Counting Unique-Sink Orientations

Unique-sink orientations (USOs) are an abstract class of orientations of the n-cube graph. We consider some classes of USOs that are of interest in connection with the linear complementarity problem. We summarise old and show new lower and upper bounds on the sizes of some such classes. Furthermore, we provide a characterisation of K-matrices in terms of their corresponding USOs.Comment: 13 pages; v2: proof of main theorem expanded, plus various other corrections. Now 16 pages; v3: minor correction

Protein interference applications in cellular and developmental biology using DARPins that recognize GFP and mCherry

Protein–protein interactions are crucial for cellular homeostasis and play important roles in the dynamic execution of biological processes. While antibodies represent a well-established tool to study protein interactions of extracellular domains and secreted proteins, as well as in fixed and permeabilized cells, they usually cannot be functionally expressed in the cytoplasm of living cells. Non-immunoglobulin protein-binding scaffolds have been identified that also function intracellularly and are now being engineered for synthetic biology applications. Here we used the Designed Ankyrin Repeat Protein (DARPin) scaffold to generate binders to fluorescent proteins and used them to modify biological systems directly at the protein level. DARPins binding to GFP or mCherry were selected by ribosome display. For GFP, binders with KD as low as 160 pM were obtained, while for mCherry the best affinity was 6 nM. We then verified in cell culture their specific binding in a complex cellular environment and found an affinity cut-off in the mid-nanomolar region, above which binding is no longer detectable in the cell. Next, their binding properties were employed to change the localization of the respective fluorescent proteins within cells. Finally, we performed experiments in Drosophila melanogaster and Danio rerio and utilized these DARPins to either degrade or delocalize fluorescently tagged fusion proteins in developing organisms, and to phenocopy loss-of-function mutations. Specific protein binders can thus be selected in vitro and used to reprogram developmental systems in vivo directly at the protein level, thereby bypassing some limitations of approaches that function at the DNA or the RNA level

ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata

<p>Abstract</p> <p>Background</p> <p>The guppy, <it>Poecilia reticulata</it>, is a well-known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for studying this important model were not previously widely available.</p> <p>Results</p> <p>With the aim of generating molecular markers for genetic mapping of the guppy, cDNA libraries were constructed from embryos and different adult organs to generate expressed sequence tags (ESTs). About 18,000 ESTs were annotated according to BLASTN and BLASTX results and the sequence information from the 3' UTRs was exploited to generate PCR primers for re-sequencing of genomic DNA from different wild type strains. By comparison of EST-linked genomic sequences from at least four different ecotypes, about 1,700 polymorphisms were identified, representing about 400 distinct genes. Two interconnected MySQL databases were built to organize the ESTs and markers, respectively. A robust phylogeny of the guppy was reconstructed, based on 10 different nuclear genes.</p> <p>Conclusion</p> <p>Our EST and marker databases provide useful tools for genetic mapping and phylogenetic studies of the guppy.</p

Platelet-Rich Plasma as an Autologous and Proangiogenic Cell Delivery System

Angiogenesis is a key factor in early stages of wound healing and is crucial for the repair of vascularized tissues such as the bone. However, supporting timely revascularization of the defect site still presents a clinical challenge. Tissue engineering approaches delivering endothelial cells or prevascularized constructs may overcome this problem. In the current study, we investigated platelet-rich plasma (PRP) gels as autologous, injectable cell delivery systems for prevascularized constructs. PRP was produced from human thrombocyte concentrates. GFP-expressing human umbilical vein endothelial cells (HUVECs) and human bone marrow-derived mesenchymal stem cells (MSCs) were encapsulated in PRP gels in different proportions. The formation of cellular networks was assessed over 14 days by time-lapse microscopy, gene expression analysis, and immunohistology. PRP gels presented a favorable environment for the formation of a three-dimensional (3D) cellular network. The formation of these networks was apparent as early as 3 days after seeding. Networks increased in complexity and branching over time but were only stable in HUVEC-MSC cocultures. The high cell viability together with the 3D capillary-like networks observed at early time points suggests that PRP can be used as an autologous and proangiogenic cell delivery system for the repair of vascularized tissues such as the bone

Romantic ideals, mate preferences, and anticipation of future difficulties in marital life: a comparative study of young adults in India and America

This article has been made available through open access by the Brunel Open Access Publishing Fund.Previous studies have established that Indians tend to be greater in collectivism and gender role traditionalism than Americans. The purpose of the present study was to examine whether these differences explained further cultural differences in romantic beliefs, traditional mate preferences, and anticipation of future difficulties in marital life. Results revealed that Indians reported greater collectivism than Americans and, in turn, held stronger romantic beliefs. Additionally, Indians’ greater collectivism and endorsement of more traditional gender roles in part predicted their preferences for a marital partner possessing traditional characteristics, and fully accounted for their heightened concerns about encountering future difficulties in marital life. These results shed light on the processes underlying cultural differences in relationship attitudes and preferences, and point to culture-specific therapies to enhance marital functioning

Influence of head size on the development of metallic wear and on the characteristics of carbon layers in metal-on-metal hip joints

Background and purpose Particles originating from the articulating surfaces of hip endoprostheses often induce an inflammatory response, which can be related to implant failure. We therefore analyzed the metal content in capsular tissue from 44 McKee-Farrar metal-on-metal hip prostheses (with 3 different head sizes) and we also analyzed the morphological structure of layers located on articulating surfaces

25th annual computational neuroscience meeting: CNS-2016

The same neuron may play different functional roles in the neural circuits to which it belongs. For example, neurons in the Tritonia pedal ganglia may participate in variable phases of the swim motor rhythms [1]. While such neuronal functional variability is likely to play a major role the delivery of the functionality of neural systems, it is difficult to study it in most nervous systems. We work on the pyloric rhythm network of the crustacean stomatogastric ganglion (STG) [2]. Typically network models of the STG treat neurons of the same functional type as a single model neuron (e.g. PD neurons), assuming the same conductance parameters for these neurons and implying their synchronous firing [3, 4]. However, simultaneous recording of PD neurons shows differences between the timings of spikes of these neurons. This may indicate functional variability of these neurons. Here we modelled separately the two PD neurons of the STG in a multi-neuron model of the pyloric network. Our neuron models comply with known correlations between conductance parameters of ionic currents. Our results reproduce the experimental finding of increasing spike time distance between spikes originating from the two model PD neurons during their synchronised burst phase. The PD neuron with the larger calcium conductance generates its spikes before the other PD neuron. Larger potassium conductance values in the follower neuron imply longer delays between spikes, see Fig. 17.Neuromodulators change the conductance parameters of neurons and maintain the ratios of these parameters [5]. Our results show that such changes may shift the individual contribution of two PD neurons to the PD-phase of the pyloric rhythm altering their functionality within this rhythm. Our work paves the way towards an accessible experimental and computational framework for the analysis of the mechanisms and impact of functional variability of neurons within the neural circuits to which they belong