Binding of S-layer homology modules from Clostridium thermocellum SdbA to peptidoglycans

S-layer homology (SLH) module polypeptides were derived from Clostridium josui xylanase Xyn10A, Clostridium stercorarium xylanase Xyn10B, and Clostridium thermocellum scafoldin dockerin binding protein SdbA as rXyn10A-SLH, rXyn10B-SLH, and rSdbA-SLH, respectively. Their binding specificities were investigated using various cell wall preparations. rXyn10A-SLH and rXyn10B-SLH bound to native peptidoglycan-containing sacculi consisting of peptidoglycan and secondary cell wall polymers (SCWP) prepared from these bacteria but not to hydrofluoric acid-extracted peptidoglycan-containing sacculi (HF-EPCS) lacking SCWP, suggesting that SCWP are responsible for binding with SLH modules. In contrast, rSdbA-SLH interacted with HF-EPCS, suggesting that this polypeptide had an affinity for peptidoglycans but not for SCWP. The affinity of rSdbA-SLH for peptidoglycans was confirmed by a binding assay using a peptidoglycan fraction prepared from Escherichia coli cells. The SLH modules of SdbA must be useful for cell surface engineering in bacteria that do not contain SCWP.     

Separation of plasmid DNA isoforms using centrifugal ultrafiltration

Centrifugal ultrafiltration is a well-established method for concentrating and purifying DNA. Here, we describe the use of centrifugal ultrafiltration for the separation of plasmid DNA isoforms based on differences in elongational flexibility of the supercoiled, open-circular, and linear plasmids. Transmission of each isoform is minimal below a critical value of the filtration velocity, which is directly related to the magnitude of the centrifugal speed and the system geometry. A discontinuous diafiltration process was used to enrich the desired isoform, as determined by agarose gel electrophoresis. The simplicity and efficacy of this membrane-based separation are attractive for multiple applications requiring the use of separated DNA isoforms.     

Delta-6 desaturase makes a different fatty acid profile of seed oil in Iranian borage (Echium amoenum Fisch. and Mey.)

Iranian borage (Echium amoenum) from Boraginaceae is a valuable medicinal plant native to Iran and Syria. We determined fatty acid profile and individual fatty acid contents in E. amoenum seed oil using gas chromatography. Nevertheless, the cumulative amount of ω-6 and ω-3 fatty acids in E. amoenum (78.5 %) was in great accordance with those of other species of Echium, Stearidonic acid (SDA, C18:4ω3) and gamma-linolenic acid (GLA, C18:3ω6) constituted only 9.7 % of seed oil in this plant. This observation elucidated the weak activity of delta-6 desaturase (D6DES) in E. amoenum compared with D6DESs of other species. As D6DES enzyme is responsible for converting linoleic acid (LA, C18:2ω6) and alpha-linolenic acid (ALA, C18:3ω3) to GLA and SDA, we isolated coding sequence of D6DES gene and characterized primary structure of the translated protein to probably find some evidences explaining the weak activity of D6DES enzyme in E. amoenum. Gene sequence from E. amoenum showed a high identity of 94–96 % with the other Echium species and the amino acid homology increased by 98 %. All the expected signatures including cytochrome b5 domain and three conserved histidine-rich motifs were found in the translated amino acid sequence. Protein alignment revealed that all the conserved motifs in D6DES sequence from E. amoenum are coincident with its counterparts from other Echium species. However, secondary structure of the enzyme deduced from its primary structure using computational simulation represented obvious differences with D6DES proteins of the other species.     

Assessment of genetic mutations in the XRCC2 coding region by high resolution melting curve analysis and the risk of differentiated thyroid carcinoma in Iran

Homologous recombination (HR) is the major pathway for repairing double strand breaks (DSBs) in eukaryotes and XRCC2 is an essential component of the HR repair machinery. To evaluate the potential role of mutations in gene repair by HR in individuals susceptible to differentiated thyroid carcinoma (DTC) we used high resolution melting (HRM) analysis, a recently introduced method for detecting mutations, to examine the entire XRCC2 coding region in an Iranian population. HRM analysis was used to screen for mutations in three XRCC2 coding regions in 50 patients and 50 controls. There was no variation in the HRM curves obtained from the analysis of exons 1 and 2 in the case and control groups. In exon 3, an Arg(188)His polymorphism (rs3218536) was detected as a new melting curve group (OR: 1.46; 95%CI: 0.432-4.969; p = 0.38) compared with the normal melting curve. We also found a new Ser(150)Arg polymorphism in exon 3 of the control group. These findings suggest that genetic variations in the XRCC2 coding region have no potential effects on susceptibility to DTC. However, further studies with larger populations are required to confirm this conclusion.     

Spike-timing in primary sensory neurons: a model of somatosensory transduction in the rat

In previous work, we constructed a simple electro-mechanical model of transduction in the rat mystacial follicle that was able to replicate primary afferent response profiles to a variety of whisker deflection stimuli. Here, we update that model to fit newly available spike-timing response data, and demonstrate that the new model produces appropriate responses to richer stimuli, including pseudo white noise and natural textures, at a spike-timing level of detail. Additionally, we demonstrate reliable distributed encoding of multi-component oscillatory signals. No modifications were necessary to the mechanical model of the physical components of the follicle–sinus complex, supporting its generality. We conclude that this model, and its continued development, will aid the understanding both of somatosensory systems in general, and of physiological results from higher (e.g. thalamocortical) systems by accurately characterising the signals on which they operate.     

Heavy metals in the Rosetta estuary of the Nile and the adjoining Mediterranean waters: evidence of removal of dissolved heavy metals from waters as a result of possible binding to suspended matter

The Rosetta estuary was partially separated from the Rosetta branch of the Nile by Edfina Barrage, which controls the Nile discharge into the Mediterranean Sea. The study area covers the Rosetta estuary (lotic environment) and the adjoining seawaters (lentic environment) to investigate the local and seasonal distribution of dissolved and particulate copper and zinc, as well as dissolved cadmium in this estuary and to illustrate its influence on the distribution of these metal forms in the inshore seawaters. Besides, emphasis on the removal of dissolved heavy metals from waters by their adsorption onto suspended matter (SM) was also considered. Contrary to particulate copper (PCu), the vertical values of dissolved copper (DCu) decreased generally with depth. Planktonic scavenging and regeneration processes might determine the vertical profiles of the copper forms. The copper data suggest that the surface sources of DCu exceeded the bottom sources, contrary to the sources of PCu. The markedly high and maximum seasonal averages of DCu in the estuary and inshore seawater in July inspite of the high uptake in summer possibly reflect higher amounts of humic materials. The lowest seasonal average value of DCu in the inshore seawater in January suggests removal of copper in presence of maximum value of SM during highest discharge. The highest regional average of DCu at the estuarine mouth coincided with desorption process during mixing of the fresh and salt waters. The vertical values of dissolved zinc (DZn) and particulate zinc (PZn) showed irregular variations and their high concentrations in the surface of the estuarine and inshore seawater indicate possible land-based sources. The high bottom DZn values, however, resulted from its contribution from the interstitial water of the sediments. The data suggest that the surface sources of DZn exceeded the bottom sources and PZn showed the opposite trend in the open sea area. In the estuary, the maximum seasonal average value of DZn accompanied by the lowest seasonal average of PZn in April inspite of the high uptake in spring suggest that desorption was the dominant process. The minimum regional averages of both zinc forms at the estuarine opening and the highest average of PZn near Edfina Barage are correlated with the amounts of SM, which decreased toward the estuarine mouth. The vertical values of dissolved cadmium (DCd) were much lower in the estuary than the other metals. They showed in both environments irregular variations with depth. The bottom maximum value of DCd can be attributed mainly to contamination from the sediments. There was a distinct seasonal variation of DCd. The minimum seasonal average value of DCd in the estuary in April seems to be caused by its specific binding to living plankton found in abundance. The minimum regional average of DCd value was found at the estuarine mouth. The decrease in Cd concentration due to removal from dissolved state is most pronounced in the early stage of mixing. The correlation coefficients of DCd were positive with salinity and negative with SM, indicating that Cd increased seaward. Statistical correlation between Cd and Zn concludes that the factors affecting their distribution are generally the same.     

Optimization of Bacillus subtilis natto growth parameters in glycerol-based medium for vitamin K (Menaquinone-7) production in biofilm reactors

Bioprocess and Biosystems Engineering - Menaquinone-7 (MK-7) is the key form of vitamin K used as a dietary supplement and its production revolves around Bacillus subtilis natto. Current...     

Implementation of fed-batch strategies for vitamin K (menaquinone-7) production by Bacillus subtilis natto in biofilm reactors

Recent studies show the essential health benefits associated with vitamin K, especially menaquinone-7 (MK-7). These benefits include reducing risks of cardiovascular diseases, osteoporosis, and even cancer. However, MK-7 production on an industrial level is only possible through bacterial fermentation and also current static fermentation strategies are not potent enough with difficulties to scale up. Biofilm reactors, however, may be a practical alternative. Biofilm reactors provide a controlled environment for the microorganisms to form mature and robust biofilms that enable them to produce value-added products with enhanced efficiencies. In this study, fed-batch addition of glucose and glycerol were investigated to the base media in biofilm reactors, as carbon source addition seemed crucial in batch fermentations. Results indicated that fed-batch strategies can be significantly effective in glucose-based medium, increasing the end-product concentrations to 28.7 ± 0.3 mg/L of MK-7 which was 2.3 fold higher than the level produced in suspended-cell bioreactors and renders the biofilm reactors as a potential replacement for static fermentation strategies. Moreover, morphological changes of B. subtilis were tracked during the 12-day long fermentation runs and finally, SEM investigations confirmed significant biofilm and extracellular matrices formed on the plastic composite support (PCS) in the biofilm reactors. In conclusion, biofilm reactors especially with fed-batch fermentation regimes seem to be an effective tool for MK-7 production at industrial scales.

     

Length‐weight and length‐length relationships of three indigenous fish species in Persian Gulf,Iran

In this study, length‐length relationships (LLRs) and weight‐length relationships (WLRs) were established for a Carangidae species: Uraspis helvola and tow Flatfishes: Pseudorhombus elevatus and Psettodes erumei that are substantial marine fish species to commercial fisheries in Persian Gulf that are indigenous marine fish species in the region. Samples were collected by non‐selective fish bottom trawler with stretch mesh size of 4 centimeters at the cod‐end area, which helped us to obtain such a broad range size that included small, medium and large size classes during June to August 2017. Hitherto, the length‐weight model presented in this study for Pseudorhombus elevatus and Uraspis helvola were not documented on Fishbase. Additionally, new records of maximum length are presented as 64.5 and 30 centimeters for P. erumei and P. elevatus respectively. A comprehensive size distribution and highly significant fitted model (r²>0.95) in this research provides useful insight for future studies on fish biology, fisheries assessment and ecological modeling.