Correlated Phenotypic Transitions to Competence in Bacterial Colonies

Genetic competence is a phenotypic state of a bacterial cell in which it is capable of importing DNA, presumably to hasten its exploration of alternate genes in its quest for survival under stress. Recently, it was proposed that this transition is uncorrelated among different cells in the colony. Motivated by several discovered signaling mechanisms which create colony-level responses, we present a model for the influence of quorum-sensing signals on a colony of B. Subtilis cells during the transition to genetic competence. Coupling to the external signal creates an effective inhibitory mechanism, which results in anti-correlation between the cycles of adjacent cells. We show that this scenario is consistent with the specific experimental measurement, which fails to detect some underlying collective signaling mechanisms. Rather, we suggest other parameters that should be used to verify the role of a quorum-sensing signal. We also study the conditions under which phenotypic spatial patterns may emerge

Cell Motility Dynamics: A Novel Segmentation Algorithm to Quantify Multi-Cellular Bright Field Microscopy Images

Confocal microscopy analysis of fluorescence and morphology is becoming the standard tool in cell biology and molecular imaging. Accurate quantification algorithms are required to enhance the understanding of different biological phenomena. We present a novel approach based on image-segmentation of multi-cellular regions in bright field images demonstrating enhanced quantitative analyses and better understanding of cell motility. We present MultiCellSeg, a segmentation algorithm to separate between multi-cellular and background regions for bright field images, which is based on classification of local patches within an image: a cascade of Support Vector Machines (SVMs) is applied using basic image features. Post processing includes additional classification and graph-cut segmentation to reclassify erroneous regions and refine the segmentation. This approach leads to a parameter-free and robust algorithm. Comparison to an alternative algorithm on wound healing assay images demonstrates its superiority. The proposed approach was used to evaluate common cell migration models such as wound healing and scatter assay. It was applied to quantify the acceleration effect of Hepatocyte growth factor/scatter factor (HGF/SF) on healing rate in a time lapse confocal microscopy wound healing assay and demonstrated that the healing rate is linear in both treated and untreated cells, and that HGF/SF accelerates the healing rate by approximately two-fold. A novel fully automated, accurate, zero-parameters method to classify and score scatter-assay images was developed and demonstrated that multi-cellular texture is an excellent descriptor to measure HGF/SF-induced cell scattering. We show that exploitation of textural information from differential interference contrast (DIC) images on the multi-cellular level can prove beneficial for the analyses of wound healing and scatter assays. The proposed approach is generic and can be used alone or alongside traditional fluorescence single-cell processing to perform objective, accurate quantitative analyses for various biological applications

Validation of a survey to examine drinking-water access, practices and policies in schools

ObjectiveEnsuring ready access to free drinking-water in schools is an important strategy for prevention of obesity and dental caries, and for improving student learning. Yet to date, there are no validated instruments to examine water access in schools. The present study aimed to develop and validate a survey of school administrators to examine school access to beverages, including water and sports drinks, and school and district-level water-related policies and practices.DesignSurvey validity was measured by comparing results of telephone surveys of school administrators with on-site observations of beverage access and reviews of school policy documents for any references to beverages. The semi-structured telephone survey included items about free drinking-water access (sixty-four items), commonly available competitive beverages (twenty-nine items) and water-related policies and practices (twenty-eight items). Agreement between administrator surveys and observation/document review was calculated using kappa statistics for categorical variables, and Pearson correlation coefficients and t tests for continuous variables.SettingPublic schools in the San Francisco Bay Area, California, USA.SubjectsSchool administrators (n 24).ResultsEighty-one per cent of questions related to school beverage access yielded κ values indicating substantial or almost perfect agreement (κ>0·60). However, only one of twenty-eight questions related to drinking-water practices and policies yielded a κ value representing substantial or almost perfect agreement.ConclusionsThis school administrator survey appears reasonably valid for questions related to beverage access, but less valid for questions on water-related practices and policies. This tool provides policy makers, researchers and advocates with a low-cost, efficient method to gather national data on school-level beverage access

Self-assisted Amoeboid Navigation in Complex Environments

Background: Living cells of many types need to move in response to external stimuli in order to accomplish their functional tasks; these tasks range from wound healing to immune response to fertilization. While the directional motion is typically dictated by an external signal, the actual motility is also restricted by physical constraints, such as the presence of other cells and the extracellular matrix. The ability to successfully navigate in the presence of obstacles is not only essential for organisms, but might prove relevant in the study of autonomous robotic motion. Methodology/principal findings: We study a computational model of amoeboid chemotactic navigation under differing conditions, from motion in an obstacle-free environment to navigation between obstacles and finally to moving in a maze. We use the maze as a simple stand-in for a motion task with severe constraints, as might be expected in dense extracellular matrix. Whereas agents using simple chemotaxis can successfully navigate around small obstacles, the presence of large barriers can often lead to agent trapping. We further show that employing a simple memory mechanism, namely secretion of a repulsive chemical by the agent, helps the agent escape from such trapping. Conclusions/significance: Our main conclusion is that cells employing simple chemotactic strategies will often be unable to navigate through maze-like geometries, but a simple chemical marker mechanism (which we refer to as "self-assistance") significantly improves success rates. This realization provides important insights into mechanisms that might be employed by real cells migrating in complex environments as well as clues for the design of robotic navigation strategies. The results can be extended to more complicated multi-cellular systems and can be used in the study of mammalian cell migration and cancer metastasis

Стилистический эффект разговорной речи и его составляющие

В обучении русскому языку как иностранному на современном этапе большое внимание уделяется особенностям русской разговорной речи. Это обусловлено целым рядом причин, среди которых, на наш взгляд, можно выделить следующие: во-первых, разговорная речь всегда отличается активностью проникновения во все сферы жизнедеятельности людей и функционирует как в повседневном общении, так и в различных сферах (литературе, кино, политике и т.д.). Во-вторых, разговорная речь носит многожанровый характер, что зачастую затрудняет ее понимание иностранными студентами. В-третьих, в разговорную речь помимо слов нейтрального стиля все активнее стала проникать арготическая лексика. Именно в связи с этим особый интерес у нас вызывает разговорный стиль речи в преломлении на инофонную аудиторию

The B7 family member B7-H6 is a tumor cell ligand for the activating natural killer cell receptor NKp30 in humans

Cancer development is often associated with the lack of specific and efficient recognition of tumor cells by the immune system. Natural killer (NK) cells are lymphocytes of the innate immune system that participate in the elimination of tumors. We report the identification of a tumor cell surface molecule that binds NKp30, a human receptor which triggers antitumor NK cell cytotoxicity and cytokine secretion. This previously unannotated gene belongs to the B7 family and, hence, was designated B7-H6. B7-H6 triggers NKp30-mediated activation of human NK cells. B7-H6 was not detected in normal human tissues but was expressed on human tumor cells, emphasizing that the expression of stress-induced self-molecules associated with cell transformation serves as a mode of cell recognition in innate immunity

A Practical Guide for the Effective Evaluation of Twitter User Geolocation

Geolocating Twitter users---the task of identifying their home locations---serves a wide range of community and business applications such as managing natural crises, journalism, and public health. Many approaches have been proposed for automatically geolocating users based on their tweets; at the same time, various evaluation metrics have been proposed to measure the effectiveness of these approaches, making it challenging to understand which of these metrics is the most suitable for this task. In this paper, we propose a guide for a standardized evaluation of Twitter user geolocation by analyzing fifteen models and two baselines in a controlled experimental setting. Models are evaluated using ten metrics over four geographic granularities. We use rank correlations to assess the effectiveness of these metrics. Our results demonstrate that the choice of effectiveness metric can have a substantial impact on the conclusions drawn from a geolocation system experiment, potentially leading experimenters to contradictory results about relative effectiveness. We show that for general evaluations, a range of performance metrics should be reported, to ensure that a complete picture of system effectiveness is conveyed. Given the global geographic coverage of this task, we specifically recommend evaluation at micro versus macro levels to measure the impact of the bias in distribution over locations. Although a lot of complex geolocation algorithms have been applied in recent years, a majority class baseline is still competitive at coarse geographic granularity. We propose a suite of statistical analysis tests, based on the employed metric, to ensure that the results are not coincidental.Comment: Accepted in the journal of ACM Transactions on Social Computing (TSC). Extended version of the ASONAM 2018 short paper. Please cite the TSC/ASONAM version and not the arxiv versio

A BioBricks Metabolic Engineering Platform for the Biosynthesis of Anthracyclinones in <i>Streptomyces coelicolor</i>

Actinomycetes produce a variety of clinically indispensable molecules, such as antineoplastic anthracyclines. However, the actinomycetes are hindered in their further development as genetically engineered hosts for the synthesis of new anthracycline analogues due to their slow growth kinetics associated with their mycelial life cycle and the lack of a comprehensive genetic toolbox for combinatorial biosynthesis. In this report, we tackled both issues via the development of the BIOPOLYMER (BIOBricks POLYketide Metabolic EngineeRing) toolbox: a comprehensive synthetic biology toolbox consisting of engineered strains, promoters, vectors, and biosynthetic genes for the synthesis of anthracyclinones. An improved derivative of the production host Streptomyces coelicolor M1152 was created by deleting the matAB gene cluster that specifies extracellular poly-β-1,6-N-acetylglucosamine (PNAG). This resulted in a loss of mycelial aggregation, with improved biomass accumulation and anthracyclinone production. We then leveraged BIOPOLYMER to engineer four distinct anthracyclinone pathways, identifying optimal combinations of promoters, genes, and vectors to produce aklavinone, 9-epi-aklavinone, auramycinone, and nogalamycinone at titers between 15-20 mg/L. Optimization of nogalamycinone production strains resulted in titers of 103 mg/L. We structurally characterized six anthracyclinone products from fermentations, including new compounds 9,10-seco-7-deoxy-nogalamycinone and 4-O-β-d-glucosyl-nogalamycinone. Lastly, we tested the antiproliferative activity of the anthracyclinones in a mammalian cancer cell viability assay, in which nogalamycinone, auramycinone, and aklavinone exhibited moderate cytotoxicity against several cancer cell lines. We envision that BIOPOLYMER will serve as a foundational platform technology for the synthesis of designer anthracycline analogues