抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of casual variants for disease phenotypes. Different classes of sequence variations at the nucleotide level are involved in human diseases, including substitutions, insertions, deletions, frameshifts, and non-sense mutations. Frameshifts and non-sense mutations are likely to cause a negative effect on protein function. Existing prediction tools primarily focus on studying the deleterious effects of single amino acid substitutions through examining amino acid conservation at the position of interest among related sequences, an approach that is not directly applicable to insertions or deletions. Here, we introduce a versatile alignment-based score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in-frame insertions, deletions, and multiple amino acid substitutions. This alignment-based score measures the change in sequence similarity of a query sequence to a protein sequence homolog before and after the introduction of an amino acid variation to the query sequence. Our results showed that the scoring scheme performs well in separating disease-associated variants (n = 21,662) from common polymorphisms (n = 37,022) for UniProt human protein variations, and also in separating deleterious variants (n = 15,179) from neutral variants (n = 17,891) for UniProt non-human protein variations. In our approach, the area under the receiver operating characteristic curve (AUC) for the human and non-human protein variation datasets is ∼0.85. We also observed that the alignment-based score correlates with the deleteriousness of a sequence variation. In summary, we have developed a new algorithm, PROVEAN (Protein Variation Effect Analyzer), which provides a generalized approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions, and in-frame insertions and deletions. The PROVEAN tool is available online at http://provean.jcvi.org.

/pdf/predicting-the-functional-effect-of-amino-acid-substitutions-o8vslfnjzv.pdf

Predicting the Functional Effect of Amino Acid Substitutions and Indels

Understanding relationships between sets is an important analysis task that has received widespread attention in the visualization community. The major challenge in this context is the combinatorial explosion of the number of set intersections if the number of sets exceeds a trivial threshold. In this paper we introduce UpSet, a novel visualization technique for the quantitative analysis of sets, their intersections, and aggregates of intersections. UpSet is focused on creating task-driven aggregates, communicating the size and properties of aggregates and intersections, and a duality between the visualization of the elements in a dataset and their set membership. UpSet visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes. Sorting according to various measures enables a task-driven analysis of relevant intersections and aggregates. The elements represented in the sets and their associated attributes are visualized in a separate view. Queries based on containment in specific intersections, aggregates or driven by attribute filters are propagated between both views. We also introduce several advanced visual encodings and interaction methods to overcome the problems of varying scales and to address scalability. UpSet is web-based and open source. We demonstrate its general utility in multiple use cases from various domains.

/pdf/upset-visualization-of-intersecting-sets-4iov8vohcq.pdf

UpSet: Visualization of Intersecting Sets.

Design studies are an increasingly popular form of problem-driven visualization research, yet there is little guidance available about how to do them effectively. In this paper we reflect on our combined experience of conducting twenty-one design studies, as well as reading and reviewing many more, and on an extensive literature review of other field work methods and methodologies. Based on this foundation we provide definitions, propose a methodological framework, and provide practical guidance for conducting design studies. We define a design study as a project in which visualization researchers analyze a specific real-world problem faced by domain experts, design a visualization system that supports solving this problem, validate the design, and reflect about lessons learned in order to refine visualization design guidelines. We characterize two axes - a task clarity axis from fuzzy to crisp and an information location axis from the domain expert's head to the computer - and use these axes to reason about design study contributions, their suitability, and uniqueness from other approaches. The proposed methodological framework consists of 9 stages: learn, winnow, cast, discover, design, implement, deploy, reflect, and write. For each stage we provide practical guidance and outline potential pitfalls. We also conducted an extensive literature survey of related methodological approaches that involve a significant amount of qualitative field work, and compare design study methodology to that of ethnography, grounded theory, and action research.

/pdf/design-study-methodology-reflections-from-the-trenches-and-4rom330819.pdf

Design Study Methodology: Reflections from the Trenches and the Stacks

Field-deployable diagnostics based on cell-free systems have advanced greatly, but on-site quantification of target analytes remains a challenge. Here we demonstrate that Escherichia coli lysate-based cell-free biosensors coupled to a personal glucose monitor (PGM) can enable on-site analyte quantification, with the potential for straightforward reconfigurability to diverse types of analytes. We show that analyte-responsive regulators of transcription and translation can modulate production of the reporter enzyme {beta}-galactosidase, which in turn converts lactose into glucose for PGM quantification. Because glycolysis is active in the lysate and would readily deplete converted glucose, we decoupled enzyme production and glucose conversion to increase endpoint signal output. This lysate metabolism did, however, allow for one-pot removal of glucose present in complex samples (like human serum) without confounding target quantification. Taken together, we show that integrating lysate-based cell-free biosensors with PGMs enables accessible target detection and quantification at the point of need. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/449464v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@e0b629org.highwire.dtl.DTLVardef@d77bbeorg.highwire.dtl.DTLVardef@fd2cb8org.highwire.dtl.DTLVardef@182f1df_HPS_FORMAT_FIGEXP M_FIG C_FIG

/pdf/point-of-care-analyte-quantification-and-digital-readout-via-333kd29mtr.pdf

Point-of-care analyte quantification and digital readout via lysate-based cell-free biosensors interfaced with personal glucose monitors

Electroporation is a basic yet powerful method for delivering small molecules (RNA, DNA, drugs) across cell membranes by application of an electrical field. Due to its vital role, electroporation has wide applicability from genetically engineering cells, to drug- and DNA-based vaccine delivery. Despite its broad applications in biological research, the high cost of electroporators is an obstacle for many budget-conscious laboratories. To address this need, we describe a simple, inexpensive, and hand-held electroporator inspired by a common household piezoelectric gas lighter. The proposed “ElectroPen” device costs about 20 cents, is portable (13 g), is fabricated on-demand using 3D-printing, and delivers repeatable exponentially decaying pulses of about 2000 V in 5 ms. We provide a proof-of-concept demonstration by genetically transforming plasmids into E. coli strains and show comparable transformation efficiency and cell growth with commercial devices, but at a fraction of the cost. Our results are validated by an independent team across the globe, providing a real-world example of democratizing science through frugal tools. Thus, the simplicity, accessibility, and affordability of our device holds potential for making modern synthetic biology accessible in high-school, community, and field-ecology laboratories.

https://www.biorxiv.org/content/biorxiv/early/2018/12/21/448977.full.pdf

ElectroPen: An ultralow-cost piezoelectric electroporator

The regulation of metabolism is critical to many important cellular processes in higher eukaryotes, and metabolites themselves can have significant regulatory potential in complex phenotypes Thus, external control of metabolism for both biotechnological and biomedical ends is of great importance There has been increasing emphasis on using non-genetic approaches for direct, transient control of metabolism and cellular state, with particularly promising applications in stem cell biomanufacturing and cancer Metabolite-based methods have been used to facilitate expansion of stem cells, to control and prevent their differentiation, and to reprogram cells to a pluripotent state Similar approaches are also being explored to inhibit the growth of cancer cells

Manipulation of metabolism in complex eukaryotic systems to control cellular state

: Concern for the conservation of marine mammals continues to rise as they are exposed to multiple anthropogenic and natural environmental stressors (Fair and Becker, 2000; Bossart, 2006; 2011). Stress responses play a critical role in allowing animals to cope with environmental perturbations. As such, there remains a large gap in our knowledge about the pathophysiological effects of both acute and chronic stress to guide management decisions on these important species. A paucity of research exists that characterizes basic stress responses required to better understand multiple stressors and biologically significant effects. As top predators, marine mammals can serve as an integrator and intensifier of the diverse stressors and hazards present in the environment. The growing concerns about anthropogenic stress include multiple stressors faced by marine mammals from increased environmental exposures to pathogens, pollution, noise and other acoustic influences. Studies that evaluate these effects in marine mammals are lacking since much of the baseline data related to physiology and health are not available. Given the limited amount of data specific to free-ranging marine mammal populations, our study used managed-care animals to bridge this gap and generate baseline data for stress parameters to ground hypotheses regarding wild populations. The bottlenose dolphin is a particularly relevant species to study stress, as it is the most common cetacean in near coastal waters, with a cosmopolitan distribution, widely represented along the U.S. coast and an important resource for the U.S. Navy.

/pdf/pathophysiology-of-stress-in-wild-and-managed-care-vxggqjf1f2.pdf

Pathophysiology of Stress in Wild and Managed-Care Bottlenose Dolphins (Tursiops truncatus)

A whole-cell biosensor for a point-of-care assay using genetically engineered bacteria or fungi to report micronutrient, for example, zinc levels in blood samples is provided. One embodiment provides a micronutrient biosensor having a gene circuit expressing at least two different pigments in response to two different concentrations of the micronutrient, wherein expression of the pigment is visible to the naked eye and is indicative of a concentration of the micronutrient. Another embodiment provides the micronutrient biosensor expressing a third pigment in response to a different concentration of the micronutrient relative to the at least two pigments. Exemplary micronutrients include but are not limited to zinc, iron, vitamin D, vitamin B12, iodine, and folate. Representative pigments include but are not limited to violacein, lycopene, and beta-carotene.

Mark P. Styczynski

Papers

Point-of-care analyte quantification and digital readout via lysate-based cell-free biosensors interfaced with personal glucose monitors

ElectroPen: An ultralow-cost piezoelectric electroporator

Manipulation of metabolism in complex eukaryotic systems to control cellular state

Pathophysiology of Stress in Wild and Managed-Care Bottlenose Dolphins (Tursiops truncatus)

Pigment-based micronutrient biosensors