Pulse waves for a semi-discrete Morris–Lecar type model

 We establish the existence of a pulse traveling wave for an infinite system of ODEs modeling a one dimensional string of nerve cells of identical Morris–Lecar type dynamics:

A Host–Vector System for a Cellulose-Producing Acetobacter Strain

An indigenous plasmid, named pAH4, was detected in a cellulose-producing Acetobacter strain. This plasmid, consisting of 4002 bp, contained an AT-rich region and encoded several open reading frames, as deduced by the complete nucleotide sequence. One of the putative open reading frames showed homology with replication proteins of other plasmids. A shuttle vector of Escherichia coli and this strain was constructed by connecting pAH4 to pUC18. Electroporation of the shuttle vector into the strain yielded 1.7 × 10⁵ ampicillin resistant transformants per μg DNA. The shuttle plasmid was very stably maintained in the strain.     

Nasonia–microbiome associations: a model for evolutionary hologenomics research

In recent years, with the development of microbial research technologies, microbiota research has received widespread attention. The parasitoid wasp genus Nasonia is a good model organism for studying insect behavior, development, evolutionary genetics, speciation, and symbiosis. This review describes key advances and progress in the field of the Nasonia–microbiome interactions. We provide an overview of the advantages of Nasonia as a model organism for microbiome studies, list research methods to study the Nasonia microbiome, and discuss recent discoveries in Nasonia microbiome research. This summary of the complexities of Nasonia–microbiome relationships will help to contribute to a better understanding of the interactions between animals and their microbiomes and establish a clear research direction for Nasonia–microbiome interactions in the future.     

Exploring a coarse-grained distributive strategy for finite-difference Poisson–Boltzmann calculations

We have implemented and evaluated a coarse-grained distributive method for finite-difference Poisson–Boltzmann (FDPB) calculations of large biomolecular systems. This method is based on the electrostatic focusing principle of decomposing a large fine-grid FDPB calculation into multiple independent FDPB calculations, each of which focuses on only a small and a specific portion (block) of the large fine grid. We first analyzed the impact of the focusing approximation upon the accuracy of the numerical reaction field energies and found that a reasonable relative accuracy of 10⁻³ can be achieved when the buffering space is set to be 16 grid points and the block dimension is set to be at least (1/6)³ of the fine-grid dimension, as in the one-block focusing method. The impact upon efficiency of the use of buffering space to maintain enough accuracy was also studied. It was found that an “optimal” multi-block dimension exists for a given computer hardware setup, and this dimension is more or less independent of the solute geometries. A parallel version of thedistributive focusing method was also implemented. Given the proper settings, the distributive method was able to achieve respectable parallel efficiency with tested biomolecular systems on a loosely connected computer cluster.     

Advantages of a two-step enzymatic process for cotton–polyester blends

Cotton fabric samples were treated with a formulation of a total crude Trichoderma reesei cellulase in a two-step procedure. In the first step, samples were treated at a low liquor ratio by padding through the enzyme formulation at 21°C and 55°C with a wet pickup of 100% and batched for 12 h. The samples were then treated at a high liquor ratio (1:25) with an identical enzyme formulation at 55°C, with intensive agitation. The pre-treatment influenced the overall weight loss and rate of hydrolysis in samples, and the protein concentration in the liquor of the second step. The overall weight loss was 25–28% (w/w) in the two-step procedure compared to a weight loss of 22% (w/w) in the one-step batch hydrolysis.     

CRISPR–Cas system: a powerful tool for genome engineering

Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Recent advances with the RNA-mediated Cas9 endonuclease derived from clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) systems have dramatically transformed our ability to specifically modify intact genomes of diverse cells and organisms. The CRISPR–Cas system has been adapted as an efficient, facile, and robust gene-targeting technology with the potential for high-throughput and multiplexed genome engineering. Exciting breakthroughs in understanding the mechanisms of the CRISPR–Cas system and its enormous potential for applications across basic science, agricultural and biotechnology.     

Searching for Spatial Patterns in a Pollinator–Plant–Herbivore Mathematical Model

This paper deals with the spatio-temporal dynamics of a pollinator–plant–herbivore mathematical model. The full model consists of three nonlinear reaction–diffusion–advection equations defined on a rectangular region. In view of analyzing the full model, we firstly consider the temporal dynamics of three homogeneous cases. The first one is a model for a mutualistic interaction (pollinator–plant), later on a sort of predator–prey (plant–herbivore) interaction model is studied. In both cases, the interaction term is described by a Holling response of type II. Finally, by considering that the plant population is the unique feeding source for the herbivores, a mathematical model for the three interacting populations is considered. By incorporating a constant diffusion term into the equations for the pollinators and herbivores, we numerically study the spatiotemporal dynamics of the first two mentioned models. For the full model, a constant diffusion and advection terms are included in the equation for the pollinators. For the resulting model, we sketch the proof of the existence, positiveness, and boundedness of solution for an initial and boundary values problem. In order to see the separated effect of the diffusion and advection terms on the final population distributions, a set of numerical simulations are included. We used homogeneous Dirichlet and Neumann boundary conditions.     

Stain–Decolorize–Stain (SDS): a new technique for multiple staining

Multiple staining of more than one gene/antigen on a single tissue section is an indispensable tool in cell and tissue research. However, most of the available multiple staining techniques have limitations, and there has been no technique to simultaneously visualize and distinguish tissue antigens, nucleotide sequences and other chemical compounds on the same slide. Here, we present a practical and economic multiple stain technique, with which multiple cellular components including mRNA (with in situ hybridization), antigen epitope (with immunohistochemistry) and chemical molecules (with histochemistry) can be stained on a single tissue section to study their relationship. In addition, this technique also offers the possibility to evaluate morphology with an H&E staining on the same sections. We used the placenta, pancreas, breast ductal carcinoma, colon adenocarcinoma, cerebellum, tonsil and heart tissue sections to evaluate the applicability of this new technique. The sensitivity and specificity of the technique have been tested, and an optimal protocol is recommended. Its applications in surgical pathology and research are discussed. This technique offers a novel tool to evaluate the relationship among multiple components at the same or adjacent locations to meet the needs of pathology diagnosis and research.     

The cichlid–Cichlidogyrus network: a blueprint for a model system of parasite evolution

Hydrobiologia - Species interactions are a key aspect of evolutionary biology. Parasites, specifically, are drivers of the evolution of species communities and impact biosecurity and public health....     

A candidate gene for fire blight resistance in Malus × robusta 5 is coding for a CC–NBS–LRR

Fire blight is the most important bacterial disease in apple (Malus?×? domestica) and pear (Pyrus communis) production. Today, the causal bacterium Erwinia amylovora is present in many apple- and pear-growing areas. We investigated the natural resistance of the wild apple Malus?×? robusta 5 against E. amylovora, previously mapped to linkage group 3. With a fine-mapping approach on a population of 2,133 individuals followed by phenotyping of the recombinants from the region of interest, we developed flanking markers useful for marker-assisted selection. Open reading frames were predicted on the sequence of a BAC spanning the resistance locus. One open reading frame coded for a protein belonging to the NBS–LRR family. The in silico investigation of the structure of the candidate resistance gene against fire blight of M.?×? robusta 5, FB_MR5, led us hypothesize the presence of a coiled-coil region followed by an NBS and an LRR-like structure with the consensus ‘LxxLx[IL]xxCxxLxxL’. The function of FB_MR5 was predicted in agreement with the decoy/guard model, that FB_MR5 monitors the transcribed RIN4_MR5, a homolog of RIN4 of Arabidopsis thaliana that could interact with the previously described effector AvrRpt2_EA of E. amylovora.     

Force–velocity relationship for multiple kinesin motors pulling a magnetic bead

Although the velocity of single kinesin motors against an opposing force F of 0–10 pN is well known, the behavior of multiple kinesin motors working to overcome a larger load is still poorly understood. We have carried out gliding assays in which 3–7 Drosophila kinesin-1 motors moved a microtubule at 200–700 μm/s against a 0–31 pN load at saturating [ATP]. The load F was generated by applying a spatially uniform magnetic field gradient to a superparamagnetic bead attached to the (+) end of the microtubule. When F was scaled by the average number of motors 〈n〉, the force–velocity relationship for multiple motors was similar to the force–velocity relationship for a single motor, supporting a minimal load-sharing model. The velocity distribution at low load has a single mode consistent with rapid fluctuations of n. However, against a load of 2.5–4.7 pN/motor, additional modes appeared at lower velocity. These observations support the Klumpp–Lipowsky model of multimotor transport [Proc Natl Acad Sci USA 102. 17284–17289 (2005)].     

Treating colon cancer with injectable PLGA–PEG–PLGA as a carrier for iodine-125

Purpose of work

Provide a safer way for treating various cancers with PLGA-PEG-PLGA (PPP)-embedded iodine-125. To improve the safety of iodine treatment for colon cancer, iodine-125 solution was embedded into PLGA–PEG–PLGA (PPP) (synthesized by bulk co-polymerization of dl-polylactide glycolide and PEG). Xenograft-carrying nude mice were then treated with iodine-125-PPP. Proliferating cell nuclear antigen and Terminal Transferase dUTP Nick-End Labeling were used to measure proliferation and apoptosis in the tumors, respectively. Simultaneously, immunohistochemistry SP was used to detect the expression levels of p53. In addition, the microvessel density (MVD) of the tumors was recorded. PPP-embedded iodine-125 induced apoptosis by increasing the expression of p53, and by decreasing the levels of VEGF and MVD in the colon cancer tumors (P < 0.01). Significant inhibition of tumor growth is seen with iodine-125 from 0.4 to 0.8 mCi. PPP-embedded iodine-125 has a similar inhibitory efficiency to using the iodine-125 seeds for the treatment of colon tumors (P > 0.05). The findings therefore provide a potentially safer method for treating various tumors with radioactive iodine.     

Adaptive Control Based Harvesting Strategy for a Predator–Prey Dynamical System

This paper deals with designing a harvesting control strategy for a predator–prey dynamical system, with parametric uncertainties and exogenous disturbances. A feedback control law for the harvesting rate of the predator is formulated such that the population dynamics is asymptotically stabilized at a positive operating point, while maintaining a positive, steady state harvesting rate. The hierarchical block strict feedback structure of the dynamics is exploited in designing a backstepping control law, based on Lyapunov theory. In order to account for unknown parameters, an adaptive control strategy has been proposed in which the control law depends on an adaptive variable which tracks the unknown parameter. Further, a switching component has been incorporated to robustify the control performance against bounded disturbances. Proofs have been provided to show that the proposed adaptive control strategy ensures asymptotic stability of the dynamics at a desired operating point, as well as exact parameter learning in the disturbance-free case and learning with bounded error in the disturbance prone case. The dynamics, with uncertainty in the death rate of the predator, subjected to a bounded disturbance has been simulated with the proposed control strategy.     

Functional–structural plant models: a growing paradigm for plant studies

A number of research groups in various areas of plant biology as well as computer science and applied mathematics have addressed modelling the spatiotemporal dynamics of growth and development of plants. This has resulted in development of functional–structural plant models (FSPMs). In FSPMs, the plant structure is always explicitly represented in terms of a network of elementary units. In this respect, FSPMs are different from more abstract models in which a simplified representation of the plant structure is frequently used (e.g. spatial density of leaves, total biomass, etc.). This key feature makes it possible to build modular models and creates avenues for efficient exchange of model components and experimental data. They are being used to deal with the complex 3-D structure of plants and to simulate growth and development occurring at spatial scales from cells to forest areas, and temporal scales from seconds to decades and many plant generations. The plant types studied also cover a broad spectrum, from algae to trees. This special issue of Annals of Botany features selected papers on FSPM topics such as models of morphological development, models of physical and biological processes, integrated models predicting dynamics of plants and plant communities, modelling platforms, methods for acquiring the 3-D structures of plants using automated measurements, and practical applications for agronomic purposes.     

Protein microarrays as a discovery tool for studying protein–protein interactions

Exploring the function of the genome and the encoded proteins has emerged as a new and exciting challenge in the postgenomic era. Novel technologies come into view that promise to be valuable for the investigation not only of single proteins, but of entire protein networks. Protein microarrays are the innovative assay platform for highly parallel in vitro studies of protein–protein interactions. Due to their flexibility and multiplexing capacity, protein microarrays benefit basic research, diagnosis and biomedicine. This review provides an overview on the basic principles of protein microarrays and their potential to multiplex protein–protein interaction studies.     

Host–parasite interactions: a litmus test for ocean acidification?

The effects of ocean acidification (OA) on marine species and ecosystems have received significant scientific attention in the past 10 years. However, to date, the effects of OA on host-parasite interactions have been largely ignored. As parasites play a multidimensional role in the regulation of marine population, community, and ecosystem dynamics, this knowledge gap may result in an incomplete understanding of the consequences of OA. In addition, the impact of stressors associated with OA on host-parasite interactions may serve as an indicator of future changes to the biodiversity of marine systems. This opinion article discusses the potential effects of OA on host and parasite species and proposes the use of parasites as bioindicators of OA disturbance.     

Bayesian Inference for Functional Response in a Stochastic Predator–Prey System

We present a Bayesian method for functional response parameter estimation starting from time series of field data on predator–prey dynamics. Population dynamics is described by a system of stochastic differential equations in which behavioral stochasticities are represented by noise terms affecting each population as well as their interaction. We focus on the estimation of a behavioral parameter appearing in the functional response of predator to prey abundance when a small number of observations is available. To deal with small sample sizes, latent data are introduced between each pair of field observations and are considered as missing data. The method is applied to both simulated and observational data. The results obtained using different numbers of latent data are compared with those achieved following a frequentist approach. As a case study, we consider an acarine predator–prey system relevant to biological control problems.     

The development of a radioimmunoassay for Tamm–Horsfall glycoprotein in serum

The Tamm–Horsfall glycoprotein prepared by salt precipitation from urine was found to comprise a heterogeneous collection of aggregates. These could be disaggregated with 8m-urea, following which chromatography on a column of Bio-Gel A.15m yielded a homogeneous glycoprotein of mol.wt. 73000 together with several unidentified impurities. Gel filtration of normal plasma showed the glycoprotein to exist predominantly in a form that is eluted identically with the purified preparation. In one case, material of higher molecular weight was also detected. The purified glycoprotein was used to develop a rapid specific radioimmunoassay for its measurement in human serum or plasma by the use of the Tamm–Horsfall glycoprotein, labelled with ¹²⁵I by the chloramine-t method as the tracer, an antiserum raised in rabbits, and separation of the bound and free fractions by a second antibody covalently linked to magnetizable particles. Parallelism was demonstrated between the standard preparation and samples. Recovery of added standard to serum varied between 99 and 109%. Total assay time was less than 4h with an intra-assay and inter-assay coefficient of variation of less than 10%. There were no significant differences in the ranges covered with regard to either age or sex, and no circadian rhythm was observed in normal subjects. A physiological range of 70–540ng/ml was established based on serum samples from 95 subjects with normal renal function, as defined by their serum creatinine and urea concentrations. No Tamm–Horsfall glycoprotein was detected in the serum of six anephric patients.     

Baitmet,a computational approach for GC–MS library-driven metabolite profiling

Introduction

Current computational tools for gas chromatography—mass spectrometry (GC–MS) metabolomics profiling do not focus on metabolite identification, that still remains as the entire workflow bottleneck and it relies on manual data reviewing. Metabolomics advent has fostered the development of public metabolite repositories containing mass spectra and retention indices, two orthogonal properties needed for metabolite identification. Such libraries can be used for library-driven compound profiling of large datasets produced in metabolomics, a complementary approach to current GC–MS non-targeted data analysis solutions that can eventually help to assess metabolite identities more efficiently.

Results

This paper introduces Baitmet, an integrated open-source computational tool written in R enclosing a complete workflow to perform high-throughput library-driven GC–MS profiling in complex samples. Baitmet capabilities were assayed in a metabolomics study involving 182 human serum samples where a set of 61 metabolites were profiled given a reference library.

Conclusions

Baitmet allows high-throughput and wide scope interrogation on the metabolic composition of complex samples analyzed using GC–MS via freely available spectral data. Baitmet is freely available at http://CRAN.R-project.org/package=baitmet.