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Search Results: 1 - 10 of 326049 matches for " Samantha S. Orchard "
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An encoded N-terminal extension results in low levels of heterologous protein production in Escherichia coli
Samantha S Orchard, Heidi Goodrich-Blair
Microbial Cell Factories , 2005, DOI: 10.1186/1475-2859-4-22
Abstract: Short-form Tdk complemented the E. coli tdk mutant strain, resulting in FUdR sensitivity of the strain. However, the E. coli tdk mutant expressing the long form of tdk remained FUdR resistant, indicating it did not have a functional deoxythymidine kinase enzyme. We report that long-form Tdk is at least 13-fold less abundant than short-form Tdk, the limited protein produced was as stable as short-form Tdk and the long-form transcript was 1.7-fold less abundant than short-form transcript. Additionally, we report that the long-form extension was sufficient to decrease heterologous production of a different X. nematophila protein, NilC.We conclude that the difference in the FUdR growth phenotype between the E. coli tdk mutant carrying the long-or short-form X. nematophila tdk is due to a difference in Tdk levels. The lower long-form protein level does not result from protein instability, but instead from reduced transcript levels possibly combined with reduced translation efficiency. Because the observed effect of the encoded N-terminal extension is not specific to Tdk production and can be overcome with induction of gene expression, these results may have particular relevance to researchers attempting to limit production of toxic proteins under non-inducing conditions.Proteins from one organism are often expressed in a different species for the purpose of protein purification or complementation studies. When such efforts fail due to non-production of the protein, the underlying cause of failure is often unclear [1]. Protein overproduction is known to induce a heat shock-like response, which results in increased proteolysis in the cell and therefore possible degradation of the desired protein [2]. Other factors such as degradation of the RNA transcript, efficiency of translation and toxic nature of the desired protein may also influence the level of protein production. Thus, common Escherichia coli strains used for protein overproduction include protease mutants (e.g. B
Penicillium menonorum, a new species related to P. pimiteouiense
S.W. Peterson,S.S. Orchard,S. Menon
IMA Fungus , 2011,
Abstract: Penicillium menonorum is described as a new monoverticillate, non-vesiculate species that resembles P. restrictum and P. pimiteouiense. On the basis of phylogenetic analysis of DNA sequences from four loci, P. menonorum occurs in a clade with P. pimiteouiense, P. vinaceum, P. guttulosum, P. rubidurum, and P. parvum. Genealogical concordance analysis was applied to P. pimiteouiense and P. parvum, substantiating the phenotypically defined species. The species P. rubidurum, P. guttulosum, and P. menonorum were on distinct branches statistically excluded from inclusion in other species and have distinct phenotypes.
Exploring Possible Encounters between New Governance, Law and Constitutionalism in the European Union  [PDF]
Samantha Velluti
Beijing Law Review (BLR) , 2013, DOI: 10.4236/blr.2013.41002

The current European Union (EU) is a highly institutionalized template for integration, equipped with a whole spectrum of different modes of regulation ranging from “hard” to “soft” which, particularly in recent years, have been pragmatically combined together to develop a hybrid and multi-tiered EU system. The dramatic expansion of the EU’s governance tool-kit and the variety of objectives and internal structures of these EU governance tools have relied on a non-clearly identifiable mix of legal and policy instruments. These changes in EU governance pose a challenge to the rule of law and its main tenets and do not sit well with the jurisprudence of the Court of Justice of the European Union (CJEU) because they occupy an unsettled constitutional space. This space is characterized by a range of possible encounters between constitutionalism and governance. In this context, New Governance forces European scholars to rethink the way the EU system operates and the way Europeanization is being pursued. The paper explores the relationship between New Governance, law and constitutionalism and the problems concerning their conceptualization and further understanding. Its main argument is that a stronger dialogue between what are known as “soft” and “hard” regulatory mechanisms may lead to a hybridized EU governance regime in which all governance tools are designed to achieve the same set of goals.

The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes
John M. Chaston, Garret Suen, Sarah L. Tucker, Aaron W. Andersen, Archna Bhasin, Edna Bode, Helge B. Bode, Alexander O. Brachmann, Charles E. Cowles, Kimberly N. Cowles, Creg Darby, Limaris de Léon, Kevin Drace, Zijin Du, Alain Givaudan, Erin E. Herbert Tran, Kelsea A. Jewell, Jennifer J. Knack, Karina C. Krasomil-Osterfeld, Ryan Kukor, Anne Lanois, Phil Latreille, Nancy K. Leimgruber, Carolyn M. Lipke, Renyi Liu, Xiaojun Lu, Eric C. Martens, Pradeep R. Marri, Claudine Médigue, Megan L. Menard, Nancy M. Miller, Nydia Morales-Soto, Stacie Norton, Jean-Claude Ogier, Samantha S. Orchard, Dongjin Park, Youngjin Park, Barbara A. Qurollo, Darby Renneckar Sugar, Gregory R. Richards, Zoé Rouy, Brad Slominski, Kathryn Slominski, Holly Snyder, Brian C. Tjaden, Ransome van der Hoeven, Roy D. Welch, Cathy Wheeler, Bosong Xiang, Brad Barbazuk, Sophie Gaudriault, Brad Goodner, Steven C. Slater, Steven Forst, Barry S. Goldman, Heidi Goodrich-Blair
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027909
Abstract: Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points.
A Comparison between Australian Football League (AFL) Injuries in Australian Indigenous versus Non-indigenous Players
Jessica Orchard,John Orchard,Hugh Seward
Sports , 2013, DOI: 10.3390/sports1030069
Abstract: It has previously been shown that being of aboriginal descent is a risk factor for hamstring injuries in Australian football. The aim of this study was to review the Australian Football League (AFL) injury database to determine whether there were any injuries where indigenous players had different relative risks to non-indigenous players. Analysis was conducted using data from the AFL injury database, which included data from 4,492 players over 21 years (1992–2012), covering 162,683 player-matches at AFL level, 91,098 matches at lower levels and 328,181 weeks (possible matches) of exposure. Compared to non-indigenous players, indigenous players had a significantly higher risk of hamstring injuries (RR 1.52, 95% CI 1.32–1.73) and calf strains (RR 1.30, 95% CI 1.00–1.69). Conversely, indigenous players had a significantly lower risk of lumbar/thoracic spine injuries (RR 0.61, 95% CI 0.41–0.91), groin strains/osteitis pubis (RR 0.75, 95% CI 0.58–0.96) and Achilles tendon injuries (RR 0.32, 95% CI 0.12–0.86). The results for the above injuries were also significant in terms of games missed. There was no difference between overall risk of injury (RR 1.03, 95% CI 0.96–1.10) or missed games (RR 1.00, 95% CI 0.97–1.04). This suggests that indigenous AFL players have the same overall number of injuries and missed games, but a slightly different injury profile.
Homicídio seguido de suicídio na cidade de Porto Alegre
Sá, Samantha Dubugras;Werlang, Blanca Susana Guevara;
Estudos de Psicologia (Campinas) , 2007, DOI: 10.1590/S0103-166X2007000200005
Abstract: this paper intended to characterize the profile of individuals who have committed homicide followed by suicide in porto alegre, during an 8-year period. the information about the events were gotten by newspaper articles and police inquiries researches, and through informants' interviews. in the 14 cases located, the event seems to be a gender-related phenomenon, as men were the killers, while women and children were the victims. the most used method for both the homicide and suicide was gunshot. the victim's home was the place where most homicides and suicides were committed, usually during the morning. in five cases, the event triggers were jealousy, threats or end of a relationship. the aggressor had problems in his primary support group, signs of impulsiveness , aggressiveness, alcohol abuse and criminal records, especially due to violence against his own family.
Universitas Psychologica , 2007,
Abstract: homicide followed by suicide (h/s) is a complex and poorly studied phenomenon. this research aims at identifying h/s cases occurred in porto alegre from 1996 throughout 2004. information on h/s was extracted from newspapers, police reports and interviews with the informants. from the 14 identified cases, men were the killers/suicides and women and children their victims. the most frequently used weapons were firearms. in general, the aggressor was an impulsive, aggressive individual showing problems within its primary supporting group, possibly suffering depression and alcohol-addicted with criminal backgrounds (violence against the family). events were mainly triggered by jealousy, threats or the end of a love relationship.
Efficient and Correct Stencil Computation via Pattern Matching and Static Typing
Dominic Orchard,Alan Mycroft
Electronic Proceedings in Theoretical Computer Science , 2011, DOI: 10.4204/eptcs.66.4
Abstract: Stencil computations, involving operations over the elements of an array, are a common programming pattern in scientific computing, games, and image processing. As a programming pattern, stencil computations are highly regular and amenable to optimisation and parallelisation. However, general-purpose languages obscure this regular pattern from the compiler, and even the programmer, preventing optimisation and obfuscating (in)correctness. This paper furthers our work on the Ypnos domain-specific language for stencil computations embedded in Haskell. Ypnos allows declarative, abstract specification of stencil computations, exposing the structure of a problem to the compiler and to the programmer via specialised syntax. In this paper we show the decidable safety guarantee that well-formed, well-typed Ypnos programs cannot index outside of array boundaries. Thus indexing in Ypnos is safe and run-time bounds checking can be eliminated. Program information is encoded as types, using the advanced type-system features of the Glasgow Haskell Compiler, with the safe-indexing invariant enforced at compile time via type checking.
Elevated Cerebral Spinal Fluid Cytokine Levels in Boys with Cerebral Adrenoleukodystrophy Correlates with MRI Severity
Troy C. Lund, Paul S. Stadem, Angela Panoskaltsis-Mortari, Gerald Raymond, Weston P. Miller, Jakub Tolar, Paul J. Orchard
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0032218
Abstract: Background X-linked adrenoleukodystrophy (ALD) is a metabolic, peroxisomal disease that results from a mutation in the ABCD1 gene. The most severe course of ALD progression is the cerebral inflammatory and demyelinating form of the disease, cALD. To date there is very little information on the cytokine mediators in the cerebral spinal fluid (CSF) of these boys. Methodology/Principal Findings Measurement of 23 different cytokines was performed on CSF and serum of boys with cerebral ALD and patients without ALD. Significant elevations in CSF IL-8 (29.3±2.2 vs 12.8±1.1 pg/ml, p = 0.0001), IL-1ra (166±30 vs 8.6±6.5 pg/ml, p = 0.005), MCP-1 (610±47 vs 328±34 pg/ml, p = 0.002), and MIP-1b (14.2±1.3 vs 2.0±1.4 pg/ml, p<0.0001) were found in boys with cALD versus the control group. The only serum cytokine showing an elevation in the ALD group was SDF-1 (2124±155 vs 1175±125 pg/ml, p = 0.0001). The CSF cytokines of IL-8 and MCP-1b correlated with the Loes MRI severity score (p = 0.04 and p = 0.008 respectively), as well as the serum SDF-1 level (p = 0.002). Finally, CSF total protein was also significantly elevated in boys with cALD and correlated with both IL-8, MCP-1b (p = 0.0001 for both), as well as Loes MRI severity score (p = 0.0007). Conclusions/Significance IL-8, IL-1ra, MCP-1, MIP-1b and CSF total protein were significantly elevated in patients with cALD; IL-8, MCP-1b, and CSF total protein levels correlated with disease severity determined by MRI. This is the largest report of CSF cytokine levels in cALD to date, and identification of these key cytokines will provide further insight into disease progression and perhaps lead to improved targeted therapies.
The Role of Interferon Antagonist, Non-Structural Proteins in the Pathogenesis and Emergence of Arboviruses
Bradley S. Hollidge,Susan R. Weiss,Samantha S. Soldan
Viruses , 2011, DOI: 10.3390/v3060629
Abstract: A myriad of factors favor the emergence and re-emergence of arthropod-borne viruses (arboviruses), including migration, climate change, intensified livestock production, an increasing volume of international trade and transportation, and changes to ecosystems (e.g., deforestation and loss of biodiversity). Consequently, arboviruses are distributed worldwide and represent over 30% of all emerging infectious diseases identified in the past decade. Although some arboviral infections go undetected or are associated with mild, flu-like symptoms, many are important human and veterinary pathogens causing serious illnesses such as arthritis, gastroenteritis, encephalitis and hemorrhagic fever and devastating economic loss as a consequence of lost productivity and high mortality rates among livestock. One of the most consistent molecular features of emerging arboviruses, in addition to their near exclusive use of RNA genomes, is the inclusion of viral, non-structural proteins that act as interferon antagonists. In this review, we describe these interferon antagonists and common strategies that arboviruses use to counter the host innate immune response. In addition, we discuss the complex interplay between host factors and viral determinants that are associated with virus emergence and re-emergence, and identify potential targets for vaccine and anti-viral therapies.
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