Outbreak of Phytophthora cinnamomi causing severe decline of avocado trees in southern Turkey

Since the summer 2017, severe decline symptoms have been observed on 10- to 25-year-old avocado trees in almost all commercial orchards planted in the Mediterranean coastal region of Turkey. Young, newly planted trees in infected orchards were also affected by the disease. Affected trees showed wilting, leaf discoloration, defoliation and severe dieback. Some trees were completely desiccated. Although fine roots of symptomatic trees usually were decayed, reddish brown cankers also occurred on taproots and lateral roots of heavily infected trees. The pathogens were isolated from necrotic root and soil samples of symptomatic trees, using selective medium and soil baiting, and were identified based on morphological features and DNA sequences of the internal transcribed spacer (ITS) region. One isolate each of Phytophthora cryptogea and P. palmivora was identified, while all other isolates were P. cinnamomi. In addition, a subcortical fan-shaped mycelium, characteristic of Armillaria spp., was observed in the stem base of a symptomatic tree and identified as Armillaria gallica by DNA sequences of the internal transcribed spacer (ITS) and the translational elongation factor 1-α (EF 1-α) gene regions. Pathogenicity of Phytophthora isolates was tested by stem inoculation on one-year-old avocado seedlings. Two months after inoculation, canker lesions developed on stems of seedlings inoculated by any of the three Phytophthora spp. In contrast, collenchyma callus formed over the wound points on control plants over the same time period. This is the first report of P. cinnamomi, P. cryptogea, P. palmivora and A. gallica causing root rot of avocado trees in Turkey. In addition, P. cryptogea and A. gallica are reported for the first time associated with disease on this host. Due to the severe symptoms and widespread occurrence, P. cinnamomi should be considered a potential threat to avocado cultivation and natural ecosystems of this region of Turkey.     

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.     

First Report of Rhizoctonia solani AG 8 on Wheat in Turkey

A survey was conducted in Ankara and Eskisehir provinces of Turkey for determining anastomosis groups and pathogenicity of Rhizoctonia species associated with root and crown rot of wheat. Pathogenicity tests revealed that Rhizoctonia solani AG 8 caused the common symptoms of damping‐off and stunting.     

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.     

The influence of water level on macrophyte growth and trophic interactions in eutrophic Mediterranean shallow lakes: a mesocosm experiment with and without fish

1. Water‐level fluctuations are typical of lakes located in the semi‐arid Mediterranean region, which is characterised by warm rainy winters and hot dry summers. Ongoing climate change may exacerbate fluctuations and lead to more severe episodes of drought, so information on the effects of water level on the functioning of lake ecosystems in such regions is crucial. 2. In eutrophic Lake Eymir, Turkey, we conducted a 4‐month (summer) field experiment using cylindrical 0.8‐m‐ (low‐water‐level) and 1.6‐m‐deep (high‐water‐level) mesocosms (kept open to the sediment and atmosphere). Fish (tench, Tinca tinca, and bleak, Alburnus escherichii) were added to half of the mesocosms, while the rest were kept fishless. Ten shoots of Potamogeton pectinatus were transplanted to each mesocosm. 3. Sampling for physicochemical variables, chlorophyll a (chl‐a), zooplankton and per cent plant volume inhabited (PVI%) by macrophytes was conducted weekly during the first 5 weeks, and subsequently biweekly. Macrophytes were harvested on the last sampling date. During the course of the experiment, the water level decreased by 0.41 ± 0.06 m. 4. Throughout the experiment, fish affected zooplankton abundance (?), nutrient concentrations (+), chl‐a (+) and water clarity (?) most strongly in the low‐water‐level mesocosms and the zooplankton community shifted towards dominance of small‐sized forms. The fishless mesocosms had a higher zooplankton/phytoplankton ratio, suggesting higher grazing. 5. Greatest macrophyte growth was observed in the low‐water‐level fishless mesocosms. However, despite high nutrient concentrations and low water clarity, macrophytes were also abundant in the fish mesocosms and particularly increased following a water‐level decrease from midsummer onwards. Macrophyte growth was poor in the high‐water‐level mesocosms, even in the fishless ones with high water clarity. This was ascribed to extensive periphyton development reducing light availability for the macrophytes. 6. Our results indicate that a reduction in water level during summer may help maintain the growth of macrophytes in Mediterranean eutrophic shallow lakes, despite a strong negative effect of fish predation on water clarity. It is therefore probable that an expected negative effect of global climate change on water clarity because of eutrophication and enhanced top‐down control of fish may be, at least partly, counteracted by reduced water level, provided that physical disturbance is not severe.     

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.     

Boron Contents of Some Wild-Growing Mushrooms Collected from the Vicinity of Boron Mines in Balikesir,Turkey

The aim of the study was to determine the boron contents of some wild-growing mushrooms collected from the vicinity of several boron mines located in Balikesir, Turkey and compare the boron contents of some mushroom and soil samples. The locations of the mushroom samples collected were within the distance of 0–100, 100–500, and 500–1,000 m to the mines. Soil samples were taken from beneath randomly selected fungal fruit bodies. A total of 40 mushroom samples were found in the study area and 37 different species were identified. Among the 40 samples analyzed, the highest boron content was detected to be 273 mg kg⁻¹ in Suillus collinitus. Also, Tricholoma terreum (69.52 mg kg⁻¹), Myxomphalia maura (36.52 mg kg⁻¹), Otidea concinna (30.70 mg kg⁻¹), Sepultaria arenosa (28.94 mg kg⁻¹), Melanoleuca paedida (28.33 mg kg⁻¹), and Lycoperdon lividum (28.31 mg kg⁻¹) relatively have high levels of boron and these species are proposed as candidates for boron accumulation. The boron contents of the other mushrooms varied and a pattern was observed where the boron content was found to be decreased as the distance from the mines increased.     

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.     

Impact of tropospheric ozone on the Euro‐Mediterranean vegetation

The impact of ozone (O₃) on European vegetation is largely under‐investigated, despite huge areas of Europe are exposed to high O₃ levels and which are expected to increase in the next future. We studied the potential effects of O₃ on photosynthesis and leaf area index (LAI) as well as the feedback between vegetation and atmospheric chemistry using a land surface model (ORCHIDEE) at high spatial resolution (30 km) coupled with a chemistry transport model (CHIMERE) for the whole year 2002. Our results show that the effect of tropospheric O₃ on vegetation leads to a reduction in yearly gross primary production (GPP) of about 22% and a reduction in LAI of 15–20%. Larger impacts have been found during summer, when O₃ reaches higher concentrations. During these months the maximum GPP decrease is up to 4 g C m^?2 day^?1, and the maximum LAI reduction is up to 0.7 m² m^?2. Since CHIMERE uses the LAI computed by ORCHIDEE to estimate the biogenic emissions, a LAI reduction may have severe implications on the simulated atmospheric chemistry. We found a large change in O₃ precursors that however leads to small changes in tropospheric O₃ concentration, while larger changes have been found for surface NO₂ concentrations.