Ultrastructural changes at gap junctions between lesioned crayfish axons

Summary In crayfish, the severed distal segment of single lateral giant axon (SLGA) often survives for at least 10 months after lesioning if this segment retains a septal region of apposition with an adjacent, intact SLGA. In control (unsevered) SLGAs, this septal region usually contains gap junctions and 50–60 nm vesicles near the axolemma of both SLGAs. From 1–14 days after lesioning, the distal segment of a severed SLGA undergoes obvious ultrastructural changes in mitochondria and neurotubular organization compared to control SLGAs or to adjacent, intact SLGAs in the same animal. Gap junctions are very difficult to locate in severed SLGAs within 24 h after lesioning. From two weeks to ten months after lesioning, the surviving stumps of severed SLGAs often appear remarkably normal except that structures normally associated with the presence of gap junctions remain very difficult to find.These and other data suggest that SLGA distal segments receive trophic support from adjacent, intact SLGAs. The mechanism of this support probably could not be via diffusion across gap junctions between intact and severed SLGAs since gap junctions largely disappear after lesioning. However, trophic maintenance could occur via the exocytotic — pinocytotic action of 50–60 nm vesicles which are always present on both sides of the septum between an intact SLGA and a severed SLGA distal segment.This work was supported by NIH research grant NS-14412 and and RCDA 00070 to G.D.B.     

A high density physical map of chromosome 1BL supports evolutionary studies,map-based cloning and sequencing in wheat

Background

As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning.

Results

Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome.

Conclusions

Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.     

Application of higher order statistics for atrial arrhythmia classification

Atrial fibrillation (AF) and atrial flutter (AFL) are the two common atrial arrhythmia encountered in the clinical practice. In order to diagnose these abnormalities the electrocardiogram (ECG) is widely used. The conventional linear time and frequency domain methods cannot decipher the hidden complexity present in these signals. The ECG is inherently a non-linear, non-stationary and non-Gaussian signal. The non-linear models can provide improved results and capture minute variations present in the time series. Higher order spectra (HOS) is a non-linear dynamical method which is highly rugged to noise. In the present study, the performances of two methods are compared: (i) 3rd order HOS cumulants and (ii) HOS bispectrum. The 3rd order cumulant and bispectrum coefficients are subjected to dimensionality reduction using independent component analysis (ICA) and classified using classification and regression tree (CART), random forest (RF), artificial neural network (ANN) and k-nearest neighbor (KNN) classifiers to select the best classifier. The ICA components of cumulant coefficients have provided the average accuracy, sensitivity, specificity and positive predictive value of 99.50%, 100%, 99.22% and 99.72% respectively using KNN classifier. Similarly, the ICA components of HOS bispectrum coefficients have yielded the average accuracy, sensitivity, specificity and PPV of 97.65%, 98.16%, 98.75% and 99.53% respectively using KNN. So, the ICA performed on the 3rd order HOS cumulants coupled with KNN classifier performed better than the HOS bispectrum method. The proposed methodology is robust and can be used in mass screening of cardiac patients.     

ECG beat classification using PCA,LDA, ICA and Discrete Wavelet Transform

Electrocardiogram (ECG) is the P-QRS-T wave, representing the cardiac function. The information concealed in the ECG signal is useful in detecting the disease afflicting the heart. It is very difficult to identify the subtle changes in the ECG in time and frequency domains. The Discrete Wavelet Transform (DWT) can provide good time and frequency resolutions and is able to decipher the hidden complexities in the ECG. In this study, five types of beat classes of arrhythmia as recommended by Association for Advancement of Medical Instrumentation (AAMI) were analyzed namely: non-ectopic beats, supra-ventricular ectopic beats, ventricular ectopic beats, fusion betas and unclassifiable and paced beats. Three dimensionality reduction algorithms; Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA) and Independent Component Analysis (ICA) were independently applied on DWT sub bands for dimensionality reduction. These dimensionality reduced features were fed to the Support Vector Machine (SVM), neural network (NN) and probabilistic neural network (PNN) classifiers for automated diagnosis. ICA features in combination with PNN with spread value (σ) of 0.03 performed better than the PCA and LDA. It has yielded an average sensitivity, specificity, positive predictive value (PPV) and accuracy of 99.97%, 99.83%, 99.21% and 99.28% respectively using ten-fold cross validation scheme.     

Unlocking the barley genome by chromosomal and comparative genomics

We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.     

Delaminating myelin membranes help seal the cut ends of severed earthworm giant axons

Transected axons are often assumed to seal by collapse and fusion of the axolemmal leaflets at their cut ends. Using photomicroscopy and electronmicroscopy of fixed tissues and differential interference contrast and confocal fluorescence imaging of living tissues, we examined the proximal and distal cut ends of the pseudomyelinated medial giant axon of the earthworm, Lumbricus terrestris, at 5–60 min post-transection in physiological salines and Ca²⁺-free salines. In physiological salines, the axolemmal leaflets at the cut ends do not completely collapse, much less fuse, for at least 60 min post-transection. In fact, the axolemma is disrupted for 20–100 μm from the cut end at 5–60 min post-transection. However, a barrier to dye diffusion is observed when hydrophilic or styryl dyes are placed in the bath at 15–30 min post-transection. At 30–60 min post-transection, this barrier to dye diffusion near the cut end is formed amid an accumulation of some single-layered and many multilayered vesicles and other membranous material, much of which resembles delaminated pseudomyelin of the glial sheath. In Ca²⁺-free salines, this single and multilayered membranous material does not accumulate, and a dye diffusion barrier is not observed. These and other data are consistent with the hypothesis that plasmalemmal damage in eukaryotic cells is repaired by Ca²⁺-induced vesicles arising from invaginations or evaginations of membranes of various origin which form junctional contacts or fuse with each other and/or the plasmalemma. © 1997 John Wiley & Sons, Inc. J Neurobiol 33: 945–960, 1997     

Diurnal pattern of acetaldehyde emission by flooded poplar trees

The emission of the tropospheric trace gas acetaldehyde was determined in leaves of 4-month-old poplar trees ( Populus tremula × P. alba ) grown under controlled environmental conditions in a greenhouse. Using a dynamic cuvette system together with a high sensitivity laser-based photoacoustic detection unit, rates of acetaldehyde emission were measured with the high time resolution of about 15 min. Submergence of the roots resulted in the emission of acetaldehyde by the leaves. The emission increased linearly before reaching more or less steady-state values (ca 350 nmol m⁻² min⁻¹; ca 470 ng g⁻¹ dry weight min⁻¹) after approximately 6 h. Prolonged flooding of poplar trees resulted in a clear diurnal rhythm of acetaldehyde emission. The emission rates decreased when the light was switched off in the evening and peaked in the morning after the light was turned on again. This pattern significantly correlated with diurnal rhythms of stomatal conductance, photosynthesis, transpiration and with the concentrations of ethanol, the assumed precursor of acetaldehyde, in the xylem sap of flooded poplar trees. It may be concluded that under conditions of diminished stomatal conductance, acetaldehyde emission declines because its diffusive flux is reduced. Alternatively, reduced transpiration may decrease ethanol transport from the roots to the shoots and appreciable amounts of the acetaldehyde precursor ethanol are lacking in the leaves. The present results support the view that acetaldehyde emitted by the leaves of plants is derived from ethanol produced by alcoholic fermentation in submerged roots and transported to the leaves with the transpiration stream.     

Ultrastructural studies of severed medial giant and other CNS axons in crayfish

Summary The distal stumps of severed medial giant axons (MGAs) and of non-giant axons (NGAs) in the CNS of the crayfish Procambarus clarkii show long-term (5–9 months) survival associated with disorientation of mitochondria and thickening of the glial sheath. However, the morphological responses of the two axonal types differ in that neither the proximal nor the distal stump of severed MGAs ever fills with mitochondria as is observed in some severed NGAs. Furthermore, the adaxonal glial layer never completely encircles portions of MGA axoplasm as occurs in many severed NGAs; in fact, ultrastructural changes in the adaxonal layer around severed MGAs are often difficult to detect. No multiple axonal profiles are ever seen within the glial sheath of the proximal or distal stumps of severed MGAs whereas these structures are easily located within severed NGAs.This work was supported by NIH research grant #NS-14412 and an RCDA#00070 to GDB