1,202 research outputs found
A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms
Introduction:
Combined infections from Candida albicans and Staphylococcus aureus are a leading cause of death in the developed world. Evidence suggests that Candida enhances the virulence of Staphylococcus—hyphae penetrate through tissue barriers, while S. aureus tightly associates with the hyphae to obtain entry to the host organism. Indeed, in a biofilm state, C. albicans enhances the antimicrobial resistance characteristics of S. aureus. The association of these microorganisms is also associated with significantly increased morbidity and mortality. Due to this tight association we hypothesised that metabolic effects were also in evidence.
Objectives:
To explore the interaction, we used a novel GC-Orbitrap-based mass spectrometer, the Q Exactive GC, which combines the high peak capacity and chromatographic resolution of gas chromatography with the sub-ppm mass accuracy of an Orbitrap system. This allows the capability to leverage the widely available electron ionisation libraries for untargeted applications, along with expanding accurate mass libraries and targeted matches based around authentic standards.
Methods:
Optimised C. albicans and S. aureus mono- and co-cultured biofilms were analysed using the new instrument in addition to the fresh and spent bacterial growth media.
Results:
The targeted analysis experiment was based around 36 sugars and sugar phosphates, 22 amino acids and five organic acids. Untargeted analysis resulted in the detection of 465 features from fresh and spent medium and 405 from biofilm samples. Three significantly changing compounds that matched to high scoring library fragment patterns were chosen for validation.
Conclusion:
Evaluation of the results demonstrates that the Q Exactive GC is suitable for metabolomics analysis using a targeted/untargeted methodology. Many of the results were as expected: e.g. rapid consumption of glucose and fructose from the medium regardless of the cell type. Modulation of sugar-phosphate levels also suggest that the pentose phosphate pathway could be enhanced in the cells from co-cultured biofilms. Untargeted metabolomics results suggested significant production of cell-wall biosynthesis components and the consumption of non-proteinaceous amino-acids
Towards an Efficient Finite Element Method for the Integral Fractional Laplacian on Polygonal Domains
We explore the connection between fractional order partial differential
equations in two or more spatial dimensions with boundary integral operators to
develop techniques that enable one to efficiently tackle the integral
fractional Laplacian. In particular, we develop techniques for the treatment of
the dense stiffness matrix including the computation of the entries, the
efficient assembly and storage of a sparse approximation and the efficient
solution of the resulting equations. The main idea consists of generalising
proven techniques for the treatment of boundary integral equations to general
fractional orders. Importantly, the approximation does not make any strong
assumptions on the shape of the underlying domain and does not rely on any
special structure of the matrix that could be exploited by fast transforms. We
demonstrate the flexibility and performance of this approach in a couple of
two-dimensional numerical examples
Intestinal, extra-intestinal and systemic sequelae of Toxoplasma gondii induced acute ileitis in mice harboring a human gut microbiota
Background Within seven days following peroral high dose infection with
Toxoplasma gondii susceptible conventionally colonized mice develop acute
ileitis due to an underlying T helper cell (Th) -1 type immunopathology. We
here addressed whether mice harboring a human intestinal microbiota developed
intestinal, extra-intestinal and systemic sequelae upon ileitis induction.
Methodology/Principal findings Secondary abiotic mice were generated by broad-
spectrum antibiotic treatment and associated with a complex human intestinal
microbiota following peroral fecal microbiota transplantation. Within three
weeks the human microbiota had stably established in the murine intestinal
tract as assessed by quantitative cultural and culture-independent (i.e.
molecular 16S rRNA based) methods. At day 7 post infection (p.i.) with 50
cysts of T. gondii strain ME49 by gavage human microbiota associated (hma)
mice displayed severe clinical, macroscopic and microscopic sequelae
indicating acute ileitis. In diseased hma mice increased numbers of innate and
adaptive immune cells within the ileal mucosa and lamina propria and elevated
intestinal secretion of pro-inflammatory mediators including IFN-γ, IL-12 and
nitric oxide could be observed at day 7 p.i. Ileitis development was
accompanied by substantial shifts in intestinal microbiota composition of hma
mice characterized by elevated total bacterial loads and increased numbers of
intestinal Gram-negative commensals such as enterobacteria and Bacteroides /
Prevotella species overgrowing the small and large intestinal lumen.
Furthermore, viable bacteria translocated from the inflamed ileum to extra-
intestinal including systemic compartments. Notably, pro-inflammatory immune
responses were not restricted to the intestinal tract as indicated by
increased pro-inflammatory cytokine secretion in extra-intestinal (i.e. liver
and kidney) and systemic compartments including spleen and serum.
Conclusion/Significance With respect to the intestinal microbiota composition
“humanized” mice display acute ileitis following peroral high dose T. gondii
infection. Thus, hma mice constitute a suitable model to further dissect the
interactions between pathogens, human microbiota and vertebrate host immunity
during acute intestinal inflammation
Prevalence Rates of Mental Disorders in Chilean Prisons
PMCID: PMC371883
BPS black holes in N=2 D=4 gauged supergravities
We construct and analyze BPS black hole solutions in gauged N=2, D=4
supergravity with charged hypermultiplets. A class of solutions can be found
through spontaneous symmetry breaking in vacua that preserve maximal
supersymmetry. The resulting black holes do not carry any hair for the scalars.
We demonstrate this with explicit examples of both asymptotically flat and
anti-de Sitter black holes. Next, we analyze the BPS conditions for
asymptotically flat black holes with scalar hair and spherical or axial
symmetry. We find solutions only in cases when the metric contains ripples and
the vector multiplet scalars become ghost-like. We give explicit examples that
can be analyzed numerically. Finally, we comment on a way to circumvent the
ghost-problem by introducing also fermionic hair.Comment: 40 pages, 2 figures; v2 references added; v3 minor changes, published
versio
Patient perspectives of managing fatigue in ankylosing spondylitis, and views on potential interventions: a qualitative study
<p>Background: Fatigue is a major component of living with ankylosing spondylitis (AS), though it has been largely over-looked, and currently there are no specific agreed management strategies.</p>
<p>Methods: This qualitative exploratory study involved participants who are members of an existing population-based ankylosing spondylitis (PAS) cohort. Participants residing in South West Wales were invited to participate in a focus group to discuss; (1) effects of fatigue, (2) self-management strategies and (3) potential future interventions. The focus groups were audio-recorded and the transcripts were analysed using thematic analysis.</p>
<p>Results: Participants consisted of 3 males/4 females (group 1) and 4 males/3 females (group 2), aged between 35 and 73 years (mean age 53 years). Three main themes were identified: (1) The effects of fatigue were multi-dimensional with participants expressing feelings of being ‘drained’ (physical), ‘upset’ (emotional) and experiencing ‘low-mood’ (psychological); (2) The most commonly reported self-management strategy for fatigue was a balanced combination of activity (exercise) and rest. Medication was reluctantly taken due to side-effects and worries over dependency; (3) Participants expressed a preference for psychological therapies rather than pharmacological for managing fatigue. Information on Mindfulness-Based Stress Reduction (MBSR) was received with interest, with recommendations for delivery in a group format with the option of distance-based delivery for people who were not able to attend a group course.</p>
<p>Conclusions: Patients frequently try and manage their fatigue without any formal guidance or support. Our research indicates there is a need for future research to focus on psychological interventions to address the multi-faceted aspects of fatigue in AS.</p>
Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori
Helicobacter pylori colonizes the gastric mucosa of half of the human population, causing gastritis, ulcers, and cancer. H. pylori
is naturally competent for transformation by exogenous DNA, and recombination during mixed infections of one stomach
with multiple H. pylori strains generates extensive allelic diversity. We developed an in vitro transformation protocol to study
genomic imports after natural transformation of H. pylori. The mean length of imported fragments was dependent on the
combination of donor and recipient strain and varied between 1294 bp and 3853 bp. In about 10% of recombinant clones, the
imported fragments of donor DNA were interrupted by short interspersed sequences of the recipient (ISR) with a mean length
of 82 bp. 18 candidate genes were inactivated in order to identify genes involved in the control of import length and
generation of ISR. Inactivation of the antimutator glycosylase MutY increased the length of imports, but did not have a
significant effect on ISR frequency. Overexpression of mutY strongly increased the frequency of ISR, indicating that MutY, while
not indispensable for ISR formation, is part of at least one ISR-generating pathway. The formation of ISR in H. pylori increases
allelic diversity, and contributes to the uniquely low linkage disequilibrium characteristic of this pathogen
Characterisation of the bacterial and fungal communities associated with different lesion sizes of Dark Spot Syndrome occurring in the Coral Stephanocoenia intersepta
The number and prevalence of coral diseases/syndromes are increasing worldwide. Dark Spot Syndrome (DSS) afflicts numerous coral species and is widespread throughout the Caribbean, yet there are no known causal agents. In this study we aimed to characterise the microbial communities (bacteria and fungi) associated with DSS lesions affecting the coral Stephanocoenia intersepta using nonculture molecular techniques. Bacterial diversity of healthy tissues (H), those in advance of the lesion interface (apparently healthy AH), and three sizes of disease lesions (small, medium, and large) varied significantly (ANOSIM R = 0.052 p,0.001), apart from the medium and large lesions, which were similar in their community profile. Four bacteria fitted into the pattern expected from potential pathogens; namely absent from H, increasing in abundance within AH, and dominant in the lesions themselves. These included ribotypes related to Corynebacterium (KC190237), Acinetobacter (KC190251), Parvularculaceae (KC19027), and Oscillatoria (KC190271). Furthermore, two Vibrio species, a genus including many proposed coral pathogens, dominated the disease lesion and were absent from H and AH tissues, making them candidates as potential pathogens for DSS. In contrast, other members of bacteria from the same genus, such as V. harveyii were present throughout all sample types, supporting previous studies where potential coral pathogens exist in healthy tissues. Fungal diversity varied significantly as well, however the main difference between diseased and healthy tissues was the dominance of one ribotype, closely related to the plant pathogen, Rhytisma acerinum, a known causal agent of tar spot on tree leaves. As the corals’ symbiotic algae have been shown to turn to a darker pigmented state in DSS (giving rise to the syndromes name), the two most likely pathogens are R. acerinum and the bacterium Oscillatoria, which has been identified as the causal agent of the colouration in Black Band Disease, another widespread coral disease
Persistence of Different Forms of Transient RNAi during Apoptosis in Mammalian Cells
Gene silencing by transient or stable RNA-interference (RNAi) is used for the study of apoptosis with an assumption that apoptotic events will not influence RNAi. However, we recently reported that stable RNAi, i.e., a permanent gene-knockdown mediated by shRNA-generating DNA vectors that are integrated in the genome, fails rapidly after induction of apoptosis due to caspase-3-mediated cleavage and inactivation of the endoribonuclease Dicer-1 that is required for conversion of shRNA to siRNA. Since apoptosis studies also increasingly employ transient RNAi models in which apoptosis is induced immediately after a gene is temporarily knocked down within a few days of transfection with RNAi-inducing agents, we examined the impact of apoptosis on various models of transient RNAi. We report here that unlike the stable RNAi, all forms of transient RNAi, whether Dicer-1-independent (by 21mer dsRNA) or Dicer-1-dependent (by 27mer dsRNA or shRNA-generating DNA vector), whether for an exogenous gene GFP or an endogenous gene poly(ADP-ribose) polymerase-1, do not fail for 2–3 days after onset of apoptosis. Our results reflect the differences in dynamics of achieving and maintaining RNAi during the early phase after transfection in the transient RNAi model and the late steady-state phase of gene-knockdown in stable RNAi model. Our results also sound a cautionary note that RNAi status should be frequently validated in the studies involving apoptosis and that while stable RNAi can be safely used for the study of early apoptotic events, transient RNAi is more suitable for the study of both early and late apoptotic events
Spin-Imbalance in a One-Dimensional Fermi Gas
Superconductivity and magnetism generally do not coexist. Changing the
relative number of up and down spin electrons disrupts the basic mechanism of
superconductivity, where atoms of opposite momentum and spin form Cooper pairs.
Nearly forty years ago Fulde and Ferrell and Larkin and Ovchinnikov proposed an
exotic pairing mechanism (FFLO) where magnetism is accommodated by formation of
pairs with finite momentum. Despite intense theoretical and experimental
efforts, however, polarized superconductivity remains largely elusive. Here we
report experimental measurements of density profiles of a two spin mixture of
ultracold 6Li atoms trapped in an array of one dimensional (1D) tubes, a system
analogous to electrons in 1D wires. At finite spin imbalance, the system phase
separates with an inverted phase profile in comparison to the three-dimensional
case. In 1D we find a partially polarized core surrounded by wings composed of
either a completely paired BCS superfluid or a fully polarized Fermi gas,
depending on the degree of polarization. Our observations are in quantitative
agreement with theoretical calculations in which the partially polarized phase
is found to be a 1D analogue of the FFLO state. This study demonstrates how
ultracold atomic gases in 1D may be used to create non-trivial new phases of
matter, and also paves the way for direct observation and further study of the
FFLO phase.Comment: 30 pages, 7 figure
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