Multidimensional chromatography: validation and efficient fishing for biomarkers and fractions containing them using the VisualCockpit software package

2-D native LC yields thousands of fractions especially when applied to sera of different origin. Checking reproducibility of repeated separation of the same serum or searching for biomarker candidates and fractions containing them requires finding, selection, and comparison of interesting data subsets out of huge data volumes. An innovative software package is applied that markedly enhances simplicity, velocity, and reliability of (i) check of reproducibility of the separation method and (ii) analysis of proteomes pertaining to different disease states.     

MAPRes: Mining association patterns among preferred amino acid residues in the vicinity of amino acids targeted for post-translational modifications

Post-translational modification (PTM) of a protein is an important event in regulating cellular functions. An algorithm, MAPRes, has been developed for mining associations among PTM sites and the preferred amino acids in their vicinity. The algorithm has been implemented to O-glycosylation and O-phosphorylation data (phosphorylated/glycosylated Ser/Thr/Tyr). The association patterns mined by MAPRes demonstrate significant correlations and the results are in conformity with the existing methods. These association rules/patterns will be helpful in predicting the sequences/motifs involved for specific PTMs in proteins.     

Validation and Quality Control of Protein Microarray-based Analytical Methods

Protein microarray technology is used mainly in the research laboratory and it is being used to uncover important diagnostic and prognostic markers that may one day emerge as routine clinical laboratory tests. It is important that these methods are subject to control procedures, in order to ensure that data of the highest quality are obtained. If quality is not controlled, the assay may yield erroneous results that would mask or confound meaningful diagnostic or prognostic associations. This chapter surveys the range of strategies designed to assure the analytical quality of protein microarray methods and it also highlights some of the potential pitfalls when moving these arrays into routine clinical practice. With the development of appropriate quality control and assurance measures, we anticipate protein microarray-based assays will be of substantial benefit in the future practice of laboratory medicine.     

Biological uncertainty

Heisenberg’s uncertainty relation has inspired speculations in a variety of scientific fields. Most of these speculations have wandered significantly far from the original formulation; yet, they may have been useful for a critical examination of methodological issues. As molecular genetics and its complexities evolve amid a backdrop of technological innovation, new “uncertainties” may have emerged. We present some of these uncertainties not as impediments, but as challenges to be recognized and managed.     

Evolution and biogeography of New Zealand's longjaw galaxiids (Osmeriformes: Galaxiidae): the genetic effects of glaciation and mountain building

1. The biological impact of glaciation in Southern Hemisphere freshwaters is poorly understood. Several large rivers of eastern South Island, New Zealand, represent a mosaic of glaciated and non-glaciated regions, and are thus well-suited for studies of post-glacial recolonization.
2. We conducted mtDNA analyses of South Island's endemic non-migratory longjaw galaxiids Galaxias prognathus and G. cobitinis (Osmeriformes: Galaxiidae) to test hypotheses of post-glacial recolonization, and to assess the vicariant effects of Pleistocene mountain building.
3. We analysed the phylogeography of longjaw cytochrome b sequences from 38 sites in central South Island ( n  = 83). On the basis of our sampling it seems that G. prognathus and G. cobitinis have a parapatric distribution in the Waitaki River system, their disjunction broadly coinciding with three large post-glacial lakes. Waitaki clades of both species are deeply divergent relative to conspecific taxa in drainages to the north and south.
4. Tests for recent population growth – predicted under post-glacial expansion of G. prognathus – do not refute recent recolonization of streams above glaciated lakes in the Waitaki River drainage. The apparent absence of potential 'source' populations from non-glaciated regions suggests a post-glacial population decline for G. prognathus below the Waitaki lakes.
5. Molecular clock calibrations based on several freshwater vicariant events elsewhere in New Zealand supported the geologically-derived hypothesis of Waitaki–Canterbury drainage isolation approximately 300 ka.     

Phytosociological data give biased estimates of species richness

Abstract. Large phytosociological data sets of three types of grassland and three types of forest vegetation from the Czech Republic were analysed with a focus on plot size used in phytosociological sampling and on the species‐area relationship. The data sets included 12975 relevés, sampled by different authors in different parts of the country between 1922 and 1999. It was shown that in the grassland data sets, the relevés sampled before the 1960s tended to have a larger plot size than the relevés made later on. No temporal variation in plot sizes used was detected in forest relevés. Species‐area curves fitted to the data showed unnatural shapes, with levelling‐off or even decrease in plot sizes higher than average. This distortion is explained by the subjective, preferential method of field sampling used in phytosociology. When making relevés in species‐poor vegetation, researchers probably tend to use larger plots in order to include more species. The reason for this may be that a higher number of species gives a higher probability of including presumed diagnostic species, so that the relevé can be more easily classified in the Braun‐Blanquet classification system. This attitude of phytosociologists has at least two consequences: (1) in phytosociological data bases species‐poor vegetation types are underrepresented or relevés are artificially biased towards higher species richness; (2) the suitability of phytosociological data for species richness estimation is severely limited.     

Ultra‐High Surface Area Activated Porous Asphalt for CO2 Capture through Competitive Adsorption at High Pressures

This study reports an improved method for activating asphalt to produce ultra‐high surface area porous carbons. Pretreatment of asphalt (untreated Gilsonite, uGil ) at 400 °C for 3 h removes the more volatile organic compounds to form pretreated asphalt ( uGil‐P ) material with a larger fraction of higher molecular weight π‐conjugated asphaltenes. Subsequent activation of uGil‐P at 900 °C gives an ultra‐high surface area (4200 m² g^?1) porous carbon material ( uGil‐900 ) with a mixed micro and mesoporous structure. uGil‐900 shows enhanced room temperature CO₂ uptake capacity at 54 bar of 154 wt% (35 mmol g^?1). The CH₄ uptake capacity is 37.5 wt% (24 mmol g^?1) at 300 bar. These are relevant pressures in natural gas production. The room temperature working CO₂ uptake capacity for uGil‐900 is 19.1 mmol g^?1 (84 wt%) at 20 bar and 32.6 mmol g^?1 (143 wt%) at 50 bar. In order to further assess the reliability of uGil‐900 for CO₂ capture at elevated pressures, the authors study competitive sorption of CO₂ and CH₄ on uGil‐900 at pressures from 1 to 20 bar at 25 °C. CO₂/CH₄ displacement constants are measured at 2 to 40 bar, and found to increase significantly with pressure and surface area.     

History cleans up messes: The impact of time in driving divergence and introgression in a tropical suture zone

Contact zones provide an excellent arena in which to address questions about how genomic divergence evolves during lineage divergence. They allow us to both infer patterns of genomic divergence in allopatric populations isolated from introgression and to characterize patterns of introgression after lineages meet. Thusly motivated, we analyze genome‐wide introgression data from four contact zones in three genera of lizards endemic to the Australian Wet Tropics. These contact zones all formed between morphologically cryptic lineage‐pairs within morphologically defined species, and the lineage‐pairs meeting in the contact zones diverged anywhere from 3.1 to 5.8 million years ago. By characterizing patterns of molecular divergence across an average of 11K genes and fitting geographic clines to an average of 7.5K variants, we characterize how patterns of genomic differentiation and introgression change through time. Across this range of divergences, we find that genome‐wide differentiation increases but becomes no less heterogeneous. In contrast, we find that introgression heterogeneity decreases dramatically, suggesting that time helps isolated genomes “congeal.” Thus, this work emphasizes the pivotal role that history plays in driving lineage divergence.     

Real‐time monitoring and control of the load phase of a protein A capture step

The load phase in preparative Protein A capture steps is commonly not controlled in real‐time. The load volume is generally based on an offline quantification of the monoclonal antibody (mAb) prior to loading and on a conservative column capacity determined by resin‐life time studies. While this results in a reduced productivity in batch mode, the bottleneck of suitable real‐time analytics has to be overcome in order to enable continuous mAb purification. In this study, Partial Least Squares Regression (PLS) modeling on UV/Vis absorption spectra was applied to quantify mAb in the effluent of a Protein A capture step during the load phase. A PLS model based on several breakthrough curves with variable mAb titers in the HCCF was successfully calibrated. The PLS model predicted the mAb concentrations in the effluent of a validation experiment with a root mean square error (RMSE) of 0.06 mg/mL. The information was applied to automatically terminate the load phase, when a product breakthrough of 1.5 mg/mL was reached. In a second part of the study, the sensitivity of the method was further increased by only considering small mAb concentrations in the calibration and by subtracting an impurity background signal. The resulting PLS model exhibited a RMSE of prediction of 0.01 mg/mL and was successfully applied to terminate the load phase, when a product breakthrough of 0.15 mg/mL was achieved. The proposed method has hence potential for the real‐time monitoring and control of capture steps at large scale production. This might enhance the resin capacity utilization, eliminate time‐consuming offline analytics, and contribute to the realization of continuous processing. Biotechnol. Bioeng. 2017;114: 368–373. © 2016 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals, Inc.     

建设适应重庆地区的区域医学影像信息和大数据分析平台

由于重庆地区的医疗水平参差不齐,所以建设重庆地区区域医疗影像信息化系统,实现各类影像信息共享,对提供高效的医疗卫生服务具有非常重要的意义。目前,建设重庆地区区域医疗影像交互平台面临着整体设计集成程度和扩展性不高、医学影像标准不统一、数据安全与质量标准不完整、平台没有整合大数据分析挖掘方法等问题。为此,首先对重庆地区区域影像平台的整体结构进行了设计,提出了区域影像交互平台的五层体系结构;其次在五层体系结构基础上制定和加强了影像数据标准和信息安全体系;并且在区域影像中心的基础上,嵌入了医学影像大数据分析工具。应用结果证明,交互平台具有较高的集成程度和扩展性,平台标准的制定和加强能有效的提高交互效率,加强数据安全和质量管理,并且平台可对海量数据进行有效的分析。