Generation of accurate peptide retention data for targeted and data independent quantitative LC‐MS analysis: Chromatographic lessons in proteomics

The emergence of data‐independent quantitative LC‐MS/MS analysis protocols further highlights the importance of high‐quality reproducible chromatographic procedures. Knowing, controlling and being able to predict the effect of multiple factors that alter peptide RP‐HPLC separation selectivity is critical for successful data collection for the construction of ion libraries. Proteomic researchers have often regarded RP‐HPLC as a “black box”, while vast amount of research on peptide separation is readily available. In addition to obvious parameters, such as the type of ion‐pairing modifier, stationary phase and column temperature, we describe the “mysterious” effects of gradient slope, column size and flow rate on peptide separation selectivity. Retention time variations due to these parameters are governed by the linear solvent strength (LSS) theory on a peptide level by the value of its slope S in the basic LSS equation—a parameter that can be accurately predicted. Thus, the application of shallower gradients, higher flow rates, or smaller columns will each increases the relative retention of peptides with higher S‐values (long species with multiple positively charged groups). Simultaneous changes to these parameters that each drive shifts in separation selectivity in the same direction should be avoided. The unification of terminology represents another pressing issue in this field of applied proteomics that should be addressed to facilitate further progress.     

Use of cyclodextrins as chiral selectors for direct resolution of the enantiomers of fluoxetine and its metabolite norfluoxetine by HPLC

The goal of this work is to investigate the direct chromatographic separation of the enantiomers of fluoxetine and its active metabolite norfluoxetine. The liquid chromatographic retention behavior of these enantiomers on a β-cyclodextrin bonded-phase column was investigated with respect to mobile phase composition, pH, ionic strength, and solvent selectivity. Relationships were established between these factors and the three most important chromatographic parameters: retention time, resolution, and selectivity. Most of the evidence suggests that the unique selectivity of this column isdue to inclusion complex formation, which provides the physical basis for enantiomeric resolution. After these studies a set of optimum chromatographic conditions was chosen for the simultaneous separation/determination of a mixture of the four enantiomers using fluorescence detector. © 1993 Wiley-Liss, Inc.     

An iterative approach from the standpoint of the additive hypothesis to the dendrogram problem posed by molecular data sets

The problem of constructing a dendrogram depicting phylogenetic relationships for a collection of contemporary species is considered. An approach was developed based on the additive hypothesis in which each “length” between two species can be described by the shortest sum of lengths for the individual links on the dendrogram topology which connect the two species. The additive hypothesis holds equally well if the dendro gram is replaced by its corresponding (rootless) network. Network topologies are defined set theoretically in terms of the initial, contemporary species, and a coefficient is defined for each point of any conceivable network. It is proved mathematically that each point of an additive network gives a coefficient value of zero, whereas each point not belonging to an additive network gives a coefficient value greater than zero. This suggests an iterative procedure in which “false” network points are replaced by “true” ones, or more generally in which “very false” network points are replaced by “nearly true” ones. The first procedure follows from the mathematical proof and the second is confirmed by simulation. Since most real data sets are not additive in the strict sense, a real data example was presented in which the iterative procedure produced a plausible network topology.     

Two shades of boldness: novel object and anti-predator behavior reflect different personality dimensions in domestic rabbits

It is increasingly common to quantify and describe behavioral variation in domestic and wild animals in terms of “personality”. Correlating behavioral traits are referred to as personality “dimensions” or “factors” and different dimensions have been reported in different species. “Boldness” is a well-described personality dimension in several species, although some issues remain unclear. Previous models of boldness include both novelty and risk taking, but recent studies indicate that these types of behaviors may reflect separate personality dimensions. In this study, we developed a behavioral test battery for domestic rabbits, and recorded behaviors of 61 individuals in four different situations (novel object, novel arena, social, and predator interactions). We used domestic rabbits as a model because behavioral variation in rabbits has rarely been quantified in terms of personality dimensions, although rabbit behavior is described. We also wanted to investigate behavioral variation in a Swedish rabbit breed of conservation concern — the Gotland rabbit. Factor analysis of the behavioral test measures suggested three personality dimensions: “exploration”, “boldness”, and “anxiety”. Novel object scores clustered in the exploration and boldness factors, whereas scores associated with predator interactions were explained by “anxiety”, indicating that novel object and anti-predator behavior reflect different personality dimensions in rabbits.     

Optimization of throughput in semipreparative chiral liquid chromatography using stacked injection

An interesting mode of chromatography for preparation of pure enantiomers from pure samples is the method of stacked injection as a pseudocontinuous procedure. Maximum throughput and minimal production costs can be achieved by the use of total chiral column length in this mode of chromatography. To maximize sample loading, often touching bands of the two enantiomers is automatically achieved. Conventional equations show direct correlation between touching‐band loadability and the selectivity factor of two enantiomers. The important question for one who wants to obtain the highest throughput is “How to optimize different factors including selectivity, resolution, run time, and loading of the sample in order to save time without missing the touching‐band resolution?” To answer this question, tramadol and propranolol were separated on cellulose 3,5‐dimethyl phenyl carbamate, as two pure racemic mixtures with low and high solubilities in mobile phase, respectively. The mobile phase composition consisted of n‐hexane solvent with alcohol modifier and diethylamine as the additive. A response surface methodology based on central composite design was used to optimize separation factors against the main responses. According to the stacked injection properties, two processes were investigated for maximizing throughput: one with a poorly soluble and another with a highly soluble racemic mixture. For each case, different optimization possibilities were inspected. It was revealed that resolution is a crucial response for separations of this kind. Peak area and run time are two critical parameters in optimization of stacked injection for binary mixtures which have low solubility in the mobile phase.     

Get a grip: Podosomes as potential players in phagocytosis

Podosomes have been known for several decades as micron-sized, F-actin-rich structures that play a pivotal role in cell migration and invasion, as they are able to mediate both cell-matrix attachment as well as extracellular matrix degradation. Particularly in monocytic cells, podosomes have been shown to fulfill a variety of additional functions such as sensing of substrate rigidity and topography, or cell-cell fusion. Increasing evidence now points to the involvement of podosome-like structures also during phagocytosis by immune cells such as macrophages, dendritic cells, and neutrophils. Here, we compare the different cell models and experimental set ups where “phagocytic podosomes” have been described. We also discuss the composition and architecture of these structures, their potential involvement in mechanosensing and particle disruption, as well as the pros and cons for addressing them as bona fide podosomes.     

A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography

The limitation of using low electron doses in non-destructive cryo-electron tomography of biological specimens can be partially offset via averaging of aligned and structurally homogeneous subsets present in tomograms. This type of sub-volume averaging is especially challenging when multiple species are present. Here, we tackle the problem of conformational separation and alignment with a “collaborative” approach designed to reduce the effect of the “curse of dimensionality” encountered in standard pair-wise comparisons. Our new approach is based on using the nuclear norm as a collaborative similarity measure for alignment of sub-volumes, and by exploiting the presence of symmetry early in the processing. We provide a strict validation of this method by analyzing mixtures of intact simian immunodeficiency viruses SIV mac239 and SIV CP-MAC. Electron microscopic images of these two virus preparations are indistinguishable except for subtle differences in conformation of the envelope glycoproteins displayed on the surface of each virus particle. By using the nuclear norm-based, collaborative alignment method presented here, we demonstrate that the genetic identity of each virus particle present in the mixture can be assigned based solely on the structural information derived from single envelope glycoproteins displayed on the virus surface.     

On the structure of liver ribosomes

The morphology of liver ribosomes and their subparticles, large and small, has been investigated. Analysis of the images has been carried out by successive selection of models and by X-raying them under conditions simulating negative staining. The relation between the main views has been checked by tilting the specimens in an electron microscope through ± 30 °.The small subparticle consists of an elongated body, to one of the ends of which a short “head” is attached. A model has been proposed, whose projections on rotation with respect to the longitudinal axis would satisfy all observable types of images. According to the proposed model, the “head” is tilted with respect to the elongated portion. The length of the subparticle is 230 Å. The dimensions of the elongated portion in the transverse direction are 110 Å × 75 to 80 Å.The large subparticles in lateral view resemble short “rods” 220 to 240 Å long and about 70 to 95 Å wide. At a distance of about 60 Å from the left end of the particles a projection (60 Å in length) is seen, on the inner side of which a depression, or “channel”, filled with the contrasting substance is always observed. Next to this depression a second projection is located, whose height is about 30 Å. The channel is either a cavity in the body of the large subparticle or a part of the RNA without protein. The length of the channel is about 80 Å, the width is about 50 to 60 Å. The left end of the particles is characterized by two sharpened portions; as a result, a cavity that shows an obtuse angle profile makes its appearance. The opposite end of the particles is cut off at an angle of 45 °. In another view, the subparticles appear to be almost rectangular in shape; they are characterized by dimensions of 150 Å × 220 to 240 Å. It is likely that the large projection is displaced sideways with respect to the longitudinal axis of the particles. The asymmetry associated with this displacement gives rise to preferred arrangements of the subparticles on the supporting film. An analysis has been made of the most typical images of monomeric ribosomes, on the basis of which a suggestion is made about mutual orientation of subparticles in a monomer.     

Fast separation of 16 seizure drug substances using non-aqueous capillary electrophoresis

A fast and simple method for separation of 16 seizure drug substances using capillary electrophoresis in a non-aqueous separation medium is described. The separation medium consists of a mixture of acetonitrile, methanol and glycerol with ammonium acetate/acetic acid as the electrolyte. The analytes are detected by UV detection at 214 nm. Injection from the detection end (8.5 cm to detector) combined with the usage of a short capillary (32.5 cm total length) makes it possible to separate all 16 amines within 2 min. The choice of solvents, electrolytes and viscosity increasing additives are discussed with special emphasis to their influence on the separation selectivity.     

Two-dimensional microcolumn separation platform for proteomics consisting of on-line coupled capillary isoelectric focusing and capillary electrochromatography. 1. Evaluation of the capillary-based two-dimensional platform with proteins, peptides, and human serum

In this report, an on-line coupling of capillary isoelectric focusing (CIEF) to capillary electrochromatography (CEC) is developed via a nanoinjector valve for performing two-dimensional (2D) proteomics separation. CIEF constitutes the first separation dimension, while CEC operates as the second separation dimension. Besides the orthogonal migration mechanisms of the two capillary-based separation modes, which lead to a 2D system whose overall peak capacity is the product of the peak capacity of the individual modes, the solvent of the CIEF mode is a weak eluent for the reversed-phase CEC (RP-CEC) mode, thus, allowing the transferring of focused fractions from CIEF to CEC without inducing band broadening, and instead zone sharpening would result. In fact, the transferred focused protein fraction from the CIEF column to the CEC column will stay tightly adsorbed to the inlet top of the CEC column until it will be eluted and separated into its protein components with a hydro-organic mobile phase. The theoretical peak capacity of the CIEF-CEC 2D platform is estimated at n(CIEF) (= 560) x n(CEC) (= 97) = 54 320. This peak capacity is more than needed for proteomics profiling. Also, only a fraction of this peak capacity is needed when looking at heart cuts for performing subproteomics. The 2D platform described here offers the convenience to generate the needed peak capacity to solve a given proteomic separation problem. This is facilitated by the RP-CEC dimension, which ensures rapid isocratic separation of proteins and peptides and rapid solvent change and column equilibration and avoids lengthy gradient elution. The RP-CEC column is based on neutral C17 monolith, which offers high separation efficiency and relatively high column permeability. To the best of our knowledge, the proposed 2D platform combining CIEF and CEC is reported for the first time for proteins and proteomics.     

六种沉水植物的克隆生长特征

为构建种群动态模型以指导沉水植被修复工程实践, 研究采用同质园实验方法对6种常见沉水植物(竹叶眼子菜(Potamogeton wrightii)、眼子菜(P. distinctus)、光叶眼子菜(P. lucens)、穿叶眼子菜(P. perfoliatus)、扭叶眼子菜(P. intortifolius)和苦草(Vallisneria natans)的克隆生长模式进行了连续观测研究, 获取了分株形成速率、空间扩张速率、株高增加速率等种群扩张动态参数,及分株数、间隔子长度、分株高度等克隆构件特征参数。结果表明, 6种沉水植物的分株数从28d开始增长, 其中苦草的分株形成速率最高, 平均为1.09株/d, 分株形成最大速率出现在55d之后; 穿叶眼子菜和扭叶眼子菜的分株形成速率低于苦草, 但是高于竹叶眼子菜、眼子菜和光叶眼子菜, 最大速率出现在41d之后。虽然苦草的分株最多, 但是分株的株高最低, 其株高增长速率均值为0.2 cm/d。眼子菜属物种中竹叶眼子菜和眼子菜株高增长速率最高, 光叶眼子菜的株高增长速率和分株形成速率都最低。克隆系占据面积随时间的扩张速率为穿叶眼子菜(113.22 cm2/d)>扭叶眼子菜(71.70 cm2/d)>苦草(35.48 cm2/d)>竹叶眼子菜(12.09 cm2/d)>眼子菜(3.07 cm2/d)>光叶眼子菜(0.53 cm2/d)。此外, 研究还发现眼子菜属植物普遍表现出匍匐茎上“节”的形成, 而苦草则不具备这种特性, 匍匐茎“节”的形成及随之形成的不定根在眼子菜属植物空间扩张过程中具有重要的生态功能, 并在种群构建方面与苦草等其他物种发生分异。基于眼子菜属植物匍匐茎上的“节”可以形成跳跃性的分株, 在种群面积扩张方面更具优势; 而苦草形成分株的数量更多、速度更快, 在提高种群密度保障种群稳定方面更有优势。     

OIL FLOWERS AND OIL BEES: FURTHER EVIDENCE FOR POLLINATOR ADAPTATION

We examined foreleg length and body size variation in two species of oil-collecting bees (Rediviva; Melittidae) in southern Africa. Oil-collecting bees harvest oil from host flowers by rubbing their forelegs against oil-secreting trichomes. Significant differences in foreleg length occur among populations of both species. Rediviva “pallidula” populations vary significantly in mean foreleg length (11.34 ± 0.42 mm to 12.67 ± 0.36 mm), but not in body length (10.59 ± 0.74 to 10.80 ± 0.64), and foreleg length and body size are not significantly correlated. Instead, foreleg variation appears to be a function of host plant spur length. Ninety-two percent of the variance in foreleg length of R. “pallidula” is explained by mean Diascia spur length. Rediviva rufocincta populations vary significantly in mean foreleg length (10.12 ± 0.70 mm to 12.34 ± 0.68 mm) and in body length (9.03 ± 0.26 mm to 10.56 ± 0.24 mm). Foreleg length scales allometrically with body size in this species as 90.5% of the variance in foreleg length can be explained as a function of body length. Body size appears to be constrained by the morphology of the oil-secreting host plant. Both bees collect floral oil with specially modified setae on the tarsi of their forelegs. The length of the disti- + mediotarsus (refered to here as “tarsus”) in relation to the entire foreleg is shorter in R. rufocincta and does not increase as rapidly with increasing foreleg length as for R. “pallidula.” These differences in variation can be attributed to differences in position of oil within the flowers of the respective host plants. Rediviva “pallidula” collects oil from Diascia species that have the oil deeply situated in narrow floral spurs of varying length, while R. rufocincta collects oil from the broadly saccate flowers of Bowkeria verticillata and B. citrina.     

Sex and the fixation of single favourable mutations

Sexual populations will accumulate favourable mutations more rapidly than asexual populations. This is true if it is often the case that two different favourable mutations can be found to be spreading simultaneously through populations. It is argued here that sexual species will incorporate single favourable mutations more quickly than asexual “species”, if the latter are multi-clonal. Thus one mutation can spread to fixation within a sexual species but in an asexual “species” with N_c clones at least N_c mutations must occur if the mutation is to be subsequently found in every member of the “species”. Asexual “species” may minimise this disadvantage by evolving polyploidy or occasional episodes of hybridisation. Both are in fact common in asexual “species”.     

Causal mechanisms of evolution and the capacity for niche construction

Ernst Mayr proposed a distinction between “proximate”, mechanistic, and “ultimate”, evolutionary, causes of biological phenomena. This dichotomy has influenced the thinking of many biologists, but it is increasingly perceived as impeding modern studies of evolutionary processes, including study of “niche construction” in which organisms alter their environments in ways supportive of their evolutionary success. Some still find value for this dichotomy in its separation of answers to “how?” versus “why?”questions about evolution. But “why is A?” questions about evolution necessarily take the form “how does A occur?”, so this separation is illusory. Moreover, the dichotomy distorts our view of evolutionary causality, in that, contra Mayr, the action of natural selection, driven by genotype-phenotype-environment interactions which constitute adaptations, is no less “proximate” than the biological mechanisms which are altered by naturally selected genetic variants. Mayr’s dichotomy thus needs replacement by more realistic, mechanistic views of evolution. From a mechanistic viewpoint, there is a continuum of adaptations from those evolving as responses to unchanging environmental pressures to those evolving as the capacity for niche construction, and intermediate stages of this can be identified. Some biologists postulate an association of “phenotypic plasticity” (phenotype-environment covariation with genotype held constant) with capacity for niche construction. Both “plasticity” and niche construction comprise wide ranges of adaptive mechanisms, often fully heritable and resulting from case-specific evolution. Association of “plasticity” with niche construction is most likely to arise in systems wherein capacity for complex learning and behavioral flexibility have already evolved.     

Investigation of an on-line two-dimensional chromatographic approach for peptide analysis in plasma by LC–MS–MS

Reversed phase and hydrophilic interaction chromatography (HILIC) were successfully coupled for the on-line extraction and quantitative analysis of peptides by ESI–LC–MS/MS. A total of 11 peptides were utilized to determine the conditions for proper focusing and separation on both dimensions. Minor modifications to the initial organic composition of the first reversed-phase dimension provided options between a comprehensive (generic) or more selective approach for peptide transfer to the second HILIC dimension. Ion-pairing with trifluoroacetic acid (TFA) provided adequate chromatographic retention and peak symmetry for the selected peptides on both C₁₈ and HILIC. The resulting signal suppression from TFA was partially recovered by a post-column “TFA fix” using acetic acid yielding improvements in sensitivity. Minimal sample preparation aligned with standard on-line extraction procedures provided highly reproducible and robust results for over 300 sequential matrix injections. Final optimized conditions were successfully employed for the quantitation of peptide PTHrP (1–36) in rat K₃EDTA plasma from 25.0 to 10,000 ng/mL using PTHrP (1–34) as the analog internal standard. This highly orthogonal two-dimensional configuration was found to provide the unique selectivity required to overcome issues with interfering endogenous components and minimize electrospray ionization effects in biological samples.     

Exploiting the functional and taxonomic structure of genomic data by probabilistic topic modeling

In this paper, we present a method that enable both homology-based approach and composition-based approach to further study the functional core (i.e., microbial core and gene core, correspondingly). In the proposed method, the identification of major functionality groups is achieved by generative topic modeling, which is able to extract useful information from unlabeled data. We first show that generative topic model can be used to model the taxon abundance information obtained by homology-based approach and study the microbial core. The model considers each sample as a “document,” which has a mixture of functional groups, while each functional group (also known as a “latent topic”) is a weight mixture of species. Therefore, estimating the generative topic model for taxon abundance data will uncover the distribution over latent functions (latent topic) in each sample. Second, we show that, generative topic model can also be used to study the genome-level composition of “N-mer” features (DNA subreads obtained by composition-based approaches). The model consider each genome as a mixture of latten genetic patterns (latent topics), while each functional pattern is a weighted mixture of the “N-mer” features, thus the existence of core genomes can be indicated by a set of common N-mer features. After studying the mutual information between latent topics and gene regions, we provide an explanation of the functional roles of uncovered latten genetic patterns. The experimental results demonstrate the effectiveness of proposed method.     

"Noise" as a unifying concept in the theory of schizophrenia

The psychological effects of pharmacologically active substances can only be adequately described in terms of the psychological processes upon which they act. Psychopharmacology therefore depends on the development of psychological “models”, i.e. formally stated and testable hypotheses concerning the psychological processes required for the performance of any given task. Information theory is not concerned with the physical nature of events but only with those features which confer specificity upon them. It therefore provides a suitable theoretical language in which to describe interactions between biochemical, neurophysiological and psychological events. (i) The first section of this paper defines the information-theory concept of noise. Starting from first principles with the “noisy channel” and progressing to the “noisy system”, some of its psychophysiological implications are explored. (ii) An “order-memory” task is described which was used for three years to study the thinking of acutely disturbed young adult psychiatric patients, including many with acute schizophrenia. On the basis of a simple model, it is possible to calculate the value of a “critical” noise-level which marks the dividing line between two qualitatively different modes of functioning. (iii) A number of results are either reported or summarized, which show the functional significance of a supra-critical noise-level and its connection with the acute schizophrenic state. (iv) A “control-theory” approach to schizophrenia is outlined, which shows how specific and non-specific hereditary factors could be accommodated in the hypothesis but mainly emphasizes the concept of a mutual struggle for control between parent and child, in which the “loser” overloads the regulatory capacity of the other by “going noisy”. In this way the “loser” escapes from control but is more or less disabled by his own cognitive noise.     

Ion binding to KcsA: implications in ion selectivity and channel gating

Binding of K+ and Na+ to the potassium channel KcsA has been characterized from the stabilization observed in the heat-induced denaturation of the protein as the ion concentration is increased. KcsA thermal denaturation is known to include (i) dissociation of the homotetrameric channel into its constituent subunits and (ii) protein unfolding. The ion concentration-dependent changes in the thermal stability of the protein, evaluated as the Tm value for thermal-induced denaturation of the protein, may suggest the existence of both high- and low-affinity K+ binding sites of KcsA, which lend support to the tenet that channel gating may be governed by K+ concentration-dependent transitions between different affinity states of the channel selectivity filter. We also found that Na+ binds to KcsA with a KD similar to that estimated electrophysiologically from channel blockade. Therefore, our findings on ion binding to KcsA partly account for K+ over Na+ selectivity and Na+ blockade and argue against the strict “snug fit” hypothesis used initially to explain ion selectivity from the X-ray channel structure. Furthermore, the remarkable effects of increasing the ion concentration, K+ in particular, on the Tm of the denaturation process evidence that synergistic effects of the metal-mediated intersubunit interactions at the channel selectivity filter are a major contributor to the stability of the tetrameric protein. This observation substantiates the notion of a role for ions as structural “effectors” of ion channels.     

Optimization of reversed-phase peptide liquid chromatography ultraviolet mass spectrometry analyses using an automated blending methodology.

The balance between chromatographic performance and mass spectrometric response has been evaluated using an automated series of experiments where separations are produced by the real-time automated blending of water with organic and acidic modifiers. In this work, the concentration effects of two acidic modifiers (formic acid and trifluoroacetic acid) were studied on the separation selectivity, ultraviolet, and mass spectrometry detector response, using a complex peptide mixture. Peptide retention selectivity differences were apparent between the two modifiers, and under the conditions studied, trifluoroacetic acid produced slightly narrower (more concentrated) peaks, but significantly higher electrospray mass spectrometry suppression. Trifluoroacetic acid suppression of electrospray signal and influence on peptide retention and selectivity was dominant when mixtures of the two modifiers were analyzed. Our experimental results indicate that in analyses where the analyzed components are roughly equimolar (e.g., a peptide map of a recombinant protein), the selectivity of peptide separations can be optimized by choice and concentration of acidic modifier, without compromising the ability to obtain effective sequence coverage of a protein. In some cases, these selectivity differences were explored further, and a rational basis for differentiating acidic modifier effects from the underlying peptide sequences is described.