High‐throughput SNPs for all: genotyping‐in‐thousands

Understanding the genetic structure of species is essential for conservation. It is only with this information that managers, academics, user groups and land‐use planners can understand the spatial scale of migration and local adaptation, source‐sink dynamics and effective population size. Such information is essential for a multitude of applications including delineating management units, balancing management priorities, discovering cryptic species and implementing captive breeding programmes. Species can range from locally adapted by hundreds of metres (Pavey et al. 2010 ) to complete species panmixia (Côté et al. 2013 ). Even more remarkable is that this essential information can be obtained without fully sequenced or annotated genomes, but from mere (putatively) nonfunctional variants. First with allozymes, then microsatellites and now SNPs, this neutral genetic variation carries a wealth of information about migration and drift. For many of us, it may be somewhat difficult to remember our understanding of species conservation before the widespread usage of these useful tools. However most species on earth have yet to give us that ‘peek under the curtain’. With the current diversity on earth estimated to be nearly 9 million species (Mora et al. 2011 ), we have a long way to go for a comprehensive meta‐phylogeographic understanding. A method presented in this issue by Campbell and colleagues (Campbell et al. 2015 ) is a tool that will accelerate the pace in this area. Genotyping‐in‐thousands (GT‐seq) leverages recent advancements in sequencing technology to save many hours and dollars over previous methods to generate this important neutral genetic information.     

Stability of Lycopene in Oil‐in‐Water Emulsions

Lycopene can be dissolved within the oil phase of oil‐in‐water emulsions to increase bioavailability in water‐dispersible systems. It is sensitive to oxidative conditions and easily undergoes isomerization at high temperatures. Degradation kinetics and isomerization of lycopene in oil‐in‐water‐emulsions were investigated as a function of thermal treatment and oxygen content. Lycopene degradation was found to follow a first‐order kinetics and rate constants were determined. Higher temperatures are directly correlated with increasing lycopene losses. Moreover, thermal treatment leads to a significant decrease of the concentrations of all‐trans and 13‐cis isomer, while the concentration of the 9‐cis isomer increased. Oxygen‐free conditions reduce lycopene losses significantly.     

Resonance Raman quantification of the redox state of cytochromes b and c in‐vivo and in‐vitro

We observe the redox state changes with respiration of cytochromes b and c in mitochondria in a living Saccharomyces cerevisiae cell as well as in isolated mitochondria with the very use of Raman microspectroscopy. The possibility of monitoring the respiration activity of mitochondria in vivo and in vitro by Raman microspectroscopic quantification of the cytochrome redox states is suggested. It will lead to a new means to assess mitochondrial respiration activity in vivo and in vitro without using any labelling or genetic manipulation. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

From water‐in‐oil to oil‐in‐water emulsions to optimize the production of fatty acids using ionic liquids in micellar systems

Biocatalysis is nowadays considered as one of the most important tools in green chemistry. The elimination of multiple steps involved in some of the most complex chemical synthesis, reducing the amounts of wastes and hazards, thus increasing the reaction yields and decreasing the intrinsic costs, are the major advantages of biocatalysis. This work aims at improving the enzymatic hydrolysis of olive oil to produce valuable fatty acids through emulsion systems formed by long alkyl chain ionic liquids (ILs). The optimization of the emulsion and the best conditions to maximize the production of fatty acids were investigated. The stability of the emulsion was characterized considering the effect of several parameters, namely, the IL and its concentration and different water/olive oil volumetric ratios. ILs from the imidazolium and phosphonium families were evaluated. The results suggest that the ILs effect on the hydrolysis performance varies with the water concentration and the emulsion system formed, that is, water‐in‐oil or oil‐in‐water emulsion. Although at low water concentrations, the presence of ILs does not present any advantages for the hydrolysis reaction, at high water contents (in oil‐in‐water emulsions), the imidazolium‐based IL acts as an enhancer of the lipase catalytic capacity, super‐activating 1.8 times the enzyme, and consequently promoting the complete hydrolysis of the olive oil for the highest water contents [85% (v/v)]. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1473–1480, 2015     

Common Slope Tests for Bivariate Errors‐in‐Variables Models

Likelihood ratio tests are derived for bivariate normal structural relationships in the presence of group structure. These tests may also be applied to less restrictive models where only errors are assumed to be normally distributed. Tests for a common slope amongst those from several datasets are derived for three different cases – when the assumed ratio of error variances is the same across datasets and either known or unknown, and when the standardised major axis model is used. Estimation of the slope in the case where the ratio of error variances is unknown could be considered as a maximum likelihood grouping method. The derivations are accompanied by some small sample simulations, and the tests are applied to data arising from work on seed allometry.     

Multivariate statistical monitoring as applied to clean‐in‐place (CIP) and steam‐in‐place (SIP) operations in biopharmaceutical manufacturing

Multivariate statistical process monitoring (MSPM) is becoming increasingly utilized to further enhance process monitoring in the biopharmaceutical industry. MSPM can play a critical role when there are many measurements and these measurements are highly correlated, as is typical for many biopharmaceutical operations. Specifically, for processes such as cleaning‐in‐place (CIP) and steaming‐in‐place (SIP, also known as sterilization‐in‐place), control systems typically oversee the execution of the cycles, and verification of the outcome is based on offline assays. These offline assays add to delays and corrective actions may require additional setup times. Moreover, this conventional approach does not take interactive effects of process variables into account and cycle optimization opportunities as well as salient trends in the process may be missed. Therefore, more proactive and holistic online continued verification approaches are desirable. This article demonstrates the application of real‐time MSPM to processes such as CIP and SIP with industrial examples. The proposed approach has significant potential for facilitating enhanced continuous verification, improved process understanding, abnormal situation detection, and predictive monitoring, as applied to CIP and SIP operations. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:505–515, 2014     

Simulation‐selection‐extrapolation: Estimation in high‐dimensional errors‐in‐variables models

Errors‐in‐variables models in high‐dimensional settings pose two challenges in application. First, the number of observed covariates is larger than the sample size, while only a small number of covariates are true predictors under an assumption of model sparsity. Second, the presence of measurement error can result in severely biased parameter estimates, and also affects the ability of penalized methods such as the lasso to recover the true sparsity pattern. A new estimation procedure called SIMulation‐SELection‐EXtrapolation (SIMSELEX) is proposed. This procedure makes double use of lasso methodology. First, the lasso is used to estimate sparse solutions in the simulation step, after which a group lasso is implemented to do variable selection. The SIMSELEX estimator is shown to perform well in variable selection, and has significantly lower estimation error than naive estimators that ignore measurement error. SIMSELEX can be applied in a variety of errors‐in‐variables settings, including linear models, generalized linear models, and Cox survival models. It is furthermore shown in the Supporting Information how SIMSELEX can be applied to spline‐based regression models. A simulation study is conducted to compare the SIMSELEX estimators to existing methods in the linear and logistic model settings, and to evaluate performance compared to naive methods in the Cox and spline models. Finally, the method is used to analyze a microarray dataset that contains gene expression measurements of favorable histology Wilms tumors.     

Interface Concentrated‐Confinement Suppressing Cathode Dissolution in Water‐in‐Salt Electrolyte

Mass dissolution is one main problems for cathodes in aqueous electrolytes due to the strong polarity of water molecules. In principle, mass dissolution is a thermodynamically favorable process as determined by the Gibbs free energy. However, in real situations, dissolution kinetics, which include viscosity, dissolving mass mobility, and interface properties, are also a critical factor influencing the dissolution rate. Both thermodynamic and kinetic dissolving factors can be regulated by the ratio of salt to solvent in the electrolyte. In this study, concentration‐controlled cathode dissolution is investigated in a susceptible Na₃V₂(PO₄)₃ cathode whose time‐, cycle‐, and state‐of‐charge‐dependent dissolubility are evaluated by multiple electrochemical and chemical methods. It is verified that the super‐highly concentrated water‐in‐salt electrolyte has a high viscosity, low vanadium ion diffusion, low polarity of solvated water, and scarce solute?water dissolving surfaces. These factors significantly lower the thermodynamic‐controlled solubility and the dissolving kinetics via time and physical space local mass interfacial confinement, thereby inducing a new mechanism of interface concentrated‐confinement which improves the cycling stability in real aqueous rechargeable sodium‐ion batteries.     

Universal label‐free in‐process quantification of influenza virus‐like particles

Virus‐like particles (VLPs) are becoming established as vaccines, in particular for influenza pandemics, increasing the interest in the development of VLPs manufacturing bioprocess. However, for complex VLPs, the analytical tools used for quantification are not yet able to keep up with the bioprocess progress. Currently, quantification for Influenza relies on traditional methods: hemagglutination assay or Single Radial Immunodiffusion. These analytical technologies are time‐consuming, cumbersome, and not supportive of efficient downstream process development and monitoring. Hereby we report a label‐free tool that uses Biolayer interferometry (BLI) technology applied on an Octet platform to quantify Influenza VLPs at all stages of bioprocess. Human (α2,6‐linked sialic acid) and avian (α2,3‐linked sialic acid) biotinylated receptors associated with streptavidin biosensors were used, to quantify hemagglutinin content in several mono‐ and multivalent Influenza VLPs. The applied method was able to quantify hemagglutinin from crude samples up to final bioprocessing VLP product. BLI technology confirmed its value as a high throughput analytical tool with high sensitivity and improved detection limits compared to traditional methods. This simple and fast method allowed for real‐time results, which are crucial for in‐line monitoring of downstream processing, improving process development, control and optimization.     

The membrane proteome of stroma thylakoids from Arabidopsis thaliana studied by successive in‐solution and in‐gel digestion

From individual localization and large‐scale proteomic studies, we know that stroma‐exposed thylakoid membranes harbor part of the machinery performing the light‐dependent photosynthetic reactions. The minor components of the stroma thylakoid proteome, regulating and maintaining the photosynthetic machinery, are in the process of being unraveled. In this study, we developed in‐solution and in‐gel proteolytic digestion methods, and used them to identify minor membrane proteins, e.g. transporters, in stroma thylakoids prepared from Arabidopsis thaliana (L.) Heynh Columbia‐0 leaves. In‐solution digestion with chymotrypsin yielded the largest number of peptides, but in combination with methanol extraction resulted in identification of the largest number of membrane proteins. Although less efficient in extracting peptides, in‐gel digestion with trypsin and chymotrypsin led to identification of additional proteins. We identified a total of 58 proteins including 44 membrane proteins. Almost half are known thylakoid proteins with roles in photosynthetic light reactions, proteolysis and import. The other half, including many transporters, are not known as chloroplast proteins, because they have been either curated (manually assigned) to other cellular compartments or not curated at all at the plastid protein databases. Transporters include ATP‐binding cassette (ABC) proteins, transporters for K⁺ and other cations. Other proteins either have a role in processes probably linked to photosynthesis, namely translation, metabolism, stress and signaling or are contaminants. Our results indicate that all these proteins are present in stroma thylakoids; however, individual studies are required to validate their location and putative roles. This study also provides strategies complementary to traditional methods for identification of membrane proteins from other cellular compartments.     

Enhanced detection of in‐gel released N‐glycans by MALDI‐TOF‐MS

Many biologically relevant glycoproteins need to be separated on 1D‐ or 2D‐gels prior to analysis and are available in picomole amounts. Therefore, it is important to have optimized methods to unravel the glycome that combine in‐gel digestions with MALDI‐TOF‐MS. In this technical report, we investigated how the detection of in‐gel released N‐glycans could be improved by MALDI‐TOF‐MS. First, an AnchorChip target was tested and compared to ground steel target using several reference oligosaccharides. The highest signals were obtained with an AnchorChip target and D‐arabinosazone as the matrix; a LOD of 1.3 to 10 fmol was attained. Then, the effect of octyl‐β‐glucopyranoside, a nonionic detergent, was studied during in‐gel peptide‐N⁴‐(acetyl‐ß‐glucosaminyl) asparagine amidase F digestion of standard glycoproteins and during glycan extraction. Octyl‐β‐glucopyranoside increased the intensity and the amount of detected neutral as well as acidic N‐glycans. A LOD of under 7 pmol glycoprotein could be achieved.