Diapause Induction and Termination in Eggs of the Fruit Tree Red Spider Mite Panonychus Ulmi in Northern Greece

In apple orchards in northern Greece, females of Panonychus ulmi Koch were found to lay diapause eggs from late August to the beginning of October. The course of diapause termination in the field was determined by transferring diapause eggs during winter and early spring from apple orchards with the varieties Starkinson and Firiki to short days (LD 8:16) (1992–1996), and long days (LD 16:8) (1994–1995), both at 20 °C. Percentages of diapause termination were very low to zero from October to the beginning of January, then progressively increased throughout January and February. Diapause termination in 50% of the eggs occurred in the first half of February in lowland mite populations irrespective of the year and location from which the eggs originated, and about one month earlier in a population originating from an altitude of 300 m. For each sampling date throughout the winter, the mean number of days required for 50% egg hatch at 20 °C (T_50%) was similar under either a long (LD 16:8) or a short (LD 8:16) photoperiod. Diapause eggs collected in October 1995 from two orchards and maintained at 0, 5, 10 and 15 °C for various periods were subsequently transferred to 20 °C and LD 8:16, where TP_50% was determined. It was shown that temperature, duration of maintenance at the different temperatures and the orchard from which the eggs originated had a significant effect on T_50% and therefore on diapause development. Additionally, in our strains diapause intensity was much weaker than in strains from more northern latitudes and was terminated even without any cold exposure. The variation in diapause intensity in different strains of P. ulmi may have an adaptive significance for this widespread species.     

Computer-based malignancy grading of astrocytomas employing a support vector machine classifier, the WHO grading system and the regular hematoxylin-eosin diagnostic staining procedure

OBJECTIVE: To investigate and develop an automated technique for astrocytoma malignancy grading compatible with the clinical routine. STUDY DESIGN: One hundred forty biopsies of astrocytomas were collected from 2 hospitals. The degree of tumor malignancy was defined as low or high according to the World Health Organization grading system. From each biopsy, images were digitized and segmented to isolate nuclei from background tissue. Morphologic and textural nuclear features were quantified to encode tumor malignancy. Each case was represented by a 40-dimensional feature vector. An exhaustive search procedure in feature space was utilized to determine the best feature combination that resulted in the smallest classification error. Low and high grade tumors were discriminated using support vector machines (SVMs). To evaluate the system performance, all available data were split randomly into training and test sets. RESULTS: The best vector combination consisted of 3 textural and 2 morphologic features. Low and high grade cases were discriminated with an accuracy of 90.7% and 88.9%, respectively, using an SVM classifier with polynomial kernel of degree 2. CONCLUSION: The proposed methodology was based on standards that are common in daily clinical practice and might be used in parallel with conventional grading as a second-opinion tool to reduce subjectivity in the classification of astrocytomas.     

Structure-function analysis of immunity proteins of pediocin-like bacteriocins: C-terminal parts of immunity proteins are involved in specific recognition of cognate bacteriocins

The immunity proteins of pediocin-like bacteriocins show a high degree of specificity with respect to the pediocin-like bacteriocin they recognize and confer immunity to. The aim of this study was to identify regions of the immunity proteins that are involved in this specific recognition. Six different hybrid immunity proteins were constructed from three different pediocin-like bacteriocin immunity proteins that have similar sequences but confer resistance to different bacteriocins. These hybrid immunity proteins were then tested for their ability to confer immunity to various pediocin-like bacteriocins. The specificities of the hybrid immunity proteins proved to be similar to those of the immunity proteins from which the C-terminal halves were derived, thus revealing that the C-terminal half of immunity proteins for pediocin-like bacteriocins contains a domain that is involved in specific recognition of the bacteriocins they confer immunity to. Moreover, the results also revealed that the effectiveness of an immunity protein is strain dependent and that its functionality thus depends in part on interplay with strain-dependent factors. To further investigate the structure-function relationship of these immunity proteins, the enterocin A and leucocin A immunity proteins (EntA-im and LeuA-im) were purified to homogeneity and structurally analyzed under various conditions by Circular dichroism (CD) spectroscopy. The results revealed that both immunity proteins are alpha-helical and well structured in an aqueous environment, the denaturing temperature being 78.5 degrees C for EntA-im and 58.0 degrees C for LeuA-im. The CD spectra also revealed that there was no further increase in the structuring or alpha-helical content when the immunity proteins were exposed to dodecylphosphocholine micelles or dioleoyl-L-alpha-phosphatidyl-DL-glycerol (DOPG) liposomes, indicating that the immunity proteins, in contrast to the bacteriocins, do not interact extensively with membranes. They may nevertheless be loosely associated with the membrane, possibly as peripheral membrane proteins, thus enabling them to interact with their cognate bacteriocin.     

A miniaturized column chromatography method for measuring receptor-mediated inositol phosphate accumulation

Inositol phosphates (IPs), such as 1,4,5-inositol-trisphosphate (IP(3)), comprise a ubiquitous intracellular signaling cascade initiated in response to G protein-coupled receptor-mediated activation of phospholipase C. Classical methods for measuring intracellular accumulation of these molecules include time-consuming high-performance liquid chromatography (HPLC) separation or large-volume, gravity-fed anion-exchange column chromatography. More recent approaches, such as radio-receptor and AlphaScreen assays, offer higher throughput. However, these techniques rely on measurement of IP(3) itself, rather than its accumulation with other downstream IPs, and often suffer from poor signal-to-noise ratios due to the transient nature of IP(3). The authors have developed a miniaturized, anion-exchange chromatography method for measuring inositol phosphate accumulation in cells that takes advantage of signal amplification achieved through measuring IP(3) and downstream IPs. This assay uses centrifugation of 96-well-formatted anion-exchange mini-columns for the isolation of radiolabeled inositol phosphates from cell extracts, followed by low-background dry-scintillation counting. This improved assay method measures receptor-mediated IP accumulation with signal-to-noise and pharmacological values comparable to the classical large-volume, column-based methods. Assay validation data for recombinant muscarinic receptor 1, galanin receptor 2, and rat astrocyte metabotropic glutamate receptor 5 are presented. This miniaturized protocol reduces reagent usage and assay time as compared to large-column methods and is compatible with standard 96-well scintillation counters.     

Arterial distensibility: acute changes following dynamic exercise in normal subjects

The time course of acute changes in large artery distensibility immediately and for 60 min following maximum treadmill exercise in normal subjects was characterized by simultaneously measuring upper and lower limb pulse wave velocity (PWV). A new oscillometric technique was used, which has proven to be sensitive to changes in distensibility induced by acute changes in vascular tone independently of blood pressure. The observed changes in PWV are attributable to changes in vascular tone corresponding to recovery from a systemic net constrictor response and a local net dilator response to exercise with persisting postexercise vasodilatation. They are inadequately explained by associated changes in blood pressure and cannot be attributed to changes in heart rate or viscosity. Modeled as a system of n coupled linear differential equations, the minimum (and adequate) order required to reproduce these patterns was n = 1 for the upper and n = 2 for the exercising lower limb. The economy of the solution suggests entrainment among the multiple interactive mechanisms governing vasomotor control.     

Exploring the nonlinear geometry of protein homology

The explosion of biological data resulting from genomic and proteomic research has created a pressing need for data analysis techniques that work effectively on a large scale. An area of particular interest is the organization and visualization of large families of protein sequences. An increasingly popular approach is to embed the sequences into a low-dimensional Euclidean space in a way that preserves some predefined measure of sequence similarity. This method has been shown to produce maps that exhibit global order and continuity and reveal important evolutionary, structural, and functional relationships between the embedded proteins. However, protein sequences are related by evolutionary pathways that exhibit highly nonlinear geometry, which is invisible to classical embedding procedures such as multidimensional scaling (MDS) and nonlinear mapping (NLM). Here, we describe the use of stochastic proximity embedding (SPE) for producing Euclidean maps that preserve the intrinsic dimensionality and metric structure of the data. SPE extends previous approaches in two important ways: (1) It preserves only local relationships between closely related sequences, thus allowing the map to unfold and reveal its intrinsic dimension, and (2) it scales linearly with the number of sequences and therefore can be applied to very large protein families. The merits of the algorithm are illustrated using examples from the protein kinase and nuclear hormone receptor superfamilies.