Tomographic techniques for the study of exceptionally preserved fossils

Three-dimensional fossils, especially those preserving soft-part anatomy, are a rich source of palaeontological information; they can, however, be difficult to work with. Imaging of serial planes through an object (tomography) allows study of both the inside and outside of three-dimensional fossils. Tomography may be performed using physical grinding or sawing coupled with photography, through optical techniques of serial focusing, or using a variety of scanning technologies such as neutron tomography, magnetic resonance imaging and most usefully X-ray computed tomography. This latter technique is applicable at a variety of scales, and when combined with a synchrotron X-ray source can produce very high-quality data that may be augmented by phase-contrast information to enhance contrast. Tomographic data can be visualized in several ways, the most effective of which is the production of isosurface-based 'virtual fossils' that can be manipulated and dissected interactively.     

Use of electron microscopy for aiding our understanding of wood biodegradation

Abstract: The use of electron microscopy (EM) has proved to be an invaluable tool for studying structural aspects of lignocellulose degradation by fungi and bacteria and therefore improving our understanding of wood biodegradation. The present review details the application of conventional (SEM, TEM, STEM), analytical (EM X-ray microanalysis, (EDXA)), and immunogold cytochemical EM procedures in the field and gives specific examples of its use for each of the known important types of microbial wood decay including bacterial (tunnelling and erosion), soft rot (cavity and erosion), brown rot and white rot (simultaneous decay and preferential lignin degraders), and discusses important advances made by adopting the techniques. The more recent use of immunogold cytochemistry for studying microbe and fungal enzyme-wood cell wall interactions and its application for localization of specific wood-degrading (laccase, Mn(II) and lignin peroxidases, and cellulases) and H₂O₂ producing (pyranose oxidase) enzymes in situ during white rot decay are also reviewed, as is the application of EM for studying non-enzymatic wood decay. Methods for labelling and detecting wood components (lignin, hemi- and cellulose) in situ by EDXA and enzyme immunogold cytochemistry are also outlined. The use of EM in wood biodegradation research is rapidly expanding and is seen as an important compliment to biochemical and chemical approaches. The future should see even greater advances in our understanding of wood decay as more advanced and recently developed EM techniques are also exploited.     

Aerobic and Anaerobic Biodegradation of Aged Pentachlorophenol by Indigenous Microorganisms

Pentachlorophenol (PCP) use as a general biocide, particularly for treating wood, has led to widespread environmental contamination. Biodegradation has emerged as the main mechanism for PCP degradation in soil and groundwater and a key strategy for remediation. Examining the microbial biodegrading potential for PCP at a contaminated site is crucial in determining its fate. Hundreds of studies have been published on PCP microbial degradation, but few have described the biodegradation of PCP that has been in contact with soils for many years. The bioavailability of “aged” hydrophobic organics is a significant concern. PCP- and 2,3,4,6-tetrachlorophenol (2,3,4,6-TeCP)-contaminated soil samples from several depths at a former wood treatment site were placed under varying conditions in the laboratory to determine the anaerobic and aerobic potential for biodegradation of chlorophenols at the site. PCP biodegradation occurred in both anaerobic and aerobic soil samples. Rapid aerobic degradation occurred in samples spiked with 2- and 4-chlorophenol, but not with 3-chlorophenol. Reductive dechlorination of PCP in anaerobic samples resulted in the accumulation of 3-chlorophenol. In most anaerobic replicates, 3-chlorophenol was degraded with the appearance of detectable, but not quantifiable amounts of phenol. These results indicate excellent potential for remediation at the site using the indigenous microorganisms under both aerobic and anaerobic conditions. However, a fraction of the PCP was unavailable for degradation.     

High-Dynamic-Range CT Reconstruction Based on Varying Tube-Voltage Imaging

For complicated structural components characterized by wide X-ray attenuation ranges, the conventional computed tomography (CT) imaging using a single tube-voltage at each rotation angle cannot obtain all structural information. This limitation results in a shortage of CT information, because the effective thickness of the components along the direction of X-ray penetration exceeds the limitation of the dynamic range of the X-ray imaging system. To address this problem, high-dynamic-range CT (HDR-CT) reconstruction is proposed. For this new method, the tube’s voltage is adjusted several times to match the corresponding effective thickness about the local information from an object. Then, HDR fusion and HDR-CT are applied to obtain the full reconstruction information. An accompanying experiment demonstrates that this new technology can extend the dynamic range of X-ray imaging systems and provide the complete internal structures of complicated structural components.     

Gravimetric screening method for fungal decay of paper: inoculation with <Emphasis Type="Italic">Trametes</Emphasis> <Emphasis Type="Italic">versicolor</Emphasis>

The European standard test EN 113 for fungal degradation of solid wood has been adapted for degradation of paper by white rot fungus (Trametes versicolor). Fungal degradation of paper sheets may potentially be used for screening different wood preservatives on paper instead of solid wood. The paper samples showed higher relative mass losses compared to wood, and samples pretreated with boric acid, copper sulfate and polymerized linseed oil were successfully tested for biodegradation using the paper sheet method. The results on paper degradation were compared with wood, both as wood blocks (according to standard test) and wood cut in sections forming layered structures mimicking paper layers.     

Recent developments in microbial biotransformation and biodegradation of dioxins

Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs), commonly known as dioxins (PCDD/Fs), are toxic environmental pollutants formed from various sources. Elimination of these pollutants from the environment is a difficult task due to their persistent and ubiquitous nature. Removal of dioxins by biological degradation (biodegradation) is considered a feasible method as an alternative to other expensive physicochemical approaches. Biodegradation of dioxins has been extensively studied in several microorganisms, and details concerning biodiversity, biodegradation, biochemistry and molecular biology of this process have accumulated during the last three decades. There are several microbial mechanisms responsible for biodegradation of dioxins, including oxidative degradation by dioxygenase-containing aerobic bacteria, bacterial and fungal cytochrome P-450, fungal lignolytic enzymes, reductive dechlorination by anaerobic bacteria, and direct ether ring cleavage by fungi containing etherase-like enzymes. Many attempts have been made to bioremediate PCDD/Fs using this basic knowledge of microbial dioxin degradation. This review emphasizes the present knowledge and recent advancements in the microbial biotransformation, biodegradation and bioremediation of dioxins.     

Investigation et prise en charge du nodule pulmonaire solitaire dans un environnement multidisciplinaire

For a long time, chest X-ray and chest-computed tomography have played a pivotal role in the characterization of solitary pulmonary nodule before adding an epidemiological dimension with lung cancer screening. However, computed tomography is not specific enough for most small solitary pulmonary nodules. The latest technological developments, such as multislice CT and positron emission tomography, provides important information allowing to simplify the diagnostic work-up, but also raise new questions. The exact role of positron emission tomography in the management of patients with solitary pulmonary nodule remains to be defined in the absence of evidence-based guidelines. This up-to-date review describes the state-of-the-art investigation of solitary pulmonary nodule with hybrid imaging by positron emission tomography/computed tomography and presents a few directions for clinical management in a multidisciplinary environment.     

Mechanics of linear microcracking in trabecular bone

Microcracking in trabecular bone is responsible both for the mechanical degradation and remodeling of the trabecular bone tissue. Recent results on trabecular bone mechanics have demonstrated that bone tissue microarchitecture, tissue elastic heterogeneity and tissue-level mechanical anisotropy all should be considered to obtain detailed information on the mechanical stress state. The present study investigated the influence of tissue microarchitecture, tissue heterogeneity in elasticity and material separation properties and tissue-level anisotropy on the microcrack formation process. Microscale bone models were executed with the extended finite element method. It was demonstrated that anisotropy and heterogeneity of the bone tissue contribute significantly to bone tissue toughness and the resistance of trabecular bone to microcrack formation. The compressive strain to microcrack initiation was computed to increase by a factor of four from an assumed homogeneous isotropic tissue to an assumed anisotropic heterogenous tissue.     

Nondestructive tree-ring measurements for Japanese oak and Japanese beech using micro-focus X-ray computed tomography

The purpose of this study is to establish technology for utilizing images taken by micro-focus X-ray computed tomography (CT) to perform nondestructive tree-ring measurement of wooden cultural properties. This paper covers two experiments conducted using Japanese oak as a typical example of ring-porous wood and Japanese beech as a representative example of diffuse-porous wood. In the first experiment, images of thin strip specimens of Japanese oak and Japanese beech taken by micro-focus X-ray CT are compared against those taken by soft X-ray radiography, the method conventionally used in dendrodensitometry. A discussion then follows in regard to image quality and tree-ring width measurement resulting from the two methods. In the second experiment, tomograms are taken of folk art articles made of Japanese oak and Japanese beech, demonstrating that it is possible to use nondestructive means to visualize the tree-rings of three-dimensional objects. The results show that micro-focus X-ray CT offers much promise of widespread utilization in the tree-ring dating of wooden cultural properties.     

Yield prediction and stoichiometry of multi-step biodegradation reactions involving oxygenation

Microorganisms can initiate the degradation of organic compounds by oxygenation reactions that require the investment of energy and electrons. This diversion of energy and electrons away from synthesis reactions leads to decreased overall cell yields. A thermodynamic method was developed that improves the accuracy of cell yield prediction for compounds degraded through pathways involving oxygenation reactions. This method predicts yields and stoichiometry for each step in the biodegradation pathway, thus enabling modeling a multi-step biodegradation process in which oxygenations occur and intermediates may persist. EDTA and benzene biodegradation are presented as examples. The method compares favorably with other yield prediction methods while providing additional information of yields for intermediates produced in the degradation pathway.     

Visualizing the internal structure of polyethylene glycol-impregnated wood by digital breast tomosynthesis

This study proposes digital breast tomosynthesis (DBT) as a low-tube-voltage method for imaging wood artifacts treated with polyethylene glycol (PEG). In case of general clinical X-ray Computed Tomography (X-CT), PEG-impregnated wood images typically suffer from low contrast between the PEG and the tree-ring. Because X-CT uses high-tube-voltage X-rays that have high energy, they are transmitted regardless of the X-ray absorption difference of the substance, and therefore, it is not suitable for imaging PEG-impregnated wood. Mammography uses low-tube-voltage X-rays, and therefore, it is suitable for delineating substances with small X-ray absorption differences. However, although mammography can produce high-contrast images of wood, it cannot distinguish three-dimensional (3D) structures such as tree rings, because those are projection images. DBT is a type of mammography used to enhance contrast using low-tube voltage, and it enables imaging 3D structures by exposure X-rays to objects several times changing the exposure angle, and it can obtain quasi-computed tomography. Therefore, we believe that by applying DBT to dendroarchaeology, it would be possible to obtain high-contrast, high-resolution images in the visualization of the internal structure of wood.In this study, we used clinical X-CT, mammography, and DBT to obtain images of wood after PEG impregnation, and we evaluated the internal structure of the wood and the visibility of annual rings. We obtained DBT images as a tomogram with a thickness of 1 mm, which eliminated the distortion of tree rings in the sagittal direction and duplication of the PEG and the tree-ring. Further, tree-rings were easily visualized without a noticeable blur, and the DBT contrast was improved compared to clinical X-CT contrast because DBT was performed at low voltage. Important wooden artifacts excavated from ruins were preserved by PEG. Therefore, this method can be expected to become a very useful tool for dendroarchaeology when used as a complementary tool for microfocus X-CT.     

Use of NIR and pyrolysis-MBMS coupled with multivariate analysis for detecting the chemical changes associated with brown-rot biodegradation of spruce wood

Near infrared (NIR) spectroscopy and pyrolysis-molecular beam mass spectrometry (py-MBMS) analysis can be used in conjunction with multivariate regression and principal components analysis to differentiate brown-rot-degraded wood from non-degraded spruce and to follow the temporal changes in wood undergoing brown-rot degradation. Regression of NIR test results vs. percent weight loss for Postia placenta- and Gloeophyllum trabeum-infected spruce wood blocks yielded a correlation coefficient of 0.96. Regression of MBMS test results for the same samples yielded a correlation coefficient of 0.96. Principle components analysis was used to differentiate non-infected wood and P. placenta- and G. trabeum-infected wood. These techniques may be used to detect different types of biodegradation and to develop a better understanding of the chemical changes that the wood undergoes when it is subjected to brown-rot biodegradation.     

Oxalic acid, Fe-reduction activity and oxidative enzymes detected in culture extracts recovered from Pinus taeda wood chips biotreated by Ceriporiopsis subvermispora

Pinus taeda wood chips were treated with the biopulping fungus, Ceriporiopsis subvermispora, under solid-state fermentation for periods varying from 7 to 90 days. Low molecular mass compounds and oxidative enzymes were extracted from biotreated wood samples. Manganese-dependent peroxidase was the main oxidative enzyme on all biodegradation periods. Aqueous extracts from biotreated wood presented decreasing pH values, oxalic acid being the major organic acid secreted by the fungus. Analysis of these extracts by gas chromatography coupled with mass spectrometry (GC/MS) revealed small amounts of fatty acids, several short-chain organic acids (C3–C6) and numerous sugar derivatives. 3-methoxy-4-hydroxy benzaldehyde, 3-methoxy-4-hydroxy benzoic acid, 3,4-dihydroxy benzoic acid and tricarboxy-benzene were also found in the wood extracts. A remarkable characteristic of the wood extracts was a strong Fe³⁺-reducing ability. High Fe³⁺-reducing activity and high catechol concentrations were detected in the wood extracts from the undecayed control. This reducing activity and catechol concentrations decreased during the first 7 days of biodegradation. However, from the seventh day of culturing, catechol derivatives coming from lignin degradation start to accumulate in the cultures and Fe³⁺-reduction activity increased again. The Fe³⁺-reduction activity observed in the wood extracts indicates that Fe²⁺ would be available in solution during the wood decay process. Considering that Fe²⁺ and H₂O₂ (produced by this fungus based on MnP-degradation of oxalate) were present in the wood extracts, at least some extent for degradation reactions based on Fenton-chemistry, similarly to the observed in brown-rot fungi, is supposed to occur during wood decay by C. subvermispora.     

Microbial breakdown of halogenated aromatic pesticides and related compounds.

Considerable progress has been made in the last few years in understanding the mechanisms of microbial degradation of halogenated aromatic compounds. Much is already known about the degradation mechanisms under aerobic conditions, and metabolism under anaerobiosis has lately received increasing attention. The removal of the halogen substituent is a key step in degradation of halogenated aromatics. This may occur as an initial step via reductive, hydrolytic or oxygenolytic mechanisms, or after cleavage of the aromatic ring at a later stage of metabolism. In addition to degradation, several biotransformation reactions, such as methylation and polymerization, may take place and produce more toxic or recalcitrant metabolites. Studies with pure bacterial and fungal cultures have given detailed information on the biodegradation pathways of several halogenated aromatic compounds. Several of the key enzymes have been purified or studied in cell extracts, and there is an increasing understanding of the organization and regulation of the genes involved in haloaromatic degradation. This review will focus on the biodegradation and biotransformation pathways that have been established for halogenated phenols, phenoxyalkanoic acids, benzoic acids, benzenes, anilines and structurally related halogenated aromatic pesticides. There is a growing interest in developing microbiological methods for clean-up of soil and water contaminated with halogenated aromatic compounds.     

Microbial breakdown of halogenated aromatic pesticides and related compounds

Abstract Considerable progress has been made in the last few years in understanding the mechanisms of microbial degradation of halogenated aromatic compounds. Much is already known about the degradation mechanisms under aerobic conditions, and metabolism under anaerobiosis has lately received increasing attention. The removal of the halogen substituent is a key step in degradation of halogenated aromatics. This may occur as an initial step via reductive, hydrolytic or oxygenolytic mechanisms, or after cleavage of the aromatic ring at a later stage of metabolism. In addition to degradation, several biotransformation reactions, such as methylation and polymerization, may take place and produce more toxic or recalcitrant metabolites. Studies with pure bacterial and fungal cultures have given detailed information on the biodegradation pathways of several halogenated aromatic compounds. Several of the key enzymes have been purified or studied in cell extracts, and there is an increasing understanding of the organization and regulation of the genes involved in haloaromatic degradation. This review will focus on the biodegradation and biotransformation pathways that have been established for halogenated phenols, phenoxyalkanoic acids, benzoic acids, benzenes, anilines and structurally related halogenated aromatic pesticides. There is a growing interest in developing microbiological methods for clean-up of soil and water contaminated with halogenated aromatic compounds.     

Pore-scale investigation on the response of heterotrophic respiration to moisture conditions in heterogeneous soils

The relationship between microbial respiration rate and soil moisture content is an important property for understanding and predicting soil organic carbon degradation, CO₂ production and emission, and their subsequent effects on climate change. This paper reports a pore-scale modeling study to investigate the response of heterotrophic respiration to moisture conditions in soils and to evaluate various factors that affect this response. X-ray computed tomography was used to derive soil pore structures, which were then used for pore-scale model investigation. The pore-scale results were then averaged to calculate the effective respiration rates as a function of water content in soils. The calculated effective respiration rate first increases and then decreases with increasing soil water content, showing a maximum respiration rate at water saturation degree of 0.75, which is consistent with field and laboratory observations. The relationship between the respiration rate and moisture content is affected by various factors, including pore-scale organic carbon bioavailability, the rate of oxygen delivery, soil pore structure and physical heterogeneity, soil clay content, and microbial drought resistivity. Overall, this study provides mechanistic insights into the soil respiration response to the change in moisture conditions, and reveals a complex relationship between heterotrophic microbial respiration rate and moisture content in soils that is affected by various hydrological, geophysical, and biochemical factors.     

微生物降解石油烃的功能基因研究进展

微生物对石油烃的降解在自然衰减去除土壤和地下水石油烃污染的过程中发挥了重要作用。微生物通过其产生的一系列酶来利用和降解这类有机污染物,其中,编码关键降解酶的基因称为功能基因。功能基因可作为生物标志物用于分析环境中石油烃降解基因的多样性。因此,研究石油降解功能基因是分析土著微生物群落多样性、评价自然衰减潜力与构建基因工程菌的重要基础。本文主要介绍了烷烃和芳香烃在有氧和无氧条件下的微生物降解途径,重点总结了烷烃和芳香烃降解的主要功能基因及其作用,包括参与羟化作用的单加氧酶和双加氧酶基因、延胡索酸加成反应的琥珀酸合酶基因以及中心中间产物的降解酶基因等。     

Absence of microbial mineralization of lignin in anaerobic enrichment cultures

The existence of anaerobic biodegradation of lignin was examined in mixed microflora. Egyptian soil samples, in which rapid mineralization of organic matter takes place in the presence of an important anaerobic microflora, were used to obtain the anaerobic enrichment cultures for this study. Specifically, 14CO2 or [14C]lignin wood was used to investigate the release of labeled gaseous or soluble degradation products of lignin in microbial cultures. No conversion of 14C-labeled lignin to 14CO2 or 14CH4 was observed after 6 months of incubation at 30 degrees C in anaerobic conditions with or without NO3-. A small increase in soluble radioactivity was observed in certain cultures, but it could not be related to the release of catabolic products during the anaerobic biodegradation of lignin.     

RADIONUCLIDE COMPUTED TOMOGRAPHY: APPLICATIONS IN CARDIOVASCULAR DISEASE

Tomography is an imaging modality in which information in one plane is displayed in focus while information from overlying and underlying planes is either blurred or eliminated. As a result, there is an improvement in the contrast of structures in the plane of interest. Computerized axial tomography (CAT) is an imaging modality in which a digital computer mathematically reconstructs the image of a plane or section from data collected perpendicular to the axis of that plane. The axis of the plane and the patient's long axis usually coincide so that the reconstructed images reveal transverse sections. In recent years, two types of computed tomography in medical imaging have generated a great deal of interest. These are X-ray transmission and radio-nuclide emission computed tomography.