Whole plant response of Pongamia pinnata to drought stress tolerance revealed by morpho-physiological,biochemical and transcriptome analysis

Molecular Biology Reports - Pongamia is considered an important biofuel species worldwide. Drought stress in the early growth stages of Pongamia influences negatively on the germination and...     

Predicting breast cancer using an expression values weighted clinical classifier

Background

Clinical data, such as patient history, laboratory analysis, ultrasound parameters-which are the basis of day-to-day clinical decision support-are often used to guide the clinical management of cancer in the presence of microarray data. Several data fusion techniques are available to integrate genomics or proteomics data, but only a few studies have created a single prediction model using both gene expression and clinical data. These studies often remain inconclusive regarding an obtained improvement in prediction performance. To improve clinical management, these data should be fully exploited. This requires efficient algorithms to integrate these data sets and design a final classifier.LS-SVM classifiers and generalized eigenvalue/singular value decompositions are successfully used in many bioinformatics applications for prediction tasks. While bringing up the benefits of these two techniques, we propose a machine learning approach, a weighted LS-SVM classifier to integrate two data sources: microarray and clinical parameters.

Results

We compared and evaluated the proposed methods on five breast cancer case studies. Compared to LS-SVM classifier on individual data sets, generalized eigenvalue decomposition (GEVD) and kernel GEVD, the proposed weighted LS-SVM classifier offers good prediction performance, in terms of test area under ROC Curve (AUC), on all breast cancer case studies.

Conclusions

Thus a clinical classifier weighted with microarray data set results in significantly improved diagnosis, prognosis and prediction responses to therapy. The proposed model has been shown as a promising mathematical framework in both data fusion and non-linear classification problems.     

Production of enzyme preparations on the basis of Penicillum canescens recombinant strains with a high ability for the hydrolysis of plant materials

An enzyme preparation has been produced on the basis of Penicillium canescens strains with the activity of cellibiohydrolase I, II; endo-1,4-β-gluconase of Penicillium verruculosum; and β-glucosidase of Aspergillus niger. It was shown that for the most effective hydrolysis of aspen wood pulp the optimal ratio of cellobiohydrolase and endo-1,4-β-gluconase in enzyme preparations was 8: 2 (by protein). It was also established that the homologous xylanase secreted by the Penicillium canescens fungus is a required component for the enzyme complex for hydrolysis of the hemicellulose matrix of aspen wood.     

Production of enzyme preparations on the basis of Penicillum canescens recombinant strains with a high ability for the hydrolysis of plant materials

An enzyme preparation has been produced on the basis of Penicillium canescens strains with the activity of cellibiohydrolase I, II; endo-1,4-beta-gluconase of Penicillium verruculosum; and beta-glucosidase of Aspergillus niger. It was shown that for the most effective hydrolysis of aspen wood pulp the optimal ratio of cellobiohydrolase and endo- 1,4-3-gluconase in enzyme preparations was 8 : 2 (by protein). It was also established that the homologous xylanase secreted by the Penicillium canescens fungus is a required component for the enzyme complex for hydrolysis of the hemicellulose matrix of aspen wood.     

Mitochondrial DNA Polymorphism in Natural Populations of the Drosophila virilis Species Group

Restriction fragment length polymorphism (RFLP) analysis has been used to evaluate mitochondrial DNA (mtDNA) variation in 12 sibling species forming the Drosophila virilis species group. The variation thresholds corresponding to the interspecific and interstrain levels have been determined. The results indicate that interspecific hybridization has significantly contributed to the evolutionary history of the virilis species group.     

From determination of amino acid residue conformation to reconstruction of the spatial structure of proteins (from the data of nuclear Overhauser enhancement spectroscopy

A new approach to the calculation of the spatial protein structure based on the joint utilization of the theoretical conformational analysis method and nuclear Overhauser enhancement (NOE) spectroscopy data is proposed and verified. The quality in determining various molecule structural parameters is estimated in terms of the expected NOE spectral parameters derived from the X-ray analysis data of the avian pancreatic polypeptide. The proposed approach is shown to correctly determine such structural parameters of protein molecules as local amino acid residue conformations, reciprocal spatial orientation of the C alpha atoms neighbouring along amino acid sequence and reapproached segments of the polypeptide chain. Spatially remote molecule fragments are mainly responsible for the error in determining structural parameters.     

Effect of dalargin,a synthetic leu-enkephalin analogue on synaptic transmission in the Lorenzini ampullae of rays

Effects of dalargin, a synthetic leu-enkephalin analogue and its antagonist naloxone on synaptic transmission in afferent synapses of ray electroreceptors were investigated using an isolated preparation of Lorenzini ampullae from Black sea rays. It was shown that dalargin (10^–6–10^–10 mole liter) both decreased background activity and evoked activity of an afferent fiber in a dose-dependent manner. Naloxone (10^–5 mole/liter) also inhibited afferent impulsation and completely blocked responses of the Lorenzini ampullae to dalargin application. L-glutamate-induced excitatory responses were reduced in the presence of dalargin. It is suggested that the modulatory action of dalargin on glutamatergic synaptic transmission in the Lorenzini ampullae is exerted via specific opiate receptors.Translated from Neirofiziologiya, Vol. 25, No. 1, pp. 18–21, January–February, 1993.     

Changes in the village foci of tick-borne relapsing fever in Uzbekistan over a 10-year period]

The paper presents the results of repeated investigations in the tick relapsing fever nidus (TRF) conducted after a ten-year interval in Gava settlement situated in the foothill area of the Namangan Province of Uzbekistan. A considerable deterioration in the habitat conditions of the vector, Ornithodoros papillipes Bir., due to the intensified anthropogenic effect, and decrease in its number have been noted. The distribution range of the tick (percent of infested farmsteads) in this case did not reduce. The infection rate of the vector's population with the tick relapsing fever agent decreased that points indirectly to a higher mortality of infected ticks under unfavourable conditions. Wavy course of morbidity with TRF during the period between investigations shows that changes that took place in the nidus were not uniform in their character and may have resulted to some extent from natural cycles. A similar character of anthropogenic effect on the populations of ticks in the settlement natural nidi suggests that the above changes are common to the nidi of this infection.     

Some morphological and functional properties of the lateral line system of the dwarf catfish

The peripheral and central portions of the lateral line system of the dwarf catfish were studied by morphological and electrophysiological methods. The posterior lateral line nerve, innervating the electro- and mechanoreceptors of the trunk, was shown to consist of poorly myelinated fibers 2–9 µ in diameter. The conduction velocity in this nerve varied from 10 to 15 m/sec. The lateral line nerves end in the medial nucleus of the acoustico-lateral region, which consists of dorsal and medial parts. The former is composed of circular and triangular cells measuring 6–14 µ, the second part by circular cells measuring 4–6 µ. These parts of the medial nucleus are most sharply differentiated in the region of entry of the auditory nerve. Responses to stimulation of the lateral line electro- and mechanoreceptors were recorded over the whole of the acousticolateral region in the caudal-rostral direction. The neurons studied were located at depths of 400–800 µ in the region of the medial nucleus.I. P. Pavlov Institute of Physiology, Academy of Sciences of the USSR, Leningrad, Translated from Neirofiziologiya, Vol. 7, No. 2, pp. 203–207, March–April, 1975.     

Photoinduction kinetics of electrical potential in a single chloroplast as studied with micro-electrode technique.

1. Using single chloroplasts of Peperomia metallica the kinetics of light-induced potential changes were studied. Three kinetic components (the initial fast rise, the decay in the light and the decay in the dark) were found to be characterized by time constants 4, 220 and 60 ms, respectively at light intensity 5000 1x and temperature 18 degrees C. After flash excitation the potential kept on rising for about 10 ms. Cooling of the medium down to 5 degrees C had no effect on the duration of potential rise after the flash. 2. Variations in the medium temperature in the range 2-23 degrees C had little effect on photoresponse magnitude but resulted in significant acceleration of decay in the light. 3. Addition of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (5-)0(-6) M) resulted in suppression of the magnitude of the photoresponse but was not accompanied by any change in the rate of initial rise of potential. 3-(3,4-Dichlorophenyl)-1,1-dimethylurea-inhibited photoresponse could be restored and even enhanced by subsequent addition of N-methylphenazonium methosulfate (10(-4) M). N-Methylphenazonium methosulfate essentially influenced the time course and light-intensity curves of photoresponse. 4. The chloroplast photoresponses were of different time-courses when elicited by red (640 nm) or far red (712 nm) light. This fact as well as an enhancement effect of combined illumination by two intermittent light beams indicate on the interaction of two photosynthetic pigment systems when the photoelectric response was formed. 5. An imposed electrical field resulted in stimulation or suppression of chloroplast photoresponse depending on the polarity of the field. No indications for the existance of "reversal potential" for photoelectric response were obtained. 6. A kinetic scheme of photoresponse formation is proposed, which includes two sequential photochemical reactions of photosynthesis.