On the production,elemental composition (C,N, P) and distribution of photosynthetic organic matter in the Southern Black Sea

Chemical oceanographic understanding of the southernBlack Sea has been improved by recent measurements ofthe optical transparency, phytoplankton biomass (interms of chlorophyll-a and particulate organic matter)and primary productivity. During the spring-autmunperiod of 1995–1996, light generally penetrated onlyinto the upper 15–40 m, with an attenuation coefficientvarying between 0.125 and 0.350 m^2122;1. The averagechlorophyll-a (Chl-a) concentrations for the euphoticzone ranged from 0.1 to 1.5 μg l^2122;1. Coherentsub-surface Chl-a maxima were formed near the base ofthe euphotic zone only in summer. Production rate variedbetween 247 and 1925 in the spring and between 405 and687 mgC m^2122;2 d^2122;1 in the summer-autumn period.The average POM concentrations in the euphotic zonevaried regionally and seasonally between 3.8 and28.6 μm for POC, 0.5 and 3.1 μm for PON and0.02 and 0.1 μm for PP. Atomic ratios of C/N, C/Pand N/P, derived from the regressions of POM data,ranged between 7.5 and 9.6, 109 and 165, and 11.2 and16.6, respectively. In the suboxic/anoxic interface,the elemental ratios change substantially due to anaccumulation of PP cohering to Fe and Mn oxides. Thechemocline boundaries and the distinct chemicalfeatures of the oxic/anoxic transition layer (the so-called suboxic zone) are all located at specificdensity surfaces; however, they exhibit remarkablespatial and temporal variations both in their positionand in their magnitude, which permit the definition of long-term changes in the biochemical properties of theBlack Sea upper layer. This revised version was published online in July 2006 with corrections to the Cover Date.     

An approach for the improved immobilization of penicillin G acylase onto macroporous poly(glycidyl methacrylate‐co‐ethylene glycol dimethacrylate) as a potential industrial biocatalyst

The use of penicillin G acylase (PGA) covalently linked to insoluble carrier is expected to produce major advances in pharmaceutical processing industry and the enzyme stability enhancement is still a significant challenge. The objective of this study was to improve catalytic performance of the covalently immobilized PGA on a potential industrial carrier, macroporous poly(glycidyl methacrylate‐co‐ethylene glycol dimethacrylate) [poly(GMA‐co‐EGDMA)], by optimizing the copolymerization process and the enzyme attachment procedure. This synthetic copolymer could be a very promising alternative for the development of low‐cost, easy‐to‐prepare, and stable biocatalyst compared to expensive commercially available epoxy carriers such as Eupergit or Sepabeads. The PGA immobilized on poly(GMA‐co‐EGDMA) in the shape of microbeads obtained by suspension copolymerization appeared to have higher activity yield compared to copolymerization in a cast. Optimal conditions for the immobilization of PGA on poly(GMA‐co‐EGDMA) microbeads were 1 mg/mL of PGA in 0.75 mol/L phosphate buffer pH 6.0 at 25°C for 24 h, leading to the active biocatalyst with the specific activity of 252.7 U/g dry beads. Chemical amination of the immobilized PGA could contribute to the enhanced stability of the biocatalyst by inducing secondary interactions between the enzyme and the carrier, ensuring multipoint attachment. The best balance between the activity yield (51.5%), enzyme loading (25.6 mg/g), and stability (stabilization factor 22.2) was achieved for the partially modified PGA. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 32:43–53, 2016     

Exploiting performance characterization of BLAST in the grid

Sequence analysis has become essential to the study of genomes and biological research in general. Basic Local Alignment Search Tool (BLAST) leads the way as the most accepted method for performing necessary query searches and analysis of discovered genes. Combating growing data sizes, with the goal of speeding up job runtimes, scientist are resorting to grid computing technologies. However, grid environments are characterized by dynamic, heterogeneous, and transient state of available resources causing major hindrance to users when trying to realize user-desired levels of service. This paper analyzes performance characteristics of NCBI BLAST on several resources and captures influence of resource characteristics and job parameters on BLAST job runtime across those resources. Obtained results are summarized as a set of principles characterizing performance of NCBI BLAST across homogeneous and heterogeneous environments. These principles are then applied and verified through creation of a grid-enabled BLAST wrapper application called Dynamic BLAST. Results show runtime savings up to 50% and resource utilization improvement of approximately 40%.     

Altered NADH and improved function by anesthetic and ischemic preconditioning in guinea pig intact hearts

NADH increases during ischemia because O(2) shortage limits NADH oxidation at the electron transport chain. Ischemic (IPC) and anesthetic preconditioning (APC) attenuate cardiac reperfusion injury. We examined whether IPC and APC similarly alter NADH, i.e., mitochondrial metabolism. NADH fluorescence was measured at the left ventricular wall of 40 Langendorff-prepared guinea pig hearts. IPC was achieved by two 5-min periods of ischemia and APC by exposure to 0.5 or 1.3 mM sevoflurane for 15 min, each ending 30 min before 30 min of global ischemia. During ischemia, NADH initially increased in nonpreconditioned control hearts and then gradually declined below baseline levels. This increase in NADH was lower after APC but not after IPC. The subsequent decline was slower after IPC and APC. On reperfusion, NADH was less decreased after IPC or APC, mechanical and metabolic functions were improved, and infarct size was lower compared with controls. Our results indicate that IPC and APC cause distinctive changes in mitochondrial metabolism during ischemia and thus lead to improved function and tissue viability on reperfusion.     

The effect of lycopene on oxytetracycline-induced oxidative stress and immunosuppression in rainbow trout (Oncorhynchus mykiss, W.)

The aim of this study was to determine the effects of lycopene on oxytetracycline (OTC)-induced oxidative stress and immunosuppression in rainbow trout. The experimental fish analysed in this study were divided into 6 different experimental groups. Group 1 was the control group, and groups 2, 3 and 4 received corn oil, lycopene and OTC, respectively, for 14 days. Group 5 received OTC for 14 days after lycopene pre-treatment for 14 days, while group 6 received OTC for 14 days before lycopene post-treatment for 14 days. Blood and tissue samples were collected at the end of the experiment and analysed for the oxidant-antioxidant status and changes in the immune response. There was a significant increase in the malondialdehyde level, which is an index of lipid peroxidation, and a decrease in superoxide dismutase, catalase, and glutathione peroxidase activity as well as a decrease in the glutathione level in the blood, liver, kidney and spleen of OTC-treated fish. Glutathione-S-transferase activity was significantly increased in the blood, liver, kidney and spleen samples of the group that received OTC alone. OTC also appeared to suppress specific and nonspecific immune system parameters, such as the haematocrit, leucocyte count, oxidative radical production (nitroblue tetrazolium activity), total plasma protein and immunoglobulin levels and phagocytic activity. Pre- and post-treatment with lycopene attenuated the OTC-induced oxidative stress by significantly decreasing the tissue malondialdehyde level. The superoxide dismutase, catalase and glutathione peroxidase activities as well as the glutathione levels were significantly increased with lycopene administration, while glutathione-S-transferase activity was significantly decreased. Lycopene administration was also associated with a significant increase in the OTC-suppressed immune system parameters in fish. Thus, the present results suggest that pre- and post-treatment with lycopene (10 mg per kg fish weight, delivered orally) may alleviate OTC-induced oxidative stress and immunosuppression.     

Role of S-nitrosothiol transport in the cardioprotective effects of S-nitrosocysteine in rat hearts

The objective of this study was to determine if prior exposure of rat hearts to S-nitrosocysteine (CysNO) was able to provide protection against reperfusion injury. We probed NO release using the extracellular NO scavenger oxyhemoglobin (oxyHb), and we examined the involvement of the amino acid transport system L (L-AT), a known transporter of CysNO, using the L-AT competitor, L-leucine (L-Leu). Isolated (9- to 12-week-old Wistar male) rat hearts (six to eight per group) were perfused with CysNO (10 microM) for 30 min with or without the L-AT competitor L-Leu (1 mM) before 30 min of ischemia. Cardiac function was assessed before, during, and after treatment and during 120 min of reperfusion after ischemia. Functional recovery (rate-pressure product) was significantly improved in the CysNO group compared to hearts in the CysNO+L-Leu group and the control group (p<0.05). Necrosis, measured by triphenyltetrazolium chloride staining, was significantly reduced in CysNO hearts (p<0.05) and this improvement was reversed by L-Leu. The NO scavenger oxyHb (20 microM) was perfused either concomitant with CysNO or just before ischemia. In neither case did oxyHb affect the cardioprotection afforded by CysNO. OxyHb alone, given in either time window, did not alter the course of ischemia-reperfusion injury. When nitrite was used in place of CysNO, no protective effects were observed. Perfusion with CysNO increased tissue S-nitrosothiol (RSNO) levels from an unmeasurable background to a value of about 15.7+/-4.1 pmol RSNO/mg protein, as measured by triiodide-based chemiluminescence in the presence and absence of mercury(II) chloride. In the presence of L-Leu, this value dropped to 0.4+/-0.3 pmol RSNO/mg protein. This study demonstrates that exposure to CysNO before ischemia increases tissue S-nitrosothiol levels, improves postischemic contractile dysfunction, and attenuates necrosis. The mechanism of cardioprotection requires the uptake of CysNO via the L-AT and does not seem to involve NO release either during CysNO exposure or during ischemia. This suggests that the protective effects of CysNO are mediated through the posttranslational modification of cellular proteins through an NO-independent transnitrosation mechanism.     

Ischemic preconditioning alters real-time measure of O2 radicals in intact hearts with ischemia and reperfusion

Reactive oxygen species (ROS) are believed to be involved in triggering cardiac ischemic preconditioning (IPC). Decreased formation of ROS on reperfusion after prolonged ischemia may in part underlie protection by IPC. In heart models, these contentions have been based either on the effect of ROS scavengers to abrogate IPC-induced preservation or on a measurement of oxidation products on reperfusion. Using spectrophotofluorometry at the left ventricular wall and the fluorescent probe dihydroethidium (DHE), we measured intracellular ROS superoxide (O(2)(-).) continuously in isolated guinea pig heart and tested the effect of IPC and the O(2)(-). scavenger manganese(III) tetrakis (4-benzoic acid) porphyrin chloride (MnTBAP) on O(2)(-). formation throughout the phases of preconditioning (PC), 30-min ischemia and 60-min reperfusion (I/R). IPC was evidenced by improved contractile function and reduced infarction; MnTBAP abrogated these effects. Brief PC pulses increased O(2)(-). during the ischemic but not the reperfusion phase. O(2)(-). increased by 35% within 1 min of ischemia, increased further to 95% after 20 min of ischemia, and decreased slowly on reperfusion. In the IPC group, O(2)(-). was not elevated over 35% during index ischemia and was not increased at all on reperfusion; these effects were abrogated by MnTBAP. Our results directly demonstrate how intracellular ROS increase in intact hearts during IPC and I/R and clarify the role of ROS in triggering and mediating IPC.