Peptide separation by Hydrophilic-Interaction Chromatography: a review

Recent developments in the separation of peptides by high-performance liquid chromatography (HPLC) using polar sorbents with less polar eluents are summarized in this review. This separation mode is now commonly referred to as Hydrophilic-Interaction Chromatography (HILIC). The retention mechanism and chromatographic behavior of polar solutes under HILIC conditions are studied on TSKgel Amide-80 columns, which consist of carbamoyl groups bonded to a silica gel matrix, using a mixture of acetonitrile (MeCN)–water containing 0.1% trifluoroacetic acid (TFA). Some applications are given in peptide field using Hydrophilic-Interaction Chromatography.     

Protein identification by liquid chromatography-mass spectrometry using retention time prediction

Liquid chromatography has been coupled with mass spectrometry to improve the dynamic range and to reduce the complexity of sample introduced to the mass spectrometer at any given time. The chromatographic separation also provides information on the analytes, such as peptides in enzymatic digests of proteins; information that can be used when identifying the proteins by peptide mass fingerprinting. This paper discusses a recently introduced method based on retention time prediction to extract information from chromatographic separations and the applications of this method to protein identification in organisms with small and large genomes.     

蛋白质组学分离检测技术研究进展

蛋白质组学是后基因组时代的新兴学科,是当今生命科学领域新的增长点,而其中的分离检测技术则是蛋白质组学得以迅速发展的重要基石。对蛋白质组学中的分离检测技术-双向凝胶电泳、色谱和质谱等技术近几年的发展现状及最新研究进展进行综述,并对本实验室在蛋白质组学方面的研究结合生物信息学的探索进行概述。     

A statistical method for chromatographic alignment of LC-MS data

Integrated liquid-chromatography mass-spectrometry (LC-MS) is becoming a widely used approach for quantifying the protein composition of complex samples. The output of the LC-MS system measures the intensity of a peptide with a specific mass-charge ratio and retention time. In the last few years, this technology has been used to compare complex biological samples across multiple conditions. One challenge for comparative proteomic profiling with LC-MS is to match corresponding peptide features from different experiments. In this paper, we propose a new method--Peptide Element Alignment (PETAL) that uses raw spectrum data and detected peak to simultaneously align features from multiple LC-MS experiments. PETAL creates spectrum elements, each of which represents the mass spectrum of a single peptide in a single scan. Peptides detected in different LC-MS data are aligned if they can be represented by the same elements. By considering each peptide separately, PETAL enjoys greater flexibility than time warping methods. While most existing methods process multiple data sets by sequentially aligning each data set to an arbitrarily chosen template data set, PETAL treats all experiments symmetrically and can analyze all experiments simultaneously. We illustrate the performance of PETAL on example data sets.     

农林生态系统中营养元素N、P、K流动的网络分析

对农林业系统沙兰杨-小麦-玉米群落类型中N、P、K流动网络分析表明,系统中N、P、K的循环指数分别为0.071、0.039、0.139,均小于传统的循环系数(CC等于回归量/吸收量),而在群落中的总滞留时间分别为22.41、79.72、26.57a.     

Synthesis,spectroscopic and chromatographic studies of sunflower oil biodiesel using optimized base catalyzed methanolysis

Methyl esters from vegetable oils have attracted a great deal of interest as substitute for petrodiesel to reduce dependence on imported petroleum and provide an alternate and sustainable source for fuel with more benign environmental properties. In the present study biodiesel was prepared from sunflower seed oil by transesterification by alkali-catalyzed methanolysis. The fuel properties of sunflower oil biodiesel were determined and discussed in the light of ASTM D6751 standards for biodiesel. The sunflower oil biodiesel was chemically characterized with analytical techniques like FT-IR, and NMR (¹H and ¹³C). The chemical composition of sunflower oil biodiesel was determined by GC–MS. Various fatty acid methyl esters (FAMEs) were identified by retention time data and verified by mass fragmentation patterns. The percentage conversion of triglycerides to the corresponding methyl esters determined by ¹H NMR was 87.33% which was quite in good agreement with the practically observed yield of 85.1%.     

Nutritional ecology of dimorphic herbivores: digestion and passage rates in Nubian ibex

We compared forage digestion and passage rates among three groups of Nubian ibex (Capra ibex nubiana) — mature males, non-lactating females, and lactating females — to test hypotheses relating intraspecific digestive ability to body mass and reproduction costs. We hypothesized that large males (60 kg) would exhibit longer forage retention times and more complete digestion of fermentable cell walls than adult females (23 kg). We tested these predictions by measuring digestion and retention of a grass hay and an alfalfa hay, forages that exhibited contrasting rates and extents of cell wall digestion. Consistent with predictions, males retained both forages longer than non-lactating females. However, by substantially increasing gut fill, lactating females increased both intake and retention time with respect to non-lactating females. Contrary to predictions, all three groups digested the grass (66% digestible) and alfalfa hay (63%) equally well. Alfalfa cell wall was less digestible than that of grass hay (60% vs 69% digestible), and retention time of alfalfa was consistently, but not statistically significantly, shorter. Fiber digestion was not correlated with retention time, emphasizing the ability of behavioral processes to modify digestion rate. We postulate that females achieved their greater digestion rate by masticating forages much more thoroughly than males.     

农林生态系统中营养元素N,P,K流动的网络分析

对农林业系统沙兰杨－小麦－玉米群落类型中Ｎ、Ｐ、Ｋ流动网络分析表明,系统中Ｎ、Ｐ、Ｋ的循环指数分别为０．０７１、０．０３９、０．１３９,均小于传统的循环系数（ＣＣ等于回归量／吸收量）,而在群落中的总滞留时间分别为２２．４１、７９．７２、２６．５７ａ．     

Preparation of high adsorption capacity bio-chars from waste biomass

Bio-chars with high adsorption capacity derived from rice-husks and corncobs were prepared at different retention times (RTs) in a pyrolysis reactor. At a fixed pyrolysis temperature, the pyrolysis RT is a key factor influencing the surface areas and functional group contents of the bio-chars, and further influencing their adsorption capacities. The results indicate that the bio-char prepared at RT of 1.6 s exhibits a higher phenol adsorption capacity (589 mg g⁻¹) than other bio-chars and many activated carbons reported in the literature. An adsorption mechanism based on acid-base interaction and hydrogen binding between phenol and the functional groups was proposed to elucidate the adsorption process. An economic evaluation of the use of bio-chars as adsorbents was made.     

The functional significance of the browser-grazer dichotomy in African ruminants

The allometric relationships for the fermentation rate of dry matter, the total energy concentration of volatile fatty acids (VFAs), the energy supplied from VFA production and the mass of the digesta contents within the rumen or caecum and proximal colon (hindgut) were used to test whether the digestive strategies of grazing and browsing African ruminants differ. The wet and dry mass of the contents of the rumen and hindgut were allometrically related to body mass (BM). These relationships did not differ between browsing and grazing ruminants. The fermentation rates in the rumen were strongly allometric and the intercepts of the relationships did not differ between browsers and grazers. The fermentation rates in the hindgut were not allometrically related to BM and did not differ between ruminants with different feeding habits. Likewise, the total energy concentration of the VFAs in the rumen and hindgut showed no allometric scaling and did not differ between browsing and grazing ruminants. The energy supplied by VFA production in both the rumen and hindgut of African ruminants scaled at around 0.8 with BM. Only in the case of the energy supplied by VFAs in the rumen were there significantly different intercepts for browsing and grazing ruminants. The energy supplied by VFA production in the rumen was inadequate to meet the energy requirements for maintenance of browsers and small grazers. The retention time of digesta in the alimentary tract was positively related to BM although there was no difference in the allometric relationships for grazers and browsers. The results of these analyses suggest that, after controlling for the effects of body mass, there is little difference in digestive strategy between African ruminants with different morphological adaptations of the gut.     

An economical device for carbon supplement in large-scale micro-algae production

One simple but efficient carbon-supplying device was designed and developed, and the correlative carbon-supplying technology was described. The absorbing characterization of this device was studied. The carbon-supplying system proved to be economical for large-scale cultivation of Spirulina sp. in an outdoor raceway pond, and the gaseous carbon dioxide absorptivity was enhanced above 78%, which could reduce the production cost greatly.     

Digestive constraints on an aquatic carnivore: effects of feeding frequency and prey composition on harbor seals

We hypothesized that increased feeding frequency in captive harbor seals would increase nutrient loads and thus reduce retention time and the digestive efficiency of natural prey. We measured daily feed intake and excretion during 6 feeding trials and fed herring (49% lipid), pollock (22% lipid) or an equal mix of each diet over 24 months. Animals were accustomed to feeding at either high or low frequency. Body mass and intake did not vary with season. Although mean retention times were similar between diets and feeding frequencies, solute and particulate digesta markers separated at high feeding frequency. Consistent dry matter digestibility resulted in greater gut fill from pollock than from herring. Digestible energy intakes from pollock were approximately 25% greater than from either herring or the mixed diet. Lipid digestibility of herring declined from 90% to 50% when lipid intake exceeded 60 g kg^–0.75 day^–1. Our hypothesis of a trade-off between intake and digestion was not supported for protein but was supported for lipid. Results of this study imply that a flexible digestive system for harbor seals can compensate for ingesting prey of lower energy density by increasing gut fill and enhancing protein and lipid assimilation, to sustain digestible energy intake.Abbreviations DM dry matter - DEI digestible energy intake - DIT diet-induced thermogenesis - FF feeding frequency - MRT mean retention time Communicated by: G. Heldmaier     

生物信息学及其在环境微生物研究中的应用

生物信息学的快速发展,推动了微生物信息学的建立。模式微生物基因组学的研究,极大地丰富了生物信息学的内容。微生物结构基因组学和功能基因组学研究试图揭示基因结构与功能的内在联系,绘制出基因调控网络图。基因组功能注释是功能基因组学研究的主要目的。基因芯片技术的运用,成为环境微生物生态研究和功能酶基因定位的有力工具。生物信息学为环境微生物的研究和发展提供了一个崭新的信息平台和技术手段。介绍了一些相关数据库和专业网站。