Design and evaluation of 16S rRNA sequence based oligonucleotide probes for the detection and quantification of Comamonas testosteroni in mixed microbial communities

Background The β-proteobacterial species Comamonas testosteroni is capable of biotransformation and also biodegradation of a range of chemical compounds and thus potentially useful in chemical manufacturing and bioremediation. The ability to detect and quantify members of this species in mixed microbial communities thus may be desirable. Results We have designed an oligonucleotide probe for use in fluorescent in situ hybridization (FISH) and two pairs of PCR primers targeting a C. testosteroni subgroup. The FISH probe and one of the PCR primer pairs are suitable for quantification of C. testosteroni in mixed microbial communities using FISH followed by quantitative image analysis or real-time quantitative PCR, respectively. This has been shown by analysis of samples from an enrichment of activated sludge on testosterone resulting in an increase in abundance and finally isolation of C. testosteroni. Additionally, we have successfully used quantitative PCR to follow the C. testosteroni abundance during a laboratory scale wastewater bioaugmentation experiment. Conclusion The oligonucleotides presented here provide a useful tool to study C. testosteroni population dynamics in mixed microbial communities

Centrality dependence of high energy jets in p+Pb collisions at the LHC

The recently measured centrality dependence of high energy jets in proton-lead collisions at the LHC is investigated. We hypothesize that events with jets of very high energy (a few hundred GeV) are characterized by a suppressed number of soft particles, thus shifting these events into more peripheral bins. This naturally results in the suppression (enhancement) of the nuclear modification factor, $R_{pA}$, in central (peripheral) collisions. Our calculations suggest that a moderate suppression of the order of $20\%$, for $10^{3}$ GeV jets, can quantitatively reproduce the experimental data. We further extract the suppression factor as a function of jet energy and test our conjecture using available $R_{pA}$ data for various centralities.Comment: 5 pages, 4 figures; extended discussion, comparison with data adde

Conformational Dynamics of Supramolecular Protein Assemblies in the EMDB

The Electron Microscopy Data Bank (EMDB) is a rapidly growing repository for the dissemination of structural data from single-particle reconstructions of supramolecular protein assemblies including motors, chaperones, cytoskeletal assemblies, and viral capsids. While the static structure of these assemblies provides essential insight into their biological function, their conformational dynamics and mechanics provide additional important information regarding the mechanism of their biological function. Here, we present an unsupervised computational framework to analyze and store for public access the conformational dynamics of supramolecular protein assemblies deposited in the EMDB. Conformational dynamics are analyzed using normal mode analysis in the finite element framework, which is used to compute equilibrium thermal fluctuations, cross-correlations in molecular motions, and strain energy distributions for 452 of the 681 entries stored in the EMDB at present. Results for the viral capsid of hepatitis B, ribosome-bound termination factor RF2, and GroEL are presented in detail and validated with all-atom based models. The conformational dynamics of protein assemblies in the EMDB may be useful in the interpretation of their biological function, as well as in the classification and refinement of EM-based structures.Comment: Associated online data bank available at: http://lcbb.mit.edu/~em-nmdb

An investigation into the efficacy of kinematics and kinetics method for stride-characteristic measurements of horses trotting on a treadmill

The aim of this study was to investigate the validity of stride characteristic measurements taken from the sternum by means of an Optical Motion Capture System (OMCS) and an Inertia Measurement Unit (IMU), in comparison with OMCS hoof markers. Measurements were taken from sound horses of a range of breeds, trotting at self-selected speeds on a treadmill (OMCS N=15; IMU N=4). Hoof marker trajectories were compared in terms of dorsoventral position (pZ), craniocaudal velocity (vX) and dorsoventral velocity (vZ). Contra-laterally coupled limbs were compared at beginning and end of stance according to vX. A Girth Marker (GM) placed over the sternum was used to identify beginning and end of stance of each diagonal using dorsoventral acceleration (aZ) and dorsoventral velocity (vZ) respectively. These were compared with hoof marker vX. GM aZ and vZ were then validated against the same measurements taken by an IMU measuring at the same time from the same location. No significant difference (p < 0.05) was found by ANOVA between hoof marker trajectories pZ, vX or vZ at beginning or end of stance. No significant difference was found by t-test or ICC between contralaterally coupled limbs at beginning or end of stance. GM aZ and vZ could be used to identify beginning and end of stance for each diagonal without significant difference from hoof vX timings according to t-test and ICC. OMCS GM and IMU did not differ in terms of velocity (peak or trough timing or amplitude, or absolute difference: peak minus trough), or acceleration peak timing, trough timing or trough amplitude according to t-test or ICC. However, OMCS GM and IMU differed significantly in terms of acceleration peak amplitude (p = .01, ICC = 0.46) and absolute difference (p = .04, ICC = 0.66). The sternum can be used as a site to collect data providing accurate information on beginning or end of stance of horses with no advanced placement of contralaterally coupled limbs, whilst trotting at self selected speeds on a treadmill. Temporal acceleration data, and temporal or amplitudal velocity data are sufficient to identify beginning and end of stance from the sternum using an IMU. Amplitudal acceleration data from an IMU should be further investigated before assumed valid under these conditions

Geometrically nonlinear analysis of thin-walled composite box beams

A general geometrically nonlinear model for thin-walled composite space beams with arbitrary lay-ups under various types of loadings has been presented by using variational formulation based on the classical lamination theory. The nonlinear governing equations are derived and solved by means of an incremental Newton–Raphson method. A displacement-based one-dimensional finite element model that accounts for the geometric nonlinearity in the von Kármán sense is developed. Numerical results are obtained for thin-walled composite box beam under vertical load to investigate the effect of geometric nonlinearity and address the effects of the fiber orientation, laminate stacking sequence, load parameter on axial–flexural–torsional response