Using the Discrete Dipole Approximation and Holographic Microscopy to Measure Rotational Dynamics of Non-spherical Colloidal Particles

We present a new, high-speed technique to track the three-dimensional translation and rotation of non-spherical colloidal particles. We capture digital holograms of micrometer-scale silica rods and sub-micrometer-scale Janus particles freely diffusing in water, and then fit numerical scattering models based on the discrete dipole approximation to the measured holograms. This inverse-scattering approach allows us to extract the the position and orientation of the particles as a function of time, along with static parameters including the size, shape, and refractive index. The best-fit sizes and refractive indices of both particles agree well with expected values. The technique is able to track the center of mass of the rod to a precision of 35 nm and its orientation to a precision of 1.5$^\circ$, comparable to or better than the precision of other 3D diffusion measurements on non-spherical particles. Furthermore, the measured translational and rotational diffusion coefficients for the silica rods agree with hydrodynamic predictions for a spherocylinder to within 0.3%. We also show that although the Janus particles have only weak optical asymmetry, the technique can track their 2D translation and azimuthal rotation over a depth of field of several micrometers, yielding independent measurements of the effective hydrodynamic radius that agree to within 0.2%. The internal and external consistency of these measurements validate the technique. Because the discrete dipole approximation can model scattering from arbitrarily shaped particles, our technique could be used in a range of applications, including particle tracking, microrheology, and fundamental studies of colloidal self-assembly or microbial motion.Comment: 11 pages, 9 figures, 2 table

Development of a quantitative PCR assay for the detection and enumeration of a potentially ciguatoxin-producing dinoflagellate, Gambierdiscus lapillus (Gonyaulacales, Dinophyceae)

© 2019 Public Library of Science. All rights reserved. Ciguatera fish poisoning (CFP) is an illness contracted through the ingestion of seafood containing ciguatoxins. It is prevalent in tropical regions worldwide, including in Australia. Ciguatoxins are produced by some species of Gambierdiscus. Therefore, screening of Gambierdiscus species identification through quantitative PCR (qPCR), along with the determination of species toxicity, can be useful in monitoring potential ciguatera risk in these regions. In Australia, CFP is prevalent in tropical Queensland and increasingly in sub-tropical regions of Australia, but has a report rate of approximately 10%. Yet the identity, distribution and abundance of ciguatoxin producing Gambierdiscus spp. is largely unknown. In this study, we developed a rapid qPCR assay to quantify the presence and abundance of Gambierdiscus lapillus, a likely ciguatoxic species first described from Australia. We assessed the specificity and efficiency of the qPCR assay. The assay was tested on 25 environmental samples from the Heron Island reef in the southern Great Barrier Reef, a ciguatera endemic region, to determine the presence and patchiness of this species across samples from Chnoospora sp., Padina sp. and Sargassum sp. macroalgal hosts

Proteomic analysis of the cerebrospinal fluid of patients with Creutzfeldt-Jakob disease

So far, only the detection of 14-3-3 proteins in cerebrospinal fluid (CSF) has been accepted as diagnostic criterion for Creutzfeldt-Jakob disease (CJD). However, this assay cannot be used for screening because of the high rate of false-positive results, whereas patients with variant CJD are often negative for 14-3-3 proteins. The aim of this study was to compare the spot patterns of CSF by 2-dimensional polyacrylamide gel electrophoresis (2D-PAGE) to search for a CJD-specific spot pattern. We analyzed the CSF of 28 patients {[}11 CJD, 9 Alzheimer's disease ( AD), 8 nondemented controls (NDC)] employing 2D-PAGE which was optimized for minimal volumes of CSF (0.1 ml; 7-cm strips). All samples were run at least three times, gels were silver stained and analyzed by an analysis software and manually revised. We could consistently match 268 spots which were then compared between all groups. By the use of 5 spots, we were able to differentiate CJD from AD or NDC with a sensitivity of 100%. CJD could also be distinguished from both groups by using a heuristic clustering algorithm of 2 spots. We conclude that this proteomic approach can differentiate CJD from other diseases and may serve as a model for other neurodegenerative diseases. Copyright (C) 2007 S. Karger AG, Basel

Association between cartilage degeneration and subchondral bone remodeling in patients with knee osteoarthritis comparing MRI and 99mTc-DPD-SPECT/CT

SummaryObjectiveThe purpose of this retrospective cross-sectional study was to investigate the association between cartilage lesions assessed with 3T-MRI and remodeling of the subchondral bone detected by 99mTc-DPD-SPECT/CT.Design99mTc-DPD-SPECT/CT and MRI of 27 knees of 25 patients with chronic knee pain and risk factors for osteoarthritis (OA) were evaluated by one nuclear physician and one radiologist. Six regions of the knee (in total 162 regions in 27 knees) were assessed according to structural joint lesions graded with a modified Whole Organ MR imaging score (WORMS) and according to subchondral 99mTc-DPD-SPECT uptake. Relationships between regional WORMS scores and uptake were quantified using general estimating equations. In a secondary analysis the uptake sum with the WORMS sum per joint was compared using Spearman correlations.ResultsElevated subchondral uptake was significantly associated with the grade of cartilage lesions (P < 0.0001). Mean uptake was significantly higher subjacent to full thickness cartilage lesions compared to partial thickness lesions (P < 0.0001). A similar association was observed between bone marrow edema pattern (BMEP) and cartilage lesions. The sum of uptakes per joint was positively correlated to the WORMS sum (rs = 0.42) and to the sum of cartilage lesions per joint (rs = 0.50).ConclusionBoth functional and structural changes of the subchondral bone in terms of scintigraphic osseous activity and the presence and degree of BMEP were significantly associated with cartilage lesions in patients with OA of the knee. This association was pronounced with full thickness lesions, indicating a possible protective effect of the cartilage layer for the subjacent bone

Link and subgraph likelihoods in random undirected networks with fixed and partially fixed degree sequence

The simplest null models for networks, used to distinguish significant features of a particular network from {\it a priori} expected features, are random ensembles with the degree sequence fixed by the specific network of interest. These "fixed degree sequence" (FDS) ensembles are, however, famously resistant to analytic attack. In this paper we introduce ensembles with partially-fixed degree sequences (PFDS) and compare analytic results obtained for them with Monte Carlo results for the FDS ensemble. These results include link likelihoods, subgraph likelihoods, and degree correlations. We find that local structural features in the FDS ensemble can be reasonably well estimated by simultaneously fixing only the degrees of few nodes, in addition to the total number of nodes and links. As test cases we use a food web, two protein interaction networks (\textit{E. coli, S. cerevisiae}), the internet on the autonomous system (AS) level, and the World Wide Web. Fixing just the degrees of two nodes gives the mean neighbor degree as a function of node degree, $_k$, in agreement with results explicitly obtained from rewiring. For power law degree distributions, we derive the disassortativity analytically. In the PFDS ensemble the partition function can be expanded diagrammatically. We obtain an explicit expression for the link likelihood to lowest order, which reduces in the limit of large, sparse undirected networks with $L$ links and with $k_{\rm max} \ll L$ to the simple formula $P(k,k') = kk'/(2L + kk')$. In a similar limit, the probability for three nodes to be linked into a triangle reduces to the factorized expression $P_{\Delta}(k_1,k_2,k_3) = P(k_1,k_2)P(k_1,k_3)P(k_2,k_3)$.Comment: 17 pages, includes 11 figures; first revision: shortened to 14 pages (7 figures), added discussion of subgraph counts, deleted discussion of directed network

Thermodynamic properties of sea air

Very accurate thermodynamic potential functions are available for fluid water, ice, seawater and humid air covering wide ranges of temperature and pressure conditions. They permit the consistent computation of all equilibrium properties as, for example, required for coupled atmosphere-ocean models or the analysis of observational or experimental data. With the exception of humid air, these potential functions are already formulated as international standards released by the International Association for the Properties of Water and Steam (IAPWS), and have been adopted in 2009 for oceanography by IOC/UNESCO. &lt;br&gt;&lt;br&gt; In this paper, we derive a collection of formulas for important quantities expressed in terms of the thermodynamic potentials, valid for typical phase transitions and composite systems of humid air and water/ice/seawater. Particular attention is given to equilibria between seawater and humid air, referred to as "sea air" here. In a related initiative, these formulas will soon be implemented in a source-code library for easy practical use. The library is primarily aimed at oceanographic applications but will be relevant to air-sea interaction and meteorology as well. &lt;br&gt;&lt;br&gt; The formulas provided are valid for any consistent set of suitable thermodynamic potential functions. Here we adopt potential functions from previous publications in which they are constructed from theoretical laws and empirical data; they are briefly summarized in the appendix. The formulas make use of the full accuracy of these thermodynamic potentials, without additional approximations or empirical coefficients. They are expressed in the temperature scale ITS-90 and the 2008 Reference-Composition Salinity Scale

Cryopreservation of grapevine (Vitis spp.) shoot tips from growth chamber-sourced plants and histological observations

Many genebanks rely on cryopreservation as a method to preserve vulnerable field collections of vegetatively propagated crops. Effective cryopreservation procedures have been identified for Vitis; however, they usually use in vitro plantlets as the shoot tip source materials. It is costly to establish Vitis collections in vitro prior to cryopreservation. We sought to determine if growth chamber derived Vitis plants could serve as the source of shoot tips for cryopreservation. Nodal sections from growth chamber derived plants were surface-disinfected and placed in tissue culture on pre-treatment medium for 2 weeks. Uniform apical shoot tips (1 mm) were first obtained from the nodal sections and then precultured for 3 days on medium containing 0.3 M sucrose, salicylic acid, glutathione (reduced form), ascorbic acid and plant preservative mixture. Half-strength PVS2 was applied for 30 min at 22 °C, prior to full-strength PVS2 treatment at 0 °C. Cryopreserved shoot tips had the highest average regrowth of 50 and 55 % without and with cold-acclimation followed with a full-strength PVS2 exposure duration of 40 and 30 min at 0 °C, respectively. This cryopreservation protocol achieved high percentages of regrowth in V. vinifera 'Chardonnay' and 'Riesling' and V. hybrid 'Oppenheim'. Histological observations revealed that shoot tips from growth chamber plants had apical as well as multiple lateral meristems that survived LN immersion. The preservation of multiple meristems in each shoot tip may increase the capacity of shoot tip regeneration in cryopreserved Vitis that originates from ex vitro sources. The high percentage of regrowth after shoot tip cryopreservation using Vitis shoot tips derived from growth chamber source plants suggest that it may be possible to cryopreserve Vitis shoot tips without first introducing each accession into tissue culture

Ion dynamics in perturbed quadrupole ion traps

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