Evaluation of the Possible Contribution of Various Regulatory Genes to Determination of Carpel Number as a Potential Mechanism for Optimal Agricultural Yield.

Various regulatory genes encoding transcription factors and miRNAs regulate carpel number. Multicarpelly is normally associated with increased size of the floral meristem, and several genetic factors have been discovered that influence this characteristic. A fundamental understanding of the regulatory genes affecting carpel number can facilitate strategies for agricultural yield improvement, which is crucial, given that the global population is growing rapidly. A multicarpellate plant may provide a significantly higher yield than a plant bearing fewer carpels. Higher yields can be achieved via various means; in this review, we provide an overview of the current knowledge of the various regulatory factors that contribute to multicarpelly and the potential of increasing carpel number to achieve an increased yield.

Isolation and characterization of the most abundant rhizobacterial species associated with Vuralia turcica (Fabaceae: Papilionoideae).

Vurali turcica is naturally grown in a limited area in Central Anatolia in Turkey and was categorized as a critically endangered plant in the Red Data Book of Turkish Plants. This study aimed to analyze whether the symbiotic and mutualistic relation between V. turcica rhizomes and present microflora in the habitat can be active on its distribution. Plant growth-promoting rhizobacteria (PGPRs) colonize the rhizosphere and promote plant growth and physiology. In this paper, the diversity of PGPRs of rhizomes of V. turcica was analyzed. Rhizome samples were obtained from the natural habitats of V. turcica by the workers of Nezahat Gökyigit Botanical Garden, and bacterial isolation was conducted on the collected samples. MIS analysis, 16S rRNA, and 16S-23S rRNA ITS region sequencing were implemented, and as a result, Bacillus megaterium was found to be one of the most abundant bacterial species of the rhizomes of V. turcica based on nucleotide homology. This study is the first report on the identification of rhizobacterial species in V. turcica.

Guided screen for synergistic three-drug combinations.

Combinations of three or more drugs are routinely used in various medical fields such as clinical oncology and infectious diseases to prevent resistance or to achieve synergistic therapeutic benefits. The very large number of possible high-order drug combinations presents a formidable challenge for discovering synergistic drug combinations. Here, we establish a guided screen to discover synergistic three-drug combinations. Using traditional checkerboard and recently developed diagonal methods, we experimentally measured all pairwise interactions among eight compounds in Erwinia amylovora, the causative agent of fire blight. Showing that synergy measurements of these two methods agree, we predicted synergy/antagonism scores for all possible three-drug combinations by averaging the synergy scores of pairwise interactions. We validated these predictions by experimentally measuring 35 three-drug interactions. Therefore, our guided screen for discovering three-drug synergies is (i) experimental screen of all pairwise interactions using diagonal method, (ii) averaging pairwise scores among components to predict three-drug interaction scores, (iii) experimental testing of top predictions. In our study, this strategy resulted in a five-fold reduction in screen size to find the most synergistic three-drug combinations.

Diagonal Method to Measure Synergy Among Any Number of Drugs.

A synergistic drug combination has a higher efficacy compared to the effects of individual drugs. Checkerboard assays, where drugs are combined in many doses, allow sensitive measurement of drug interactions. However, these assays are costly and do not scale well for measuring interaction among many drugs. Several recent studies have reported drug interaction measurements using a diagonal sampling of the traditional checkerboard assay. This alternative methodology greatly decreases the cost of drug interaction experiments and allows interaction measurement for combinations with many drugs. Here, we describe a protocol to measure the three pairwise interactions and one three-way interaction among three antibiotics in duplicate, in five days, using only three 96-well microplates and standard laboratory equipment. We present representative results showing that the three-antibiotic combination of Levofloxacin + Nalidixic Acid + Penicillin G is synergistic. Our protocol scales up to measure interactions among many drugs and in other biological contexts, allowing for efficient screens for multi-drug synergies against pathogens and tumors.

Screening of new antileukemic agents from essential oils of algae extracts and computational modeling of their interactions with intracellular signaling nodes.

Microalgae are very rich in bioactive compounds, minerals, polysaccharides, poly-unsaturated fatty acids and vitamins, and these rich constituents make microalgae an important resource for the discovery of new bioactive compounds with applications in biotechnology. In this study, we studied the antileukemic activity of several chosen microalgae species at the molecular level and assessed their potential for drug development. Here we identified Stichococcus bacillaris, Phaeodactylum tricornutum, Microcystis aeruginosa and Nannochloropsis oculata microalgae extracts with possible antileukemic agent potentials. Specifically we studied the effects of these extracts on intracellular signal nodes and apoptotic pathways. We characterized the composition of essential oils of these fifteen different algae extracts using gas chromatography-mass spectrometry (GC-MS). Finally, to identify potential molecular targets causing the phenotypic changes in leukemic cell lines, we docked a selected group of these essential oils to several key intracellular proteins. According to results of rank score algorithm, five of these essential oils analyzed might be considered as in silico plausible candidates to be used as antileukemic agents.

Challenges facing European agriculture and possible biotechnological solutions.

Agriculture faces many challenges to maximize yields while it is required to operate in an environmentally sustainable manner. In the present study, we analyze the major agricultural challenges identified by European farmers (primarily related to biotic stresses) in 13 countries, namely Belgium, Bulgaria, the Czech Republic, France, Germany, Hungary, Italy, Portugal, Romania, Spain, Sweden, UK and Turkey, for nine major crops (barley, beet, grapevine, maize, oilseed rape, olive, potato, sunflower and wheat). Most biotic stresses (BSs) are related to fungi or insects, but viral diseases, bacterial diseases and even parasitic plants have an important impact on yield and harvest quality. We examine how these challenges have been addressed by public and private research sectors, using either conventional breeding, marker-assisted selection, transgenesis, cisgenesis, RNAi technology or mutagenesis. Both national surveys and scientific literature analysis followed by text mining were employed to evaluate genetic engineering (GE) and non-GE approaches. This is the first report of text mining of the scientific literature on plant breeding and agricultural biotechnology research. For the nine major crops in Europe, 128 BS challenges were identified with 40% of these addressed neither in the scientific literature nor in recent European public research programs. We found evidence that the private sector was addressing only a few of these "neglected" challenges. Consequently, there are considerable gaps between farmer's needs and current breeding and biotechnology research. We also provide evidence that the current political situation in certain European countries is an impediment to GE research in order to address these agricultural challenges in the future. This study should also contribute to the decision-making process on future pertinent international consortia to fill the identified research gaps.

Cytotoxic effect of extract from Dunaliella salina against SH-SY5Y neuroblastoma cells.

Cytotoxic effects of essential oils extracted from Dunaliella salina on SH-SY5Y human neuroblastoma cells were investigated in this study. GC-MS analysis was used for determination of the composition of essential oils found in Dunaliella salina extract. All experimented concentrations of Dunaliella salina extract on SH-SY5Y human neuroblastoma cells were significantly more cytotoxic than the tested concentrations of the extract on ECV304 human endothelial cells used as a control. Fifthy compounds were detected in GC-MS analysis of the extract, and five major compounds were predominantly found as follows: octadecanoic acid, methyl ester (27.43%); hexadecanoic acid, methyl ester (Cas) methyl palmitate (24.82%); 9,12,15-octadecatrienoic acid, ethyl ester, (Z,Z,Z)- (7.39%); octadecanoic acid (5.03%), pentadecanoic acid (3.60%). The cytotoxic activity of Dunaliella salina extract on SH-SY5Y human neuroblastoma cells might be due to high concentrations of octadecanoic acid and hexadecanoic acid. Furthermore, results indicate that the extract demonstrates some proliferative effect on ECV304 cells in a dose-dependent manner between 0.25 and 5 µg/ml. These results suggest that Dunaliella salina may have anticancer potential against human neuroblastoma cells.

Large-scale identification and analysis of suppressive drug interactions.

One drug may suppress the effects of another. Although knowledge of drug suppression is vital to avoid efficacy-reducing drug interactions or discover countermeasures for chemical toxins, drug-drug suppression relationships have not been systematically mapped. Here, we analyze the growth response of Saccharomyces cerevisiae to anti-fungal compound ("drug") pairs. Among 440 ordered drug pairs, we identified 94 suppressive drug interactions. Using only pairs not selected on the basis of their suppression behavior, we provide an estimate of the prevalence of suppressive interactions between anti-fungal compounds as 17%. Analysis of the drug suppression network suggested that Bromopyruvate is a frequently suppressive drug and Staurosporine is a frequently suppressed drug. We investigated potential explanations for suppressive drug interactions, including chemogenomic analysis, coaggregation, and pH effects, allowing us to explain the interaction tendencies of Bromopyruvate.

Oxidative stress is a mediator for increased lipid accumulation in a newly isolated Dunaliella salina strain.

Green algae offer sustainable, clean and eco-friendly energy resource. However, production efficiency needs to be improved. Increasing cellular lipid levels by nitrogen depletion is one of the most studied strategies. Despite this, the underlying physiological and biochemical mechanisms of this response have not been well defined. Algae species adapted to hypersaline conditions can be cultivated in salty waters which are not useful for agriculture or consumption. Due to their inherent extreme cultivation conditions, use of hypersaline algae species is better suited for avoiding culture contamination issues. In this study, we identified a new halophilic Dunaliella salina strain by using 18S ribosomal RNA gene sequencing. We found that growth and biomass productivities of this strain were directly related to nitrogen levels, as the highest biomass concentration under 0.05 mM or 5 mM nitrogen regimes were 495 mg/l and 1409 mg/l, respectively. We also confirmed that nitrogen limitation increased cellular lipid content up to 35% under 0.05 mM nitrogen concentration. In order to gain insight into the mechanisms of this phenomenon, we applied fluorometric, flow cytometric and spectrophotometric methods to measure oxidative stress and enzymatic defence mechanisms. Under nitrogen depleted cultivation conditions, we observed increased lipid peroxidation by measuring an important oxidative stress marker, malondialdehyde and enhanced activation of catalase, ascorbate peroxidase and superoxide dismutase antioxidant enzymes. These observations indicated that oxidative stress is accompanied by increased lipid content in the green alga. In addition, we also showed that at optimum cultivation conditions, inducing oxidative stress by application of exogenous H2O2 leads to increased cellular lipid content up to 44% when compared with non-treated control groups. Our results support that oxidative stress and lipid overproduction are linked. Importantly, these results also suggest that oxidative stress mediates lipid accumulation. Understanding such relationships may provide guidance for efficient production of algal biodiesels.

Rediscovery of historical Vitis vinifera varieties from the South Anatolia region by using amplified fragment length polymorphism and simple sequence repeat DNA fingerprinting methods.

Anatolia played an important role in the diversification and spread of economically important Vitis vinifera varieties. Although several biodiversity studies have been conducted with local cultivars in different regions of Anatolia, our aim is to gain a better knowledge on the biodiversity of endangered historical V. vinifera varieties in the northern Adana region of southern Anatolia, particularly those potentially displaying viticulture characteristics. We also demonstrate the genetic relatedness in a selected subset of widely cultivated and commercialized V. vinifera collection cultivars, which were obtained from the National Grapevine Germplasm located at the Institute of Viticulture, Turkey. In the present study, microsatellites were used in narrowing the sample size from 72 accessions down to a collection of 27 varieties. Amplified fragment length polymorphisms were then employed to determine genetic relatedness among this collection and local V. vinifera cultivars. The unweighted pair group method with arithmetic mean cluster and principal component analyses revealed that Saimbeyli local cultivars form a distinct group, which is distantly related to a selected subset of V. vinifera collection varieties from all over Turkey. To our knowledge, this is the first study conducted with these cultivars. Further preservation and use of these potential viticultural varieties will be helpful to avoid genetic erosion and to promote continued agriculture in the region.