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.     

Growth promoting influence of siderophore-producing Pseudomonas strains GRP3A and PRS9 in maize (Zea mays L.) under iron limiting conditions

Maize seeds were bacterized with siderophore-producing pseudomonads with the goal to develop a system suitable for better iron uptake under iron-stressed conditions. Siderophore production was compared in fluorescent Pseudomonas spp. GRP3A, PRS9 and P. chlororaphis ATCC 9446 in standard succinate (SSM) and citrate (SCM) media. Succinate was better suited for siderophore production, however, deferration of media resulted in increased siderophore production in all the strains. Maximum siderophore level (216.23 microg/ml) was observed in strain PRS9 in deferrated SSM after 72 h of incubation. Strains GRP3A and PRS9 were used for plant growth promotion experiments. Strains GRP3A and PRS9 were also antagonistic against the phytopathogens, Colletotrichum dematium, Rhizoctonia solani and Sclerotium rolfsii. Bacterization of maize seeds with strains GRP3A and PRS9 showed significant increase in germination percentage and plant growth. Maximum shoot and root length and dry weight were observed with 10 microM Fe3+ along with bacterial inoculants suggesting application of siderophore producing plant growth promoting rhizobacterial strains in crop productivity in calcareous soil system.     

Experimental infection of Nematospiroides dubius in Swiss albino mice. IX. Effect of dose break up on the serum protein patterns

The present study concerns with the effects of larval inoculation with either a single dose or two or more spaced doses of 200 larvae on the serum protein profiles. No significant difference occurred in the various fractions among the three groups indicating that the total quantity of antigenic stimulation in the most important factor in eliciting such changes, no matter whether the dose is given once or spaced in two or three small doses. Serum protein fractions of Swiss albino mice undergoing experimental infection of Nematospiroides dubius do not tend to rise further due to repeated exposures in comparison to those that received a challenge dose only (1). Hence, experiments were designed to ascertain whether there is any difference in serum protein patterns due to breaking up of the infective dose into two or three spaced doses of N. dubius larvae.     

Experimental infection of Nematospiroides dubius in Swiss albino mice. VII. Worm burdens and serum protein fractions

The paper deals with the alterations in serum protein profiles and its possible correlation with the worm burden in Swiss white mice infected with single and repeated doses of N. dubius infective larvae. Marked changes observed in serum protein fractions in all the groups were found to be further raised with increase in dose levels. However, maximum (optimal) changes of different fractions depend on the total number of larvae inoculated irrespective of the number of inoculations given. Percentage of worm retention was found to be inversely proportional to the number of larvae inoculated. Worm expulsion during repeated infections was attributed to the therefore, participation of increased amount of immunoglobulins and, humoral immunity (immediate type) has been suggested to play a major role in the immune mechanism of this model.     

In vitro Responses of Embryoids ofEschscholzia californica

Thein vitro embryoids ofEschscholzia californica do not form normal plantlets in cultures. However, 6-benzylaminopurine and gibberellic acid, when added to the medium, partially alleviate this inhibition. Experiments involving decotylization, and culture of embryoids at different stages, indicated the cardinal role of cotyledons in plumular growth.     

Cell-density-dependent Changes in the Metabolism of Chloronema Cell Cultures: I. Relationship between Cell Density and Enzymic Activities

In the growing chloronema cell suspension cultures of the moss Funaria hygrometrica Hedw., activities of several enzymes have been found to be cell-density-dependent. Cyclic nucleotide phosphodiesterase (cNPDE), nitrate reductase (NR), and protein kinase showed highest activity at a low cell density (1 to 2 milligrams per milliliter) while indoleacetic acid (IAA) oxidase and peroxidase were highest at a high cell density (>10 milligrams per milliliter). 3′-Nucleotidase and the glycolytic enzymes (aldolase, hexokinase, phosphofructokinase, phosphoglucoisomerase, pyruvate kinase, and triose phosphate isomerase) showed no significant dependence on the cell density. Alternatively, if the NR and peroxidase activities were determined as a function of time in batch cultures, their levels were maximal 60 to 70 and 320 hours after subculture, respectively, the corresponding cell densities being 1 to 2 and 23 milligrams per milliliter. The relationship between cell density and NR and peroxidase activities is the same, whether these enzymes are measured in batch cultures during a growth cycle or in the cells cultured at different initial inoculum densities for a constant time. Conventionally enzymic changes have been correlated with growth phases; however, it is felt that the pattern of enzymic activities can also be interpreted as cell-density-dependent.     

Growth rate and oxygen regulate the interactions of group B Streptococcus with polarized respiratory epithelial cells

We investigated growth conditions that regulate the ability of group B Streptococcus (GBS) to attach to, invade, and translocate through polarized human respiratory epithelial cells (RECs). GBS grown in a chemostat at a fast cell mass doubling time (t(d) = 1.8 h), invaded RECs from both the apical and basolateral surfaces in higher numbers compared with those held at a t(d) = 11 h. With the exception of adherence from the basolateral surface, GBS reached peak adherence to, invasion of, and translocation through RECs when held at the fast t(d) with 15% dissolved oxygen compared with 0% dissolved oxygen. Growth rate and oxygen level strongly influence the interaction of GBS with polarized RECs and likely GBS pathogenicity.     

Analysis of time-dependent recovery from beryllium toxicity following chelation therapy and antioxidant supplementation

Efforts have been made to minimize the toxic effect caused by beryllium. Adult cyclic rats of Sprague Dawley strain were administered a bolus dose of 50mg/kg beryllium nitrate intramuscularly. The chelation therapy with glutathione (GSH), dimercapto propane sulfonic acid (DMPS)+ selenium (Se) and D-Penicillamine (DPA) + Se was given for 3 days followed by a rest of 1,3 and 7 days respectively. The results revealed a significant fall in the blood sugar level, serum alkaline phosphatase activity, serum proteins. A significant rise in the transaminases i.e. aspartate aminotranferase and alanine aminotranferase pattern is indicative of leakage of enzymes from liver resulting in alterations in the cell permeability. A rise in the hepatic lipid peroxidation activity is a direct indication of oxidative damage resulting in free radical generation. Results of the distribution studies by atomic absorption spectrophotometry reveal an increased concentration of beryllium in liver and kidney followed by lung and uterus. The relative ability of 3 chelating agents to act as antagonists for acute beryllium poisoning have been examined in liver, kidney, lungs and uterus. The appreciable change in the beryllium concentration in various organs is duration-dependent during the entire period being highly significant after 7 days rest. From the biochemical assays, and distribution studies it can be assumed that DPA+Se was the most effective therapeutic agent followed by DMPS+Se and GSH. Thus it can be concluded that DPA+Se is a better therapeutic agent as compared to DMPS+Se and GSH.     

A mass mortality of fishes caused by receding water levels in the vegetated littoral zone of the West Kleinemonde Estuary,South Africa

On 15 November 2017 the mouth of the West Kleinemonde Estuary breached following heavy catchment rains and increased river flow. The water level in the estuary following mouth opening decreased by 1.65 m within 24 h, resulting in an almost complete draining of the littoral zone where large beds of the aquatic macrophyte Ruppia cirrhosa and mats of the associated filamentous algae were present. As the water depth within the plant beds decreased, the macrophytes, together with the algal filaments, created an increasingly dense mat, trapping fish that were resident, foraging or passing through the littoral zone. By 16 November 2017 large numbers of fishes belonging to at least 20 species were trapped in pools and depressions within the littoral, as well as within the R. cirrhosa beds and filamentous algal mats in the lower reaches of this system. Other affected taxa included crustaceans, especially isopods, and large numbers of small bivalves attached to macrophyte vegetation. Beneficiaries of the fish kill, in terms of unexpected food availability, included a variety of piscivorous bird species and the Cape clawless otter Aonyx capensis. This is the first documented account of a diverse species fish kill associated with estuary mouth breaching.