Tips on improving the efficiency of electrotransfer of target proteins from Phos‐tag SDS‐PAGE gel

The sensitivity of Western blotting analysis after Phos‐tag SDS‐PAGE is occasionally inferior to that after normal (Phos‐tag‐free) SDS‐PAGE under similar experimental conditions, possibly as a result of inefficient electrotransfer from the Phos‐tag gel to the blotting membrane. We therefore present tips on improving the efficiency of electrotransfer of proteins in semidry and wet‐tank blotting. When model samples containing several standard phosphoproteins were subjected to semidry blotting, their electrotransfer efficiencies after Phos‐tag SDS‐PAGE were markedly inferior to those of their dephosphorylated counterparts in the same gel. This was ameliorated by immersing the electrophoresed Phos‐tag gel in a transfer buffer containing 1 mM EDTA for 30 min before electroblotting. Similarly, phosphoproteomes in crude cell extracts were inefficiently transferred by semidry blotting, but the efficiencies of their electrotransfer were improved by pretreatment with EDTA. In contrast, the efficiencies of wet‐tank blotting of the same samples were not dependent on the degree of phosphorylation, and the efficiencies of electrotransfer of all proteins from Phos‐tag gels were similar to those from normal gels. In some cases involving the use of a Phos‐tag gel, addition of 0.1% w/v of SDS to the transfer buffer significantly improved the electrotransfer.     

Polysialic acid production using Escherichia coli K1 in a disposable bag reactor

Polysialic acid (polySia), consisting of α‐(2,8)‐linked N‐acetylneuraminic acid monomers plays a crucial role in many biological processes. This study presents a novel process for the production of endogenous polySia using Escherichia coli K1 in a disposable bag reactor with wave‐induced mixing. Disposable bag reactors provide easy and fast production in terms of regulatory requirements as GMP, flexibility, and can easily be adjusted to larger production capacities not only by scale up but also by parallelization. Due to the poor oxygen transfer rate compared to a stirred tank reactor, pure oxygen was added during the cultivation to avoid oxygen limitation. During the exponential growth phase the growth rate was 0.61 h^?1. Investigation of stress‐related product release from the cell surface showed no significant differences between the disposable bag reactor with wave‐induced mixing and the stirred tank reactor. After batch cultivation a cell dry weight of 6.8 g L^?1 and a polySia concentration of 245 mg L^?1 were reached. The total protein concentration in the supernatant was 132 mg L^?1. After efficient and time‐saving downstream processing characterization of the final product showed a protein content of below 0.04 mg_protein/g_polySia and a maximal chain length of ～90 degree of polymerization.     

坦克作业对乘员肾脏功能的影响

目的：观察坦克作业对乘员肾脏功能的影响。方法：在我军某坦克部队随机选取152名坦克乘员为观察组,在同一部队选取非坦克作业战士37名为对照组。留取24h尿和晨尿,检测尿中α1-微球蛋白（α1-MG）、β2-微球蛋白（β2-MG）、IgG、N-乙酰-β-葡萄糖苷酶（NAG）和尿微量白蛋白（UAE）排泄率。结果：与对照组比较,观察组尿α1-．MG、β2-MG、尿NAG、尿UAE均明显升高,且平均值均超过临床检验正常值,尿IgG无明显升高。其中从事坦克作业50摩托小时以上的坦克乘员尿中β2-MG、NAG、UAE均高于对照组（P〈0．05）,从事坦克作业51～100摩托小时的尿中α1-MG虽有升高,但未有统计学差异且平均值在正常范围内,从事坦克作业大于301摩托小时的坦克乘员尿中α1-MG显著高于对照组。脱离坦克作业3年后乘员尿中β2-MG、NAG、UAE降低至正常水平,但大于10年者尿中β2-MG再度出现升高,与6—10年组比较有显著差异（P〈0．05）。脱离坦克作业后坦克乘员尿中α1-MG虽有下降,但始终未降至正常水平。结论：坦克作业对乘员肾脏功能有一定影响,脱离坦克作业后乘员肾功能可得到较好的恢复,但远期仍遗留一定程度的肾小管重吸收功能障碍。     

Environmental DNA metabarcoding primers for freshwater fish detection and quantification: In silico and in tanks

Environmental DNA (eDNA) techniques refer to utilizing the organisms’ DNA extracted from environment samples to genetically identify target species without capturing actual organisms. eDNA metabarcoding via high‐throughput sequencing can simultaneously detect multiple fish species from a single water sample, which is a powerful tool for the qualitative detection and quantitative estimates of multiple fish species. However, sequence counts obtained from eDNA metabarcoding may be influenced by many factors, of which primer bias is one of the foremost causes of methodological error. The performance of 18 primer pairs for COI, cytb, 12S rRNA, and 16S rRNA mitochondrial genes, which are all frequently used in fish eDNA metabarcoding, were evaluated in the current study. The ribosomal gene markers performed better than the protein‐coding gene markers during in silico screening, resulting in higher taxonomic coverage and appropriate barcode lengths. Four primer pairs—AcMDB07, MiFish‐U, Ve16S1, and Ve16S3—designed for various regions of the 12S and 16S rRNA genes were screened for tank metabarcoding in a case study targeting six freshwater fish species. The four primer pairs were able to accurately detect all six species in different tanks, while only MiFish‐U, Ve16S1, and Ve16S3 revealed a significant positive relationship between species biomass and read count for the pooled tank data. The positive relationship could not be found in all species within the tanks. Additionally, primer efficiency differed depending on the species while primer preferential species varied in different fish assemblages. This case study supports the potential for eDNA metabarcoding to assess species diversity in natural ecosystems and provides an alternative strategy to evaluate the performance of candidate primers before application of eDNA metabarcoding in natural ecosystems.     

Pyranose 2-oxidase (P2O): Production from Trametes versicolor in Stirred Tank Reactor andits Partial Characterization

Abstract

Optimization of pyranose-2-oxidase (P2O) production conditions from Trametes versicolor was carried out in shaking cultures containing glucose, malt, and yeast extracts; the optimum concentration values were found to be 1.5% glucose, 1.0% yeast extract, and 1.0% malt extract, pH 5.0, temperature, 26°C, and agitation rate 150 rpm. For the first time, P2O production was also carried out in a stirred tank reactor (STR) with 2.2 L working volume in the optimized medium composition, and biomass, P2O activity, protein, nitrogen and glucose concentrations were also monitored besides pH and dissolved oxygen (DO). In the STR, P2O activity peaked on day 9. Partial enzyme characterization occurred and optimum pH and temperature were detected as 7.0 and 37°C, respectively. K _m value was found to be 1.009 mM.     

Rainfall and hydrological stability alter the impact of top predators on food web structure and function

Climate change will alter the distribution of rainfall, with potential consequences for the hydrological dynamics of aquatic habitats. Hydrological stability can be an important determinant of diversity in temporary aquatic habitats, affecting species persistence and the importance of predation on community dynamics. As such, prey are not only affected by drought‐induced mortality but also the risk of predation [a non‐consumptive effect (NCE)] and actual consumption by predators [a consumptive effect (CE)]. Climate‐induced changes in rainfall may directly, or via altered hydrological stability, affect predator–prey interactions and their cascading effects on the food web, but this has rarely been explored, especially in natural food webs. To address this question, we performed a field experiment using tank bromeliads and their aquatic food web, composed of predatory damselfly larvae, macroinvertebrate prey and bacteria. We manipulated the presence and consumption ability of damselfly larvae under three rainfall scenarios (ambient, few large rainfall events and several small rainfall events), recorded the hydrological dynamics within bromeliads and examined the effects on macroinvertebrate colonization, nutrient cycling and bacterial biomass and turnover. Despite our large perturbations of rainfall, rainfall scenario had no effect on the hydrological dynamics of bromeliads. As a result, macroinvertebrate colonization and nutrient cycling depended on the hydrological stability of bromeliads, with no direct effect of rainfall or predation. In contrast, rainfall scenario determined the direction of the indirect effects of predators on bacteria, driven by both predator CEs and NCEs. These results suggest that rainfall and the hydrological stability of bromeliads had indirect effects on the food web through changes in the CEs and NCEs of predators. We suggest that future studies should consider the importance of the variability in hydrological dynamics among habitats as well as the biological mechanisms underlying the ecological responses to climate change.     

Hydrodynamic stress induces monoterpenoid oxindole alkaloid accumulation by Uncaria tomentosa (Willd) D. C. cell suspension cultures via oxidative burst

Uncaria tomentosa cell suspension cultures were grown in a 2-L stirred tank bioreactor operating at a shear rate gamma(.)(avg)=86 s(-1). The cultures showed an early monophasic oxidative burst measured as H2O2 production (2.15 micromol H2O2 g(-1) dw). This response was followed by a transient production of monoterpenoid oxindole alkaloids (178 +/- 40 microg L(-1) at 24 h). At the stationary phase (144 h), the increase of the shear rate gamma(.)(avg) up to 150 s(-1) and/or oxygen tension up to 85% generated H2O2, restoring oxindole alkaloid production. U. tomentosa cells cultured in Erlenmeyer flasks also exhibited the monophasic oxidative burst but the H2O2 production was 16-fold lower and the alkaloids were not detected. These cells exposed to H2O2 generated in situ produced oxindole alkaloids reaching a maximum of 234 +/- 40 microg L(-1). A positive correlation was observed between the oxindole alkaloid production and the endogenous H2O2 level. On the other hand, addition of 1 microM diphenyleneiodonium (NAD(P)H oxidase inhibitor) or 10 microM sodium azide (peroxidases inhibitor) reduced both H2O2 production and oxindole alkaloids build up, suggesting that these enzymes might play a role in the oxidative burst induced by the hydrodynamic stress.     

Acclimation Strategy of a Biohydrogen Producing Population in a Continuous‐Flow Reactor with Carbohydrate Fermentation

Poor startup of biological hydrogen production systems can cause an ineffective hydrogen production rate and poor biomass growth at a high hydraulic retention time (HRT), or cause a prolonged period of acclimation. In this paper a new startup strategy was developed in order to improve the enrichment of the hydrogen‐producing population and the efficiency of hydrogen production. A continuously‐stirred tank reactor (CSTR) and molasses were used to evaluate the hydrogen productivity of the sewage sludge microflora at a temperature of 35 °C. The experimental results indicated that the feed to microorganism ratio (F/M ratio) was a key parameter for the enrichment of hydrogen producing sludge in a continuous‐flow reactor. When the initial biomass was inoculated with 6.24 g of volatile suspended solids (VSS)/L, an HRT of 6 h, an initial organic loading rate (OLR) of 7.0 kg chemical oxygen demand (COD)/(m³ × d) and an feed to microorganism ratio (F/M) ratio of about 2–3 g COD/(g of volatile suspended solids (VSS) per day) were maintained during startup. Under these conditions, a hydrogen producing population at an equilibrium state could be established within 30 days. The main liquid fermentation products were acetate and ethanol. Biogas was composed of H₂ and CO₂. The hydrogen content in the biogas amounted to 47.5 %. The average hydrogen yield was 2.01 mol/mol hexose consumed. It was also observed that a special hydrogen producing population was formed when this startup strategy was used. It is supposed that the population may have had some special metabolic pathways to produce hydrogen along with ethanol as the main fermentation products.     

Protein crystallization in stirred systems—scale‐up via the maximum local energy dissipation

Macromolecular bioproducts like therapeutic proteins have usually been crystallized with µL‐scale vapor diffusion experiments for structure determination by X‐ray diffraction. Little systematic know‐how exists for technical‐scale protein crystallization in stirred vessels. In this study, the Fab‐fragment of the therapeutic antibody Canakinumab was successfully crystallized in a stirred‐tank reactor on a 6 mL‐scale. A four times faster onset of crystallization of the Fab‐fragment was observed compared to the non‐agitated 10 µL‐scale. Further studies on a liter‐scale with lysozyme confirmed this effect. A 10 times faster onset of crystallization was observed in this case at an optimum stirrer speed. Commonly suggested scale‐up criteria (i.e., minimum stirrer speed to keep the protein crystals in suspension or constant impeller tip speed) were shown not to be successful. Therefore, the criterion of constant maximum local energy dissipation was applied for scale‐up of the stirred crystallization process for the first time. The maximum local energy dissipation was estimated by measuring the drop size distribution of an oil/surfactant/water emulsion in stirred‐tank reactors on a 6 mL‐, 100 mL‐, and 1 L‐scale. A comparable crystallization behavior was achieved in all stirred‐tank reactors when the maximum local energy dissipation was kept constant for scale‐up. A maximum local energy dissipation of 2.2 W kg^?1 was identified to be the optimum for lysozyme crystallization at all scales under study. Biotechnol. Bioeng. 2013; 110: 1956–1963. © 2013 Wiley Periodicals, Inc.