Segmentation and measurement of fat volumes in murine obesity models using X-ray computed tomography

Obesity is associated with increased morbidity and mortality as well as reduced metrics in quality of life. Both environmental and genetic factors are associated with obesity, though the precise underlying mechanisms that contribute to the disease are currently being delineated. Several small animal models of obesity have been developed and are employed in a variety of studies. A critical component to these experiments involves the collection of regional and/or total animal fat content data under varied conditions. Traditional experimental methods available for measuring fat content in small animal models of obesity include invasive (e.g. ex vivo measurement of fat deposits) and non-invasive (e.g. Dual Energy X-ray Absorptiometry (DEXA), or Magnetic Resonance (MR)) protocols, each of which presents relative trade-offs. Current invasive methods for measuring fat content may provide details for organ and region specific fat distribution, but sacrificing the subjects will preclude longitudinal assessments. Conversely, current non-invasive strategies provide limited details for organ and region specific fat distribution, but enable valuable longitudinal assessment. With the advent of dedicated small animal X-ray computed tomography (CT) systems and customized analytical procedures, both organ and region specific analysis of fat distribution and longitudinal profiling may be possible. Recent reports have validated the use of CT for in vivo longitudinal imaging of adiposity in living mice. Here we provide a modified method that allows for fat/total volume measurement, analysis and visualization utilizing the Carestream Molecular Imaging Albira CT system in conjunction with PMOD and Volview software packages.     

Non-destructive quantification of cereal roots in soil using high-resolution X-ray tomography

One key constraint to further understanding plant root development is the inability to observe root growth in situ due to the opaque nature of soil. Of the present non-destructive techniques, computed tomography (CT) is best able to capture the complexities of the edaphic environment. This study compared the accuracy and impact of X-ray CT measurement of in situ root systems with standard technology (soil core washing and WinRhizo analysis) in the context of treatments that differed in the vertical placement of phosphorus fertilizers within the soil profile. Although root lengths quantified using WinRhizo were 8% higher than that observed in the same plants using CT, measurements of root length by the two methodologies were highly correlated. Comparison of scanned and unscanned plants revealed no effect of repeated scanning on plant growth and CT was not able to detect any changes in roots between phosphorus treatments that was observed using WinRhizo. Overall, the CT technique was found to be fast, safe, and able to detect roots at high spatial resolutions. The potential drawbacks of CT relate to the software to digitally segment roots from soil and air, which will improve significantly as automated segmentation algorithms are developed. The combination of very fast scans and automated segmentation will allow CT methodology to realize its potential as a high-throughput technique for the quantification of roots in soils.     

Spatio-temporal leaf growth patterns of Arabidopsis thaliana and evidence for sugar control of the diel leaf growth cycle

Leaf growth dynamics are driven by diel rhythms. The analysis of spatio-temporal leaf growth patterns in Arabidopsis thaliana wild type and mutants of interest is a promising approach to elucidate molecular mechanisms controlling growth. The diel availability of carbohydrates is thought to affect diel growth. A digital image sequence processing (DISP)-based noninvasive technique for visualizing and quantifying highly resolved spatio-temporal leaf growth was adapted for the model plant A. thaliana. Diel growth patterns were analysed for the wild type and for a mutant with altered diel carbohydrate metabolism. A. thaliana leaves showed highest relative growth rates (RGRs) at dawn and lowest RGRs at the beginning of the night. Along the lamina, a clear basipetal gradient of growth rate distribution was found, similar to that in many other dicotyledonous species. The starch-free 1 (stf1) mutant revealed changed temporal growth patterns with reduced nocturnal, and increased afternoon, growth activity. The established DISP technique is presented as a valuable tool to detect altered temporal growth patterns in A. thaliana mutants. Endogenous changes in the diel carbohydrate availability of the starch-free mutant clearly affected its diel growth rhythms.     

Application of X-ray computed tomography to quantify fresh root decomposition in situ

Background and aims

Much of our understanding of plant root decomposition and related carbon cycling come from mass loss rates calculated from roots buried in litter bags. However, this may not reflect what actually happens in the soil, where the interactions between root and soil structure presents a more complex physico-chemical environment compared to organic matter isolated in a porous bag buried in disturbed soil. This work investigates the potential of using X-ray micro-computed tomography (CT) to measure root decomposition in situ.

Methods

Roots of Vicia faba L. were excised from freshly germinated seeds, buried in re-packed soil cores and cores incubated for 60 days. Changes in root volume and surface area were measured using repeated scans. Additional samples were destructively harvested and roots weighed to correlate root mass with root volume. The method was further applied to an experiment to investigate the effects of soil bulk density and soil moisture on root decomposition.

Results

Root volume (X-ray CT) and root mass (destructive harvest) decreased by 90 % over the 60 day incubation period, by which stage, root volume and mass had stabilised. There was a strong correlation (R ²?=?0.97) between root volume and root mass.

Conclusions

X-ray CT visualization and analysis provides a unique toolbox to understand root decomposition in situ.     

Magnetic resonance imaging, computed tomography, and conventional X-ray in 3 cases of symmelia

BACKGROUND: Symmelia is a rare birth defect, often combined with severe malformations of the urogenital system and the lower gastrointestinal tract. Additionally, a deformed pelvis and various degrees of separation of the lower limbs are present. CASES: We report the examination findings of 3 autopsy specimens of symmelia using magnetic resonance imaging (MRI) and computed tomography (CT) with 3-dimensional (3D) reconstructions, and conventional X-ray. CONCLUSIONS: MRI and CT with the addition of 3D visualization can be used additionally with autopsy and conventional X-ray images in the investigation of such complex anatomical abnormalities.     

Localized compliance of small airways in excised rat lungs using microfocal X-ray computed tomography.

Airway compliance is a key factor in understanding lung mechanics and is used as a clinical diagnostic index. Understanding such mechanics in small airways physiologically and clinically is critical. We have determined the "morphometric change" and "localized compliance" of small airways under "near"-physiological conditions; namely, the airways were embedded in parenchyma without dehydration and fixation. Previously, we developed a two-step method to visualize small airways in detail by staining the lung tissue with a radiopaque solution and then visualizing the tissue with a cone-beam microfocal X-ray computed tomography system (Sera et al. J Biomech 36: 1587-1594, 2003). In this study, we used this technique to analyze changes in diameter and length of the same small airways ( approximately 150 microm ID) and then evaluated the localized compliance as a function of airway generation (Z). For smaller (<300-microm-diameter) airways, diameter was 36% larger at end-tidal inspiration and 89% larger at total lung capacity; length was 18% larger at end-tidal inspiration and 43% larger at total lung capacity than at functional residual capacity. Diameter, especially at smaller airways, did not behave linearly with V(1/3) (where V is volume). With increasing lung pressure, diameter changed dramatically at a particular pressure and length changed approximately linearly during inflation and deflation. Percentage of airway volume for smaller airways did not behave linearly with that of lung volume. Smaller airways were generally more compliant than larger airways with increasing Z and exhibited hysteresis in their diameter behavior. Airways at higher Z deformed at a lower pressure than those at lower Z. These results indicated that smaller airways did not behave homogeneously.     

Quantifying the effect of soil moisture content on segmenting root system architecture in X-ray computed tomography images

Aims

A commonly accepted challenge when visualising plant roots in X-ray micro Computed Tomography (μCT) images is the similar X-ray attenuation of plant roots and soil phases. Soil moisture content remains a recognised, yet currently uncharacterised source of segmentation error. This work sought to quantify the effect of soil moisture content on the ability to segment roots from soil in μCT images.

Methods

Rice (Oryza sativa) plants grown in contrasting soils (loamy sand and clay loam) were μCT scanned daily for nine days whilst drying from saturation. Root volumes were segmented from μCT images and compared with volumes derived by root washing.

Results

At saturation the overlapping attenuation values of root material, water-filled soil pores and soil organic matter significantly hindered segmentation. However, in dry soil (ca. six days of drying post-saturation) the air-filled pores increased image noise adjacent to roots and impeded accurate visualisation of root material. The root volume was most accurately segmented at field capacity.

Conclusions

Root volumes can be accurately segmented from μCT images of undisturbed soil without compromising the growth requirements of the plant providing soil moisture content is kept at field capacity. We propose all future studies in this area should consider the error associated with scanning at different soil moisture contents.     

On the diel rhythms in metabolism and activity of post-hatching lesser spotted dogfish, Scyliorhinus canicula

The diel rhythms in metabolic rate ( M_R ) and activity level ( A_L ) were measured for single post-hatching dogfish (weight range, 2.76–10.61 g) at 15° C by the indirect calorimetric method of rate of oxygen consumption ( V O₂) and by video-observation respectively, over a period of 72 b. The mean VO ₂ increased from 62.0 (s.e. 2.9) mg O₂ kg⁻¹ h⁻¹ in the daylight hours to 85.5 (s.e. 3.1) mg O₂ kg⁻¹ h⁻¹ during the dark (light regíme, 12 h L: 12 h D). The simultaneous measurement of A _L also showed mean night elevation from 0.6 (s.e. 0.2) min h⁻¹ in the light phase to 14.5 (s.e. 1.6) min h⁻¹ during the darkness. Bimodal nocturnal activity (BNA) was exhibited by the post-hatching dogfish within the 12 h dark period, with V O₂ increasing from 71.4 (s.e. 2.8) mg O₂ kg⁻¹ h⁻¹ before 01.00 hours to 99.5 (s.e. 4.2) mg O₂ kg⁻¹ h⁻¹ after 01.00 hours. Similarly, A _L also increased from 8.9 (s.e. I.7)min h⁻¹ before 01.00 hours to 21.1 (s.e. 2.8) min h⁻¹ after 01.00 hours. The importance of the results presented to the natural behavioural ecology of the hatching dogfish are discussed.     

X-ray quantitative computed tomography: the relations to physical properties of proximal tibial trabecular bone specimens

Cylindrical bone specimens from the proximal epiphysis of ten normal human proximal tibiae were randomly assigned to a destructive axial compression test-series (N = 94) or to a protocol of standardized mechanical conditioning followed by non-destructive repeated testing to 0.6% strain and a final destructive test (N = 121). Specimen X-ray quantitative computed tomography (QCT) obtained at different scanning energies (100, 120 and 140 kVp) yielded closely related results (r = 1.00). Accordingly, predictions of physically measured densities or mechanical properties were not improved by using more than one scanning energy. QCT and physically measured densities were intimately related (QCT at 140 kVp to apparent density using linear regression: r = 0.94, and to apparent ash density: r = 0.95) and did not differ significantly in their ability to predict the mechanical properties, thus favouring the more easily implemented QCT for routine work. Evaluation of the relation of apparent density to Young's modulus and ultimate strength suggested that a power law regression model is preferable to a linear model, although linear model prediction of mechanical properties does not have significantly worse accuracy within the narrow density range investigated. The effect of conditioning on the behaviour of bone specimens subjected to destructive compression tests was to increase the stiffness and strength by approximately 50 and 20% respectively.     

A laboratory study of diel and annual activity rhythms and vertical distribution in the perch,Perca fluviatilis,at the Arctic circle

Synopsis Diel and annual rhythms of activity and vertical distribution of a group of perch in a large laboratory tank were measured for 15 months under a natural light regime at the Arctic circle (Messaure, Swedish-Lappland, 66°42N, 20°25E). Perch were found to be mainly day-active at all seasons. The activity level was correlated with temperature and duration of activity with day length. During winter, the perch group stayed at the bottom of the tank. During the summer, the group spent about as much time in the upper part of the tank as in the lower. The behavior of perch in the laboratory is assumed roughly to mirror their behavior in the field.     

The naso-frontal joint in snakes as revealed by high-resolution X-ray computed tomography of intact and complete skulls

The naso-frontal joint of snakes is described on the basis of high-resolution X-ray computed tomography scans of single individuals of spirit-preserved snake specimens. The suspension of the snout unit from the braincase at the naso-frontal joint shows some broad evolutionary trends among snakes with potential phylogenetic implications, such as sutured or fused medial frontal flanges formed by the medial frontal pillars and the frontal subolfactory processes (in alethinophidians), the restriction of the usually extended dorsoventral contact of the medial nasal flange with the medial frontal flanges to a dorsal or ventral contact (in macrostomatans), and the transfer of the main element of snout suspension from the nasal to the septomaxilla (in colubroids). Some phylogenetic implications of the morphological characters identified in this study are outlined and discussed.     

Chemical inhibition of the glycolate pathway in soybean leaf cells

Isolated soybean (Glycine max [L.] Merr.) leaf cells were treated with three inhibitors of the glycolate pathway in order to evaluate the potential of such inhibitors for increasing photosynthetic efficiency. Preincubation of cells under acid conditions in α-hydroxypyridinemethanesulfonic acid increased ¹⁴CO₂ incorporation into glycolate, but severely inhibited photosynthesis. Isonicotinic acid hydrazide (INH) increased the incorporation of ¹⁴CO₂ into glycine and reduced label in serine, glycerate, and starch. Butyl 2-hydroxy-3-butynoate (BHB) completely and irreversibly inhibited glycolate oxidase and increased the accumulation of ¹⁴C into glycolate. Concomitant with glycolate accumulation was the reduction of label in serine, glycerate, and starch, and the elimination of label in glycine. The inhibitors INH and BHB did not eliminate serine synthesis, suggesting that some serine is synthesized by an alternate pathway. The per cent incorporation of ¹⁴CO₂ into glycolate by BHB-treated cells or glycine by INH-treated cells was determined by the O₂/CO₂ ratio present during assay. Photosynthesis rate was not affected by INH or BHB in the absence of O₂, but these compounds increased the O₂ inhibition of photosynthesis. This finding suggests that the function of the photorespiratory pathway is to recycle glycolate carbon back into the Calvin cycle, so if glycolate metabolism is inhibited, Calvin cycle intermediates become depleted and photosynthesis is decreased. Thus, chemicals which inhibit glycolate metabolism do not reduce photorespiration and increase photosynthetic efficiency, but rather exacerbate the problem of photorespiration.     

The effect of zeaxanthin on the thickness of dimyristoylphosphatidylcholine bilayer: X-ray diffraction study

Multilayers of dimyristoylphosphatidylcholine (DMPC) modified with a carotenoid pigment zeaxanthin were analyzed by means of small-angle X-ray diffractometry. The results are discussed in terms of the superlattice theory developed recently for metallic multilayers. Inclusion of zeaxanthin to a DMPC bilayer increases thickness of the hydrophobic core by about 3 Å in the whole lipid-pigment miscibility range. The thickness increases very sharply as pigment concentration approaches the threshold of miscibility. Zeaxanthin aggregation within a layer causes further changes in the thickness of the membrane: a local decrease followed by a gradual rise.     

Spiral computed tomography in the diagnosis of limb osteomyelitis

The results of radiation studies in 121 patients of different age (4 to 75 years) examined for limb osteomyelitis are analyzed. All the patients underwent routine X-ray study and computed tomography (CT), 26 patients had X-ray fistulography; 8, linear tomography; 10, CT fistulography; 6, scintigraphy, and 15, ultrasound study. Acute hematogenous osteomyelitis (AHO), chronic hematogenous osteomyelitis (CHO), and atypical (here Garre's sclerosing osteomyelitis and Brodie's abscess) osteomyelitis were ascertained in 10.6, 26.4, and 10.1% of cases, respectively. Posttraumatic osteomyelitis was diagnosed in almost 50% of the patients. CT defined the phase of chronic limb osteomyelitis. Spiral CT has proven to be the most effective technique for diagnosing limb osteomyelitis as compared with routine X-ray study: the accuracy of X-ray study was 81.8%, its sensitivity, 84.9%, and specificity, 60.0% and those of computed tomography were 96.7, 99.1, and 80.0%, respectively.