Physical and biochemical differences in Agrobacterium rhizogenes-mediated transgenic hairy root lines of Echinacea purpurea

In Vitro Cellular & Developmental Biology - Plant - Echinacea (Echinacea purpurea L.), also known as purple coneflower, is one of the important medicinal plants commonly used for respiratory...     

Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel

Potato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Niğde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r2 value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world’s population.     

Effectiveness of different cleaning agents on the adherence of Candida albicans to acrylic denture base resin

doi: 10.1111/j.1741‐2358.2010.00379.x
Effectiveness of different cleaning agents on the adherence of Candida albicans to acrylic denture base resin Objective:  To evaluate the ability of three alkaline peroxide‐type (Polident, Efferdent, Fittydent) and two mouth rinse cleaning agents (CloSYSII and Corsodyl) to inhibit Candida albicans on acrylic denture base resin. Background:  Appropriate routine cleaning of dentures is necessary to prevent denture stomatitis and maintenance of healthy supporting tissues. Materials and methods:  A total of 180 acrylic resin specimens (10 × 10 × 2 mm) were prepared and divided into six groups. Candida albicans was incubated on Sabouraud dextrose agar (SDA) at 37°C for 48 h. After dilution, a final yeast suspension of approximately 10 6 C. albicans per millimetre was prepared. Ten acrylic resin specimens for each group were placed in a sterile Petri dish covered with 20 ml of fungal suspension and incubated at 37°C for 90 min. Then, the specimens were immersed in 40 ml of the test solution at 37°C for 15, 30 and 60 min. Fungal cells adhering to acrylic resin surfaces were fixed in formaldehyde and counted microscopically. Results:  Mouth rinses showed the highest removal activity for all the treatment times and completely eliminated the adherence of C. albicans. Conclusions:  The use of mouth rinse may be a suitable method for cleaning dentures.     

Taxonomic relationships among Turkish water frogs as revealed by phylogenetic analyses using mtDNA gene sequences

We assessed taxonomic relationships among Turkish water frogs through estimation of phylogenetic relationships among 62 adult specimens from 44 distinct populations inhabiting seven main geographical regions of Turkey using 2897 bp sequences of the mitochondrial Cytb, 12S rRNA and 16S rRNA genes with equally-weighted parsimony, likelihood, and Bayesian methods of inference. Monophyletic clade (Clade A) of the northwesternmost (Thrace) samples is identified as Pelophylax ridibundus. The other clade (Clade B) consisted of two monophyletic subclades. One of these contains specimens from southernmost populations that are regarded as an unnamed species. The other subclade consists of two lineages, of which one corresponds to P. caralitanus and another to P. bedriagae. Taxonomic relationships of these two species are discussed and recognition of P. caralitanus as a subspecies of P. bedriagae is proposed.     

Screening of tree leaves as annual renewable green biomass for phenol oxidase production and biochemical characterization of mulberry (Morus alba) leaf phenol oxidases

Fruit tree leaf tissues were screened in a search for determination of an alternative source(s) for commercial phenol oxidase (PO) production considering the importance of utilization of green biomass for production of value-added products. Mulberry, pear, sour cherry and apricot leaves were identified as promising PO production sources, due to their comparable enzyme activities with respect to mushroom (Agaricus bisporus), a well-known PO source. Within the scope of this research, further biochemical characterization was only performed for mulberry (Morus alba) leaf tissue due to its high PO activity (ca. 19 EU g⁻¹ tissue) and also its known non-toxic and edible nature which are important properties of an enzyme source to be used without detailed purification. In mulberry leaves, presence of three different PO activities, laccase, peroxidase and catechol oxidase of 62–64 kDa molecular weights, were identified. Since simple extraction/concentration steps without fractionation/purification was aimed as PO production process, operational parameters such as optimal temperature, pH and kinetic studies of overall PO activity were investigated using concentrated crude extract. The highest PO activity against 4-methyl catechol was observed at 45°C and pH 7. Michaelis–Menten kinetic parameters, K _m and V _max, of PO activity were determined as 6 mM 4-methyl catechol and 2.2 μmol quinone produced min⁻¹ ml⁻¹, respectively. PO activity of mulberry leaves increased up to late November. Consequently, mulberry leaves seem as a suitable PO source for industrial applications in which a wide range of substrate utilization is necessary.     

Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA

Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit. Using biochemical, structural and cellular approaches, we show here that BlaS inhibits both translation elongation and termination in Mammalia. Bound to mammalian terminating ribosomes, BlaS distorts the 3′CCA tail of the P-site tRNA to a larger extent than previously reported for bacterial ribosomes, thus delaying both, peptide bond formation and peptidyl-tRNA hydrolysis. While BlaS does not inhibit stop codon recognition by the eukaryotic release factor 1 (eRF1), it interferes with eRF1’s accommodation into the peptidyl transferase center and subsequent peptide release. In human cells, BlaS inhibits nonsense-mediated mRNA decay and, at subinhibitory concentrations, modulates translation dynamics at premature termination codons leading to enhanced protein production.     

Evaluation of alkaline pretreatment temperature on a multi-product basis for the co-production of glucose and hemicellulose based films from lignocellulosic biomass

Cotton stalks were subjected to alkaline pretreatment for the co-production of glucose and hemicellulose based films with a multi-product approach. Three pretreatment temperatures (25, 60 and 90 °C) were evaluated for their effects both on the glucose yield and on the properties of hemicellulose based films. Compared to untreated cotton stalks, the glucose yields were enhanced 3.9, 4.1 and 4.2 times for pretreatments conducted at 25, 60 and 90 °C, respectively. The pretreatment temperature of 90 °C was detrimental in terms of film formation. Tensile energy to break values of the films obtained after pretreatments conducted at 25, 60 and 90 °C were 1.1, 0.8, and 0.4 MJ/m³, respectively. The hemicellulosic part of the process, which considers the production of hemicellulose based films, should govern the pretreatment temperature since it was more responsive to the changes in the pretreatment temperature compared to the cellulosic part that accounts for glucose production.     

Enhancing the value of nitrogen from rapeseed meal for microbial oil production

Rapeseed meal, a major byproduct of biodiesel production, has been used as a low-cost raw material for the production of a generic microbial feedstock through a consolidated bioconversion process. Various strategies were tested for the production of a novel fermentation medium, rich in free amino nitrogen (FAN): commercial enzymes (CEs) (2.7 mg g^?1 dry meal), liquid state fungal pre-treatment (LSF) using Aspergillus oryzae (4.6 mg g^?1), liquid state fungal pre-treatment followed by fungal autolysis (LSFA) (9.13 mg g^?1), liquid state pre-treatment using fungal enzymatic broth (EB) (2.1 mg g^?1), but the best strategy was a solid state fungal pre-treatment followed by fungal autolysis (34.5 mg g^?1).The bioavailability of the nitrogen sources in the novel medium was confirmed in fed-batch bioreactor studies, in which 82.3 g dry cell L^?1 of the oleaginous yeast Rhodosporidium toruloides Y4 was obtained with a lipid content of 48%. The dry cell weight obtained was higher than that obtained using conventional yeast extract, due to a higher total nitrogen content in the novel biomedium. The fatty acids obtained from the microbial oil were similar to those derived from rapeseed oil.     

Protein expression changes in ovarian cancer during the transition from benign to malignant

Epithelial ovarian carcinoma has in general a poor prognosis since the vast majority of tumors are genomically unstable and clinically highly aggressive. This results in rapid progression of malignancy potential while still asymptomatic and thus in late diagnosis. It is therefore of critical importance to develop methods to diagnose epithelial ovarian carcinoma at its earliest developmental stage, that is, to differentiate between benign tissue and its early malignant transformed counterparts. Here we present a shotgun quantitative proteomic screen of benign and malignant epithelial ovarian tumors using iTRAQ technology with LC-MALDI-TOF/TOF and LC-ESI-QTOF MS/MS. Pathway analysis of the shotgun data pointed to the PI3K/Akt signaling pathway as a significant discriminatory pathway. Selected candidate proteins from the shotgun screen were further confirmed in 51 individual tissue samples of normal, benign, borderline or malignant origin using LC-MRM analysis. The MRM profile demonstrated significant differences between the four groups separating the normal tissue samples from all tumor groups as well as perfectly separating the benign and malignant tumors with a ROC-area of 1. This work demonstrates the utility of using a shotgun approach to filter out a signature of a few proteins only that discriminates between the different sample groups.