Thermodynamic modeling of the partitioning of biomolecules in aqueous two-phase systems using a modified Flory–Huggins equation

A modified Flory–Huggins equation accounting for the solvation of polymer molecules by water molecules was used to model the phase behavior of aqueous two-phase systems (ATPS) formed by poly(ethylene glycol) (PEG) and dextran. The parameters of the equation were obtained by fitting experimental equilibrium data either accounting for or disregarding dextran polidispersity. The modified equation was subsequently applied to calculate partition coefficients of biomolecules in these systems. It was found that accounting for polidispersity did not affect significantly the calculated phase equilibrium, but increased the agreement of calculated partition coefficients with experimental data. Further improvement was obtained by using a size dependent interaction parameter for dextran pseudo-components.     

Combining capture–recapture data and pedigree information to assess heritability of demographic parameters in the wild

Quantitative genetic analyses have been increasingly used to estimate the genetic basis of life‐history traits in natural populations. Imperfect detection of individuals is inherent to studies that monitor populations in the wild, yet it is seldom accounted for by quantitative genetic studies, perhaps leading to flawed inference. To facilitate the inclusion of imperfect detection of individuals in such studies, we develop a method to estimate additive genetic variance and assess heritability for binary traits such as survival, using capture–recapture (CR) data. Our approach combines mixed‐effects CR models with a threshold model to incorporate discrete data in a standard ‘animal model’ approach. We employ Markov chain Monte Carlo sampling in a Bayesian framework to estimate model parameters. We illustrate our approach using data from a wild population of blue tits (Cyanistes caeruleus) and present the first estimate of heritability of adult survival in the wild. In agreement with the prediction that selection should deplete additive genetic variance in fitness, we found that survival had low heritability. Because the detection process is incorporated, capture–recapture animal models (CRAM) provide unbiased quantitative genetics analyses of longitudinal data collected in the wild.     

On Sample Size of the Kruskal–Wallis Test with Application to a Mouse Peritoneal Cavity Study

Summary As the nonparametric generalization of the one‐way analysis of variance model, the Kruskal–Wallis test applies when the goal is to test the difference between multiple samples and the underlying population distributions are nonnormal or unknown. Although the Kruskal–Wallis test has been widely used for data analysis, power and sample size methods for this test have been investigated to a much lesser extent. This article proposes new power and sample size calculation methods for the Kruskal–Wallis test based on the pilot study in either a completely nonparametric model or a semiparametric location model. No assumption is made on the shape of the underlying population distributions. Simulation results show that, in terms of sample size calculation for the Kruskal–Wallis test, the proposed methods are more reliable and preferable to some more traditional methods. A mouse peritoneal cavity study is used to demonstrate the application of the methods.     

A test of the Darwin–Fisher theory for the evolution of male secondary sexual traits in monogamous birds

The Darwin–Fisher theory proposes that the presence of male secondary sexual traits in monogamous birds is selected for by early season breeding of females that are in good condition. These early breeding females have high fecundity because of their good condition, and they select mates based on secondary sex traits. We tested whether this hypothesis may be responsible for the presence of male sexual ornaments in the great frigatebird, a socially and genetically monogamous seabird. Consistent with the Darwin–Fisher theory, we found that reproductive success declined over the season. However, males with more exaggerated ornaments were not chosen as mates earlier in the season than males with less exaggerated ornaments, and selection gradients on these ornaments were not significantly different from zero.     

Reducing the perversion of diversion: Applying world‐standard fish screening practices to the Murray–Darling Basin

Summary The impact of water diversion on fish populations is a global issue. Many countries have invested substantial funding into research and implementation strategies to ensure fish are protected at diversions that take water out of rivers for agriculture and other human uses. The most common management action is the installation of fish screens, and a wide range of designs are presently available that suit a large range of diversions. The Murray–Darling Basin is the largest catchment in Australia and has been substantially developed over the past 100 years to store and divert water for that protect fish from escaping into the irrigation systems. Recent studies have determined that water diversions have substantial impacts on native fish populations, but there are presently no coordinated efforts for mitigation strategies. The purpose of this review is to highlight aspects of successful screening programmes worldwide and identify those that could be directly applied to the Murray–Darling Basin. The development of similar programmes in the United States, New Zealand and the United Kingdom has identified that sufficient information and technology exists to inform the development of fish screening programmes. There is no need to commence implementation from first principles, and substantial progress can be achieved by applying successful aspects of other programmes. By identifying existing designs, defining ecological targets, developing generalised guidelines appropriate for local conditions and engaging the community, a co‐ordinated and successful fish screening programme could be directly applied to the Murray–Darling Basin. This would have substantial benefits for the long‐term sustainability of native fish without compromising water supply requirements.     

A procedure for the transient expression of genes by agroinfiltration above the permissive threshold to study temperature‐sensitive processes in plant–pathogen interactions

Localized expression of genes in plants from T‐DNAs delivered into plant cells by Agrobacterium tumefaciens is an important tool in plant research. The technique, known as agroinfiltration, provides fast, efficient ways to transiently express or silence a desired gene without resorting to the time‐consuming, challenging stable transformation of the host, the use of less efficient means of delivery, such as bombardment, or the use of viral vectors, which multiply and spread within the host causing physiological alterations themselves. A drawback of the agroinfiltration technique is its temperature dependence: early studies have shown that temperatures above 29 °C are nonpermissive to tumour induction by the bacterium as a result of failure in pilus formation. However, research in plant sciences is interested in studying processes at these temperatures, above the 25 °C experimental standard, common to many host–environment and host–pathogen interactions in nature, and agroinfiltration is an excellent tool for this purpose. Here, we measured the efficiency of agroinfiltration for the expression of reporter genes in plants from T‐DNAs at the nonpermissive temperature of 30 °C, either transiently or as part of viral amplicons, and envisaged procedures that allow and optimize its use for gene expression at this temperature. We applied this technical advance to assess the performance at 30 °C of two viral suppressors of silencing in agropatch assays [Potato virus Y helper component proteinase (HCPro) and Cucumber mosaic virus 2b protein] and, within the context of infection by a Potato virus X (PVX) vector, also assessed indirectly their effect on the overall response of the host Nicotiana benthamiana to the virus.     

A molecular dynamics simulation of the flavin mononucleotide–RNA aptamer complex

We report on an unrestrained molecular dynamics simulation of the flavin mononucleotide (FMN)–RNA aptamer. The simulated average structure maintains both cross‐strand and intermolecular FMN–RNA nuclear Overhauser effects from the nmr experiments and has all qualitative features of the nmr structure including the G10–U12–A25 base triple and the A13–G24, A8–G28, and G9–G27 mismatches. However, the relative orientation of the hairpin loop to the remaining part of the molecule differs from the nmr structure. The simulation predicts that the flexible phosphoglycerol part of FMN moves toward G27 and forms hydrogen bonds. There are structurally long‐lived water molecules in the FMN binding pocket forming hydrogen bonds within FMN and between FMN and RNA. In addition, long‐lived water is found bridging primarily RNA backbone atoms. A general feature of the environment of long‐lived “structural” water is at least two and in most cases three or four potential acceptor atoms. The 2′‐OH group of RNA usually acts as an acceptor in interactions with the solvent. There are almost no intrastrand O2′H(n)⋮O4′(n + 1) hydrogen bonds within the RNA backbone. In the standard case the preferred orientation of the 2′‐OH hydrogen atoms is approximately toward O3′ of the same nucleotide. However, a relatively large number of conformations with the backbone torsional angle γ in the trans orientation is found. A survey of all experimental RNA x‐ray structures shows that this backbone conformation occurs but is less frequent than found in the simulation. Experimental nmr RNA aptamer structures have a higher fraction of this conformation as compared to the x‐ray structures. The backbone conformation of nucleotide n + 1 with the torsional angle γ in the trans orientation leads to a relatively short distance between 2′‐OH(n) and O5′(n + 1), enabling hydrogen‐bond formation. In this case the preferred orientation of the 2′‐OH hydrogen atom is approximately toward O5′(n + 1). We find two relatively short and dynamically stable types of backbone–backbone next‐neighbor contacts, namely C2′(H)(n)⋮O4′(n + 1) and C5′(H)(n + 1)⋮O2′(n). These interactions may affect both backbone rigidity and thermodynamic stability of RNA helical structures. © 1999 John Wiley & Sons, Inc. Biopoly 50: 287–302, 1999     

Comparative motility of X and Y chromosome–bearing bovine sperm separated on the basis of DNA content by flow sorting

A combination of flow cytometric sperm sorting of X and Y chromosome–bearing sperm (X and Y sperm) and computer-assisted sperm analysis (CASA) for measuring sperm motility allows assessment of motion parameters in the two populations. Bull sperm were separated into X and Y populations by flow cytometry following staining with the DNA-binding dye Hoechst 33342. The motion parameters differed depending on sperm concentration. Decreasing sperm concentration resulted in higher velocities and straighter trajectories. The concentrations of control (stained-unsorted and unstained-unsorted) and flow-sorted sperm were therefore adjusted to similar numbers (5 × 10⁶ sperm per milliliter). Samples of sorted X and Y sperm and control sperm were transferred to prewarmed slides on a heated stage (37°C) and their motion video recorded for 2 min using a magnification of ×100 and a high-resolution camera. The sperm analysis was carried out on a Hobson Sperm Tracker (HST) using HST 7 software. The following motion parameters were measured: curvilinear, straight-line, and average path velocity; mean angular displacement (MAD); beat cross-frequency; amplitude of lateral head displacement; linearity (LIN); and straightness of path (STR). Sperm movement was unaffected by staining with Hoechst 33342, excitation by ultraviolet (UV) light, or the physical process of cell sorting. Significant differences were seen between X and Y sperm for MAD, LIN, and STR. No difference was observed for the other parameters. The results indicate that in a simple salts solution, Y bull sperm do not swim faster than X sperm but may be distinguished from X sperm on the basis of LIN and STR. Mol. Reprod. Dev. 50:323–327, 1998. Published 1998 Wiley-Liss, Inc.     

Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study

T e in the amount of ‘omics’ data available and in our ability to interpret those data. The aim of this paper was to consider how omics techniques can be used to improve and refine microbiological risk assessment, using dose–response models for RNA viruses, with particular reference to norovirus through the oral route as the case study. The dose–response model for initial infection in the gastrointestinal tract is broken down into the component steps at the molecular level and the feasibility of assigning probabilities to each step assessed. The molecular mechanisms are not sufficiently well understood at present to enable quantitative estimation of probabilities on the basis of omics data. At present, the great strength of gene sequence data appears to be in giving information on the distribution and proportion of susceptible genotypes (for example due to the presence of the appropriate pathogen‐binding receptor) in the host population rather than in predicting specificities from the amino acid sequences concurrently obtained. The nature of the mutant spectrum in RNA viruses greatly complicates the application of omics approaches to the development of mechanistic dose–response models and prevents prediction of risks of disease progression (given infection has occurred) at the level of the individual host. However, molecular markers in the host and virus may enable more broad predictions to be made about the consequences of exposure in a population. In an alternative approach, comparing the results of deep sequencing of RNA viruses in the faeces/vomitus from donor humans with those from their infected recipients may enable direct estimates of the average probability of infection per virion to be made.     

Neuron death in the developing avian isthmo–optic nucleus,and its relation to the establishment of functional circuitry

The present review covers all the published data on neuron death in the developing avian isthmo–optic nucleus (ION), which provides a particularly convenient situation for studying the causes and consequences of neuron death in the development of the vertebrate central nervous system. The main conclusions are as follows: The naturally occurring neuron death in the ION is related both temporally and causally to the ION's formation of afferent and efferent connections. The ION neurons need to obtain both anterograde and retrograde survival signals in order to survive during a critical period in embryogenesis. They may compete, at least for the retrograde signals, but the nature of the competition is still unclear. The retrograde signals are modified by action potentials. Neurons dying from a lack of anterograde survival signals can be distinguished morphologically from ones dying from a lack of retrograde signals. The neuron death refines circuitry by selectively eliminating neurons with “aberrant” axons projecting to the “wrong” (i.e., ipsilateral) retina or to the “wrong” (topographically inappropriate) part of the contralateral retina. © 1992 John Wiley & Sons, Inc.     

Synthetic, structural and solution speciation studies on binary Al(III)–(carboxy)phosphonate systems. Relevance to the neurotoxic potential of Al(III)

Efforts to delineate the interactions of neurotoxic Al(III) with low molecular mass substrates relevant to neurodegenerative processes, led to the investigation of the pH-specific synthetic chemistry of the binary Al(III)-[N-(phosphonomethyl) iminodiacetic acid] (Al-NTAP), Al(III)-[nitrilo-tris(methylene-phosphonic acid)] (Al-NTA3P), and Al(III)-[1-hydroxy ethylidene-1,1-diphosphonic acid] (Al-HEDP) systems, in correlation with solution speciation studies. Reaction of Al(NO₃)₃·9H₂O with NTAP at pH 7.0 and 4.0 afforded the new species (CH₆N₃)₄[Al₂(C₅H₆NPO₇)₂(OH)₂]·8H₂O (1) and (NH₄)₂[Al₂(C₅H₆NPO₇)₂(H₂O)₂]·4H₂O (2), while reaction of Al(NO₃)₃·9H₂O with NTA3P led to K₈[Al₂(C₃H₆NP₃O₉)₂(OH)₂]·20H₂O (3). Complexes 1–3 were characterized by elemental analysis, FT-IR, ¹³C, ³¹P, ¹H NMR (for 1–2 solid state and solution NMR where feasible), and X-ray crystallography. The structures of 1–3 reveal the presence of uniquely defined dinuclear complexes of octahedral Al(III) bound to fully deprotonated phosphonate ligands, water and hydroxo moieties. The aqueous solution speciation studies on the aforementioned binary systems project a clear picture of the binary Al(III)–(carboxy)phosphonate interactions and species under variable pH-conditions and specific Al(III):ligand stoichiometry. The concurrent solid state and solution work (a) exemplifies essential structural and chemical attributes of soluble aqueous species, reflecting well-defined interactions of Al(III) with phosphosubstrates and (b) strengthens the potential linkage of neurotoxic Al(III) chemical reactivity toward O,N-containing (carboxy)phosphate-rich cellular targets.     

Role of CXCR4/SDF-1α in the migratory phenotype of hepatoma cells that have undergone epithelial–mesenchymal transition in response to the transforming growth factor-β

Treatment of FaO rat hepatoma cells with TGF-β selects cells that survive to its apoptotic effect and undergo epithelial–mesenchymal transitions (EMT). We have established a cell line (TβT-FaO, from TGF-β-treated FaO) that shows a mesenchymal, de-differentiated, phenotype in the presence of TGF-β and is refractory to its suppressor effects. In the absence of this cytokine, cells revert to an epithelial phenotype in 3–4 weeks and recover the response to TGF-β. TβT-FaO show higher capacity to migrate than that observed in the parental FaO cells. We found that FaO cells express low levels of CXCR4 and do not respond to SDF-1α. However, TGF-β up-regulates CXCR4, through a NFkappaB-dependent mechanism, and TβT-FaO cells show elevated levels of CXCR4, which is located in the presumptive migration front. A specific CXCR4 antagonist (AMD3100) attenuates the migratory capacity of TβT-FaO cells on collagen gels. Extracellular SDF-1α activates the ERKs pathway in TβT-FaO, but not in FaO cells, increasing cell scattering and protecting cells from apoptosis induced by serum deprivation. Targeted knock-down of CXCR4 with specific siRNA blocks the TβT-FaO response to SDF-1α. Thus, the SDF-1/CXCR4 axis might play an important role in mediating cell migration and survival after a TGF-β-induced EMT in hepatoma cells.     

Cloning, expression, purification and functional characterization of the oligomerization domain of Bcr–Abl oncoprotein fused to the cytoplasmic transduction peptide

Protein-based cellular therapeutics have been limited by getting molecules into cells and the fact that many proteins require accurate cellular localization for function. Cytoplasmic transduction peptide (CTP) is a newly designed transduction peptide that carries molecules across the cell membrane with a preference to localize in the cytoplasmic compartment and is, therefore, applicable for cytoplasmic targeting. The Bcr–Abl fusion protein, playing major causative role in chronic myeloid leukemia (CML), is a cytoplasmic oncoprotein that contains an N-terminus oligomerization domain (OD) mediating homodimerization of Bcr–Abl proteins, and an intact OD in Bcr–Abl is required both for the activation of its transforming activity and tyrosine kinase. Therefore, disrupting Bcr–Abl oligomerization represents a potential therapeutic strategy for inhibiting Bcr–Abl oncogenicity. In this study, we explored the possible homodimerization-disrupting and tyrosine kinase inhibiting effect of the transduction of OD in Bcr–Abl positive K562 cells. By expressing in Escherichia coli a CTP-OD-HA fusion protein followed by Ni⁺–NTA affinity purification, immunoblot identification and enterokinase cleavage, we showed that the CTP-OD-HA protein was structurally and functionally active in that it potently transduced and primarily localized into the cytoplasmic compartment, heterodimerized with Bcr–Abl, and potently inhibited the phospho-tyrosine pathways of Bcr–Abl oncoprotein at a low concentration of 4 μM. These results delineate strategies for the expression and purification of therapeutic molecules for intracytoplasmic protein based therapeutics and the CTP-OD-HA-mediated killing strategy could be explored as a promising anti-leukemia agent or an adjuvant to the conventional therapeutic modalities in chronic myeloid leukemia, such as in vitro purging.     

Replication of an association of variation in the FOXO3A gene with human longevity using both case–control and longitudinal data

Genetic variation in FOXO3A has previously been associated with human longevity. Studies published so far have been case–control studies and hence vulnerable to bias introduced by cohort effects. In this study we extended the previous findings in the cohorts of oldest old Danes (the Danish 1905 cohort, N = 1089) and middle‐aged Danes (N = 736), applying a longitudinal study design as well as the case–control study design. Fifteen SNPs were chosen in order to cover the known common variation in FOXO3A. Comparing SNP frequencies in the oldest old with middle‐aged individuals, we found association (after correction for multiple testing) of eight SNPs; 4 (rs13217795, rs2764264, rs479744, and rs9400239) previously reported to be associated with longevity and four novel SNPs (rs12206094, rs13220810, rs7762395, and rs9486902 (corrected P‐values 0.001–0.044). Moreover, we found association of the haplotypes TAC and CAC of rs9486902, rs10499051, and rs12206094 (corrected P‐values: 0.01–0.03) with longevity. Finally, we here present data applying a longitudinal study design; when using follow‐up survival data on the oldest old in a longitudinal analysis, we found no SNPs to remain significant after the correction for multiple testing (Bonferroni correction). Hence, our results support and extent the proposed role of FOXO3A as a candidate longevity gene for survival from younger ages to old age, yet not during old age.