteobacteria, where the active site subunit (MfrA) is localized in the periplasm, but for which a physiological role has not been identified. We show that the Campylobacter jejuni mfrABE operon is transcribed from a single promoter, with the mfrA gene preceded by a small open reading-frame (mfrX) encoding a C. jejuni-specific polypeptide of unknown function. The growth characteristics and enzyme activities of mutants in the mfrA and menaquinol : fu- marate reductase A (frdA) genes show that the cyto- plasmic facing Frd enzyme is the major fumarate reductase under oxygen limitation. The Mfr enzyme is shown to be necessary for maximal rates of growth by fumarate respiration and rates of fumarate reduction in intact cells measured by both viologen assays and 1 H-NMR were slower in an mfrA mutant. As periplas- mic fumarate reduction does not require fumarate/ succinate antiport, Mfr may allow more efficient adaptation to fumarate-dependent growth. However, a further rationale for the periplasmic location of Mfr is suggested by the observation that the enzyme also reduces the fumarate analogues mesaconate and crotonate; fermentation products of anaerobes with which C. jejuni shares its gut environment, that are unable to be transported into the cell. Both MfrA and MfrB subunits were localized in the periplasm by immunoblotting and 2D-gel electrophoresis, but an mfrE mutant accumulated unprocessed MfrA in the cytoplasm, suggesting a preassembled MfrABE holoenzyme has to be recognized by the TAT system for translocation to occur. Gene expression studies in chemostat cultures following an aerobic-anaerobic shift showed that mfrA is highly upregulated by oxygen limitation, as would be experienced in vivo. Our results indicate that in addition to a role in fuma- rate respiration, Mfr allows C. jejuni to reduce analo- gous substrates specifically present in the host gut environment.
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- 2010
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28. Has the introduction of brown trout altered disease patterns in native New Zealand fish?
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David W. Kelly, Colin R. Townsend, Rachel A. Paterson, Robert Poulin, and Daniel M. Tompkins
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Brown trout ,Trout ,Gobiomorphus breviceps ,biology ,Animal ecology ,Ecology ,Parasitism ,Parasite hosting ,Introduced species ,Aquatic Science ,Salmo ,biology.organism_classification - Abstract
Summary 1. It is well recognised that non‐indigenous species (NIS) can affect native communities via the ‘spillover’ of introduced parasites. However, two other potentially important processes, the ‘spillback’ of native parasites from a competent NIS host, where the latter acts as a reservoir leading to amplified infection in native hosts, and the ‘dilution’ of parasitism by a NIS host acting as a sink for native parasites, have either not been tested or largely overlooked. 2. We surveyed the helminth parasite fauna of native New Zealand fish in Otago streams that varied in the abundance of introduced brown trout Salmo trutta, to look for evidence of spillback and/or dilution. Spillover is not an issue in this system, with trout introduced as parasite‐free eggs. 3. Seven native parasite species were present across 12 sites; significant inverse relationships with an index of trout abundance (i.e. dilution) were documented for three species infecting the native upland bully Gobiomorphus breviceps, and one species infecting the native roundhead galaxias Galaxias anomalus. 4. An inverse relationship between bully energy status and infection intensity of one parasite species suggests that parasite dilution could have positive effects on bully populations. Our failure to detect similar relationships for the other parasites does not preclude the possibility that dilution is beneficial to native fish, since parasites may have subtle or unmeasured impacts. 5. The parasite dilution patterns reported are compelling in that they occurred across several native host and parasite species; as such they have important implications for invasion ecology, providing an interesting contrast to the largely negative impacts reported for NIS. Mechanisms potentially responsible for the patterns observed are discussed
- Published
- 2009
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29. Downregulation of connective tissue growth factor by three-dimensional matrix enhances ovarian carcinoma cell invasion
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Jaclyn A. Shepard, Angela J. Fought, Lonnie D. Shea, M. Sharon Stack, Peter Penzes, David Lee Kelly, Denise M. Scholtens, Maria V. Barbolina, and Brian P. Adley
- Subjects
Integrins ,Umbilical Veins ,Cancer Research ,Pathology ,medicine.medical_specialty ,Blotting, Western ,Integrin ,Cell Culture Techniques ,Down-Regulation ,Connective tissue ,Collagen Type I ,Article ,Immunoenzyme Techniques ,Extracellular matrix ,Downregulation and upregulation ,Spheroids, Cellular ,Biomarkers, Tumor ,Cell Adhesion ,medicine ,Animals ,Humans ,Neoplasm Invasiveness ,RNA, Messenger ,RNA, Small Interfering ,Cell adhesion ,Cells, Cultured ,Oligonucleotide Array Sequence Analysis ,Neurons ,Ovarian Neoplasms ,integumentary system ,biology ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,Connective Tissue Growth Factor ,Rats ,CTGF ,medicine.anatomical_structure ,Oncology ,Cell culture ,Cancer research ,biology.protein ,Female ,Endothelium, Vascular ,Type I collagen - Abstract
Epithelial ovarian carcinoma (EOC) is a leading cause of death from gynecologic malignancies, due mainly to the prevalence of undetected metastatic disease. The process of cell invasion during intraperitoneal anchoring of metastatic lesions requires concerted regulation of many processes, including modulation of adhesion to the extracellular matrix and localized invasion. Exploratory cDNA microarray analysis of early response genes (altered after 4 hr of 3D collagen culture) coupled with confirmatory real-time reverse-transcriptase polymerase chain reaction, multiple 3D cell culture matrices, Western blot, immunostaining, adhesion, migration and invasion assays were used to identify modulators of adhesion pertinent to EOC progression and metastasis. cDNA microarray analysis indicated a dramatic downregulation of connective tissue growth factor (CTGF) in EOC cells placed in invasion- mimicking conditions (3D Type I collagen). Examination of human EOC specimens revealed that CTGF expression was absent in 46% of the tested samples (n = 41), but was present in 100% of normal ovarian epithelium samples (n = 7). Reduced CTGF expression occurs in many types of cells and may be a general phenomenon displayed by cells encountering a 3D environment. CTGF levels were inversely correlated with invasion such that downregulation of CTGF increased, while its upregulation reduced collagen invasion. Cells adhered preferentially to a surface comprised of both collagen I and CTGF relative to either component alone using alpha6beta1 and alpha3beta1 integrins. Together these data suggest that downregulation of CTGF in EOC cells may be important for cell invasion through modulation of cell-matrix adhesion.
- Published
- 2009
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30. Effects of Intravenous Verapamil on the Haemodynamic Response to Exercise in Patients with Angina Pectoris
- Author
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David T. Kelly, Phillip J. Harris, S. Meares, N. M. B. Sadick, M. Hiroe, Gary S. Roubin, and George J. Bautovich
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Adult ,Male ,medicine.medical_specialty ,Cardiac output ,Cardiac Volume ,Angina Pectoris ,Angina ,Internal medicine ,Internal Medicine ,Humans ,Medicine ,Infusions, Parenteral ,Pulmonary Wedge Pressure ,Cardiac Output ,Pulmonary wedge pressure ,End-systolic volume ,Ejection fraction ,business.industry ,Stroke Volume ,Stroke volume ,Middle Aged ,medicine.disease ,Oxygen ,medicine.anatomical_structure ,Verapamil ,Anesthesia ,Exercise Test ,cardiovascular system ,Vascular resistance ,Cardiology ,Vascular Resistance ,business ,medicine.drug - Abstract
The effects of intravenous Verapamil (V) on exercise haemodynamics and ventricular function were compared in 13 patients with stable effort angina. Intravascular pressures, thermodilution cardiac output and radionuclide ejection fraction were measured simultaneously at rest and during exercise. At rest Verapamil produced systemic vasodilation. During exercise at identical workloads compared to control, Verapamil increased cardiac index (CI) and decreased AVO2 difference. Pulmonary artery wedge pressure was lower. Ejection fraction was higher (control-55 +/- 11% vs V-64 +/- 11%) as the disproportionate increase in end systolic volume relative to the end diastolic volume was prevented. Verapamil is effective in exercise induced angina and alters haemodynamics primarily through its vasodilating properties associated with an increased CI.
- Published
- 2009
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31. Efficient solution-phase synthesis of multiple O-phosphoseryl-containing peptides related to casein and statherin
- Author
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David P. Kelly, John W. Perich, and Eric C. Reynolds
- Subjects
Chemistry ,Stereochemistry ,Molecular Sequence Data ,Caseins ,Liquid phase ,Phosphoproteins ,Biochemistry ,Pentapeptide repeat ,Solution phase ,Phosphoserine ,chemistry.chemical_compound ,Casein ,Peptide synthesis ,Amino Acid Sequence ,Salivary Proteins and Peptides ,Peptides ,Peptide sequence ,Solution phase synthesis - Abstract
The multiple Ser(P)-containing peptides, H-Ser(P)-Ser(P)-Ser(P)-Glu-Glu-NHMe.TFA, H-Asp-Ser(P)-Ser(P)-Glu-Glu-NHMe.TFA and H-Glu-Ser(P)-Ser(P)-Glu-Glu-NHMe.TFA were prepared by the use of Boc-Ser(PO3Ph2)-OH in the Boc mode of solution phase peptide synthesis followed by platinum-mediated hydrogenolytic de-protection of the Ser(PO3Ph2)-containing peptides. The protected peptides were assembled using the mixed anhydride coupling methods with 40% TFA/CH2Cl2 used for removal of the Boc group from intermediate Boc-protected peptides.
- Published
- 2009
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32. Efficient solution phase synthesis and use of multiple O-phosphothreonyl-containing peptides for calcium phosphate binding studies
- Author
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John W. Perich, David P. Kelly, and Eric C. Reynolds
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Calcium Phosphates ,Binding Sites ,Chemistry ,Stereochemistry ,Molecular Sequence Data ,chemistry.chemical_element ,Tripeptide ,Calcium ,Biochemistry ,Pentapeptide repeat ,Solutions ,chemistry.chemical_compound ,Phosphothreonine ,Yield (chemistry) ,Methods ,Peptide synthesis ,Amino Acid Sequence ,Threonine ,Oligopeptides ,Peptide sequence ,Protein Binding - Abstract
The protected phosphothreonine derivative Boc-Thr(PO 3 Ph 2 )-OH was prepared in high yield from Boc-Thr-OH by a simple three-step procedure which involved 4-nitrobenzylcarboxyl protection,either phosphorotriester (diphenyl phosphorochloridate) or phosphite-triester (diphenyl N,N-diethylphosphoramidite) phosphorylation of the threonine hydroxyl group of Boc-Thr-ONb followed by hydrogenolytic carboxyl deprotection.The three Thr(P)-containing peptides,H-Thr(P)-Glu-Glu-NHMe.TFA, H-Thr(P)-Thr(P)-Glu-Glu-NHMe.TFA and H-Thr(P)-Thr(P)-Thr(P)-Glu-Glu-NHMe.TFA, were prepared in high yield by the use of Boc-Thr(PO 3 Ph 2 )-OH in the Boc mode of peptide synthesis (mixed anhydride method) followed by platinum-mediated hydrogenolytic deprotection of the Thr(PO 3 Ph 2 )-containing peptides.The use of the phosphopeptides in calcium phosphate binding studies showed that the triple Thr(P)-cluster was a basic structural requirement, since only the pentapeptide was able to bind calcium phosphate efficiently
- Published
- 2009
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33. Subgaleal Hematoma in a Child, without Skull Fracture
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David J. Gower, David L. Kelly, John S. Kirkpatrick, and Allen R. Chauvenet
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Hematoma ,medicine.medical_specialty ,Severe headache ,Scalp ,business.industry ,Subgaleal hematoma ,medicine.disease ,Surgery ,Head trauma ,Encephalocele ,body regions ,Skull ,medicine.anatomical_structure ,Developmental Neuroscience ,Skull fracture ,Pediatrics, Perinatology and Child Health ,Frontal Sinusitis ,Humans ,Medicine ,Female ,Blood Platelet Disorders ,Neurology (clinical) ,Child ,business - Abstract
The rare cases of subgaleal hematoma in childhood reported previously have all been related to head trauma. A case of apparently spontaneous subgaleal hematoma is reported which was associated with a qualitative platelet defect and not with trauma. Subgaleal hematoma must be differentiated from subgaleal infection and air from frontal sinusitis with bony erosion, and from an encephalocele or tumor erosion through the skull. Computed cranial tomography is useful in that differentiation. Most cases have been managed conservatively, but subgaleal tap may be indicated if there is severe headache or potential scalp necrosis.
- Published
- 2008
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34. Dermatofibrosarcoma protuberans and giant cell fibroblastoma exhibit CD99 positivity
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Alexander J. Lazar, David R. Kelly, Victor G. Prieto, Deborah Y. Sanders, Marcelo G. Horenstein, Anne H. Bussian, Henry G. Skelton, Kathleen J. Smith, Terry L. Barrett, and A. Hafeez Diwan
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medicine.medical_specialty ,Pathology ,Skin Neoplasms ,Histology ,CD99 ,CD34 ,Antigens, CD34 ,Dermatology ,12E7 Antigen ,Biology ,Pathology and Forensic Medicine ,Antigens, CD ,Biomarkers, Tumor ,Dermatofibrosarcoma protuberans ,medicine ,Humans ,Skin ,Dermatofibrosarcoma ,Giant Cell Tumors ,Anatomical pathology ,Giant-cell fibroblastoma ,medicine.disease ,Immunohistochemistry ,Sarcoma ,Fibroma ,Cell Adhesion Molecules - Abstract
According to most authors, dermatofibrosarcoma protuberans (DFSP) and giant cell fibroblastoma (GCF) represent the adult and juvenile forms, respectively, of the same disease entity, as evidenced by similar morphology, an identical chromosomal translocation, and CD34 positivity. It has been shown that DFSP and nuchal-type fibroma (NTF) (which is also CD34-positive) are related lesions, and that there might possibly be a continuum between the two. In addition, NTF exhibits CD99 positivity. It was therefore, hypothesized that both DFSP and GCF would show similar immunopositivity for CD99. Archives of pathology at several institutions were searched for DFSP and GCF tissue blocks. A total of 29 DFSP and 5 GCF were analyzed by immunohistochemistry for expression of CD99. Twenty-three of 29 DFSP (79%) and 2 of 5 GCP (40%) expressed CD99. Comparison of CD99 and CD34 showed that the non-tumoral periphery of DFSP was less probable to be CD99 positive, but this finding was not statistically significant.
- Published
- 2008
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35. Adult T-cell Leukemia/Lymphoma in an Adolescent Presenting with Skin Lesions
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Jayne Ness, Amy Theos, David R. Kelly, Catherine T. Lucas, David F. Crawford, Kendra J. Gillis, and Yuki A. Hammers
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Pathology ,medicine.medical_specialty ,Skin Neoplasms ,Adolescent ,Dermatology ,Disease ,Malignancy ,Virus ,Adult T-cell leukemia/lymphoma ,Immunophenotyping ,Fatal Outcome ,Antigens, CD ,hemic and lymphatic diseases ,Disease Transmission, Infectious ,medicine ,Humans ,Leukemia-Lymphoma, Adult T-Cell ,Skin ,Human T-lymphotropic virus 1 ,Deltaretrovirus Antibodies ,business.industry ,Transfusion Reaction ,medicine.disease ,HTLV-I Infections ,Lymphoma, T-Cell, Cutaneous ,Lymphoma ,Long latency ,Leukemia ,Pediatrics, Perinatology and Child Health ,Female ,Skin lesion ,business - Abstract
Adult T-cell leukemia/lymphoma is a T-cell malignancy caused by the human T-cell lymphotropic virus-I. Adult T-cell leukemia/lymphoma is primarily a disease of adults due to the long latency period between initial infection and development of leukemia. We present a case of acute adult T-cell leukemia/lymphoma in an adolescent. Skin lesions had appeared 3 years earlier and were the initial sign of human T-cell lymphotropic virus-I infection and T-cell malignancy. Her disease failed to respond to both intensive chemotherapy and antiviral therapy. Cutaneous lesions are sometimes the initial sign of adult T-cell leukemia/lymphoma and early recognition is imperative.
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- 2008
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36. A temperature-regulated Campylobacter jejuni gluconate dehydrogenase is involved in respiration-dependent energy conservation and chicken colonization
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Erin C. Gaynor, David J. Kelly, Stephen J. Hall, Stuart A. Thompson, Johanna E. Hall, Diane G. Newell, Mohanasundari Pajaniappan, Shaun Cawthraw, Kimberly M. Rathbun, Willie A. Agee, Joshua A. Fields, and Christopher M. Burns
- Subjects
Pectobacterium ,biology ,Strain (chemistry) ,Mutant ,Dehydrogenase ,Colonization ,biology.organism_classification ,Molecular Biology ,Microbiology ,Campylobacter jejuni ,Pathogen ,Bacteria - Abstract
Campylobacter jejuni is a gastrointestinal pathogen of humans but can asymptomatically colonize the avian gut. C. jejuni therefore grows at both 37 degrees C and 42 degrees C, the internal temperatures of humans and birds respectively. Microarray and proteomic studies on temperature regulation in C. jejuni strain 81-176 revealed the upregulation at 42 degrees C of two proteins, Cj0414 and Cj0415, orthologous to gluconate dehydrogenase (GADH) from Pectobacterium cypripedii. 81-176 demonstrated GADH activity, converting d-gluconate to 2-keto-d-gluconate, that was higher at 42 degrees C than at 37 degrees C. In contrast, cj0414 and cj0415 mutants lacked GADH activity. Wild-type but not cj0415 mutant bacteria exhibited gluconate-dependent respiration. Neither strain grew in defined media with d-gluconate or 2-keto-d-gluconate as a sole carbon source, revealing that gluconate was used as an electron donor rather than as a carbon source. When administered to chicks individually or in competition with wild-type, the cj0415 mutant was impaired in establishing colonization. In contrast, there were few significant differences in colonization of BALB/c-ByJ mice in single or mixed infections. These results suggest that the ability of C. jejuni to use gluconate as an electron donor via GADH activity is an important metabolic characteristic that is required for full colonization of avian but not mammalian hosts.
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- 2008
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37. Identifying the source of species invasions: sampling intensity vs. genetic diversity
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Jim R. Muirhead, Derek K. Gray, Sandra Ellis, Daniel D. Heath, Hugh J. MacIsaac, and David W. Kelly
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Genetic diversity ,education.field_of_study ,Ecology ,Population ,Population genetics ,Sampling (statistics) ,Biology ,Phylogeography ,Genetic variation ,Sampling design ,Genetics ,education ,Ecology, Evolution, Behavior and Systematics ,Sampling bias - Abstract
Population geneticists and community ecologists have long recognized the importance of sampling design for uncovering patterns of diversity within and among populations and in communities. Invasion ecologists increasingly have utilized phylogeographical patterns of mitochondrial or chloroplast DNA sequence variation to link introduced populations with putative source populations. However, many studies have ignored lessons from population genetics and community ecology and are vulnerable to sampling errors owing to insufficient field collections. A review of published invasion studies that utilized mitochondrial or chloroplast DNA markers reveals that insufficient sampling could strongly influence results and interpretations. Sixty per cent of studies sampled an average of less than six individuals per source population, vs. only 45% for introduced populations. Typically, far fewer introduced than source populations were surveyed, although they were sampled more intensively. Simulations based on published data forming a comprehensive mtDNA haplotype data set highlight and quantify the impact of the number of individuals surveyed per source population and number of putative source populations surveyed for accurate assignment of introduced individuals. Errors associated with sampling a low number of individuals are most acute when rare source haplotypes are dominant or fixed in the introduced population. Accuracy of assignment of introduced individuals is also directly related to the number of source populations surveyed and to the degree of genetic differentiation among them (F(ST)). Incorrect interpretations resulting from sampling errors can be avoided if sampling design is considered before field collections are made.
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- 2008
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38. Fish community responses to drying disturbances in an intermittent stream: a landscape perspective
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Andrew J. H. Davey and David J. Kelly
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Brown trout ,Gobiomorphus breviceps ,Electrofishing ,Resistance (ecology) ,biology ,Ecology ,Spatial ecology ,Environmental science ,Context (language use) ,Species richness ,Aquatic Science ,Salmo ,biology.organism_classification - Abstract
Summary 1. Refugia are critical to the persistence of individuals, populations and communities in disturbed environments, yet few studies have considered how the position of refugia within the landscape interacts with the behavioural responses of component species to determine the influence of disturbance events on mobile animals. 2. An 18-month quantitative electrofishing survey was undertaken on the Selwyn River, a stream that is intermittent in its middle reaches, to determine how the direction and distance to refugia affect the response of fish populations to drying, and how landscape context interacts with flow permanence to produce spatial patterns in communities. 3. Overall, the propensity of fish to take refuge in perennial reaches during drying episodes, and the rate and extent of recolonization from these refugia upon rewetting, depended upon the direction and distance to refugia and the behaviour of component species. 4. In the upper river, Canterbury galaxias (Galaxias vulgaris), upland bullies (Gobiomorphus breviceps) and brown trout (Salmo trutta) migrated upstream to permanent water as the stream dried from the bottom up, but frequent drying and slow recolonization by most species combined to produce a fish community in intermittent reaches that was quantitatively and qualitatively different to that in neighbouring perennial reaches. 5. In the lower river, fish did not appear to migrate downstream to permanent water as the stream dried from the top down, but a lower frequency of drying episodes and faster recolonization by upland bullies and eels (Anguilla spp.) from downstream refugia allowed the fish community in intermittent reaches to converge with that in neighbouring perennial reaches during prolonged wetted periods. 6. Longitudinal patterns of increasing fish density and species richness with flow permanence are interpreted as the product of species-specific responses to drying events and the spatial position of refugia within the riverscape.
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- 2007
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39. The tectorial membrane: Anatomical, biomechanical, and histological analysis
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Leslie Acakpo-Satchivi, John C. Wellons, E. Rita Humphrey, David R. Kelly, Jeffrey P. Blount, Gina D. Chua, Mohammadali Mohajel Shoja, W. Jerry Oakes, E. George Salter, and R. Shane Tubbs
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Male ,Histology ,Tectorial Membrane ,Lateral flexion ,Tectorial membrane ,Dissection (medical) ,Cadaver ,medicine ,Humans ,Range of Motion, Articular ,Aged ,Aged, 80 and over ,business.industry ,Craniocervical region ,Skull ,General Medicine ,Anatomy ,Middle Aged ,Elastic Tissue ,medicine.disease ,Spinal cord ,Biomechanical Phenomena ,medicine.anatomical_structure ,Membrane ,Ligaments, Articular ,Cervical Vertebrae ,Ligament ,Female ,business - Abstract
There is minimal information in the literature regarding the tectorial membrane. Further, information in the literature regarding the anatomy and function of this structure is often contradictory. We performed the current study to elucidate further this structure's detailed anatomy, function, and histology. Thirteen adult cadavers underwent dissection of their tectorial membranes and detailed observations and measurements were made of them. Ranges of motion of the craniocervical junction were performed before and after transection of this structure. Histological analysis was performed on all membranes. The tectorial membrane was found to attach much more superiorly than previously described and was found to be firmly adherent to the cranial base and body of the axis but not to the posterior aspect of the odontoid process. The mean thickness of this membrane was found to be 1 mm. Flexion of the head made the tectorial membrane fully taut at 15 degrees and extension made it fully taut at 20 degrees; however, there was a buckling effect (redundant tectorial membrane) noted at the level of the odontoid process in extension. With the alar and transverse ligaments cut and with flexion of the head, the middle portion of this membrane was stretched over the odontoid process, thus acting as a "hammock" that inhibited the odontoid process from moving posteriorly. The tectorial membrane did not limit cervical flexion per se but rather helped to insure that the odontoid process did not impinge into the cervical canal. Lateral flexion was not found to be limited by this structure. Histologically, parallel collagen fibers with spindle-shaped fibrocytes were observed within this membrane and near its attachment to the posterior axis, the collagen fibers were noted to be more homogenous with larger non-spindled fibrocytes. At the cranial attachment of the tectorial membrane, multiple calcified areas were noted that interdigitated with the underlying bone. Also near this cephalic bony attachment, there was an increase in the number of elastic fibers, which were found running parallel with the surrounding Type III collagen fibers. The tectorial membrane was found to attach much more superiorly than previously described. We would propose that the tectorial membrane provides for a second line of defense, preventing the odontoid process from compressing the spinal cord and by doing so, secondarily limits movement of the craniocervical juncture. This hypothesis is strengthened by the finding of many elastic fibers in the tectorial membrane. To our knowledge, our study is the first to perform a detailed histological analysis of the tectorial membrane. We hope that these data are useful to the clinician who investigates this ligament of the craniocervical region.
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- 2007
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40. Growth ofCampylobacter jejunion nitrate and nitrite: electron transport to NapA and NrfA via NrfH and distinct roles for NrfA and the globin Cgb in protection against nitrosative stress
- Author
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David J. Kelly, Robert K. Poole, Marc S. Pittman, Simon F. Park, Karen T. Elvers, Michael Jones, and Lucy J. Lee
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biology ,Cytochrome ,Mutant ,Wild type ,Periplasmic space ,biology.organism_classification ,Nitrite reductase ,Microbiology ,Campylobacter jejuni ,chemistry.chemical_compound ,Biochemistry ,chemistry ,biology.protein ,Globin ,Nitrite ,Molecular Biology - Abstract
Pathways of electron transport to periplasmic nitrate (NapA) and nitrite (NrfA) reductases have been investigated in Campylobacter jejuni, a microaerophilic food-borne pathogen. The nap operon is unusual in lacking napC (encoding a tetra-haem c-type cytochrome) and napF, but contains a novel gene of unknown function, napL. The iron-sulphur protein NapG has a major role in electron transfer to the NapAB complex, but we show that slow nitrate-dependent growth of a napG mutant can be sustained by electron transfer from NrfH, the electron donor to the nitrite reductase NrfA. A napL mutant possessed approximately 50% lower NapA activity than the wild type but showed normal growth with nitrate as the electron acceptor. NrfA was constitutive and was shown to play a role in protection against nitrosative stress in addition to the previously identified NO-inducible single domain globin, Cgb. However, nitrite also induced cgb expression in an NssR-dependent manner, suggesting that growth of C. jejuni with nitrite causes nitrosative stress. This was confirmed by lack of growth of cgb and nssR mutants, and slow growth of the nrfA mutant, in media containing nitrite. Thus, NrfA and Cgb together provide C. jejuni with constitutive and inducible components of a robust defence against nitrosative stress.
- Published
- 2006
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41. Impacts of fine sediment addition to tussock, pasture, dairy and deer farming streams in New Zealand
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Colin R. Townsend, Christoph D. Matthaei, Florian Weller, and David W. Kelly
- Subjects
geography ,geography.geographical_feature_category ,Ecology ,Tussock ,Environmental science ,Sediment ,Ecosystem ,Species richness ,STREAMS ,Aquatic Science ,Sedimentation ,Pasture ,Hydrobiology - Abstract
Summary 1. Increased fine sediment input caused by agricultural development is expected to act as a stressor for stream ecosystems. In a large-scale field experiment, we added fine river sand to 50-m reaches of three second-order streams in each of four categories of catchment development (ungrazed tussock grasslands, grazed pasture, dairying and deer farming) and measured the responses of macroinvertebrates and aquatic moss. 2. Before addition, fine sediment cover differed between land uses, being lowest in tussock (7%), intermediate in pasture (30%) and dairy (47%) and highest in deer streams (88%). Sediment addition increased cover by one land-use category (e.g. augmented sediment cover in tussock streams was similar to pre-existing cover in pasture streams), and cover remained high in impact reaches (compared with controls) throughout the 5-week experiment. Sediment addition did not change concentrations of phosphate, nitrate and ammonium, which were generally highest in dairy streams and lowest in tussock streams. 3. Aquatic mosses (most common in tussock, absent in dairy and deer), invertebrate density (highest in deer, lowest in tussock), taxon richness (highest in pasture, lowest in deer) and diversity (highest in pasture and tussock, lowest in dairy and deer) all differed between land uses. Sediment addition resulted in reductions of moss cover, invertebrate taxon richness and richness of Ephemeroptera, Plecoptera and Trichoptera in impact relative to control reaches. 4. The impact of sediment addition was strongest in pasture streams where pre-existing sediment cover was moderate and richness and diversity of the invertebrate community highest. However, even in the already sediment-rich and species-poor deer streams, density of one common taxon was reduced significantly by sediment addition, and another two were affected in the same way in dairy streams, the second-most intense land use. 5. Our experiment has disentangled the impact of sediment addition from other concomitant land-use effects that could not be reliably distinguished in previous research, which has mainly consisted of correlative studies or unrealistically small-scale experiments.
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- 2006
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42. Contrasting patterns in genetic diversity following multiple invasions of fresh and brackish waters
- Author
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David W. Kelly, Daniel D. Heath, Jim R. Muirhead, and Hugh J. MacIsaac
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geography ,Genetic diversity ,geography.geographical_feature_category ,Brackish water ,Ecology ,Introduced species ,Estuary ,Biology ,Invasive species ,Phylogeography ,Population bottleneck ,Habitat ,Genetics ,Ecology, Evolution, Behavior and Systematics - Abstract
Biological invasions may combine the genetic effects of population bottlenecks and selection and thus provide valuable insight into the role of such processes during novel environmental colonizations. However, these processes are also influenced by multiple invasions, the number of individuals introduced and the degree of similarity between source and receiving habitats. The amphipod Gammarus tigrinus provides a useful model to assess these factors, as its invasion history has involved major environmental transitions. This species is native to the northwest Atlantic Ocean, although it invaded both brackish and freshwater habitats in the British Isles after introduction more than 65 years ago. It has also spread to similar habitats in Western Europe and, most recently, to Eastern Europe, the Baltic Sea, and the Laurentian Great Lakes. To examine sources of invasion and patterns of genetic change, we sampled populations from 13 native estuaries and 19 invaded sites and sequenced 542 bp of the mitochondrial COI gene. Strong native phylogeographical structure allowed us to unambiguously identify three allopatrically evolved clades (2.3–3.1% divergent) in invading populations, indicative of multiple introductions. The most divergent clades occurred in the British Isles and mainland Europe and were sourced from the St Lawrence and Chesapeake/Delaware Bay estuaries. A third clade was found in the Great Lakes and sourced to the Hudson River estuary. Despite extensive sampling, G. tigrinus did not occur in freshwater at putative source sites. Some European populations showed reduced genetic diversity consistent with bottlenecks, although selection effects cannot be excluded. The habitat distribution of clades in Europe was congruent with the known invasion history of secondary spread from the British Isles. Differences in salinity tolerance among lineages were suggested by patterns of habitat colonization by different native COI clades. Populations consisting of admixtures of the two invading clades were found principally at recently invaded fresh and brackish water sites in Eastern Europe, and were characterized by higher genetic diversity than putative source populations. Further studies are required to determine if these represent novel genotypes. Our results confirm that biological invasions need not result in diminished genetic diversity, particularly if multiple source populations, each with distinctive genetic composition, contribute to the founding populations.
- Published
- 2006
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43. Invasion by the amphipod Gammarus pulex alters community composition of native freshwater macroinvertebrates
- Author
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David W. Kelly, Jaimie T. A. Dick, Calum MacNeil, Robbie A. McDonald, and Roberta J. E. Bailey
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Biomass (ecology) ,biology ,Ecology ,media_common.quotation_subject ,Species diversity ,biology.organism_classification ,Competition (biology) ,Gammarus pulex ,Pulex ,Gammarus ,Ecosystem ,Species richness ,Ecology, Evolution, Behavior and Systematics ,media_common - Abstract
Assessing the effects of invading species on native community structure is often confounded by environmental factors and weakened by lack of replicated, long-term pre- and post-invasion monitoring. Here, we uncouple the community effects of a freshwater amphipod invader from environmental differences. In Irish rivers, the introduced Gammarus pulex replaces the native Gammarus duebeni celticus. However, the River Lissan in Northern Ireland is dissected by a weir that has slowed the upstream invasion by G. pulex. This allowed us in 2000 to sample three contiguous 150-m reaches that were (1) G. pulex dominated; (2) mixed Gammarus spp.; and (3) G. duebeni celticus only. In 2003, we resampled these reaches and one additional of mixed Gammarus species and one with only G. duebeni celticus further upstream. In temperature, conductivity, and pH, there were statistically significant but no biologically relevant differences among the five reaches of 2003, and between the three reaches surveyed in both years. Although there was evidence of recovery in macroinvertebrate diversity and richness in invaded reaches between years, continued upstream invasion was associated with sustained reductions in these community metrics as compared to un-invaded sites. Community ordination indicated (1) different associations of community composition attributed to the distribution, abundance, and biomass of the invader; and (2) increasing similarity of invaded communities over time. The impact mechanisms of G. pulex on macroinvertebrate community composition may include predation and competition. The consequences of the observed community changes for ecosystem functioning require further investigation.
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- 2006
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44. The Campylobacter jejuni PEB1a adhesin is an aspartate/glutamate-binding protein of an ABC transporter essential for microaerobic growth on dicarboxylic amino acids
- Author
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David J. Kelly, Edward Guccione, Michael P. Williamson, Maria del Rocio Leon-Kempis, and Francis Mulholland
- Subjects
endocrine system diseases ,Mutant ,Glutamic Acid ,ATP-binding cassette transporter ,Microbiology ,Campylobacter jejuni ,Bacterial Proteins ,Glutamate aspartate transporter ,Animals ,Humans ,Asparagine ,Molecular Biology ,chemistry.chemical_classification ,Antigens, Bacterial ,Aspartic Acid ,biology ,Wild type ,Glutamate binding ,biology.organism_classification ,Aerobiosis ,Recombinant Proteins ,Amino Acids, Dicarboxylic ,Culture Media ,Amino acid ,chemistry ,Biochemistry ,biology.protein ,ATP-Binding Cassette Transporters ,Subcellular Fractions - Abstract
The PEB1a protein of the gastrointestinal pathogen Campylobacter jejuni mediates interactions with epithelial cells and is an important factor in host colonization. Cell fractionation and immunoblotting showed that PEB1a is most abundant in the periplasm of C. jejuni, and is detectable in the culture supernatant but not in the inner or outer membrane. The protein is homologous with periplasmic-binding proteins associated with ABC transporters and we show by fluorescence spectroscopy that purified recombinant PEB1a binds L-aspartate and L-glutamate with sub microM K(d) values. Binding of L-14C-aspartate or L-14C-glutamate was strongly out-competed by excess unlabelled aspartate or glutamate but only poorly by asparagine and glutamine. A mutant in the Cj0921c gene, encoding PEB1a, was completely unable to transport 5 microM L-14C-glutamate and showed a large reduction (approximately 20-fold) in the rate of L-14C-aspartate transport compared with the wild type. Although microaerobic growth of this mutant was little affected in complex media, growth on aspartate or glutamate in defined media was completely prevented, whereas growth with serine was similar to wild type. 1H-NMR analysis of the culture supernatants of the Cj0921c mutant showed some utilization of aspartate but not glutamate, consistent with the transport data. It is concluded that in addition to the established role of PEB1a as an adhesin, the PEB1 transport system plays a key role in the utilization of aspartate and glutamate, which may be important in vivo carbon sources for this pathogen.
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- 2006
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45. VICARIANCE AND DISPERSAL EFFECTS ON PHYLOGEOGRAPHIC STRUCTURE AND SPECIATION IN A WIDESPREAD ESTUARINE INVERTEBRATE
- Author
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Hugh J. MacIsaac, Daniel D. Heath, and David W. Kelly
- Subjects
education.field_of_study ,Species complex ,Ecology ,Population ,Allopatric speciation ,Life Sciences ,Biology ,Phylogeography ,Genetic Speciation ,Genetic structure ,Vicariance ,Genetics ,Biological dispersal ,education ,General Agricultural and Biological Sciences ,Ecology, Evolution, Behavior and Systematics - Abstract
Vicariance and dispersal can strongly influence population genetic structure and allopatric speciation, but their importance in the origin of marine biodiversity is unresolved. In transitional estuarine environments, habitat discreteness and dispersal barriers could enhance divergence and provide insight to evolutionary mechanisms underlying marine and freshwater biodiversity. We examined this by assessing phylogeographic structure in the widespread amphipod Gammarus tigrinus across 13 estuaries spanning its northwest Atlantic range from Quebec to Florida. Mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 1 phylogenies supported deep genetic structure consistent with Pliocene separation and cryptic northern and southern species. This break occurred across the Virginian-Carolinian coastal biogeographic zone, where an oceanographic discontinuity may restrict gene flow. Ten estuarine populations of the northern species occurred in four distinct clades, supportive of Pleistocene separation. Glaciation effects on genetic structure of estuarine populations are largely unknown, but analysis of molecular variance (AMOVA) supported a phylogeographic break among clades in formerly glaciated versus nonglaciated areas across Cape Cod, Massachusetts. This finding was concordant with patterns in other coastal species, though there was no significant relationship between latitude and genetic diversity. This supports Pleistocene vicariance events and divergence of clades in different northern glacial refugia. AMOVA results and private haplotypes in most populations support an allopatric distribution across estuaries. Clade mixture zones are consistent with historical colonization and human-mediated transfer. An isolation-by-distance model of divergence was detected after we excluded a suspected invasive haplotype in the St. Lawrence estuary. The occurrence of cryptic species and divergent population structure support limited dispersal, dispersed habitat distribution, and historical factors as important determinants of estuarine speciation and diversification. © 2006 The Society for the Study of Evolution. All rights reserved.
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- 2006
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46. Oligopeptides as catalysts for asymmetric epoxidation
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Stanley M. Roberts and David R. Kelly
- Subjects
Models, Molecular ,inorganic chemicals ,Biophysics ,Stereoisomerism ,Alkenes ,Biochemistry ,Catalysis ,Biomaterials ,chemistry.chemical_compound ,Chalcone ,Organic chemistry ,Enzyme kinetics ,Hydrogen peroxide ,Oligopeptide ,biology ,Chemistry ,Organic Chemistry ,Enantioselective synthesis ,Active site ,Substrate (chemistry) ,Hydrogen Peroxide ,General Medicine ,Combinatorial chemistry ,biology.protein ,Epoxy Compounds ,Stereoselectivity ,Oligopeptides - Abstract
Oligopeptides are versatile catalysts for the enantioselective epoxidation of electron deficient alkenes, (e.g. alpha,beta-unsaturated ketones) with alkaline hydrogen peroxide. This review describes optimisation of the catalyst, substrate range, synthetic applications of the products and rationalisation of the stereoselectivity by an active site model.
- Published
- 2006
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47. Complete ossification of the human falx cerebri
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W. Jerry Oakes, Robert Lott, David R. Kelly, E. George Salter, and R. Shane Tubbs
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Male ,Pathology ,medicine.medical_specialty ,Histology ,Dura mater ,Cadaver ,Meningeal Neoplasms ,medicine ,Humans ,Aged ,Ossification ,business.industry ,Ossification, Heterotopic ,Carcinoma ,Meninges ,Poorly differentiated carcinoma ,General Medicine ,Anatomy ,Frontal Lobe ,Falx cerebri ,Dissection ,Normal ossification ,medicine.anatomical_structure ,Dura Mater ,medicine.symptom ,business - Abstract
During the routine dissection of the head and neck of an adult male cadaver complete ossification of the falx cerebri was noted. Anomalous ossification was not found in any other dural component or other parts of the body. The brain appeared grossly normal. Histological sections showed normal ossification processes involving the falx cerebri. In addition, rare scattered deposits of metastatic poorly differentiated carcinoma within the trabecular spaces were seen. Reports of isolated islands of ossification involving primarily the most anterior part of the falx cerebri in man are found in the literature. Our case report represents to our knowledge, the first report of complete ossification of this dural partition. Whether this is simply an anomalous configuration or due to the few metastatic cells found within this region remains unclear.
- Published
- 2005
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48. Introduction of the non-indigenous amphipod Gammarus pulex alters population dynamics and diet of juvenile trout Salmo trutta
- Author
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Jaimie T. A. Dick and David W. Kelly
- Subjects
education.field_of_study ,Amphipoda ,biology ,Ecology ,Population ,Aquatic Science ,biology.organism_classification ,Gammarus pulex ,Trout ,Pulex ,Gammarus ,Salmo ,education ,Invertebrate - Abstract
Summary 1. The amphipod Gammarus pulex, introduced to Irish rivers with the aim of enhancing trout feeding, is displacing the native Gammarus duebeni celticus. These two species are generally associated with different environmental conditions and macroinvertebrate communities, confounding assessment of effects of the invader as compared with the native on fish populations. Here, we uncouple effects of the two Gammarus species from environmental gradients. 2. A weir dissects a lowland stretch of the River Lissan, slowing the upstream invasion by G. pulex and resulting in contiguous G. pulex, mixed species and G. d. celticus reaches. Total invertebrate abundance and biomass in the benthos were significantly higher in the G. pulex reach, driven by high invader abundance, with low abundance of other taxa. Gammarus pulex was particularly prominent in night-time drift. 3. Correspondingly, densities and biomass of 0+ trout were significantly higher in the G. pulex reach, while instantaneous loss rates were lower. Fish growth rates were similar among the three reaches. 4. In the G. pulex reach, this invader dominated the diet of 0+ trout, leading to ingestion of significantly higher invertebrate biomass than fish in the other reaches. Fish generally preyed on Gammarus in proportion to its abundance, but exhibited some positive selection for G. pulex in the invaded reach. 5. The negative effects of the invader on native invertebrates are contrasted with positive effects on juvenile trout. This indicates changes in energy flux after invasion, with differential resource use or assimilation by G. pulex probable underlying mechanisms. As the frequency of amphipod invasions increases globally, investigations of their role as strong interactors at multiple levels of ecological organisation is required if the consequences of deliberate and unintentional introductions are to be predicted, and ultimately, prevented.
- Published
- 2005
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49. Prey selection by wild birds can allow novel and conspicuous colour morphs to spread in prey populations
- Author
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David J. Kelly, Laura Amy Bartlett, Nicola M. Marples, Robert J. Thomas, and Innes C. Cuthill
- Subjects
education.field_of_study ,Fixation (population genetics) ,Extinction ,Ecology ,Population ,Small population size ,Aposematism ,Biology ,education ,Predator ,Ecology, Evolution, Behavior and Systematics ,Selection (genetic algorithm) ,Predation - Abstract
Conspicuous warning coloration helps to protect prey because it signals to potential predators that the prey is unprofitable. However, such signals only work once predators have come to associate the conspicuous colour with the unprofitability of the prey. The evolution of warning coloration is generally considered to be paradoxical, because it has traditionally been assumed that the first brightly coloured individuals would be at an immediate selective disadvantage because of their greater conspicuousness to predators that are naive to the meaning of the signal. As a result, it has been difficult to understand how a novel conspicuous colour morph could ever avoid rapid extinction, and instead survive and spread in the population until predators have become educated about the signal. In the present study, we experimentally simulated the appearance of a single novel coloured mutant in small populations (20 individuals) of palatable artificial pastry “prey”. The colour morph frequencies in each “generation” of prey (presented on successive days of a trial) were determined by the relative survival of the previous generation under predation by free-living birds. We found that the novel colour morphs regularly persisted and increased from a starting frequency of 1/20 to reach fixation (100%), despite being fully palatable, even when the novel morph was much more conspicuous against the background than the familiar morph. This was true for both green (not normally considered a warning colour) and red (a classic warning colour) novel morphs. Novel colours reached fixation significantly faster than could be accounted for by random drift, indicating differential predation in relation to prey colour by the birds. Our experiments show that the immediate demise of a fully palatable new prey morph is not an inevitable outcome of predator behaviour, because even very conspicuous prey can gain protection from conservative foragers, simply by being novel.
- Published
- 2004
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50. EFFECTS OF SOLAR ULTRAVIOLET RADIATION ON STREAM BENTHIC COMMUNITIES: AN INTERSITE COMPARISON
- Author
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David W. Schindler, Max L. Bothwell, and David J.A. Kelly
- Subjects
Canopy ,Biomass (ecology) ,geography ,geography.geographical_feature_category ,integumentary system ,biology ,Ecology ,fungi ,biology.organism_classification ,Benthos ,Algae ,Photosynthetically active radiation ,Benthic zone ,Environmental science ,Shading ,Ecology, Evolution, Behavior and Systematics ,Riparian zone - Abstract
The effects of solar ultraviolet radiation (UVR), both mid-ultraviolet (UVB; 280-320 nm) and near-ultraviolet (UVA; 320-400 nm), on benthic algal and invertebrate communities were compared in three reaches of a British Columbia coastal stream that differed in the degree of shading by riparian canopy (a full canopy, a partial canopy, and no canopy). At each of the three sites benthic communities were exposed to three different radiation treatments: photosynthetically active radiation alone (PAR; 400-700 nm), PAR1UVA, and PAR1UVA1UVB. Relative to the site with no canopy, UVR was 88% and 66% lower, and PAR was 83% and 49% lower at sites with full and partial canopy, respectively. Late summer increases in UVR to the streambed caused by declines in water level and dissolved organic carbon (DOC) were also lower at sites with high canopy. Sites with less canopy shading had greater algal accrual, decreased biomass of total invertebrates, mayflies, and stoneflies, and reduced invertebrate community diversity com- pared to the heavily shaded reach of the stream. UVR produced taxon-specific community responses that varied across sites and increased with increasing UVR as summer progressed. At the full canopy site UVR had no impact, and the final (day 91) biomass and diversity of invertebrates was highest, and algal biomass lowest. Higher UVA radiation under reduced canopies inhibited algal accrual but had little effect on algal community composition. The biomass of several invertebrate taxa (e.g., Dicosmoecus spp., Limnephilidae) and com- munity diversity were reduced by both UVA and UVB. Less sensitive taxa (e.g., Paralep- tophlebia spp., Paraleptophlebidae) were inhibited only by the highest UVB levels in late summer when water transparency to UVR was greatest. Inhibition of grazers by UVR appeared to indirectly increase algal accrual, particularly at the partial canopy site. Our results indicate that riparian shading may moderate UVR effects on benthic com- munities, mainly through impacts on invertebrates with indirect effects on algae. By re- ducing UVR exposure of streambeds, riparian canopies may be important for ameliorating UVR effects on shallow lotic systems, especially during late-summer, low-flow periods when DOC concentrations are reduced.
- Published
- 2003
- Full Text
- View/download PDF
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