Microbial indicators for sawdust and bark compost stability and humification processes

To what extent some microbial index ratios are suitable for use as early criteria for the level of compost stability during aerobic composting of coniferous sawdust and bark at mesophilic conditions was studied. Evolution of the specific respiration activity (CO₂-C/biomass C) and the ratios between some groups of microorganisms were followed as a function of composting time. The specific respiration activity was found to be an early and most reliable indicator of compost stability. The peroxidase and polyphenoloxidase enzyme activity during composting, as well as the composition of newly-formed humus substances were studied. The duration of composting increased the quality of newly-formed humus substances (C_h.a.:C_f.a ratio; Ca-complexed humic acid and resistance of organo-mineral complexes). The quality of humus substances could be used to assess compost stability. However, the results can be applied only under defined conditions.     

Fourier-transform infrared spectroscopy: a pharmacotoxicologic tool for in vivo monitoring radical aggression

Among the physico-chemical methods that can be used to investigate induced peroxidation in living cells, Fourier transform infrared (FT-IR) spectroscopy appears to be a valuable technique as it is non-destructive and sensitive for monitoring changes in the vibrational spectra of samples. We examined microsomal fractions from rat liver and brain by FT-IR to study the effect of radical aggression induced in vivo by carbon tetrachloride (CCl4). The length of the acyl chains was increased as a consequence of peroxidation induced by the xenobiotic. Moreover, an enhanced level of cholesterol esters and an increase in phospholipids were observed in the liver and the brain, respectively. The conformational structure of the membrane proteins was changed in both the liver and the brain. In the polysaccharide region, we observed an important loss in glucidic structures, such as a decrease in liver glycogen and in some brain glycolipids. These alterations are probably due to the interactions between cells and CCl4 and the metabolic changes caused by CCl4. Thus, FT-IR spectroscopy appears to be an useful tool and an accurate means for rapidly investigating the in vivo biochemical alterations induced by CCl4 in microsomes, and for correlating them with biochemical and physiological data.     

Magnetic resonance spectroscopy: an in vivo tool for monitoring cerebral injury in SIV-infected macaques

The purpose of our study was to demonstrate the feasibility of using in vivo proton Magnetic Resonance Spectroscopy (MRS) to monitor the brain manifestations of SIV infection in the macaque model of AIDS. Previous spectroscopy work on macaque brain tissue and in vivo work in humans is reviewed to provide the motivation and context for this study. We collected 34 MRS data sets on 14 uninfected rhesus macaques. From this data, we demonstrate that we are capable of detecting changes similar to those observed in human MRS studies for most metabolites using less than 10 animals. The juvenile macaques utilized in this study demonstrate age-related changes in the levels of N-acetyl aspartate (NAA), a neuronal marker. The quantity and distribution of neurochemicals in the macaque are found to be slightly, but significantly, different than in the human.     

Comparison between UV spectroscopy and Nirs to assess humification process during sewage sludge and green wastes co-composting

The humification of organic matter during composting was studied by the quantification and monitoring of the evolution of humic substances (Humic Acid-HA and Fulvic Acid-FA) by UV spectra deconvolution (UVSD) and near-infrared reflectance spectroscopy (NIRS) methods. The final aim of this work was to compare UVSD to NIRS method, already applied on the same compost samples in previous studies. Finally, UVSD predictions were good for HA and HA/FA (r² of 0.828 and 0.531) but very bad for FA (r² of 0.092). In contrary, all NIRS correlations were accurate and significant with r² of 0.817, 0.806 and 0.864 for HA, FA and HA/FA ratio respectively. From these results, HA/FA ratio being a well-used index of compost maturity, UVSD and NIRS represent two invaluable tools for the monitoring of the composting process. However, we can note that NIRS predictions were more accurate than UVSD calibrations.     

Satellite imagery as a tool for monitoring species diversity: an assessment

1. A landscape of 5 × 5·5 km in the Karnataka region of the Western Ghats of India was mapped into seven landscape element types, using field identification of types as well as supervised and unsupervised classification of satellite imagery.
2. Plant communities distributed in these landscape element types were surveyed in the field using 246 quadrats of 10 × 10 m, in order to assess whether these types could be distinguished in terms of species composition. All angiosperms excluding grasses, which could not be identified accurately in the field, were recorded for this purpose.
3. Landscape element types identified in the field harboured significantly distinctive sets of species of flowering plants, and were also by and large distinctive in terms of their species richness.
4. Landscape element types could be identified accurately on the basis of supervised classification: the types thus demarcated harboured distinctive sets of flowering plants.
5. Landscape element types coupled to satellite imagery could then be used to organize a programme of monitoring biodiversity.
6. Unsupervised classification of satellite imagery did not permit classification of landscape element types with a high enough level of accuracy. In consequence, the demarcated landscape element types did not harbour significantly distinctive sets of species of flowering plants. Unsupervised classification is therefore not appropriate in a programme of monitoring biodiversity.     

Gastrointestinal ischemia monitoring through impedance spectroscopy as a tool for the management of the critically ill

Impedance spectroscopy (IS) has been proposed as a tool for monitoring mucosal tissue ischemia and damage in the gut of critically ill patients resulting from shock and hypoperfusion. A specific device and system have been developed and tested for this specific application over the past 12 years by our research group. This paper reviews previously published studies as well as unpublished experimental results, and puts the whole in context and perspective to help understand this technology. Results presented include summaries of gastric reactance measurement understanding, in vivo measurements in animal models, clinical significance of the measurement, and future perspectives of clinical use of this technology. All of the experimental work done to date has been designed to determine the evolving device prototypes’ performance and limitations from an instrumentation point of view. Although there are still questions to be answered with regard to the IS measurement, we conclude that we have reached enough confidence in the measurement and the device’s performance and safety to begin clinically oriented research to learn how this technology may be useful in the diagnosis and management of different populations of the critically ill.     

Use of Raman spectroscopy as a tool for in situ monitoring of microwave-promoted reactions

The progress of microwave-promoted reactions can be monitored by interfacing a Raman spectrometer with a scientific microwave unit. The apparatus is assembled from commercially available components. It is used in this protocol to follow the base-catalyzed reaction of salicylaldehyde with ethylacetoacetate to yield 3-acetylcoumarin. It is possible to watch the reaction spectroscopically in real time, determine when it reaches completion and thus use it as a tool for rapid reaction optimization.     

Effect of matured compost as a bulking and inoculating agent on the microbial community and maturity of cattle manure compost

Cattle manure composts were consecutively manufactured. Compost that reached maturity first was used as a bulking and inoculating agent for subsequent compost production. The microbial community was measured through phospholipid fatty acid analysis. Changes in the content of fatty acid methyl esters derived from phospholipids were similar in all the composts. The diversity index for the fatty acid methyl ester content increased in the secondary-produced compost from the onset of composting. Microbial succession was accelerated using matured compost. The proportion of biomarker fatty acids for gram-positive bacteria also increased in the secondary-produced compost from the early stage of composting. Changes in germination index indicated the maturity stage of the compost. The proportion of biomarker fatty acids for gram-positive bacteria was positively correlated to the germination index, indicating that phospholipid fatty acid analysis is an indicator for evaluating the maturity of cattle manure composts.     

The B-value: a tool for monitoring data

This paper considers the problem of monitoring slowly accruing data from a nonsequentially designed experiment. We describe the use of the B-value, which is a transformed Z-value, for the calculation of conditional power. In data monitoring, interim Z-values do not allow simple projections to the end of the study. Moreover, because of their popular association with P-values, Z-values are often misinterpreted. If observed trends are viewed as the realization of a Brownian motion process, the B-value and its decomposition allow simple extrapolations to the end of the study under a variety of hypotheses. Applications are presented to one- and two-sample Z-tests, the two-sample Wilcoxon rank sum test, and the log-rank test.     

Novel tool for characterization of noncrystalline regions in cellulose: a FTIR deuteration monitoring and generalized two-dimensional correlation spectroscopy

Our previous results indicated that noncrystalline regions in a regenerated cellulose film comprised at least three domains engaged in different manners of molecular assembly [Kondo et al. In Cellulose Derivatives; Heinze, T. J., Glasser, W. G., Eds.; ACS Symposium Series 688; American Chemical Society: Washington, DC, 1998; Chapter 12]. In this article, we attempt to characterize each of the three noncrystalline domains in the film. The method used was a FTIR monitoring of deuteration from hydroxyl (OH) groups to OD, leading to the two-dimensional (2D) correlation analysis. The time-scan spectra in the OH-OD exchanging reaction were transformed into two kinds of 2D correlation spectra, the synchronous and the asynchronous spectra. Of the two, some cross-peaks were found in the latter spectrum. This suggests that the asynchronous 2D correlation spectrum could differentiate the contribution of OH groups due to different frequencies of hydrogen bonds in each domain. Here we will show the validity of this 2D correlation method as a powerful tool to predict hydrogen-bonding networks of the noncrystalline domains in cellulose.     

Stability and maturity of a green waste and biowaste compost assessed on the basis of a molecular study using spectroscopy,thermal analysis,thermodesorption and thermochemolysis

The organic matter (OM) of a green waste and bio waste compost was characterised over 8 months and the observed evolution was correlated with physico-chemical parameters (temperature, pH, carbon content, C/N ratio). Thermochemolysis and thermodesorption were used to monitor bacterial activity (stability) whereas diffuse reflectance infrared fourier transform spectroscopy (DRIFTS) and thermodifferential analysis (TDA) permitted to determine the degree of OM humification (maturity). DRIFT spectroscopy and TDA provide two indicators of maturity since, with these two techniques, the signals associated with the biodegradable organic matter decrease relatively to the signals associated with refractory organic matter. This increase in R_TG and R_IR ratios between aromatic to aliphatic signals constitutes a proof for OM complexification. It correlates with humic acids/fulvic acids ratio known to be a maturity index.     

Surface plasmon resonance spectroscopy: an emerging tool for the study of peptide-membrane interactions

The interactions between peptides and membranes mediate a wide variety of biological processes, and characterization of the molecular details of these interactions is central to our understanding of cellular events such as protein trafficking, cellular signaling and ion-channel formation. A wide variety of biophysical techniques have been combined with the use of model membrane systems to study peptide-membrane interactions, and have provided important information on the relationship between membrane-active peptide structure and their biological function. However, what has generally not been reported is a detailed analysis of the affinity of peptide for different membrane systems, which has largely been due to the difficulty in obtaining this information. To address this issue, surface plasmon resonance (SPR) spectroscopy has recently been applied to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. This article provides an overview of these recent applications that demonstrate the potential of SPR to enhance our molecular understanding of membrane-mediated peptide function.     

Maturity assessment of composted olive mill wastes using UV spectra and humification parameters

In this study, two olive mill wastes - exhausted olive cake (EOC) and paste of olive mill wastewater naturally dehydrated (POMW) - were co-composted and mixed with 25% sesame bark (SB). The humification process was evidenced by quantifying the humic substances and the generally accepted humification indices: (i) the ratio of humic acid (HA) carbon to fulvic acid (FA) carbon (CHA/CFA), (ii) the ratio of water soluble organic carbon (CW) to total organic nitrogen (Cw/Norg), (iii) and the ratio of humic acid carbon to total organic carbon CHA/Corg and by determining the absorbance ratios: E2/E4, E2/E6 and E4/E6. The results showed that the time required to reach maturity was dependant on the chemical properties of the initial raw materials used. The compost including EOC had more nitrogen and synthesised more polymerised HA, the POMW compost also had acceptable degrees of stability and maturity at the end of the process. Maturation was confirmed by a decline in Cw below 1.7, an increase in nitrogen, in HA, in CHA/CFA and an elimination of phytotoxicity. Composts produced with olive mill wastes, experimented on potato culture in the field, can be considered beneficial to soils because of their humification indexes and no toxicity.     

FTIR and UV spectroscopy in real-time monitoring of S. cerevisiae cell culture

A combination of FTIR and UV spectroscopy is proposed as a novel technique for integrated real-time monitoring of metabolic activity and growth rates of cell cultures, required for systematic studies of cellular low-frequency (LF) electric and magnetic field (EMF) effects. As an example, we investigated simultaneous influence of periodic LF 3D EMFs on a culture of Saccharomyces cerevisiae (baker's yeast) cells. Amplitudes, frequencies and phases of the field components were the variable parameters. Electromagnetic fields were found to efficiently control the activity of the yeast cells, with the resulting CO₂ production rates, as monitored by FTIR spectroscopy, varying by at least one order of magnitude due to the field action. Additionally, population dynamics of the yeast cells was monitored by UV absorption of the yeast culture at λ_prob = 320 nm, and compared to the CO₂ production rates. The detected physiologically active frequencies are all below 1 kHz, namely, 800 Hz excitation was effective in reducing the metabolic rates and arresting cell proliferation, whereas 200 Hz excitation was active in accelerating both cell proliferation and overall metabolic rates. The proposed methods produce objective, reliable and quantitative real-time results within minutes and may be used in various tasks that could benefit from a rapid feedback they provide in the form of metabolic and growth rates. Amplitude and frequency dependences of the LF EMF effects from individual field components with different polarizations were recorded and qualitatively interpreted based on a simple model, describing ion diffusion through a membrane channel.     

Composting of animal manures and chemical criteria for compost maturity assessment. A review

New livestock production systems, based on intensification in large farms, produce huge amount of manures and slurries without enough agricultural land for their direct application as fertilisers. Composting is increasingly considered a good way for recycling the surplus of manure as a stabilised and sanitised end-product for agriculture, and much research work has been carried out in the last decade. However, high quality compost should be produced to overcome the cost of composting.     

FTIR and UV spectroscopy in real-time monitoring of S. cerevisiae cell culture

A combination of FTIR and UV spectroscopy is proposed as a novel technique for integrated real-time monitoring of metabolic activity and growth rates of cell cultures, required for systematic studies of cellular low-frequency (LF) electric and magnetic field (EMF) effects. As an example, we investigated simultaneous influence of periodic LF 3D EMFs on a culture of Saccharomyces cerevisiae (baker's yeast) cells. Amplitudes, frequencies and phases of the field components were the variable parameters. Electromagnetic fields were found to efficiently control the activity of the yeast cells, with the resulting CO(2) production rates, as monitored by FTIR spectroscopy, varying by at least one order of magnitude due to the field action. Additionally, population dynamics of the yeast cells was monitored by UV absorption of the yeast culture at λ(prob)?=?320?nm, and compared to the CO(2) production rates. The detected physiologically active frequencies are all below 1?kHz, namely, 800?Hz excitation was effective in reducing the metabolic rates and arresting cell proliferation, whereas 200?Hz excitation was active in accelerating both cell proliferation and overall metabolic rates. The proposed methods produce objective, reliable and quantitative real-time results within minutes and may be used in various tasks that could benefit from a rapid feedback they provide in the form of metabolic and growth rates. Amplitude and frequency dependences of the LF EMF effects from individual field components with different polarizations were recorded and qualitatively interpreted based on a simple model, describing ion diffusion through a membrane channel.     

Effect of inoculation with Penicillium expansum on the microbial community and maturity of compost

Compost prepared from wheat straw and cattle/chicken mature was inoculated with the lignocellulolytic fungus, Penicillium expansum. Compared to uninoculated compost, the inoculated compost exhibited a 150% higher germination index, more than 1.2 g kg(-1)-dw of changes in NH(4)(+)-N concentrations, a ca. 12.0% higher humus content and a lignocellulose degradation that proceeded 57.5% faster. Culture-based determinations of microbial populations demonstrated that aerobic heterotrophic bacteria and fungi were about 1-2 orders of magnitude higher in inoculated than in uninoculated compost. The number of ammonifying, ammonium-oxidizing, nitrite-oxidizing, denitrifying bacteria and cellulose-decomposing bacteria was 6.1-9.0 log(10) CFU g(-1)-dw, 1.2-4.3 log(10) MPN g(-1)-dw, 3.5-6.8 log(10) MPN g(-1)-dw, 3.58-4.34 log(10) MPN g(-1)-dw, 1.4-3.8 log(10)MPN g(-1)-dw, and 4.2-8.8 log(10) CFU g(-1)-dw higher in the compost inoculated with P. expansum.     

SRMBuilder: a user-friendly tool for selected reaction monitoring data analysis

With high sensitivity and reproducibility, selected reaction monitoring (SRM) has become increasingly popular in proteome research for targeted quantification of low abundance proteins and post translational modification. SRM is also well accepted in other mass-spectrometry based research areas such as lipidomics and metabolomics, which necessitates the development of easy-to-use software for both post-acquisition SRM data analysis and quantification result validation. Here, we introduce a software tool SRMBuilder, which can automatically parse SRM data in multiple file formats, assign transitions to compounds, match light/heavy transition/compound pairs and provide a user-friendly graphic interface to manually validate the quantification result at transition/compound/sample level. SRMBuilder will greatly facilitate processing of the post-acquisition data files and validation of quantification result for SRM. The software can be downloaded for free from http://www.proteomics.ac.cn/software/proteomicstools/index.htm as part of the software suite ProteomicsTools.