69 research outputs found
The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity
Background: Multiple factors can influence stool sample integrity upon sample
collection. Preservation of faecal samples for microbiome studies is therefore an
important step, particularly in tropical regions where resources are limited and
high temperatures may significantly influence microbiota profiles. Freezing is the
accepted standard to preserve faecal samples however, cold chain methods are often
unfeasible in fieldwork scenarios particularly in low and middle-income countries
and alternatives are required. This study therefore aimed to address the impact of
different preservative methods, time-to-freezing at ambient tropical temperatures,
and stool heterogeneity on stool microbiome diversity and composition under
real-life physical environments found in resource-limited fieldwork conditions.
Methods: Inner and outer stool samples collected from one specimen obtained from
three children were stored using different storage preservation methods (raw, ethanol
and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these
techniques and frozen at different time-to-freezing intervals post-collection from
0–32 h. Metataxonomic profiling was used to profile samples, targeting the V1–V2
regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed,
combined and aligned to the Greengenes database. Microbial diversity and
composition data were generated and analysed using Quantitative Insights Into
Microbial Ecology and R software.
Results: Child donor was the greatest predictor of microbiome variation between the
stool samples, with all samples remaining identifiable to their child of origin
despite the stool being stored under a variety of conditions. However, significant
differences were observed in composition and diversity between preservation
techniques, but intra-preservation technique variation was minimal for all
preservation methods, and across the time-to-freezing range (0–32 h) used. Stool
heterogeneity yielded no apparent microbiome differences.
Conclusions: Stool collected in a fieldwork setting for comparative microbiome
analyses should ideally be stored as consistently as possible using the same
preservation method throughout
Harnessing technology and portability to conduct molecular epidemiology of endemic pathogens in resource-limited settings
Improvements in genetic and genomic technology have enabled field-deployable molecular laboratories and these have been deployed in a variety of epidemics that capture headlines. In this editorial, we highlight the importance of building physical and personnel capacity in low and middle income countries to deploy these technologies to improve diagnostics, understand transmission dynamics and provide feedback to endemic communities on actionable timelines. We describe our experiences with molecular field research on schistosomiasis, trypanosomiasis and rabies and urge the wider tropical medicine community to embrace these methods and help build capacity to benefit communities affected by endemic infectious diseases
Broken-Symmetry States in Quantum Hall Superlattices
We argue that broken-symmetry states with either spatially diagonal or
spatially off-diagonal order are likely in the quantum Hall regime, for clean
multiple quantum well (MQW) systems with small layer separations. We find that
for MQW systems, unlike bilayers, charge order tends to be favored over
spontaneous interlayer coherence. We estimate the size of the interlayer
tunneling amplitude needed to stabilize superlattice Bloch minibands by
comparing the variational energies of interlayer-coherent superlattice miniband
states with those of states with charge order and states with no broken
symmetries. We predict that when coherent miniband ground states are stable,
strong interlayer electronic correlations will strongly enhance the
growth-direction tunneling conductance and promote the possibility of Bloch
oscillations.Comment: 9 pages LaTeX, 4 figures EPS, to be published in PR
Small Polarons in Transition Metal Oxides
The formation of polarons is a pervasive phenomenon in transition metal oxide
compounds, with a strong impact on the physical properties and functionalities
of the hosting materials. In its original formulation the polaron problem
considers a single charge carrier in a polar crystal interacting with its
surrounding lattice. Depending on the spatial extension of the polaron
quasiparticle, originating from the coupling between the excess charge and the
phonon field, one speaks of small or large polarons. This chapter discusses the
modeling of small polarons in real materials, with a particular focus on the
archetypal polaron material TiO2. After an introductory part, surveying the
fundamental theoretical and experimental aspects of the physics of polarons,
the chapter examines how to model small polarons using first principles schemes
in order to predict, understand and interpret a variety of polaron properties
in bulk phases and surfaces. Following the spirit of this handbook, different
types of computational procedures and prescriptions are presented with specific
instructions on the setup required to model polaron effects.Comment: 36 pages, 12 figure
Comprehensive lung injury pathology induced by mTOR inhibitors
Molecular Targets in Oncology[Abstract] Interstitial lung disease is a rare side effect of temsirolimus treatment in renal cancer patients. Pulmonary fibrosis is characterised by the accumulation of extracellular matrix collagen, fibroblast proliferation and migration, and loss of alveolar gas exchange units. Previous studies of pulmonary fibrosis have mainly focused on the fibro-proliferative process in the lungs. However, the molecular mechanism by which sirolimus promotes lung fibrosis remains elusive. Here, we propose an overall cascade hypothesis of interstitial lung diseases that represents a common, partly underlying synergism among them as well as the lung pathogenesis side effects of mammalian target of rapamycin inhibitors
Vascular Remodeling in Health and Disease
The term vascular remodeling is commonly used to define the structural changes in blood vessel geometry that occur in response to long-term physiologic alterations in blood flow or in response to vessel wall injury brought about by trauma or underlying cardiovascular diseases.1, 2, 3, 4 The process of remodeling, which begins as an adaptive response to long-term hemodynamic alterations such as elevated shear stress or increased intravascular pressure, may eventually become maladaptive, leading to impaired vascular function. The vascular endothelium, owing to its location lining the lumen of blood vessels, plays a pivotal role in regulation of all aspects of vascular function and homeostasis.5 Thus, not surprisingly, endothelial dysfunction has been recognized as the harbinger of all major cardiovascular diseases such as hypertension, atherosclerosis, and diabetes.6, 7, 8 The endothelium elaborates a variety of substances that influence vascular tone and protect the vessel wall against inflammatory cell adhesion, thrombus formation, and vascular cell proliferation.8, 9, 10 Among the primary biologic mediators emanating from the endothelium is nitric oxide (NO) and the arachidonic acid metabolite prostacyclin [prostaglandin I2 (PGI2)], which exert powerful vasodilatory, antiadhesive, and antiproliferative effects in the vessel wall
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