Saline-saturated DMSO-EDTA as a storage medium for microbial DNA analysis from coral mucus swab samples

The mucus surface layer of corals plays a number of integral roles in their overall health and fitness. This mucopolysaccharide coating serves as vehicle to capture food, a protective barrier against physical invasions and trauma, and serves as a medium to host a community of microorganisms distinct from the surrounding seawater. In healthy corals the associated microbial communities are known to provide antibiotics that contribute to the coral’s innate immunity and function metabolic activities such as biogeochemical cycling. Culture-dependent (Ducklow and Mitchell, 1979; Ritchie, 2006) and culture-independent methods (Rohwer, et al., 2001; Rohwer et al., 2002; Sekar et al., 2006; Hansson et al., 2009; Kellogg et al., 2009) have shown that coral mucus-associated microbial communities can change with changes in the environment and health condition of the coral. These changes may suggest that changes in the microbial associates not only reflect health status but also may assist corals in acclimating to changing environmental conditions. With the increasing availability of molecular biology tools, culture-independent methods are being used more frequently for evaluating the health of the animal host. Although culture-independent methods are able to provide more in-depth insights into the constituents of the coral surface mucus layer’s microbial community, their reliability and reproducibility rely on the initial sample collection maintaining sample integrity. In general, a sample of mucus is collected from a coral colony, either by sterile syringe or swab method (Woodley, et al., 2008), and immediately placed in a cryovial. In the case of a syringe sample, the mucus is decanted into the cryovial and the sealed tube is immediately flash-frozen in a liquid nitrogen vapor shipper (a.k.a., dry shipper). Swabs with mucus are placed in a cryovial, and the end of the swab is broken off before sealing and placing the vial in the dry shipper. The samples are then sent to a laboratory for analysis. After the initial collection and preservation of the sample, the duration of the sample voyage to a recipient laboratory is often another critical part of the sampling process, as unanticipated delays may exceed the length of time a dry shipper can remain cold, or mishandling of the shipper can cause it to exhaust prematurely. In remote areas, service by international shipping companies may be non-existent, which requires the use of an alternative preservation medium. Other methods for preserving environmental samples for microbial DNA analysis include drying on various matrices (DNA cards, swabs), or placing samples in liquid preservatives (e.g., chloroform/phenol/isoamyl alcohol, TRIzol reagent, ethanol). These methodologies eliminate the need for cold storage, however, they add expense and permitting requirements for hazardous liquid components, and the retrieval of intact microbial DNA often can be inconsistent (Dawson, et al., 1998; Rissanen et al., 2010). A method to preserve coral mucus samples without cold storage or use of hazardous solvents, while maintaining microbial DNA integrity, would be an invaluable tool for coral biologists, especially those in remote areas. Saline-saturated dimethylsulfoxide-ethylenediaminetetraacetic acid (20% DMSO-0.25M EDTA, pH 8.0), or SSDE, is a solution that has been reported to be a means of storing tissue of marine invertebrates at ambient temperatures without significant loss of nucleic acid integrity (Dawson et al., 1998, Concepcion et al., 2007). While this methodology would be a facile and inexpensive way to transport coral tissue samples, it is unclear whether the coral microbiota DNA would be adversely affected by this storage medium either by degradation of the DNA, or a bias in the DNA recovered during the extraction process created by variations in extraction efficiencies among the various community members. Tests to determine the efficacy of SSDE as an ambient temperature storage medium for coral mucus samples are presented here.

Risk analysis in aquaculture: A step-by-step introduction with worked examples

This publication is based on materials covered and outputs generated during the Workshop on Risk Assessment Methodologies and Tools for Aquaculture in Sub-Saharan Africa, which was jointly held by WorldFish and FAO in Siavonga, Zambia on 28 June - 2 July 2010. The workshop was delivered as a training exercise to 17 participants from seven sub-Saharan countries and was designed to highlight current methodologies and tools available for environmental risk analysis in aquaculture development. A key focus of the workshop was to encourage participants to consider hypothetical but realistic scenarios and to discuss issues relevant to evaluating the environmental risks of a given activity or scenario. This publication presents selected scenarios from the workshop and the outcomes of the deliberative process as developed by the participants. This publication is factual but not comprehensive, therefore any statements or estimations of risk do not represent the actual risks arising from the described scenario. It is intended to serve as an easily readable introduction to risk analysis, highlighting worked examples that will provide guidance on how a risk analysis may be approached in a similar situation.

Commodity and product identification for value chain analysis.

This commodity and product identification research was undertaken in the context of the CGIAR Research Program on Aquatic Agricultural Systems (AAS). AAS seeks to reduce poverty and improve food security for the millions of small-scale fishers and farmers who depend on the world’s floodplains, deltas and coasts. The objective of this research is to strengthen the capacity of AAS to undertake value chain studies with high potential impact on smallholders. The capacity-building aspect of this research was focused on the process of commodity and product identification for value chain analysis. Its scope was limited to fish and other aquatic animals and products in the Tonle Sap area identified for AAS intervention. The result of the identification process was the selection of a number of commodities and products that were deemed to involve a high number of smallholders along the value chain and that have high market development potential.

Axial compressor response to inlet flow distortions by a CFD analysis

The usual approach to compressor design considers uniform inlet flow characteristics. Especially in aircraft applications, the inlet flow is quite often non uniform, and this can result in severe performance degradation. The magnitude of this phenomenon is amplified in military engines due to the complexity of inlet duct configurations and the extreme flight conditions. CFD simulation is an innovative and powerful tool for studying inlet distortions and can bring this inside the very early phases of the design process. This project attempts to study the effects of inlet flow distortions in an axial flow compressor trying to minimize the use computer resources and computational time. The first stage of a low bypass ratio compressor has been analyzed and its clean and distorted performance compared outlining the principal changes due to uneven flow distribution: drop in mass flow, increase in pressure and temperature ratios, decrease in surge margin. Three different studies have then been conducted to better understand the effects of the level, the type and the frequency of the distortion.

Cluster analysis of heterogeneous rank data

Cluster analysis of ranking data, which occurs in consumer questionnaires, voting forms or other inquiries of preferences, attempts to identify typical groups of rank choices. Empirically measured rankings are often incomplete, i.e. different numbers of filled rank positions cause heterogeneity in the data. We propose a mixture approach for clustering of heterogeneous rank data. Rankings of different lengths can be described and compared by means of a single probabilistic model. A maximum entropy approach avoids hidden assumptions about missing rank positions. Parameter estimators and an efficient EM algorithm for unsupervised inference are derived for the ranking mixture model. Experiments on both synthetic data and real-world data demonstrate significantly improved parameter estimates on heterogeneous data when the incomplete rankings are included in the inference process.

Analysis of basic processes inside the keyhole during deep penetration ND-YAG CW laser welding

During laser welding, the keyhole is generated by the recoil pressure induced by the evaporation processes occurring mainly on the front keyhole wall (KW). In order to characterize the evaporation process, we have measured this recoil pressure by using a plume deflection technique, where the plume generated for static conditions (i. e. with no sample displacement) is deflected by a transverse side gas jet. From the measurement of the plume deflection angle, the recoil pressure can be determined as a function of incident intensity and sample material. From these data one can estimate the pressure generated on the front KW, during laser welding. Therefore, the corresponding dynamic pressure exerted by the vapor plume expansion on the rear KW, in contact with the melt pool, can be also estimated. These pressures appear to be in close agreement with those generated by an additional side jet that has been used in previous experiments, for stabilizing the observed melt pool oscillations or fluctuations.

Investigation of extinction in unsteady flames in turbulent combustion by 2D-LIF of OH radials and flamelet analysis

An experimental and theoretical investigation of premixed turbulent combustion in an engine simulator is presented. The distribution of hydroxyl radicals formed in the combustion of propane/air mixtures was visualized by 2D-LIF and used to monitor the progress of the combustion process. For stoichiometric mixtures, images showed a continuous wrinkled flame front, while in lean (λ=1.5) mixtures, local flame extinction was observed as discontinuities in the reaction zone. A bright active reaction zone was still observed in flame inlets and closed concave structures. The effects of self-absorption and of collisional quenching on the fluorescence signal are considered and appear to have only a minor net influence on the shape and width of the flame front. The images are evaluated and interpreted in terms of the Lewis number effect and the laminar flamelet model. Analysis was performed by determining the contour lines of the images (specifically, the ratios of average maximum to equilibrium OH concentration) and comparing with corresponding ratios from unstrained flame simulations. The results show that although the degree of turbulence is not high enough for straining effects to be important, flamelet curvature does play a significant role in the combustion of lean mixtures; this is manifested by a mean effective flame velocity that is less than the laminar burning velocity. © 1991 Combustion Institute.

SOI diode temperature sensor operated at ultra high temperatures-a critical analysis

This paper investigates the performance of diode temperature sensors when operated at ultra high temperatures (above 250°C). A low leakage Silicon On Insulator (SOI) diode was designed and fabricated in a 1 μm CMOS process and suspended within a dielectric membrane for efficient thermal insulation. The diode can be used for accurate temperature monitoring in a variety of sensors such as microcalorimeters, IR detectors, or thermal flow sensors. A CMOS compatible micro-heater was integrated with the diode for local heating. It was found that the diode forward voltage exhibited a linear dependence on temperature as long as the reverse saturation current remained below the forward driving current. We have proven experimentally that the maximum temperature can be as high as 550°C. Long term continuous operation at high temperatures (400°C) showed good stability of the voltage drop. Furthermore, we carried out a detailed theoretical analysis to determine the maximum operating temperature and exlain the presence of nonlinearity factors at ultra high temperatures. © 2008 IEEE.

Proteomic Analysis of Proteins Involved in Spermiogenesis in Mouse

Spermiogenesis is a unique process in mammals during which haploid round spermatids mature into spermatozoa in the testis. Its successful completion is necessary for fertilization and its malfunction is an important cause of male infertility. Here, we report the high-confidence identification of 2116 proteins in mouse haploid germ cells undergoing spermiogenesis: 299 of these were testis-specific and 155 were novel. Analysis of these proteins showed many proteins possibly functioning in unique processes of spermiogenesis. Of the 84 proteins annotated to be involved in vesicle-related events, VAMP4 was shown to be important for acrosome biogenesis by in vivo knockdown experiments. Knockdown of VAMP4 caused defects of acrosomal vesicle fusion and significantly increased head abnormalities in spermatids from testis and sperm from the cauda epididymis. Analysis of chromosomal distribution of the haploid genes showed underrepresentation on the X chromosome and overrepresentation on chromosome 11, which were due to meiotic sex chromosome inactivation and expansion of testis-expressed gene families, respectively. Comparison with transcriptional data showed translational regulation during spermiogenesis. This characterization of proteins involved in spermiogenesis provides an inventory of proteins useful for understanding the mechanisms of male infertility and may provide candidates for drug targets for male contraception and male infertility.

Numerical analysis of the current and voltage sharing issues for resistive fault current limiter using YBCO coated conductors

YBaCuO-coated conductors offer great potential in terms of performance and cost-saving for superconducting fault current limiter (SFCL). A resistive SFCL based on coated conductors can be made from several tapes connected in parallel or in series. Ideally, the current and voltage are shared uniformly by the tapes when quench occurs. However, due to the non-uniformity of property of the tapes and the relative positions of the tapes, the currents and the voltages of the tapes are different. In this paper, a numerical model is developed to investigate the current and voltage sharing problem for the resistive SFCL. This model is able to simulate the dynamic response of YBCO tapes in normal and quench conditions. Firstly, four tapes with different Jc 's and n values in E-J power law are connected in parallel to carry the fault current. The model demonstrates how the currents are distributed among the four tapes. These four tapes are then connected in series to withstand the line voltage. In this case, the model investigates the voltage sharing between the tapes. Several factors that would affect the process of quenches are discussed including the field dependency of Jc, the magnetic coupling between the tapes and the relative positions of the tapes. © 2010 IEEE.

Mandrel peeling of a flexible laminate with a pressure-sensitive adhesive: Comparison of experiment with numerical analysis

Mandrel peel tests with mandrels or rollers of varying diameters have been carried out using Mylar backing of several thicknesses and a commercial synthetic acrylic adhesive. The results are critically compared with the numerical predictions of the peeling software package ICPeel. In addition, a finite element model of the mandrel peeling process has been completed which gives good agreement with experiment provided appropriate mechanical properties of adherend and adhesive are used which must include the effects of adherent constraint. The influence of the thickness of the backing is also considered and both experiment and analysis confirm that there is a backing thickness at which the peel force for a laminate of this sort will show a maximum. © 2010 Blackwell Publishing Ltd.

Tracing the Origins of Hakka and Chaoshanese by Mitochondrial DNA Analysis

Hakka and Chaoshanese are two unique Han populations residing in southern China but with northern Han (NH) cultural traditions and linguistic influences. Although most of historical records indicate that both populations migrated from northern China in the last two thousand years, no consensus on their origins has been reached so far. To shed more light on the origins of Hakka and Chaoshanese, mitochondrial DNAs (mtDNAs) of 170 Hakka from Meizhou and 102 Chaoshanese from Chaoshan area, Guangdong Province, were analyzed. Our results show that some southern Chinese predominant haplogroups, e.g. B, F, and M7, have relatively high frequencies in both populations. Although median network analyses show that Hakka/Chaoshanese share some haplotypes with NH, interpopulation comparison reveals that both populations show closer affinity with southern Han (SH) populations than with NH. In consideration of previous results from nuclear gene (including Y chromosome) research, it is likely that matrilineal landscapes of both Hakka and Chaoshanese have largely been shaped by the local people during their migration southward and/or later colonization in southern China, and factors such as cultural assimilation, patrilocality, and even sex-bias in the immigrants might have played important roles during the process. Am J Phys Anthropol 141:124-130, 2010. (C) 2009 Wiley-Liss, Inc.

Breathers and thermal relaxation as a temporal process: A possible way to detect breathers in experimental situations

Breather stability and longevity in thermally relaxing nonlinear arrays is investigated under the scrutiny of the analysis and tools employed for time series and state reconstruction of a dynamical system. We briefly review the methods used in the analysis and characterize a breather in terms of the results obtained with such methods. Our present work focuses on spontaneously appearing breathers in thermal Fermi-Pasta-Ulam arrays but we believe that the conclusions are general enough to describe many other related situations; the particular case described in detail is presented as another example of systems where three incommensurable frequencies dominate their chaotic dynamics (reminiscent of the Ruelle-Takens scenario for the appearance of chaotic behavior in nonlinear systems). This characterization may also be of great help for the discovery of breathers in experimental situations where the temporal evolution of a local variable (like the site energy) is the only available/measured data. © 2005 American Institute of Physics.

An analysis of factors improving technology roadmap credibility: A communications theory assessment of roadmapping processes

In recent years, many industrial firms have been able to use roadmapping as an effective process methodology for projecting future technology and for coordinating technology planning and strategy. Firms potentially realize a number of benefits in deploying technology roadmapping (TRM) processes. Roadmaps provide information identifying which new technologies will meet firms' future product demands, allowing companies to leverage R&D investments through choosing appropriately out of a range of alternative technologies. Moreover, the roadmapping process serves an important communication tool helping to bring about consensus among roadmap developers, as well as between participants brought in during the development process, who may communicate their understanding of shared corporate goals through the roadmap. However, there are few conceptual accounts or case studies have made the argument that roadmapping processes may be used effectively as communication tools. This paper, therefore, seeks to elaborate a theoretical foundation for identifying the factors that must be considered in setting up a roadmap and for analyzing the effect of these factors on technology roadmap credibility as perceived by its users. Based on the survey results of 120 different R&D units, this empirical study found that firms need to explore further how they can enable frequent interactions between the TRM development team and TRM participants. A high level of interaction will improve the credibility of a TRM, with communication channels selected by the organization also positively affecting TRM credibility. © 2011 Elsevier Inc.

The development of a hot rolling process for variable cross-section I-beams

To meet targeted reductions in CO 2 emissions by 2050, demand for metal must be cut, for example through the use of lightweight technologies. However, the efficient production of weight optimized components often requires new, more flexible forming processes. In this paper, a novel hot rolling process is presented for forming I-beams with variable cross-section, which are lighter than prismatic alternatives. First, the new process concept is presented and described. A detailed computational and experimental analysis is then conducted into the capabilities of the process. Results show that the process is capable of producing defect free I-beams with variations in web depth of 30-50%. A full analysis of the process then indicates the likely failure modes, and identifies a safe operating window. Finally, the implications of these results for producing lightweight beams are discussed. © 2012 Elsevier B.V. All rights reserved.