Alper Devrim Ozkan

Differential effects of nitrogen and sulfur deprivation on growth and biodiesel feedstock production of Chlamydomonas reinhardtii

Biodiesel production from microalgae is a promising approach for energy production; however, high cost of its process limits the use of microalgal biodiesel. Increasing the levels of triacylglycerol (TAG) levels, which is used as a biodiesel feedstock, in microalgae has been achieved mainly by nitrogen starvation. In this study, we compared effects of sulfur (S) and nitrogen (N) starvation on TAG accumulation and related parameters in wild‐type Chlamydomonas reinhardtii CC‐124 mt(−) and CC‐125 mt(+) strains. Cell division was interrupted, protein and chlorophyll levels rapidly declined while cell volume, total neutral lipid, carotenoid, and carbohydrate content increased in response to nutrient starvation. Cytosolic lipid droplets in microalgae under nutrient starvation were monitored by three‐dimensional confocal laser imaging of live cells. Infrared spectroscopy results showed that relative TAG, oligosaccharide and polysaccharide levels increased rapidly in response to nutrient starvation, especially S starvation. Both strains exhibited similar levels of regulation responses under mineral deficiency, however, the degree of their responses were significantly different, which emphasizes the importance of mating type on the physiological response of algae. Neutral lipid, TAG, and carbohydrate levels reached their peak values following 4 days of N or S starvation. Therefore, 4 days of N or S starvation provides an excellent way of increasing TAG content. Although increase in these parameters was followed by a subsequent decline in N‐starved strains after 4 days, this decline was not observed in S‐starved ones, which shows that S starvation is a better way of increasing TAG production of C. reinhardtii than N starvation. Biotechnol. Bioeng. 2012; 109:1947–1957.

Label-Free Nanometer-Resolution Imaging of Biological Architectures through Surface Enhanced Raman Scattering

Label free imaging of the chemical environment of biological specimens would readily bridge the supramolecular and the cellular scales, if a chemical fingerprint technique such as Raman scattering can be coupled with super resolution imaging. We demonstrate the possibility of label-free super-resolution Raman imaging, by applying stochastic reconstruction to temporal fluctuations of the surface enhanced Raman scattering (SERS) signal which originate from biomolecular layers on large-area plasmonic surfaces with a high and uniform hot-spot density (>1011/cm2, 20 to 35 nm spacing). A resolution of 20 nm is demonstrated in reconstructed images of self-assembled peptide network and fibrilated lamellipodia of cardiomyocytes. Blink rate density is observed to be proportional to the excitation intensity and at high excitation densities (>10 kW/cm2) blinking is accompanied by molecular breakdown. However, at low powers, simultaneous Raman measurements show that SERS can provide sufficient blink rates required for image reconstruction without completely damaging the chemical structure.

Chromium(VI) Biosorption and Bioaccumulation by Live and Acid-Modified Biomass of a Novel Morganella morganii Isolate

Conventional methods of chromium removal are often insufficient for the remediation of chromium-contaminated natural environments, necessitating the development of alternative strategies. In this paper, we report the isolation of a novel Morganella morganii strain capable of reducing hexavalent chromium to its less-toxic and less-soluble trivalent form. Cr(VI) reduction by this strain was evaluated in both acidic environments and conditions reflecting natural freshwater sources. The isolate achieved equilibrium within 3 h and displayed a specific uptake rate of 24.30 ± 1.67 mg Cr(VI)/g biomass following HCl treatment. Without acid treatment, a reduction of over 90% was recorded within 72 h for an initial Cr(VI) concentration 20 mg/L, corresponding to a Cr(VI) removal capacity of 19.36 ± 1.89 mg/g. Absorption data of acid-treated STB5 biomass most closely followed the Toth and Langmuir models. FTIR results indicate that hydroxyl groups and extracellular or cell membrane polysaccharides may be potential adsorption sites for hexavalent chromium. Our results suggest that the isolate may be used in situ for treatment of polluted freshwater environments.

Tissue Distribution and Correlation Profiles of Heavy-Metal Accumulation in the Freshwater Crayfish Astacus leptodactylus

The present work details the analysis of heavy-metal and metalloid concentrations in exoskeleton, gill, hepatopancreas, and abdominal muscle tissues of 60 crayfish (Astacus leptodactylus) specimens collected from Lake Hirfanlı, a dam lake located in Kırşehir (Turkey) with a low metal-contamination profile. Concentrations of 11 metals (aluminum [Al], chromium [Cd], manganese [Mn], cobalt [Co], nickel [Ni], copper [Cu], molybdenum [Mo], silver [Ag], cadmium [Cd], mercury [Hg], and lead [Pb]) and a metalloid (arsenic [As]) were measured by inductively coupled plasma–mass spectrometry, and the relative frequencies of the most abundant isotopes of Cr, Cu, Ag, Cd, Hg, and Pb were evaluated. Three correlation trends were evaluated between the following: (1) different elements in the each individual tissue, (2) individual elements in different tissues, and (3) different elements in different tissues. In addition, correlation rates of growth parameters (weight, cephalothorax length, and total length) with heavy-metal and metalloid concentrations in each tissue were investigated. Our results suggest that substantial differences in metal and metalloid-accumulation levels exist between male and female specimens, with stronger correlations between the heavy-metal concentrations observed in the male cohort. It is notable that correlation trends of Co, Cu, 52As, Cr, and Ni in exoskeleton of the male specimens display strong similarities. Likewise, a very strong correlation is present in Ni–Cd and Ni–Pb accumulations in abdominal muscle of the male specimens; a similar trend is present between Cd and Pb concentrations in the same tissue of female specimens. For correlation rates of different heavy metals and metalloid in different tissues, the strongest positive association observed was between 63Cu in gill and As in hepatopancreas, whereas the strongest negative correlation was between accumulated Ni in abdominal muscle and As in exoskeleton. Strong correlations between metals and metalloid accumulations were observed between exoskeleton and gill. In many cases, metal and metalloid accumulation was negatively correlated with growth parameters. Preferential accumulation of Cr and Cu isotopes was observed in different tissues, suggesting that significant amounts of isotope fractionation occur during heavy-metal accumulation. Relatively low correlation rates were observed between 52Cr/53Cr and 63Cu/65Cu concentrations in several tissue types in both male and female cohorts, whereas no such trend was observed between Cd and Pb isotopes.

Removal of a reactive dye and hexavalent chromium by a reusable bacteria attached electrospun nanofibrous web

A contaminant resistant Lysinibacillus sp. NOSK was isolated from a soil sample and its Reactive Black 5 (RB5) and Cr(VI) removal efficiencies were investigated as a function of changes in the initial pH values, temperature, static/shaking conditions, reactive dye and Cr(VI) concentrations. In this study, an electrospun polysulfone nanofibrous web (PSU-NFW) was found to be effective in attachment of bacterial cells. Bacteria attached PSU-NFWs (bacteria/PSU-NFW) have shown highly efficient removal of RB5, as 99.7 ± 0.9% and 35.8 ± 0.4% for the pristine PSU-NFW. Moreover, the highest Cr(VI) removal efficiencies measured were 98.2 ± 0.6% for bacteria attached PSU-NFW and 32.6 ± 0.6% for the pristine PSU-NFW. Simultaneous removal of RB5 and Cr(VI) were also investigated. Reusability test results indicate that, bacteria/PSU-NFW can be reused for at least 7 cycles with 28.1 ± 0.6% and 66.7 ± 0.8% removal efficiencies for RB5 and Cr(VI), respectively.

Nitrogen and sulfur deprivation differentiate lipid accumulation targets of Chlamydomonas reinhardtii

Nitrogen (N) and sulfur (S) have inter-related and distinct impacts on microalgal metabolism; with N starvation having previously been reported to induce elevated levels of the biodiesel feedstock material triacylglycerol (TAG), while S deprivation is extensively studied for its effects on biohydrogen production in microalgae.1,2 We have previously demonstrated that N- and S-starved cells of Chlamydomonas reinhardtii display different metabolic trends, suggesting that different response mechanisms exist to compensate for the absence of those two elements.3 We used C. reinhardtii CC-124 mt(-) and CC-125 mt(+) strains to test possible metabolic changes related to TAG accumulation in response to N and S deprivation, considering that gamete differentiation in this organism is mainly regulated by N.4 Our findings contribute to the understanding of microalgal response to element deprivation and potential use of element deprivation for biodiesel feedstock production using microalgae, but much remains to be elucidated on the precise contribution of both N and S starvation on microalgal metabolism.

Accumulation trends of metals and a metalloid in the freshwater crayfish Astacus leptodactylus from Lake Yeniçağa (Turkey)

This study aims to determine the extent of metal pollution in Lake Yeniçağa (Bolu, Turkey) by investigating the accumulation trends of five metals (Al, Cu, Fe, Ni and Zn) and a metalloid (As) in gills, exoskeleton, hepatopancreas and abdominal muscles of the freshwater crayfish Astacus leptodactylus. Principal component analysis (PCA), cluster analysis (CA), correlation analysis and analysis of variance (ANOVA) were utilised to determine the accumulation profiles of each element over four seasons. The greatest element accumulation was found to occur in the gills. All elements in exoskeletal tissue displayed positive correlations with each other, a similar trend was also observed in the hepatopancreas samples. Strong (r=0.868) and very strong (r=0.960) positive correlations were found between the accumulations of Al and Fe in gills and the exoskeleton, respectively. Correlations in tissue accumulation rates are discussed in the context of metabolic roles and impacts associated with the elements tested. Elemental compositions of Yeniçağa water and sediment samples were also investigated to determine whether the composition of the surrounding environment matches the metal accumulation trends of tissue samples. We demonstrate that, by the criteria set by the United States Environmental Protection Agency, Lake Yeniçağa is heavily polluted in terms of As and Ni.

Effects of laser ablated silver nanoparticles on Lemna minor

The present study investigates and models the effect of laser ablated silver nanoparticles (AgNPs) on the development of the aquatic macrophyte Lemna minor. Toxic effects of five different AgNP concentrations (8, 16, 32, 96 and 128 μg L(-1)) on L. minor were recorded over seven days under simulated natural conditions. Biosorption of AgNPs by L. minor was modeled using four sorption isotherms, and the sorption behavior was found to agree most closely with the Langmuir-Freundlich model (R(2)=0.997). While toxic effects of AgNPs could be observed in all models and concentrations, the greatest increase in toxicity was in the 8-32 μg L(-1) range. Dry weight- and frond number-based inhibition experiments suggest that growth inhibition does not necessarily scale with AgNP concentration, and that slight fluctuations in inhibition rates exist over certain concentration ranges. Very close fits (R(2)=0.999) were obtained for all removal models, suggesting that the fluctuations are not caused by experimental variation. In addition, L. minor was found to be a successful bioremediation agent for AgNPs, and displayed higher removal rates for increasing AgNP doses. FT-IR spectroscopy suggests that carbonyl groups are involved in AgNP remediation.

Heparin mimetic peptide nanofiber gel promotes regeneration of full thickness burn injury

Burn injuries are one of the most common types of trauma worldwide, and their unique physiology requires the development of specialized therapeutic materials for their treatment. Here, we report the use of synthetic, functional and biodegradable peptide nanofiber gels for the improved healing of burn wounds to alleviate the progressive loss of tissue function at the post-burn wound site. These bioactive nanofiber gels form scaffolds that recapitulate the structure and function of the native extracellular matrix through signaling peptide epitopes, which can trigger angiogenesis through their affinity to basic growth factors. In this study, the angiogenesis-promoting properties of the bioactive scaffolds were utilized for the treatment of a thermal burn model. Following the excision of necrotic tissue, bioactive gels and control solutions were applied topically onto the wound area. The wound healing process was evaluated at 7, 14 and 21 days following injury through histological observations, immunostaining and marker RNA/protein analysis. Bioactive peptide nanofiber-treated burn wounds formed well-organized and collagen-rich granulation tissue layers, produced a greater density of newly formed blood vessels, and exhibited increased re-epithelialization and skin appendage development with minimal crust formation, while non-bioactive peptide nanofibers and the commercial wound dressing 3M™ Tegaderm™ did not exhibit significant efficiency over sucrose controls. Overall, the heparin-mimetic peptide nanofiber gels increased the rate of repair of burn injuries and can be used as an effective means of facilitating wound healing.

Atomic force microscopy for the investigation of molecular and cellular behavior.

The present review details the methods used for the measurement of cells and their exudates using atomic force microscopy (AFM) and outlines the general conclusions drawn by the mechanical characterization of biological materials through this method. AFM is a material characterization technique that can be operated in liquid conditions, allowing its use for the investigation of the mechanical properties of biological materials in their native environments. AFM has been used for the mechanical investigation of proteins, nucleic acids, biofilms, secretions, membrane bilayers, tissues and bacterial or eukaryotic cells; however, comparison between studies is difficult due to variances between tip sizes and morphologies, sample fixation and immobilization strategies, conditions of measurement and the mechanical parameters used for the quantification of biomaterial response. Although standard protocols for the AFM investigation of biological materials are limited and minor differences in measurement conditions may create large discrepancies, the method is nonetheless highly effective for comparatively evaluating the mechanical integrity of biomaterials and can be used for the real-time acquisition of elasticity data following the introduction of a chemical or mechanical stimulus. While it is currently of limited diagnostic value, the technique is also useful for basic research in cancer biology and the characterization of disease progression and wound healing processes.