Mutation detection analysis of a region of 16S-like ribosomal RNA gene of Entamoeba histolytica, Entamoeba dispar and Entamoeba moshkovskii

<p>Abstract</p> <p>Background</p> <p>The level of intra-species genetic variation in <it>Entamoeba histolytica, Entamoeba dispar </it>and <it>Entamoeba moshkovskii </it>populations in a localized geographic area, like Puducherry, India, remains unknown.</p> <p>Methods</p> <p>In the present study the existence of genetic variation in the nested multiplex polymerase chain reaction (NM-PCR) amplified region of the 16S-like ribosomal RNA genes of <it>E. histolytica, E. dispar </it>and <it>E. moshkovskii </it>was investigated by riboprinting and single strand conformation polymorphism (SSCP) analysis.</p> <p>Results</p> <p>We found that 70 stool specimens were positive for <it>E. histolytica</it>, 171 stool specimens were positive for <it>E. dispar</it>, and 37 stool specimens were positive for <it>E. moshkovskii </it>by NM-PCR. Ninety liver abscess pus specimens, 21 urine specimens, and 8 saliva specimens were positive for <it>E. histolytica </it>by NM-PCR. Riboprinting analysis detected a mutation in the PCR product of only one <it>E. histolytica </it>isolate from a stool specimen. However, SSCP analysis detected mutations in the PCR products of five <it>E. histolytica </it>isolates and three <it>E. moshkovskii </it>isolates from stool specimens, and one <it>E. histolytica </it>isolate from a saliva specimen. The mutations detected by riboprinting and SSCP analysis were confirmed by sequencing. All the nucleotide sequences showing mutations in this study have already been deposited into the NCBI GenBank database under accession numbers [GenBank: <ext-link ext-link-type="gen" ext-link-id="EF682200">EF682200</ext-link> to GenBank: <ext-link ext-link-type="gen" ext-link-id="EF682208">EF682208</ext-link>].</p> <p>Conclusion</p> <p>The present study has revealed the subsistence of mutations in the ribosomal RNA genes of <it>E. histolytica </it>and <it>E. moshkovskii</it>, which points towards the existence of intra-species genetic variation in <it>E. histolytica </it>and <it>E. moshkovskii </it>isolates infecting humans.</p

Cumulative signal transmission in nonlinear reaction-diffusion networks

Quantifying signal transmission in biochemical systems is key to uncover the mechanisms that cells use to control their responses to environmental stimuli. In this work we use the time-integral of chemical species as a measure of a network’s ability to cumulatively transmit signals encoded in spatiotemporal concentrations. We identify a class of nonlinear reaction-diffusion networks in which the time-integrals of some species can be computed analytically. The derived time-integrals do not require knowledge of the solution of the reaction-diffusion equation, and we provide a simple graphical test to check if a given network belongs to the proposed class. The formulae for the time-integrals reveal how the kinetic parameters shape signal transmission in a network under spatiotemporal stimuli. We use these to show that a canonical complex-formation mechanism behaves as a spatial low-pass filter, the bandwidth of which is inversely proportional to the diffusion length of the ligand

In situ Biological Dose Mapping Estimates the Radiation Burden Delivered to ‘Spared’ Tissue between Synchrotron X-Ray Microbeam Radiotherapy Tracks

Microbeam radiation therapy (MRT) using high doses of synchrotron X-rays can destroy tumours in animal models whilst causing little damage to normal tissues. Determining the spatial distribution of radiation doses delivered during MRT at a microscopic scale is a major challenge. Film and semiconductor dosimetry as well as Monte Carlo methods struggle to provide accurate estimates of dose profiles and peak-to-valley dose ratios at the position of the targeted and traversed tissues whose biological responses determine treatment outcome. The purpose of this study was to utilise γ-H2AX immunostaining as a biodosimetric tool that enables in situ biological dose mapping within an irradiated tissue to provide direct biological evidence for the scale of the radiation burden to ‘spared’ tissue regions between MRT tracks. Γ-H2AX analysis allowed microbeams to be traced and DNA damage foci to be quantified in valleys between beams following MRT treatment of fibroblast cultures and murine skin where foci yields per unit dose were approximately five-fold lower than in fibroblast cultures. Foci levels in cells located in valleys were compared with calibration curves using known broadbeam synchrotron X-ray doses to generate spatial dose profiles and calculate peak-to-valley dose ratios of 30–40 for cell cultures and approximately 60 for murine skin, consistent with the range obtained with conventional dosimetry methods. This biological dose mapping approach could find several applications both in optimising MRT or other radiotherapeutic treatments and in estimating localised doses following accidental radiation exposure using skin punch biopsies

SIMS: A Hybrid Method for Rapid Conformational Analysis

Proteins are at the root of many biological functions, often performing complex tasks as the result of large changes in their structure. Describing the exact details of these conformational changes, however, remains a central challenge for computational biology due the enormous computational requirements of the problem. This has engendered the development of a rich variety of useful methods designed to answer specific questions at different levels of spatial, temporal, and energetic resolution. These methods fall largely into two classes: physically accurate, but computationally demanding methods and fast, approximate methods. We introduce here a new hybrid modeling tool, the Structured Intuitive Move Selector (SIMS), designed to bridge the divide between these two classes, while allowing the benefits of both to be seamlessly integrated into a single framework. This is achieved by applying a modern motion planning algorithm, borrowed from the field of robotics, in tandem with a well-established protein modeling library. SIMS can combine precise energy calculations with approximate or specialized conformational sampling routines to produce rapid, yet accurate, analysis of the large-scale conformational variability of protein systems. Several key advancements are shown, including the abstract use of generically defined moves (conformational sampling methods) and an expansive probabilistic conformational exploration. We present three example problems that SIMS is applied to and demonstrate a rapid solution for each. These include the automatic determination of ﾑﾑactiveﾒﾒ residues for the hinge-based system Cyanovirin-N, exploring conformational changes involving long-range coordinated motion between non-sequential residues in Ribose- Binding Protein, and the rapid discovery of a transient conformational state of Maltose-Binding Protein, previously only determined by Molecular Dynamics. For all cases we provide energetic validations using well-established energy fields, demonstrating this framework as a fast and accurate tool for the analysis of a wide range of protein flexibility problems

Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems

Mesoscopic oscillatory reaction systems, for example in cell biology, can exhibit stochastic oscillations in the form of cyclic random walks even if the corresponding macroscopic system does not oscillate. We study how the intrinsic noise from molecular discreteness influences the frequency spectrum of mesoscopic oscillators using as a model system a cascade of coupled Brusselators away from the Hopf bifurcation. The results show that the spectrum of an oscillator depends on the level of noise. In particular, the peak frequency of the oscillator is reduced by increasing noise, and the bandwidth increased. Along a cascade of coupled oscillators, the peak frequency is further reduced with every stage and also the bandwidth is reduced. These effects can help understand the role of noise in chemical oscillators and provide fingerprints for more reliable parameter identification and volume measurement from experimental spectra

Differential livelihood adaptation to social-ecological change in coastal Bangladesh

Social-ecological changes, brought about by the rapid growth of the aquaculture industry and the increased occurrence of climatic stressors, have significantly affected the livelihoods of coastal communities in Asian mega-deltas. This paper explores the livelihood adaptation responses of households of different wealth classes, the heterogeneous adaptation opportunities, barriers and limits (OBLs) faced by these households and the dynamic ways in which these factors interact to enhance or impede adaptive capacities. A mixed methods approach was used to collect empirical evidence from two villages in coastal Bangladesh. Findings reveal that households’ adaptive capacities largely depend on their wealth status, which not only determine their availability of productive resources, but also empower them to navigate social-ecological change in desirable ways. Households operate within a shared response space, which is shaped by the broader socio-economic and political landscape, as well as their previous decisions that can lock them in to particular pathways. While an adaptive response may be effective for one social group, it may cause negative externalities that can undermine the adaptation options and outcomes of another group. Adaptation OBLs interact in complex ways; the extent to which these OBLs affect different households depend on the specific livelihood activities being considered and the differential values and interests they hold. To ensure more equitable and environmentally sustainable livelihoods in future, policies and programs should aim to expand households’ adaptation space by accounting for the heterogeneous needs and complex interdependencies between response processes of different groups

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns