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Search Results: 1 - 10 of 2523 matches for " Sophie Cotton "
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Susceptibility to Predation Affects Trait-Mediated Indirect Interactions by Reversing Interspecific Competition
Sophie L. Mowles, Simon D. Rundle, Peter A. Cotton
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0023068
Abstract: Numerous studies indicate that the behavioral responses of prey to the presence of predators can have an important role in structuring assemblages through trait-mediated indirect interactions. Few studies, however, have addressed how relative susceptibility to predation influences such interactions. Here we examine the effect of chemical cues from the common shore crab Carcinus maenas on the foraging behavior of two common intertidal gastropod molluscs. Of the two model consumers studied, Littorina littorea is morphologically more vulnerable to crab predation than Gibbula umbilicalis, and it exhibited greater competitive ability in the absence of predation threat. However, Littorina demonstrated a greater anti-predator response when experimentally exposed to predation cues, resulting in a lower level of foraging. This reversed the competitive interaction, allowing Gibbula substantially increased access to shared resources. Our results demonstrate that the susceptibility of consumers to predation can influence species interactions, and suggest that inter-specific differences in trait-mediated indirect interactions are another mechanism through which non-consumptive predator effects may influence trophic interactions.
Defense peptides secreted by helminth pathogens: antimicrobial and/or immunomodulator molecules?
Sophie Cotton,Sheila Donnelly,Mark W. Robinson,John P. Dalton,Karine Thivierge
Frontiers in Immunology , 2012, DOI: 10.3389/fimmu.2012.00269
Abstract: Host defense peptides (HDPs) are an evolutionarily conserved component of the innate immune response found in all living species. They possess antimicrobial activities against a broad range of organisms including bacteria, fungi, eukaryotic parasites, and viruses. HDPs also have the ability to enhance immune responses by acting as immunomodulators. We discovered a new family of HDPs derived from pathogenic helminth (worms) that cause enormous disease in animals and humans worldwide. The discovery of these peptides was based on their similar biochemical and functional characteristics to the human defense peptide LL-37. We propose that these new peptides modulate the immune response via molecular mimicry of mammalian HDPs thus providing a mechanism behind the anti-inflammatory properties of helminth infections.
Cysteine Peptidases as Schistosomiasis Vaccines with Inbuilt Adjuvanticity
Rashika El Ridi, Hatem Tallima, Sahar Selim, Sheila Donnelly, Sophie Cotton, Bibiana Gonzales Santana, John P. Dalton
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0085401
Abstract: Schistosomiasis is caused by several worm species of the genus Schistosoma and afflicts up to 600 million people in 74 tropical and sub-tropical countries in the developing world. Present disease control depends on treatment with the only available drug praziquantel. No vaccine exists despite the intense search for molecular candidates and adjuvant formulations over the last three decades. Cysteine peptidases such as papain and Der p 1 are well known environmental allergens that sensitize the immune system driving potent Th2-responses. Recently, we showed that the administration of active papain to mice induced significant protection (P<0.02, 50%) against an experimental challenge infection with Schistosoma mansoni. Since schistosomes express and secrete papain-like cysteine peptidases we reasoned that these could be employed as vaccines with inbuilt adjuvanticity to protect against these parasites. Here we demonstrate that sub-cutaneous injection of functionally active S. mansoni cathepsin B1 (SmCB1), or a cathepsin L from a related parasite Fasciola hepatica (FhCL1), elicits highly significant (P<0.0001) protection (up to 73%) against an experimental challenge worm infection. Protection and reduction in worm egg burden were further increased (up to 83%) when the cysteine peptidases were combined with other S. mansoni vaccine candidates, glyceraldehyde 3-phosphate dehydrogenase (SG3PDH) and peroxiredoxin (PRX-MAP), without the need to add chemical adjuvants. These studies demonstrate the capacity of helminth cysteine peptidases to behave simultaneously as immunogens and adjuvants, and offer an innovative approach towards developing schistosomiasis vaccines
Emissions Mitigation Schemes in Australia—The Past, Present and Future  [PDF]
Deborah Cotton, Stefan Trück
Low Carbon Economy (LCE) , 2013, DOI: 10.4236/lce.2013.42009
Abstract:

Australia was one of the first countries in the world to adopt mandatory emissions trading schemes as part of its emissions mitigation program. To date there have been six states and one federal emissions mitigation schemes. Some state schemes operate in conjunction with other states or the federal scheme and some operate independently. This complex set of regulations and requirements for emitters has led to a deficiency in nationwide coverage with no firm target set for Australia. In July 2011 the Federal Labor Government released details of a carbon tax proposal which was passed by the two houses of Parliament by the end of 2011 and was introduced in July 2012. The Government states that an emissions trading scheme will be introduced in 2015 with a possible link to the European Emissions Trading Scheme (EU ETS). This paper provides a critical overview of Australian responses to climate change, with a particular emphasis on the numerous emissions mitigation schemes.

Homologous recombination in animal mitochondria
James Cotton
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-10-reports0034
Abstract: This is rather surprising, as this paradigm is based on indirect evidence and is challenged by a growing body of data. The original observation that paternal mitochondria do not penetrate the egg is now known to be in error, with paternal organelles persisting for several hours after fertilization. It is also known that mammalian mitochondria contain the necessary enzymatic machinery for homologous recombination, and mitochondrial fusion is well known in Drosophila. Non-homologous recombination (unequal crossing-over) has been held responsible for variation in the number of tandem repeats in a number of animal mitochondrial genomes, and has been directly observed in a nematode. Two recent population studies have also suggested that recombination has occurred in human mtDNA.With all this evidence, it would seem likely that homologous recombination does occur in animal mitochondria, but the publication of human population studies last year provoked considerable debate, emphasizing that there is much interest in whether animal mtDNA does show homologous recombination, and considerable skepticism. Many authors will no doubt remain skeptical, despite the results of this paper, in which Ladoukakis and Zouros have exploited the unusual genetic system of the mussel to uncover direct evidence for homologous recombination within animal mitochondria.The unusual biparental inheritance of mitochondria in mussels of the families Unionidea and Mytilidaehas been known for about a decade, and is an interesting exception to the otherwise universal rule of maternal inheritance for animal mtDNA. Normally, female (F) and male (M) mitochondrial sequences differ by 20% - too great an amount to expect to observe homologous recombination. Luckily, a quirk of the Mytilus system allows a unique opportunity to observe mtDNA recombination in action. Occasionally, F genomes become 'masculinized', invading the M transmission route in sperm (see Figure 1). These MF genomes can now diverge from the
A new profusion of planktonic eukaryotes
James Cotton
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-7-reports0016
Abstract: These methods have been very little used on eukaryotic microorganisms, however. Despite a growing sense of our ignorance of the extent of biodiversity, the feeling seems to have been that the largest branches of the tree of eukaryotic life are largely described. Recent culture-based studies have, however, identified two new groups of marine planktonic eukaryotes, raising expectations that tiny plankton may harbor more surprises. Moon-van der Staay and colleagues report one of the first large-scale molecular studies of marine picoplankton (microorganisms of < 3 μm diameter), revealing for the first time the true diversity of eukaryotes in this environment.Moon-van der Staay et al. used primers to regions of the 18S rRNA gene conserved across most, but not all, eukaryotes, to clone 103 and sequence 35 almost full-length 18S sequences derived from picoplankton of the equatorial Pacific. Only two of the sequences showed 99% identity to known organisms, but phylogenetic analysis revealed that most of the sequences are either from new members of known eukaryotic lineages or are related to known organisms. The results confirm the importance of autotrophic groups such as haptophytes and prasinophytes in this environment. Among the more arresting discoveries is a new lineage that appears to be very common among the picoplankton: 6 out of 35 sequenced clones belong to a lineage related to both the dinoflagellates and the parasitic Perkinsozoa. This clade could be related to the currently unsequenced heterotroph Oxyrrhis. Also well represented are acantharians, stramenopiles and dinoflagellates. In most cases, it is unclear whether the divergent environmental clones belong to auto- or heterotrophic clades within these groups, although the majority of dinoflagellate sequences seem, rather surprisingly, to form a lineage with a parasitic organism, Amoebophrya.The full text of Moon-van der Staay et al's article together with a similar article on Antarctic picoplankton by a differ
Oldest archaea?
James Cotton
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-6-reports0076
Abstract: The existence of new uncultured types of archaea was first suggested in 1992, when two separate studies revealed archaea-like small-subunit (SSU) rRNA sequences in two different samples of seawater. These sequences were related to both the Crenarchaeota and Euryarchaeota, the two known lineages of archaea. Further work confirmed that these sequences represented organisms that were native to, and abundant in, cold seawater. Since this discovery, novel lineages of both archaean groups have been identified in a wide variety of marine, freshwater and terrestrial environments, confirming that the cultured archaea represent only a fraction of the group's diversity. Another surprise was to come, however, when Norman Pace and colleagues reported some particularly unusual archaeal sequences from a hot spring in Yellowstone National Park. These sequences were difficult to place phylogenetically, even when full-length SSU rRNA sequences became available, and are either very deeply branching crenarchaeotes, or an entirely new division of archaea (which they called 'korarchaeota'), or even a sister group to the Eukaryota. Using similar techniques, Kim et al. have now identified another branch of archaean diversity, even more ancient than the korarchaeote lineage.Kim et al. have twice previously reported unusual archaeal SSU rRNA sequences from diversity analyses of paddy-field soil archaeal communities. They have now designed PCR primers specific for these sequences, revealing the presence of similar molecules in paddy soils from around Japan. Using standard techniques, the researchers failed to produce amplification products using any primer pairs more than 700 base pairs apart, but succeeded in cloning 10 samples of around 645 nucleotides long. Phylogenies produced using a variety of different methods place these 10 sequences at the base of the Archaea (see Figure 1), below the Korarchaeota (which appear as basal crenarchaeotes in all of these analyses). The failure to detect
Evolution without sex
James Cotton
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-3-reports0068
Abstract: The cycle of meiosis and syngamy observed in the vast majority of eukaryotes prevents alleles from accumulating any great number of mutations independent from one another, as mutations will become either fixed or extinct as a result of genetic drift. Welch and Meselson have realized that, in a completely asexual organism in which meiotic recombination has ceased, this relationship will break down, allowing formerly allelic sequences to diverge as they effectively become distinct, haploid loci. Very little recombination should be necessary to maintain an allelic relationship, so observing a greater degree of diversity between such loci in a single individual than between the same loci in two related species would be powerful evidence that the organisms have been evolving asexually since before the species' common ancestor. Welch and Meselson measured substitutional changes at selectively neutral sites in four genes from four species of bdelloids, and found exactly this pattern of extreme divergence between former alleles. They were especially careful to use multiple PCR reactions and to clone many molecules from each reaction, to ensure that all copies of these genes were sampled. This allowed them to show that, for two of the genes, existing copies form two distinct lineages in the asexual bdelloids, presumably descended from the alleles of a diploid sexual ancestor.A perspective article (Judson and Normark Science 2000, 288:1185-1186) commenting on Welch and Meselson's finding appeared in the same issue of Science and is available to subscribers.Bdelloid rotifers have uniquely strange genomes, differing completely from obligately or facultatively sexual rotifers. The lack of allele pairs on homologous chromosomes excludes the possibility that bdelloid rotifers are ordinary diploids engaging in very rare or cryptic sex. A few exotic possibilities remain that could produce this pattern in a sexual species - for example, an ancestral genome duplication in a lineage wi
Retroviruses from retrotransposons
James Cotton
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-2-reports0006
Abstract: Much research has focused on the vertebrate retroviruses, where the Env proteins are important antigenic sites. Unfortunately, this involvement in mediating host immune responses produces strong selective pressure for polymorphism, producing rapid sequence divergence at this locus. It has therefore proved impossible to ascertain the origins of the env gene of these retroviruses. It is not even certain whether the vertebrate retroviruses acquired these genes in a single event or as multiple independent horizontal transfers. It has been established that the plant caulimoviruses, derived from a retrotransposon lineage, have cell-to-cell movement proteins related to those of a number of plant viruses. Now, Malik et al. present convincing evidence for the origins of the env genes of three distinct lineages of invertebrate retroviruses.Database searches with a conserved block of amino acids from the divergent Env proteins of insect errantiviruses identified similarity to ORFs from some baculoviruses (a group of double-stranded DNA insect viruses). The baculoviral ORFs have the transmembrane regions and signal peptides expected of viral envelope proteins, and tend to occur in viruses lacking the described baculoviral 'envelope analogous' gp64 gene, suggesting that the identified ORFs represent a second, unrelated envelope protein of baculoviruses. The fact that the errantiviruses are derived from a lineage of retrotransposons, whereas all known baculoviruses are infectious, strongly suggests that these genes originally evolved in a baculoviral genome and have subsequently been acquired by the errantiviruses. Cer elements from Caenorhabditis elegans are members of the BEL clade of LTR retrotransposons, and contain env genes showing strong similarity to phlebovirus G2 glycoproteins, whereas the closely related Tas element from Ascaris shows some limited similarity to herpesvirus gB glycoprotein, the herpesvirus protein primarily implicated in infection. The low similarity be
Towards uncultured-microbe genomics
James Cotton
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-2-reports0060
Abstract: The authors constructed two BAC libraries from environmental DNA samples, termed metagenomic libraries. The first library contained a total of approximately 100 Mb of environmental DNA with a mean fragment size of 27 kb, while the second, constructed using a refined technique, contained 24,576 cloned fragments of mean size 44.5 kb - making a total of around 1000 Mb of environmental DNA. Antibacterial, lipase, amylase, nuclease, and hemolytic activity could all be detected from the smaller of these libraries, and DNase and antibacterial genes from two clones were successfully sequenced. Seven of the clones from the smaller library had detectable 16S rRNA genes, which could be used to place the clones in a wide diversity of bacterial phyla - low G+C Gram-positives, cytophagales, proteobacteria and acidobacteria.Environmental DNA was extracted using fairly standard methods, although pulsed-field gel electrophoresis was used to isolate only high-molecular weight DNA for use in the second library. The major advance in this paper is the use of BAC vectors, which allows significant expression of heterologous environmental DNA in Escherichia coli, making it possible to screen the library for novel functional genes using standard, quick biochemical assays. The authors also use an interesting PCR protocol involving competitive oligonucleotides to amplify 16S rRNA genes in the presence of E. coli DNA, which they intend to describe in detail elsewhere.A strategy of BAC cloning of large environmental DNA fragments allows both traditional and functional genomic studies of uncultured microorganisms to be carried out.As with any new technique, there are many unanswered questions about this work. Most important, perhaps, is to investigate how efficiently genes from different bacteria are expressed in BACs. Clearly the efficiency of expression will depend on the size of inserts, on how completely environmental genomic DNA is sampled in the library and on how similar the protein trans
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