An integrating sphere leaf chamber

Abstract. A combination of an optical integrating sphere and leaf chamber is described, and some principles of its design are given. It is shown that the number of quanta absorbed by the leaf inside the sphere can be found from measurements of the quantum flux density inside the sphere with and without the leaf present, when certain constant parameters of the sphere are known. Methods for finding these are given. It is not necessary to know leaf area or absorptivity for the quantum yield for photosynthesis to be derived from additional measurement of CO₂, fixation.     

Corals as light collectors: an integrating sphere approach

An integrating sphere was used to estimate the fraction of the incident quantum flux absorbed by a coral colony placed within it. This method allows one to examine the in vivo light absorption of intact coral colonies. We used this method to study effects of colony morphology, size, and photoacclimation status on the light harvesting efficiency by the zooxanthellae. Light absorption per unit of coral surface area decreased with increase in colony size, with a clear effect of different coral morphologies. In branched colonies, shading among branches reduced the absorbed light per unit area and per zooxanthellae. Photoacclimation to low light resulted in increased cellular chlorophyll concentrations in the zooxanthellae. In shade acclimated colonies, areal chlorophyll concentrations increased significantly, leading to more overlap among the optical cross-sections of pigments within cells and mutual shading among cells. These package effects showed up as a decrease in the in vivo, chlorophyll-a specific, spectral average, effective optical cross-section, a*. An integrating sphere is a useful tool for collecting optical information on corals.     

An entropy-based measure for QTL mapping using extreme samples of population

Quantitative trait locus (QTL) mapping can be accomplished through the method of selective genotyping, which is based on the differences of frequencies between an upper sample and a lower sample in population. However, amplifying the differences in marker allele frequencies in extreme samples may increase the probability for QTL mapping. Shannon entropy, which is a nonlinear function of allele frequencies, can be used to amplify the differences in marker allele frequencies. In this paper, we present a novel measure for linkage disequilibrium (LD) between a marker and single QTL, that is based on the comparison of the entropy and conditional entropy in a marker in extreme samples of population. This measure of LD between the marker and the trait locus can be used when the marker allele frequencies are known in the extreme samples of a population. We investigate the mapping performance in both analytic and simulation scenarios of a single QTL linked to a single marker. Our results show that the measure has very reasonable performance. In addition, a simulation study is performed on the basis of the haplotype frequencies of 10 SNPs of angiotensin-I converting enzyme (ACE) genes.     

Functional assay to measure yessotoxins in contaminated mussel samples

Yessotoxin (YTX) treatment of MCF-7 cells results in the accumulation of a 100-kDa fragment of E-cadherin (ECRA(100)) without a parallel loss of the intact protein in cytosoluble extracts. As a consequence, concentration-dependent increases in the total immunoreactivity detectable by anti-E-cadherin antibodies relative to controls (RTI) and in the relative immunoreactivity of ECRA(100) (RI) are observed. These responses have been exploited to develop a functional assay to measure YTX in samples from contaminated mussels by a three-step procedure, consisting of (i) treatment of MCF-7 cells with YTX standard in the concentration range 0-1nM and of unknown samples; (ii) preparation of cellular extracts, fractionation of proteins by polyacrylamide gel electrophoresis under denaturing conditions, and immunoblotting with anti-E-cadherin antibodies, followed by densitometric analyses of autoradiographies and calculation of RI of ECRA(100) and of RTI of the samples; and (iii) interpolation of the YTX concentrations in unknown samples on standard curves, by the RI of ECRA(100) and the RTI of the samples. The procedure has been used to measure yessotoxins in contaminated mussel samples, and the results obtained show that this functional assay is very sensitive (limit of detection of about 100ng equivalent YTX/g of digestive gland), and robust, as (i) it is insensitive to matrix effects in the range of toxin concentrations relevant for risk assessment to protect humans from exposure to YTX, (ii) calculations are based on a molecular parameter (the RI of ECRA(100)) which is not affected by errors in sample preparation, (iii) it can be performed by the use of antibodies commercially available from different companies, and (iv) it does not show an absolute need of calibration by a pure standard within each assay.     

To best measure cell proliferation in samples from the intestine

Arrangement of the intestinal cell lining, as it is, into distinct anatomically defined zones where proliferation is confined to the crypts, makes it an ideal tissue to study growth control mechanisms. While many methods have been used to quantify cell proliferation in the gut, several of them have severe limitations and others (although potentially better) have been misused and misinterpreted. Here, correct use and interpretation of labelling studies will be described as will a well established alternative method that provides equivalent results for one-sixth of the effort.     

IJ_Rhizo: an open-source software to measure scanned images of root samples

Background and aims

This paper provides an overview of the measuring capabilities of IJ_Rhizo, an ImageJ macro that measures scanned images of washed root samples. IJ_Rhizo is open-source, platform-independent and offers a simple graphic user interface (GUI) for a main audience of non-programmer scientists. Being open-source based, it is also fully modifiable to accommodate the specific needs of the more computer-literate users. A comparison of IJ_Rhizo’s performance with that of the widely used commercial package WinRHIZO? is discussed.

Methods

We compared IJ_Rhizo’s performance with that of the commercial package WinRHIZO? using two sets of images, one comprising test-line images, the second consisting of images of root samples collected in the field. IJ_Rhizo and WinRHIZO? estimates were compared by means of correlation and regression analysis.

Results

IJ_Rhizo “Kimura” and WinRHIZO? “Tennant” were the length estimates that were best linearly correlated with each other. Correlation between average root diameter estimates was weaker, due to the sensitivity of this parameter to thresholding and filtering of image background noise.

Conclusions

Overall, IJ_Rhizo offers new opportunities for researchers who cannot afford the cost of commercial software packages to carry out automated measurement of scanned images of root samples, without sacrificing accuracy.     

The repetitive use of samples to measure multiple cytokines: the sequential ELISA

The inexpensive and highly effective enzyme-linked immunosorbant assay (ELISA) is widely used for the quantification of biomarkers in a variety of biological samples. The applicability of the standard ELISA is difficult when experiments yield low volume samples. In such studies, the capacity of sample collection system does not meet the sample volume requirements to measure multiple different cytokines by the traditional ELISA protocol. In the modified methodology of the sequential ELISA, samples are re-used in multiple successive cycles, dramatically increasing the number of biomarkers which may be measured. Although the protocols presented to date were developed for quantification of cytokines in either blood plasma or cerebrospinal fluid, the sequential ELISA protocol has wide potential for further uses. When only limited quantities of samples are available for analysis, the sequential ELISA technique based on commercially available antibody pairs can be an attractive alternative to more advanced, costly multiplex methods. Additionally, any laboratory that currently runs traditional ELISAs has all the necessary equipment and reagents to perform the sequential ELISA.     

Different methods for extracting bacteria from freshwater sediment and a simple method to measure bacterial production in sediment samples

The efficiency of different treatments was tested to extract bacterial cells from freshwater sediment samples. The influence of sonication, density gradient centrifugation, fixation by formalin and centrifugation speed on bacterial recovery was investigated. The method developed by Smith and Azam [Mar. Microb. Food Webs 6 (1992) 107] to measure microbial activity on bacterioplankton (3H-leucine incorporation), was also evaluated in sediment samples. After 1 min of sonication bacterial abundance was reduced by about 47% in diluted sediments with tetrasodium pyrophosphate. With the addition of Percoll after sonication, bacterial counts were not significantly different (P<0.05). Fixation by formalin increased bacterial counts using sonication. However, higher bacterial abundance was estimated in non-sonicated samples. Bacterial abundance in samples centrifuged at 7000xg with and without Percoll was not significantly different (P<0.05). Highest bacterial abundance was obtained after centrifugation at low speed (750xg). Bacterial abundance decreased with higher centrifugation speed (750, 1500 and 3000xg), the difference, however, was not significant. Bacterial production ranged from 0.10 microg C cm(-3) d(-1) in autoclaved sediment to 0. 27 microg C cm(-3) d(-1) in untreated sediment. The radioactivity measured in controls of both untreated and autoclaved sediment was high (70 and 91%, respectively), indicating a high level of leucine adsorption in sediment particles. In contrast, radioactivity in control samples previously centrifuged was markedly lower (6%). Despite the high values of radioactivity in the controls, bacterial production in untreated sediment was significantly higher than in centrifuged sediment (P<0.05).     

An improved method for concentrating rotavirus from water samples

A modified adsorption-elution method for the concentration of seeded rotavirus from water samples was used to determine various factors which affected the virus recovery. An enzyme-linked immunosorbent assay was used to detect the rotavirus antigen after concentration. Of the various eluents compared, 0.05M glycine, pH 11.5 gave the highest rotavirus antigen recovery using negatively charged membrane filtration whereas 2.9% tryptose phosphate broth containing 6% glycine; pH 9.0 was found to give the greatest elution efficiency when a positively charged membrane was used. Reconcentration of water samples by a speedVac concentrator showed significantly higher rotavirus recovery than polyethylene glycol precipitation through both negatively and positively charged filters (p-value <0.001). In addition, speedVac concentration using negatively charged filtration resulted in greater rotavirus recovery than that using positively charged filtration (p-value = 0.004). Thirty eight environmental water samples were collected from river, domestic sewage, canals receiving raw sewage drains, and tap water collected in containers for domestic use, all from congested areas of Bangkok. In addition, several samples of commercial drinking water were analyzed. All samples were concentrated and examined for rotavirus antigen. Coliforms and fecal coliforms (0->1,800 MPN/100 ml) were observed but rotavirus was not detected in any sample. This study suggests that the speedVac reconcentration method gives the most efficient rotavirus recovery from water samples.     

Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments

Microbial assessment of natural biodiversity is usually achieved through polymerase chain reaction (PCR) amplification. Deoxyribonucleic acid (DNA) sequences from natural samples are often difficult to amplify because of the presence of PCR inhibitors or to the low number of copies of specific sequences. In this study, we propose a non-specific preamplification procedure to overcome the presence of inhibitors and to increase the number of copies prior to carrying out standard amplification by PCR. The pre-PCR step is carried out through a multiple displacement amplification (MDA) technique using random hexamers as priming oligonucleotides and phi 29 DNA polymerase in an isothermal, whole-genome amplification reaction. Polymerase chain reaction amplification using specific priming oligonucleotides allows the selection of the sequences of interest after a preamplification reaction from complex environmental samples. The procedure (MDA-PCR) has been tested on a natural microbial community from a hypogean environment and laboratory assemblages of known bacterial species, in both cases targeting the small subunit ribosomal RNA gene sequences. Results from the natural community showed successful amplifications using the two steps protocol proposed in this study while standard, direct PCR amplification resulted in no amplification product. Amplifications from a laboratory assemblage by the two-step proposed protocol were successful at bacterial concentrations >or= 10-fold lower than standard PCR. Amplifications carried out in the presence of different concentrations of fulvic acids (a soil humic fraction) by the MDA-PCR protocol generated PCR products at concentrations of fulvic acids over 10-fold higher than standard PCR amplifications. The proposed procedure (MDA-PCR) opens the possibility of detecting sequences represented at very low copy numbers, to work with minute samples, as well as to reduce the negative effects on PCR amplifications of some inhibitory substances commonly found in environmental samples.     

Quantitative competitive-PCR assay to measure human parvovirus B19-DNA load in serum samples

The B19 virus can persist in immunocompromised patients for several months and sometimes even years because of impaired immune response. Viremia in persistent and recurrent infection may range from very low to high titers and may be associated with chronic clinical manifestations, such as chronic anemia. Several recently developed techniques that quantify B19-DNA have improved laboratory diagnosis of the infection and can help guide the choice of treatment in persistent infections (i.e., intravenous immunoglobulin (IVIG) treatment vs immunosuppression reduction). Here we describe the development of a reliable internally controlled quantitative competitive (QC)-polymerase chain reaction (PCR) assay that measures B19-DNA load in serum samples by densitometric analysis of the amplification products for monitoring B19 infection in high-risk patients. A retrospective quantification of B19-DNA in the serum samples from 48 anemic transplanted patients by the QC-PCR assay we developed in our laboratory confirmed the presence of B19-DNA in 11 of 48 samples and showed a viral DNA load between 10³ and 10⁸ B19-DNA copies/mL depending on the patients' serostatus (the highest viral load was found in IgM-positive/IgG-negative patients that is, in patients with active B19 infection at onset). The assay also confirmed B19-DNA negative patients. Our QC-PCR assay may be easily relation between active B19 infection and occurrence of anemia and to assess the efficacy of IVIG therapy or immunosuppression reduction in clearing the virus in high-risk patients.     

An ultrasensitive electrometric system to measure membrane-bound acetylcholinesterase activity

A very sensitive method for the determination of membrane-bound acetylcholinesterase from sarcoplasmic reticulum is described. The acetic acid which is released by the enzymatic hydrolysis of acetylcholine is measured by means of an electrometric system. Diluted hydrochloric acid is used as the standard to evaluate the amount of H+ produced during the time course of the reaction. With the use of a bucking voltage device the sensitivity of the method permits one to follow changes in H+ concentration below 1 microM. Therefore the enzyme activity can be estimated using a very small amount of sarcoplasmic reticulum protein. This procedure is very simple, accurate and reproducible, and it can be applied to measure membrane-bound acetylcholinesterase where the membrane suspension makes it difficult to employ spectrophotometric techniques.     

An acoustic plethysmograph to measure total infant body volume

An acoustic plethysmograph intended to measure the body volume of premature infants has been developed using the principle of the Helmholtz resonator, in which the resonance frequency is dependent on the volume of the resonating cavity. A prototype system was built and used to measure the volume of inanimate objects and newborn miniature pigs. Results for inanimate objects agree within 1 percent with comparable measurements by water displacement. Results of the animal body volume measurements compare favorably (within an average of 1.1 percent) with those obtained using hydrostatic weighing.