A mass conserved reaction-diffusion system captures properties of cell polarity

Various molecules exclusively accumulate at the front or back of migrating eukaryotic cells in response to a shallow gradient of extracellular signals. Directional sensing and signal amplification highlight the essential properties in the migrating cells, known as cell polarity. In addition to these, such properties of cell polarity involve unique determination of migrating direction (uniqueness of axis) and localized gradient sensing at the front edge (localization of sensitivity), both of which may be required for smooth migration. Here we provide the mass conservation system based on the reaction-diffusion system with two components, where the mass of the two components is always conserved. Using two models belonging to this mass conservation system, we demonstrate through both numerical simulation and analytical approximations that the spatial pattern with a single peak (uniqueness of axis) can be generally observed and that the existent peak senses a gradient of parameters at the peak position, which guides the movement of the peak. We extended this system with multiple components, and we developed a multiple-component model in which cross-talk between members of the Rho family of small GTPases is involved. This model also exhibits the essential properties of the two models with two components. Thus, the mass conservation system shows properties similar to those of cell polarity, such as uniqueness of axis and localization of sensitivity, in addition to directional sensing and signal amplification.Comment: PDF onl

Moving Beyond CHO: Alternative host systems may be the future of biotherapeutics

CHO cells are the primary expression system for recombinant proteins with significant investment over the last three decades resulting in robust cell lines and processes. The flexible nature of CHO has lent itself to multiple process formats, such as fed batch, perfusion and continuous cultures, and advances in omics technology has enabled customization of media formulations and targeted engineering of CHO cells. This knowledge has led to large gains in protein productivity that can be captured with culture duration and/or scale. Despite this, constant pressure exists to reduce cost of manufacturing and improve per batch productivity to meet the needs of increased patient populations and increase accessibility of these therapeutics. Biogen has partnered with MIT to take a holistic view of the potential future of biomanufacturing to identify technologies that can make step changes in productivity and cost reduction. This effort has identified the host system as the most important factor to enabling this vision. Specifically, a non-mammalian host could be the key to realizing the most significant gains in productivity and reduction in cost of manufacturing. Through this initiative, we sought to take a more comprehensive approach to investigate alternative hosts for recombinant antibody production. Eight non-mammalian hosts were selected based on several properties, including proven secretion of recombinant protein products, ability to glycosylate proteins, established genome or molecular biology toolkit, amongst others. The final panel of organisms included yeast, filamentous fungi, a diatom, and a trypanosome. In collaboration with Amyris, we evaluated these eight non-mammalian host cell lines to compare their suitability as a potential primary host for the biotechnology industry. Only non-engineered, wild-type strains were used as a starting point for this evaluation, which assessed the ability of each host to express the same IgG1 model antibody. The outcome of this comparative analysis demonstrated that several of the alternative hosts could express full length antibody with acceptable glycoforms. Additionally, the ease of culture, ability to engineer the genome, and flexibility of carbon source were assessed. As an output of this work, the most productive strains will be made available for use without restrictions to allow others in the community to freely work with these hosts. Based on this initial assessment, a strategy to further investigate the potential of the most promising hosts will be shared

Beyond CHO – Non-mammalian hosts could be the future expression systems of choice for recombinant biotherapeutics

Over the last 30 years there have been tremendous advances in CHO cell culture process engineering. Novel process concepts, such as fed batch, perfusion and continuous cultures, evolved from a deep understand of CHO metabolic needs and extensive media/feed formulation development. This knowledge has led to large gains in protein productivity that can be captured with culture duration and/or scale. The biotechnology industry is consistently pressured to reduce cost of manufacturing and improve per batch productivity. Independent, but related to this burden, is the ability to support an ever growing patient population with high doses of therapeutic protein. As such, Biogen partnered with MIT to take a holistic view of the potential future of biomanufacturing to identify technologies that can make step changes in productivity and cost reduction. These efforts have cast doubt that CHO would be the optimal host in the future, whereas a non-mammalian host could be a key to realizing the most significant gains in productivity and reduction in cost of manufacturing. Recombinant antibody production from non-mammalian hosts has been reported in the past, for example from the yeast pichia and filamentous fungi Trichoderma, and antibody material produced from pichia has been used in clinical trials. In the next phase of this initiative, we sought to take a more comprehensive approach to investigate alternative hosts in recombinant antibody production. Eight non-mammalian hosts were selected based on a number of properties, including proven secretion of recombinant protein products, ability to glycosylate proteins, established genome or molecular biology toolkit, amongst other characteristics. We designed an experimental plan that would enable more straightforward comparative analysis between hosts and included two main criteria to maintain a level playing field. First, only non-engineered, wild-type strains would be used as a starting point for all eight hosts of interest. Second, a single IgG1 model antibody was selected to be expressed by all hosts. In this presentation, the outcome of this comparative analysis will be discussed, including productivity values and details of the model antibody product quality. Based on this data the most productive strains will be made available for use without restrictions to allow others in the community to freely work with these hosts

Co-construction of the family-focused support conversation: a participatory learning and action research study to implement support for family members whose relatives are being discharged for end-of-life care at home or in a nursing home.

BACKGROUND: Many people move in and out of hospital in the last few weeks of life. These care transitions can be distressing for family members because they signify the deterioration and impending death of their ill relative and forthcoming family bereavement. Whilst there is evidence about psychosocial support for family members providing end-of-life care at home, there is limited evidence about how this can be provided in acute hospitals during care transitions. Consequently, family members report a lack of support from hospital-based healthcare professionals. METHODS: The aim of the study was to implement research evidence for family support at the end-of-life in acute hospital care. Informed by Participatory Learning and Action Research and Normalization Process Theory (NPT) we co-designed a context-specific intervention, the Family-Focused Support Conversation, from a detailed review of research evidence. We undertook a pilot implementation in three acute hospital Trusts in England to assess the potential for the intervention to be used in clinical practice. Pilot implementation was undertaken during a three-month period by seven clinical co-researchers - nurses and occupational therapists in hospital specialist palliative care services. Implementation was evaluated through data comprised of reflective records of intervention delivery (n = 22), in-depth records of telephone implementation support meetings between research team members and co-researchers (n = 3), and in-depth evaluation meetings (n = 2). Data were qualitatively analysed using an NPT framework designed for intervention evaluation. RESULTS: Clinical co-researchers readily incorporated the Family-Focused Support Conversation into their everyday work. The intervention changed family support from being solely patient-focused, providing information about patient needs, to family-focused, identifying family concerns about the significance and implications of discharge and facilitating family-focused care. Co-researchers reported an increase in family members' involvement in discharge decisions and end-of-life care planning. CONCLUSION: The Family-Focused Support Conversation is a novel, evidenced-based and context specific intervention. Pilot implementation demonstrated the potential for the intervention to be used in acute hospitals to support family members during end-of-life care transitions. This subsequently informed a larger scale implementation study. TRIAL REGISTRATION: n/a

Antibody production in micro-organisms

Global demand for monoclonal antibody-based therapeutics (Mab’s) far exceeds current production capacity, and is expected to continue to grow based on current development pipelines. Despite their proven efficacy in a large number of indications, equitable use of these drugs is limited by the high cost of CHO-cell based production and purification. Micro-organisms such as yeasts and filamentous fungi present an attractive alternative for antibody production, but will require extensive genetic modification to achieve both high titers and mammalian-like glycosylation patterns in a secreted product that is easily purified. Towards this end, we developed state-of-the-art genetic engineering tools for eight micro-organisms to enable the highly efficient, targeted multiplexed integrations necessary for antibody production in these hosts. We demonstrated successful antibody production in several of these micro-organisms, paving the way to low-cost microbial fermentation to replace CHO fermentation

Repeatable Dynamic Rollover Roof Test Fixture”,

ABSTRACT Experimental rollover tests have been criticized for their poor emulation of actual rollovers and for their lack of repeatability. We have designed and built a test fixture that overcomes both of these criticisms. The fixture holds a passenger compartment, weighted to match the inertia characteristics of a complete vehicle, or a complete vehicle at the appropriate pitch and yaw. The compartment is then rotated about its principal (longitudinal) axis through an arc that mimics the rolling motion of an entire vehicle. At the appropriate roll angle and falling velocity, the roof strikes a moving patch of concrete. The compartment is controlled throughout the sequence and is suspended after the impact, so that a sequence of impacts can be individually studied in separate tests. Initial tests have shown that we can achieve repeatable impacts. Test variables include pitch, yaw, roll rate and vehicle center of gravity motion (both lateral and vertical velocity). This test device addresses the various shortcomings of previous rollover tests, fixtures and the various static and drop tests of vehicles conducted to determine rollover performance

Cover to Volume 3

The fibroblast mitogen platelet-derived growth factor -BB (PDGF-BB) induces a transient expression of the orphan nuclear receptor NR4A1 (also named Nur77, TR3 or NGFIB). The aim of the present study was to investigate the pathways through which NR4A1 is induced by PDGF-BB and its functional role. We demonstrate that in PDGF-BB stimulated NIH3T3 cells, the MEK1/2 inhibitor CI-1040 strongly represses NR4A1 expression, whereas Erk5 downregulation delays the expression, but does not block it. Moreover, we report that treatment with the NF-κB inhibitor BAY11-7082 suppresses NR4A1 mRNA and protein expression. The majority of NR4A1 in NIH3T3 was found to be localized in the cytoplasm and only a fraction was translocated to the nucleus after continued PDGF-BB treatment. Silencing NR4A1 slightly increased the proliferation rate of NIH3T3 cells; however, it did not affect the chemotactic or survival abilities conferred by PDGF-BB. Moreover, overexpression of NR4A1 promoted anchorage-independent growth of NIH3T3 cells and the glioblastoma cell lines U-105MG and U-251MG. Thus, whereas NR4A1, induced by PDGF-BB, suppresses cell growth on a solid surface, it increases anchorage-independent growth

eGIFT: Mining Gene Information from the Literature

<p>Abstract</p> <p>Background</p> <p>With the biomedical literature continually expanding, searching PubMed for information about specific genes becomes increasingly difficult. Not only can thousands of results be returned, but gene name ambiguity leads to many irrelevant hits. As a result, it is difficult for life scientists and gene curators to rapidly get an overall picture about a specific gene from documents that mention its names and synonyms.</p> <p>Results</p> <p>In this paper, we present eGIFT (<url>http://biotm.cis.udel.edu/eGIFT</url>), a web-based tool that associates informative terms, called <it>i</it>Terms, and sentences containing them, with genes. To associate <it>i</it>Terms with a gene, eGIFT ranks <it>i</it>Terms about the gene, based on a score which compares the frequency of occurrence of a term in the gene's literature to its frequency of occurrence in documents about genes in general. To retrieve a gene's documents (Medline abstracts), eGIFT considers all gene names, aliases, and synonyms. Since many of the gene names can be ambiguous, eGIFT applies a disambiguation step to remove matches that do not correspond to this gene. Another additional filtering process is applied to retain those abstracts that focus on the gene rather than mention it in passing. eGIFT's information for a gene is pre-computed and users of eGIFT can search for genes by using a name or an EntrezGene identifier. <it>i</it>Terms are grouped into different categories to facilitate a quick inspection. eGIFT also links an <it>i</it>Term to sentences mentioning the term to allow users to see the relation between the <it>i</it>Term and the gene. We evaluated the precision and recall of eGIFT's <it>i</it>Terms for 40 genes; between 88% and 94% of the <it>i</it>Terms were marked as salient by our evaluators, and 94% of the UniProtKB keywords for these genes were also identified by eGIFT as <it>i</it>Terms.</p> <p>Conclusions</p> <p>Our evaluations suggest that <it>i</it>Terms capture highly-relevant aspects of genes. Furthermore, by showing sentences containing these terms, eGIFT can provide a quick description of a specific gene. eGIFT helps not only life scientists survey results of high-throughput experiments, but also annotators to find articles describing gene aspects and functions.</p

Azimuthal anisotropy in Au+Au collisions at sqrtsNN = 200 GeV

The results from the STAR Collaboration on directed flow (v_1), elliptic flow (v_2), and the fourth harmonic (v_4) in the anisotropic azimuthal distribution of particles from Au+Au collisions at sqrtsNN = 200 GeV are summarized and compared with results from other experiments and theoretical models. Results for identified particles are presented and fit with a Blast Wave model. Different anisotropic flow analysis methods are compared and nonflow effects are extracted from the data. For v_2, scaling with the number of constituent quarks and parton coalescence is discussed. For v_4, scaling with v_2^2 and quark coalescence is discussed.Comment: 26 pages. As accepted by Phys. Rev. C. Text rearranged, figures modified, but data the same. However, in Fig. 35 the hydro calculations are corrected in this version. The data tables are available at http://www.star.bnl.gov/central/publications/ by searching for "flow" and then this pape