Citropin 1.1 Trifluoroacetate to Chloride Counter-Ion Exchange in HCl-Saturated Organic Solutions: An Alternative Approach

In view of the increasing interest in peptides in various market sectors, a stronger emphasis on topics related to their production has been seen. Fmoc-based solid phase peptide synthesis, although being fast and efficient, provides final products with significant amounts of trifluoroacetate ions in the form of either a counter-ion or an unbound impurity. Because of the proven toxicity towards cells and peptide activity inhibition, ion exchange to more biocompatible one is purposeful. Additionally, as most of the currently used counter-ion exchange techniques are time-consuming and burdened by peptide yield reduction risk, development of a new approach is still a sensible solution. In this study, we examined the potential of peptide counter-ion exchange using non-aqueous organic solvents saturated with HCl. Counter-ion exchange of a model peptide, citropin 1.1 (GLFDVIKKVASVIGGL-NH₂), for each solvent was conducted through incubation with subsequent evaporation under reduced pressure, dissolution in water and lyophilization. Each exchange was performed four times and compared to a reference method—lyophilization of the peptide from an 0.1 M HCl solution. The results showed superior counter-ion exchange efficiency for most of the organic solutions in relation to the reference method. Moreover, HCl-saturated acetonitrile and tert-butanol provided a satisfying exchange level after just one repetition. Thus, those two organic solvents can be potentially introduced into routine peptide counter-ion exchange.     

Dimensionality of Social Networks Using Motifs and Eigenvalues

We consider the dimensionality of social networks, and develop experiments aimed at predicting that dimension. We find that a social network model with nodes and links sampled from an m-dimensional metric space with power-law distributed influence regions best fits samples from real-world networks when m scales logarithmically with the number of nodes of the network. This supports a logarithmic dimension hypothesis, and we provide evidence with two different social networks, Facebook and LinkedIn. Further, we employ two different methods for confirming the hypothesis: the first uses the distribution of motif counts, and the second exploits the eigenvalue distribution.     

Dimensionality Reduction of Bistable Biological Systems

Time hierarchies, arising as a result of interactions between system’s components, represent a ubiquitous property of dynamical biological systems. In addition, biological systems have been attributed switch-like properties modulating the response to various stimuli across different organisms and environmental conditions. Therefore, establishing the interplay between these features of system dynamics renders itself a challenging question of practical interest in biology. Existing methods are suitable for systems with one stable steady state employed as a well-defined reference. In such systems, the characterization of the time hierarchies has already been used for determining the components that contribute to the dynamics of biological systems. However, the application of these methods to bistable nonlinear systems is impeded due to their inherent dependence on the reference state, which in this case is no longer unique. Here, we extend the applicability of the reference-state analysis by proposing, analyzing, and applying a novel method, which allows investigation of the time hierarchies in systems exhibiting bistability. The proposed method is in turn used in identifying the components, other than reactions, which determine the systemic dynamical properties. We demonstrate that in biological systems of varying levels of complexity and spanning different biological levels, the method can be effectively employed for model simplification while ensuring preservation of qualitative dynamical properties (i.e., bistability). Finally, by establishing a connection between techniques from nonlinear dynamics and multivariate statistics, the proposed approach provides the basis for extending reference-based analysis to bistable systems.     

Dimensionality reduction for visualization of normal and pathological speech data

For an adequate analysis of pathological speech signals, a sizeable number of parameters is required, such as those related to jitter, shimmer and noise content. Often this kind of high-dimensional signal representation is difficult to understand, even for expert voice therapists and physicians. Data visualization of a high-dimensional dataset can provide a useful first step in its exploratory data analysis, facilitating an understanding about its underlying structure. In the present paper, eight dimensionality reduction techniques, both classical and recent, are compared on speech data containing normal and pathological speech. A qualitative analysis of their dimensionality reduction capabilities is presented. The transformed data are also quantitatively evaluated, using classifiers, and it is found that it may be advantageous to perform the classification process on the transformed data, rather than on the original. These qualitative and quantitative analyses allow us to conclude that a nonlinear, supervised method, called kernel local Fisher discriminant analysis is superior for dimensionality reduction in the actual context.     

Cochlear Responses to Condensation and Rarefaction Clicks

Auditory nerve responses to condensation and rarefaction clicks (CC and RC) have been recorded over a wide intensity range with gross electrodes. At low intensities the RC responses are nearly identical to CC responses. At high intensities RC and CC response waveforms are similar, but the latency of the N₁ peak in the RC response is 0.2 msec. shorter than that for the corresponding CC response. At intermediate intensities the RC and CC response waveforms are quite different. These results can be interpreted in terms of a model in which there are two excitatory mechanisms for the neural response, which are operative in different intensity ranges. The cochlear microphonic potential and a “slow” potential are suggested as possible excitatory mechanisms.     

Thermodynamics of Polyethylenimine-DNA Binding and DNA Condensation

In this study, polyethylenimine (PEI) binding to DNA was examined by isothermal titration calorimetry. Two types of binding modes were found to describe the interactions between these polyelectrolytes in buffers and in water. One type of binding involves PEI binding to the DNA groove because the enthalpy change of this binding mode is positive, and PEI is deprotonated to bind to DNA. Another likely binding mode involves external binding of PEI to the DNA phosphate backbone, accompanied with DNA condensation. The enthalpy change is negative and PEI is protonated when it binds to DNA in this mode. The intrinsic enthalpy change of first binding mode is 1.1 kJ/mol and −0.88 kJ/mol for the second binding mode. This result implies that the PEI is rearranged from the groove to the phosphate backbone of DNA when DNA is condensed. The mechanism of DNA condensation caused by PEI is discussed in this study.     

Condensation of mononucleotides by imidazole

Summary The condensation of thymidine-5-monophosphate was carried out in the presence of imidazole in aqueous solutions at neutral pH. Formation of oligo-deoxyribonucleotides up to four units was observed.     

Effect of Cell Shape and Dimensionality on Spindle Orientation and Mitotic Timing

The formation and orientation of the mitotic spindle is a critical feature of mitosis. The morphology of the cell and the spatial distribution and composition of the cells'' adhesive microenvironment all contribute to dictate the position of the spindle. However, the impact of the dimensionality of the cells'' microenvironment has rarely been studied. In this study we present the use of a microwell platform, where the internal surfaces of the individual wells are coated with fibronectin, enabling the three-dimensional presentation of adhesive ligands to single cells cultured within the microwells. This platform was used to assess the effect of dimensionality and cell shape in a controlled microenvironment. Single HeLa cells cultured in circular microwells exhibited greater tilting of the mitotic spindle, in comparison to cells cultured in square microwells. This correlated with an increase in the time required to align the chromosomes at the metaphase plate due to prolonged activation of the spindle checkpoint in an actin dependent process. The comparison to 2D square patterns revealed that the dimensionality of cell adhesions alone affected both mitotic timings and spindle orientation; in particular the role of actin varied according to the dimensionality of the cells'' microenvironment. Together, our data revealed that cell shape and the dimensionality of the cells'' adhesive environment impacted on both the orientation of the mitotic spindle and progression through mitosis.     

Birefringence and DNA Condensation of Liquid Crystalline Chromosomes

DNA can self-assemble in vitro into several liquid crystalline phases at high concentrations. The largest known genomes are encoded by the cholesteric liquid crystalline chromosomes (LCCs) of the dinoflagellates, a diverse group of protists related to the malarial parasites. Very little is known about how the liquid crystalline packaging strategy is employed to organize these genomes, the largest among living eukaryotes—up to 80 times the size of the human genome. Comparative measurements using a semiautomatic polarizing microscope demonstrated that there is a large variation in the birefringence, an optical property of anisotropic materials, of the chromosomes from different dinoflagellate species, despite their apparently similar ultrastructural patterns of bands and arches. There is a large variation in the chromosomal arrangements in the nuclei and individual karyotypes. Our data suggest that both macroscopic and ultrastructural arrangements affect the apparent birefringence of the liquid crystalline chromosomes. Positive correlations are demonstrated for the first time between the level of absolute retardance and both the DNA content and the observed helical pitch measured from transmission electron microscopy (TEM) photomicrographs. Experiments that induced disassembly of the chromosomes revealed multiple orders of organization in the dinoflagellate chromosomes. With the low protein-to-DNA ratio, we propose that a highly regulated use of entropy-driven force must be involved in the assembly of these LCCs. Knowledge of the mechanism of packaging and arranging these largest known DNAs into different shapes and different formats in the nuclei would be of great value in the use of DNA as nanostructural material.DNA molecules are the indispensable genetic material of every organism. Apart from having the encoding power of a 4-base double-stranded polymer, DNA also has an enormous capacity to be condensed. It is probably this ability that allowed the evolution of increasing genome sizes in the eukaryotes. Histone-mediated nucleosome-based chromatin is the prevailing method for DNA packaging, but it is not the only way that DNA is condensed in the eukaryotes. Highly compact liquid crystalline DNA has been reported in several animal sperm nuclei (11, 28) and was also found in the nucleosomeless liquid crystalline chromosomes (LCCs) of dinoflagellates. Neither animal sperm nuclei nor dinoflagellate nuclei employ histones. In fact, the histone core octamer may hinder the attainment of ultrahigh levels of condensation due to its restrictive volume. In the sperm model, protamine is a sperm-specific DNA-binding protein (∼7 kDa) that is an order of magnitude smaller than the histone core octamer, and it adopts a structural role in the organization of the male gametic genome (1, 3). It is this very reduction in the protein-to-DNA ratio that may well enable the high DNA compaction into a liquid crystalline state. The dinoflagellate chromosomes are known to have a protein-to-DNA ratio even smaller than those of the prokaryotes (24). The typical eukaryotic genome has a protein/DNA ratio of 1:1, whereas the dinoflagellate genome has a ratio of 1:10 (23, 24).The dinoflagellates, counterintuitively, have the largest known genomes among all living organisms, with a DNA content per genome ranging from 1.5 pg to 200 pg per haploid cell (19, 25, 43). An extraordinarily high level of DNA condensation must be attained in order to sequester these genomes within the bounds of the nucleus, and this is achieved through the form of LCCs. The concentration of the DNA in the dinoflagellate nucleus was estimated to be ∼200 mg ml⁻¹ (up to 80 times more than a human cell) (24), falling well within the range observed for in vitro cholesteric liquid crystalline DNA formation (40). By observing ultrathin sections of dinoflagellate chromosomes using high-resolution transmission electron microscopy (TEM), plectonemic structures with nested series of arches and bands were seen (8, 12, 39). This architecture resembles the molecular architecture of thin-section TEM in vitro cholesteric liquid crystals (12, 39, 43).Knowledge of the condensation process would not only be of interest in terms of eukaryotic genome packaging, but would also provide new insights for the use of DNA as building blocks for nanotechnology applications. Self-assembly is increasingly understood to be of great significance in the regulation of various macromolecules in the crowded environment of living cells (7, 15, 16, 35, 36). Interestingly, it was also recently reported that nucleosomes and polynucleosomes themselves can be self-assembled (17), and in liquid crystalline form (33). The formation of LCCs probably also relies upon the associated chromosomal proteins, while self-assembly of DNA molecules via neutralization of the negatively charged polyelectrolytes by counterions and the crowding effects within the permanently closed nucleus must also contribute significantly (36, 49, 50). Most of the previous studies of dinoflagellate LCCs were focused on the chromosomes of Prorocentrum micans (27, 29). Though it has been reported that not all dinoflagellate chromosomes show the same degree of birefringence (5), the relationships of different species and their DNA contents, densities, or compaction ratios to birefringence have not been reported.The presence of two indices of refraction and optical anisotropy confer on the liquid crystalline DNA the property of birefringence, or double retardance. This optical phenomenon describes the phase differences between the two resultant light rays of a given light path that pass through the liquid crystal according to its refractive indices. For any given anisotropic material, the birefringence is a direct result of its nanoarchitecture. The property of birefringence and polarizing microscopy have long been employed to study the submicroscopic molecular organizations of different biological samples, such as mitotic spindles (5), filamentous actins (22), and microtubules (38), in living cells. Polarizing microscopy also allows the documentation of dynamic cellular behavior and measurements of cellular structures to be performed in a repeated noninvasive manner, even over extended periods of time (22). Taking advantage of this, we used a recently developed automatic rotating polarizing light microscope (the Metripol system) to study the relative amounts of birefringence and the ultrastructures of the chromosomes in several dinoflagellate species. Highly diverse chromosome structures were observed among the species, and surprisingly, not all dinoflagellates exhibited birefringent chromosomes, even though they are apparently constructed with similar liquid crystalline architectures, as seen in TEM ultrathin sections. The use of a semiautomatic Metripol polarizing microscope allowed the quantification of the retardance (20, 21, 47) of individual chromosomes of different dinoflagellate species in a fixative-free environment, and the relationships between the absolute retardance, DNA content, DNA condensation, and chromosome architecture in the dinoflagellate chromosomes are established in this study.     

染色质集缩包装成染色体的过程和机制

染色质集缩包装形成染色体是有丝分裂的一个重要事件，它使母细胞的遗传物质得以平均地分配到两个子细胞中去． 本文综述了近年来在染色质集缩包装研究方面取得的进展， 参加集缩包装的几种蛋白质以及它们可能的作用方式．     

Condensation and precipitation of chromatin by multivalent cations

The condensation and the precipitation of rat liver chromatin upon addition of spermine4+, spermidine3+, hexamminecobalt(III)3+ and Mg2+ cations have been studied using solubility, fluorescence, circular dichroism, melting curves, electric dichroism and spermidine binding measurements, made on both soluble and precipitated complexes. The soluble complexes obtained with tetra- and trivalent cations were depleted from all histones and enriched in other proteins, particularly high mobility group proteins 1 and 2, which brings about an important enhancement of tryptophan fluorescence without modification of its two lifetimes 5.1 and 1.2 ns. In the precipitates the non-histone proteins are eliminated. Under precipitation by Mg2+ ions, the distribution of proteins remains practically unchanged. The electric dichroism and the melting curves indicate that the soluble complexes between polyamines and chromatin undergo important condensation and, at high ratios of cation over phosphate, are constituted by heterogeneous assemblies of non-histone proteins and DNA. On the contrary, the insoluble complexes seem to retain the main features of original chromatin. Precipitation by Mg2+ ions reveal much less drastic changes than those produced by polyamines. Precipitation by spermidine occurs when one cation is bound per eight nucleotides, which in addition to the histone positive charges brings about a complete neutralization of chromatin phosphates.     

The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction

Stimulus dimensionality-reduction methods in neuroscience seek to identify a low-dimensional space of stimulus features that affect a neuron’s probability of spiking. One popular method, known as maximally informative dimensions (MID), uses an information-theoretic quantity known as “single-spike information” to identify this space. Here we examine MID from a model-based perspective. We show that MID is a maximum-likelihood estimator for the parameters of a linear-nonlinear-Poisson (LNP) model, and that the empirical single-spike information corresponds to the normalized log-likelihood under a Poisson model. This equivalence implies that MID does not necessarily find maximally informative stimulus dimensions when spiking is not well described as Poisson. We provide several examples to illustrate this shortcoming, and derive a lower bound on the information lost when spiking is Bernoulli in discrete time bins. To overcome this limitation, we introduce model-based dimensionality reduction methods for neurons with non-Poisson firing statistics, and show that they can be framed equivalently in likelihood-based or information-theoretic terms. Finally, we show how to overcome practical limitations on the number of stimulus dimensions that MID can estimate by constraining the form of the non-parametric nonlinearity in an LNP model. We illustrate these methods with simulations and data from primate visual cortex.     

Dimensionality Reduction and Visualization of the Environmental Impacts of Domestic Appliances

There is an increasing worldwide concern about the problem of dealing with the waste electrical and electronic equipment (WEEE), given the high volume of appliances that are disposed of every day. In this article, an environmental evaluation of WEEE is performed that combines life cycle assessment (LCA) methodology and multivariate statistical techniques. Because LCA handles a large number of data in its different phases, when one is trying to uncover the structure of large multidimensional data sets, multivariate statistical techniques can provide useful information. In particular, principal‐component analysis and multidimensional scaling are two important dimension‐reducing tools that have been shown to be of help in understanding this type of complex multivariate data set. In this article, we use a variable selection method that reduces the number of categories for which the environmental impacts have to be computed; this step is especially useful when the number of impact categories or the number of products or processes to benchmark increases. We provide a detailed illustration showing how we have used the proposed approach to analyze and interpret the environmental impacts of different domestic appliances.     

Dimensionality reduction in computational demarcation of protein tertiary structures

Predictive classification of major structural families and fold types of proteins is investigated deploying logistic regression. Only five to seven dimensional quantitative feature vector representations of tertiary structures are found adequate. Results for benchmark sample of non-homologous proteins from SCOP database are presented. Importance of this work as compared to homology modeling and best-known quantitative approaches is highlighted.     

The Condensation of Alkylhalide with Senecioate

The condensation of alkylhalide with senecioic ester provides a mixture of α-alkyl-α-iso pro-pylidene and α-alkyl-α-iso propenyl acetic acid.