Effects of wild and farm-grown macroalgae on the growth of juvenile South African abalone Haliotis midae Linnaeus

The effect of various macroalgal diets on the growth of grow-out (>20 mm shell length) South African abalone Haliotis midae was investigated on a commercial abalone farm. The experiment consisted of four treatments: fresh kelp blades (Ecklonia maxima (Osbeck) Papenfuss) (c. 10% protein); farmed, protein-enriched Ulva lactuca Linnaeus (c. 26% protein) grown in aquaculture effluent; wild U. lactuca (c. 20% protein); and a combination diet of kelp blades + farmed U. lactuca. Abalone grew best on the combination diet (0.423 ± 0.02% weight d^?1 SGR [specific growth rate]; 59.593 ± 0.02 ?m d^?1 DISL [daily increment in shell length]; 1.093 final CF [condition factor]) followed by the kelp only diet (0.367 ± 0.02% weight d^?1 SGR; 53.148 ± 0.02 ?m d^?1 DISL; 1.047 final CF), then the farmed, protein-enriched U. lactuca only diet (0.290 ± 0.02% weight d^?1 SGR; 42.988 ± 0.03 um d”¹ DISL; 1.013 final CF) that in turn outperformed the wild U. lactuca only diet (-0.079 ± 0.01% weight d^?1 SGR; 3.745 ± 0.02 ?m d”^?1 DISL; 0.812 final CF). The results suggest that protein alone could not have accounted for the differences produced by the varieties of U. lactuca and that the gross energy content is probably important.     

Adjustment for exploratory cut-off selection in randomized clinical trials with survival endpoint

Defining the target population based on predictive biomarkers plays an important role during clinical development. After establishing a relationship between a biomarker candidate and response to treatment in exploratory phases, a subsequent confirmatory trial ideally involves only subjects with high potential of benefiting from the new compound. In order to identify those subjects in case of a continuous biomarker, a cut-off is needed. Usually, a cut-off is chosen that resulted in a subgroup with a large observed treatment effect in an exploratory trial. However, such a data-driven selection may lead to overoptimistic expectations for the subsequent confirmatory trial. Treatment effect estimates, probability of success, and posterior probabilities are useful measures for deciding whether or not to conduct a confirmatory trial enrolling the biomarker-defined population. These measures need to be adjusted for selection bias. We extend previously introduced Approximate Bayesian Computation techniques for adjustment of subgroup selection bias to a time-to-event setting with cut-off selection. Challenges in this setting are that treatment effects become time-dependent and that subsets are defined by the biomarker distribution. Simulation studies show that the proposed method provides adjusted statistical measures which are superior to naïve Maximum Likelihood estimators as well as simple shrinkage estimators.     

SIMEX for correction of dietary exposure effects with Box-Cox transformed data

Modelling dietary data, and especially 24-hr dietary recall (24HDR) data, is a challenge. Ignoring the inherent measurement error (ME) leads to biased effect estimates when the association between an exposure and an outcome is investigated. We propose an adapted simulation extrapolation (SIMEX) algorithm for modelling dietary exposures. For this purpose, we exploit the ME model of the NCI method where we assume the assumption of normally distributed errors of the reported intake on the Box-Cox transformed scale and of unbiased recalls on the original scale. According to the SIMEX algorithm, remeasurements of the observed data with additional ME are generated in order to estimate the association between the level of ME and the resulting effect estimate. Subsequently, this association is extrapolated to the case of zero ME to obtain the corrected estimate. We show that the proposed method fulfils the key property of the SIMEX approach, that is, that the MSE of the generated data will converge to zero if the ME variance converges to zero. Furthermore, the method is applied to real 24HDR data of the I.Family study to correct the effects of salt and alcohol intake on blood pressure. In a simulation study, the method is compared with the NCI method resulting in effect estimates with either smaller MSE or smaller bias in certain situations. In addition, we found our method to be more informative and easier to implement. Therefore, we conclude that the proposed method is useful to promote the dissemination of ME correction methods in nutritional epidemiology.     

C1188D mutation abolishes specific recognition between MLL1-CXXC domain and CpG site by inducing conformational switch of flexible N-terminal

Mixed lineage leukemia protein (MLL1 protein) recognizes the CpG site via its CXXC domain and is frequently associated with leukemia. The specific recognition is abolished by C1188D mutation, which also prevents MLL-related leukemia. In this paper, multiple molecular dynamic (MD) simulations were performed to investigate the mechanism of recognition and influences of C1188D mutation. Started from fully dissociated DNA and MLL1-CXXC domain, remarkably, the center of mass (COM) of MLL1-CXXC domain quickly concentrates on the vicinity of the CpG site in all 53 short MD simulations. Extended simulations of the wild type showed that the native complex formed in 500 ns among 4 of 53 simulations. In contrast, the C1188D mutant COM distributed broadly around the DNA and the native complex was not observed in any of the extended simulations. Simulations on the apo MLL1-CXXC domain further suggest that the wild type protein remained predominantly in an open form that closely resembles its structure in the native complex whereas C1188D mutant formed predominantly compact structures in which the N- terminal bends to D1188. This conformational switch hinders the formation of encounter complex, thus abolishes the recognition. Our study also provides clues to the study mechanism of recognition, by the CXXC domain from proteins like DNA methyltransferase and ten-eleven translocation enzymes.     

Noninvasive tool for optical online monitoring of individual biomass concentrations in a defined coculture

Cocultures bear great potential in the conversion of complex substrates and process intensification, as well as, in the formation of unique components only available due to inter-species interactions. Dynamic data of coculture composition is necessary for understanding and optimizing coculture systems. However, most standard online determined parameters measure the sum of all species in the reactor system. The kinetic behavior of the individual species remains unknown. Up to now, different offline methods are available to determine the culture composition, as well as the online measurement of fluorescence of genetically modified organisms. To avoid any genetic modification, a noninvasive online monitoring tool based on the scattered light spectrum was developed for microtiter plate cultivations. To demonstrate the potential, a coculture consisting of the bacterium Lactococcus lactis and the yeast Kluyveromyces marxianus was cultivated. Via partial least squares regression of scattered light spectra, the online determination of the individual biomass concentrations without further sampling and analyses is possible. The results were successfully validated by a Coulter counter-analysis, taking advantage of the different cell sizes of both organisms. The findings prove the applicability of the new method to follow in detail the dynamics of a coculture.     

A modified metabolic model for mixed culture fermentation with energy conserving electron bifurcation reaction and metabolite transport energy

A modified metabolic model for mixed culture fermentation (MCF) is proposed with the consideration of an energy conserving electron bifurcation reaction and the transport energy of metabolites. The production of H₂ related to NADH/NAD⁺ and Fdred/Fdox is proposed to be divided in three processes in view of energy conserving electron bifurcation reaction. This assumption could fine‐tune the intracellular redox balance and regulate the distribution of metabolites. With respect to metabolite transport energy, the proton motive force is considered to be constant, while the transport rate coefficient is proposed to be proportional to the octanol–water partition coefficient. The modeling results for a glucose fermentation in a continuous stirred tank reactor show that the metabolite distribution is consistent with the literature: (1) acetate, butyrate, and ethanol are main products at acidic pH, while the production shifts to acetate and propionate at neutral and alkali pH; (2) the main products acetate, ethanol, and butyrate shift to ethanol at higher glucose concentration; (3) the changes for acetate and butyrate are following an increasing hydrogen partial pressure. The findings demonstrate that our modified model is more realistic than previous proposed model concepts. It also indicates that inclusion of an energy conserving electron bifurcation reaction and metabolite transport energy for MCF is sound in the viewpoint of biochemistry and physiology. Biotechnol. Bioeng. 2013; 110: 1884–1894. © 2013 Wiley Periodicals, Inc.     

Environmental correlates of annual survival differ between two ecologically similar and congeneric owls

Understanding how survival is affected by the environment is essential to gain insight into population dynamics and the evolution of life‐history traits as well as to identify environmental selection pressures. However, we still have little understanding of the relative effect of different environmental factors and their interactions on demographic traits and population dynamics. Here we used two long‐term, individual‐based datasets on Tawny Owl Strix aluco (1981–2010) and Ural Owl S. uralensis (1986–2010) to undertake capture‐mark‐recapture analysis of annual survival of adult females in response to three biologically meaningful environmental variables and their two‐way interactions. Despite the similar ecology of these two species, their survival was associated with different and uncorrelated environmental drivers. The main correlate of Tawny Owl survival was an inverse association with snow depth (winter severity). For Ural Owl, high food (vole) abundance improved survival during years with deep snow, but was less important during years with little snow. In addition, Ural Owl survival was strongly density‐dependent, whereas Tawny Owl survival was not. Our findings advise caution in extrapolating demographic inferences from one species to another, even when they are very closely related and ecologically similar. Analyses including only one or few potential environmental drivers of a species' survival may lead to incomplete conclusions because survival may be affected by several factors and their interactions.     

农林废弃物混配基质的理化性质及其对油茶幼苗生长效应的综合评价

以腐熟的甘蔗渣( SB)、木薯皮( CP)、花生壳( PS)和火炭灰( BA)及园土( GS)为原料,按照不同体积比配制成9种混配基质,并以等体积比泥炭和园土混配基质为对照,对各基质的理化性质及基质中油茶( Camellia oleifera Abel)幼苗的生长状况进行比较;在对基质理化指标和油茶幼苗的壮苗指数进行线性回归分析和通径分析的基础上,采用主成分分析和综合评价法对各基质的育苗效果进行综合评价。结果表明：9种农林废弃物混配基质的容重、总孔隙度和毛管孔隙度分别为0.23~0.47 g·cm-3、60.90%~67.23%和46.53%~58.27%, pH 6.72~pH 7.14,各基质的速效氮含量、速效磷含量、速效钾含量、pH值、电导率和通气孔隙度均高于或显著高于对照,容重则显著低于对照。在不同基质中油茶幼苗的茎粗、单株叶片数、叶长、叶宽、叶绿素相对含量( SPAD)、单株茎叶干质量、单株根干质量和壮苗指数均存在一定差异,而株高和根冠比却无显著差异;其中S9混配基质也V( SB)：V( CP)：V( BA)=2：1：1页中幼苗的大部分生长指标较高,表现出明显的生长优势。线性回归和通径分析结果显示：除通气孔隙度外,基质的其他8个理化指标基本涵盖了影响幼苗壮苗指数的关键因素;其中,速效钾含量是对壮苗指数直接影响最大的负相关因子,而速效磷含量、电导率和总孔隙度对壮苗指数则有较大的正向直接作用,并且三者通过速效钾含量对壮苗指数产生较大的负向间接作用;此外,基质容重对壮苗指数也有一定的负向直接作用。综合评价结果显示：S9和S7混配基质也V( SB)：V( BA)：V( GS)=4：3：3页对油茶育苗效果的综合得分较高,分别为14.363和14.337,建议将S9混配基质作为油茶育苗的首选替代基质,S7混配基质作为备选基质。     

外源H2O2对盐碱混合胁迫下裸燕麦幼苗生长和抗性生理的影响

为探讨信号分子过氧化氢（H₂O₂）增强裸燕麦盐碱耐性的作用及其生理机制,以裸燕麦品种‘定莜6号’为材料,在日光温室内用珍珠岩培养幼苗至三叶一心期时叶面喷施0.01 mmol·L^-1 H₂O₂的同时根部浇灌75 mmol·L^-1盐碱混合溶液（NaCl：Na₂SO₄：NaHCO₃：Na₂CO₃=12：8：9：1）或添加H₂O₂淬灭剂二甲基硫脲（DMTU）,研究对幼苗生长及叶片光合色素含量、活性氧代谢和渗透调节物质积累的影响。结果表明：喷施H₂O₂能够缓解盐碱混合胁迫对裸燕麦幼苗生长的抑制,提高幼苗根长、株高和植株干重及叶片叶绿素a、叶绿素b、总叶绿素、类胡萝卜素含量和超氧化物歧化酶、过氧化物酶、过氧化氢酶、抗坏血酸过氧化物酶活性,降低超氧阴离子、H₂O₂、丙二醛、抗坏血酸、谷胱甘肽和游离氨基酸含量,促进抗氧化物质类黄酮、总酚和原花青素及渗透调节物质可溶性蛋白质、可溶性糖和脯氨酸积累。添加DMTU部分或完全逆转了H₂O₂的上述作用。采用隶属函数综合评价显示,喷施H₂O₂提高了盐碱混合胁迫下裸燕麦幼苗的综合评价值D,添加DMTU完全逆转了H₂O₂对D值的提升作用。表明外源H₂O₂通过参与活性氧代谢和渗透调节物质积累等生理代谢调控缓解盐碱混合胁迫诱导的氧化伤害和生长抑制,从而提高裸燕麦对盐碱胁迫的适应能力。