A substrate-induced growth-response method for estimating the biomass of microbial functional groups in soil and aquatic systems

Abstract A substrate-induced growth-response (SIGR) method is presented for estimating the biomass or density of microorganisms capable of carrying out specific metabolic functions in natural and human-made systems. The biomass of active organisms can be estimated based on the concentration of substrate needed to induce the growth of the standing population. Curves of substrate mineralization or depletion are used as indirect indicators of growth. Estimates of population size are obtained by using non-linear regression techniques to fit simple models, that contain biologically relevant parameters, to the substrate mineralization curves. In the present study, the SIGR method was used to estimate the numbers of organisms capable of mineralizing 2,4-dinitrophenol in soil and in a model waste-treatment system. The SIGR approach was tested by comparison of model estimates to estimates for the same parameters obtained by independent means.     

A Novel Experimental and Analytical Approach to the Multimodal Neural Decoding of Intent During Social Interaction in Freely-behaving Human Infants

Understanding typical and atypical development remains one of the fundamental questions in developmental human neuroscience. Traditionally, experimental paradigms and analysis tools have been limited to constrained laboratory tasks and contexts due to technical limitations imposed by the available set of measuring and analysis techniques and the age of the subjects. These limitations severely limit the study of developmental neural dynamics and associated neural networks engaged in cognition, perception and action in infants performing “in action and in context”. This protocol presents a novel approach to study infants and young children as they freely organize their own behavior, and its consequences in a complex, partly unpredictable and highly dynamic environment. The proposed methodology integrates synchronized high-density active scalp electroencephalography (EEG), inertial measurement units (IMUs), video recording and behavioral analysis to capture brain activity and movement non-invasively in freely-behaving infants. This setup allows for the study of neural network dynamics in the developing brain, in action and context, as these networks are recruited during goal-oriented, exploration and social interaction tasks.     

A simple and accurate method for generating co-dominant markers: an application of conformation-sensitive gel electrophoresis to linkage analysis in the silkworm

A simple and sensitive method for linkage analysis is described, which is based on conformation-sensitive gel electrophoresis (CSGE). Using urea-containing agarose gels or a commercially available polyacrylamide-derived matrix, 13 polymorphic markers were newly identified for known genes of the silkworm, Bombyx mori, which had been scored as monomorphic by PCR-RFLP analysis. This method for detecting polymorphisms is quite sensitive, and can be performed with inexpensive reagents and apparatus that is available in most molecular biology laboratories. Received: 19 November 1998 / Accepted: 2 March 1999     

A method for assessing evergreen habitats using phytodiversity and geospatial techniques in tropical rain forests of Southern Western Ghats (India)

We have used data generated using remote sensing and geographical information systems to categorize habitats, and then determined the relationship between the habitat categorizations and species-distribution patterns. A biologically rich hotspot—Kalakad-Mundanthurai Tiger Reserve, located at Southern Western Ghats, India, was chosen for this study. In order to spatially delineate areas of high species richness/diversity and endemic habitat zones, we have identified evergreen habitats in conjunction with landscape metrics, species assemblage, micro-habitats like slope, topography, species endemism, and proportion of core and edge species. A total of 236 species and 2,920 individuals were recorded using systematic stratified plots of 0.1 ha covering 47 plots. Hierarchical cluster analysis was done using Ward’s method. Plot information was used to identify clusters based on species density. The analysis showed five species assemblages that are quite distinct from each other in terms of dominant species. The distribution of endemic and edge species, land cover heterogeneity, and continuity of patches in these clusters were evaluated to understand the degree of disturbance and intactness at landscape scale. Integration of species assemblages and topography brought out four major elevation-slope complexes. Information on species composition (robust field survey) with spectral (hybrid classification) properties has shown 72% overall accuracy and distinguished four evergreen sub-groups and other land cover classes. The developed approach assumes great importance in the assessment of biodiversity and prioritizing the areas of conservation.     

A dot-blot method for quantification of apurinic/apyrimidinic sites in DNA using an avidin plate and liposomes encapsulating a fluorescence dye

A dot-blot method for quantification of apurinic/apyrimidinic (AP) sites in genomic DNA (calf thymus DNA) is described using an avidin-modified glass slip and biotinylated liposomes containing sulforhodamine B as a fluorescence marker. Aldehyde reactive probe (ARP)-tagged DNA was found to be strongly adsorbed on an avidin slip, even if treated with ethanolamine and biotin, with an efficiency of 51% due to the positive surface charge of avidin, and unbound ARP was easily washed out of the surface with Milli-Q water. In the assay protocol, calf thymus DNA containing AP sites is reacted with ARP in solution and immobilized on an ethanolamine- and biotin-treated avidin slip (EAB-avidin slip), followed by incubation with streptavidin. The AP sites were finally quantified with biotinylated liposomes containing 1.5 mM sulforhodamine B as a fluorescence marker. The mean fluorescence intensity over the surface of the slip was an analytically relevant measure of the amount of AP sites in calf thymus DNA. By using the dot-blot assay, 1-5 AP sites per 10(4) nucleotides in 5 and 100 ng of DNA were quantified. The current dot-blot method has potential for quantification of AP sites in genomic DNA at a level of several nanograms.     

A sensitive method for quantification of aceticlastic methanogens and estimation of total methanogenic cells in natural environments based on an analysis of ether-linked glycerolipids

Abstract A highly sensitive method for the quantification of methanogens in anaerobic digestor sludges was developed, based on an analysis of ether-linked glycerolipids. Core lipids were prepared from total lipids by HF treatment and mild methanolysis, and these core lipids were quantified as the corresponding 9-anthroyl derivatives by high-performance liquid chromatography with fluorescence detection. The amounts, in terms of cell carbon content, of Methanosaeta and Methanosarcina were proportional to the amounts of α-hydroxyarchaeol and β-hydroxyarchaeol, respectively. Moreover, the total amount of core lipids was well correlated with the cell mass of aceticlastic and H₂/CO₂-consuming methanogens. The limit of detection for Methanosaeta concilii was 17 ng of cell carbon when the signal/noise ratio was 3. This method allowed us to quantitate aceticlastic methanogens with high accuracy and to make a rough estimate of total methanogenic cells without any interference by the multifarious impurities that are present in anaerobic sludges. These results suggest that the present method will be a useful tool for investigations of methanogenic ecosystems.