In silico sequence analysis of predicted beta-amylase 7-like protein in Juglans regia L.

Walnut (Juglans regia L.) is a deciduous tree of the Juglandaceae family. Beta-amylase (β-amylase, EC 3.2.1.2) is an enzyme that catalyses hydrolysis of glycosidic bonds in polysaccharides. In this study; sequence, physicochemical, and three-dimensional analyses of predicted β-amylase 7-like protein in Juglans regia using various bioinformatic tools were conducted. The physicochemical properties of the predict β-amylase 7-like protein were analyzed by using ExPASy ProtParam tool that revealed the molecular weight (MW), Isoelectric Points (pI), total number of negatively charged residues (Asp + Glu), total number of positively charged residues (Arg + Lys), instability index, aliphatic index, and GRAVY (Grand Average of Hydropathy) values. Subcellular localization using CELLO v.2.5, putative phosphorylation sites using NetPhos 3.1 server, domain analysis using Pfam, and secondary structure prediction using SOPMA were accom-plished. To predict the 3D structure of the predict  β-amylase 7-like protein, homology models were applied using PSIPRED, RAMPAGE, and PyMOL programs. The results of our study provide insight into fundamental characteristics of the predicted β-amylase 7-like protein in Juglans regia. DOI: http://dx.doi.org/10.5281/zenodo.58313

Achillea millefolium L. subsp. millefolium essential oil’s antifungal effect

This study was carried out with the aim of determining the antifungal effect of the essential oil isolated from Achillea millefolium subsp. millefolium plant against pathogenic fungi. In order to test the antifungal effect of the oil, an analysis was conducted on a total of 4 pathogen fungi which included Candida albicans, Candida tropicalis, Candida parapsilosis and Saccharomyces cerevisiae, and the effect of the essential oil on the growth of these fungi was investigated. The essential oil of A. millefolium ssp. millefolium had varying degrees of effect on the tested fungi. The highest antifungal effect was found against S. cerevisiae; whereas the lowest antifungal effect was found against C. parapsilosis. Nystatin showed a higher activity than the essential oil of A. millefolium subsp. millefolium against the tested fungi. MIC values ​​of the essential oil against the tested fungi ranged from 1.25 μl/ml to 10 μl/ml. The results obtained indicate that essential oil of A. millefolium subsp. millefolium can be used as an alternative to antifungal agents such as amphotericin, ketoconazole, and fluconazole. DOI: http://dx.doi.org/10.5281/zenodo.134633

Sequence Analysis of nrDNA ITS Region in Paşa and Şah Apple (Malus × domestica) Genotypes

In this study, phylogenetic analysis of Şah and Paşa apple genotypes was performed using nrDNA ITS sequences. After the plant leaves were brought to the laboratory, gDNAs were obtained by genomic DNA isolation method. PCR amplification was performed using primers ITS4 and ITS5A. ITS sequences of some apple and Rosaceae species were retrieved from NCBI, bioinformatics analyzes were made with Bioedit 7.2.3, Finch TV 1.4.0 and MEGA 6.0 programs and phylogenetic trees were constructed. In the study, ITS sequence length of the Paşa apple genotype was 656 bp, and the ITS sequence length of the Şah apple genotype was 649 bp. Only in the maximum likelihood phylogenetic tree constructed using sequences of apple genotypes, Paşa and Şah apple genotypes appeared in the same clade as Malus domestica cultivar="Casciana'' and Malus domestica cultivar="Rotella''. In the phylogenetic tree generated including other species belonging to the Rosaceae family; apple genotypes Pyrus, Cotoneaster, Crataegus, Sorbus, Eriobotrya and Prunus were detected in a same clade. Overall results clearly suggested that the ITS sequences were both suitable for differentiation between the selected genera and were compatible with previous phylogenetic studies

Determination of total phenolic content, total flavonoid content and total antioxidant capacity in some endemic Sideritis L. (Lamiaceae) species grown in Turkey

In this study, total phenolic, total flavonoid and antioxidant activities of the some endemic species Sideritis rubriflora Hub.-Mor., Sideritis libanotica Labill. subsp. violascens (P.H.Davis) P.H.Davis, Sideritis erythrantha Boıss. Et Heldr. Apus Bentham var. cedretorum P.H.Davis, Sideritis congesta P. H. Davis Et Hub.-Mor., Sideritis brevidens P.H.Davis and Sideritis vuralii H. Duman Et Başer, which were collected from Anamur district of Mersin province in Turkey, were analyzed. Total phenolic content (TPC), total flavonoid content (TFC) and total antioxidant capacity (DPPH), (ABTS), (FRAP) of the ground surface parts were evaluated. As a result of the study, the highest TPC value was observed in S. erythrantha subsp. cedretorum and S. rubriflora extracts as being 366.9 and 328.3 mg/g DW, respectively; the highest TFC value was observed in S. rubriflora extract as being 155.7 mg/g; the highest DPPH radical scavenging activity was observed in S. congesta and S. brevidens extracts as being 39.1% and 38.9%, respectively; the highest ABTS radical scavenging activity was observed in S. erythrantha subsp. cedretorum and S. rubriflora extracts as being 54.9% and 51.9%, respectively; the highest FRAP value was observed in S. libanotica subsp. violascens extract as being 1500.2 µmol/g. In the light of the acquired findings, it is suggested that Sideritis species used in the study can be used as a possible natural source in the pharmaceutical and food industries. DOI: http://dx.doi.org/10.5281/zenodo.466007

Use of Arthrobotrys spp. in biocontrol of the root-knot nematode Meloidogyne incognita

Plant parasitic nematodes are well-known and devastating pathogens of many agricultural crops around the world. Among the plant phytoparasitic, root-knot nematodes (Meloidogyne spp.) are the economically important limiting factors in agricultural productivity and the quality of crops. One of the most destructive species of root-knot nematodes is Meloidogyne incognita among the most important plant pests which cause severe problems in economically important crops such as vegetables, fruits, and ornamental plants. Root-knot nematodes can be managed by resistant cultivars, crop rotation, cultural practices, chemical nematicides and biocontrol agents. However, the use of nematicides can cause significant problems, including environmental pollution and long-term residue issues. Therefore, biological control with fungus is agriculturally useful an exciting and rapidly developing research area and especially there is growing attention to the exploitation of fungi for the control of nematodes. Nematophagous fungi are an important group of soil microorganisms that can suppress the populations of plant parasitic nematodes. These fungi can be divided into four main categories: endoparasitic fungi, nematode-trapping fungi, fungi that parasitic egg and female, and toxin-producing fungi. Among the nematophagous fungi, nematode-trapping fungi which are natural enemies of nematodes are the most studied. The nematode-trapping fungi develop hyphal structures. Arthrobotrys spp. are a well-known nematode-trapping fungus with biocontrol potential against root-knot nematodes, including M. incognita. The objective of this paper is to summarize the data on the potential for use of Arthrobotrys spp. in biocontrol of the root-knot nematode M. incognita. DOI: http://dx.doi.org/10.5281/zenodo.1001564