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

基礎講座 電気泳動(Electrophoresis)

The use of artificial intelligence, and the deep-learning subtype in particular, has been enabled by the use of labeled big data, along with markedly enhanced computing power and cloud storage, across all sectors. In medicine, this is beginning to have an impact at three levels: for clinicians, predominantly via rapid, accurate image interpretation; for health systems, by improving workflow and the potential for reducing medical errors; and for patients, by enabling them to process their own data to promote health. The current limitations, including bias, privacy and security, and lack of transparency, along with the future directions of these applications will be discussed in this article. Over time, marked improvements in accuracy, productivity, and workflow will likely be actualized, but whether that will be used to improve the patient-doctor relationship or facilitate its erosion remains to be seen.

High-performance medicine: the convergence of human and artificial intelligence

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

正しい方法がわかる臨床基本手技 : from the New England journal of medicine

The rate constants for exchange of hydrogen for deuterium at the α-CH2 positions of 8-(N,N-dimethylaminonaphthalen-1-yl)acetic acid tert-butyl ester 1 and naphthalen-1-ylacetic acid tert-butyl ester 2 have been determined in potassium deuteroxide solutions in 1:1 D2O:CD3CN, in order to quantify the effect of the neighbouring peri-dimethylamino substituent on α-deprotonation. Intramolecular general base catalysis by the (weakly basic) neighbouring group was not detected. Second-order rate constants, kDO, for the deuterium exchange reactions of esters 1 and 2 have been determined as 1.35 × 10−4 M−1 s−1 and 3.95 × 10−3 M−1 s−1, respectively. The unexpected 29-fold decrease in the kDO value upon the introduction of a peri-dimethylamino group is attributed to an unfavourable steric and/or electronic substituent effect on intermolecular deprotonation by deuteroxide ion. From the experimental kDO values, carbon acid pKa values of 26.8 and 23.1 have been calculated for esters 1 and 2.

/pdf/peri-dimethylamino-substituent-effects-on-proton-transfer-at-1jyc6m4lrf.pdf

peri-Dimethylamino substituent effects on proton transfer at carbon in α-naphthylacetate esters: a model for mandelate racemase.

Microfluidic droplets are a unique tool for performing biological and chemical experiments. The compartmentalization of single entities, such as plasmids or cells, into microdroplets separated by an immiscible carrier fluid allows for (i) experimentation in the nL- and pL-range which reduces reagent consumption (ii) the generation of highly monodisperse droplets resulting in homogeneous reaction conditions and (iii) microdroplets can be generated with frequencies up to 10 kHz allowing high-throughput screens of up to 100 million reaction conditions per day. If ultrahigh throughput is not necessary, devices interfacing with multiple handling and optical analysis systems provide additional capabilities with more control over the content of each droplet. Microfluidic droplets are used for a variety of biochemical and biomedical assays. They can be used to encapsulate single cells in 3D hydrogel matrices to monitor the effect of specific soluble factors or drugs on differentiation, or follow clonal spheroid formation and drug response. And finally, microfluidic devices enable the high-throughput screening of millions of metagenomic genes to discover new enzymes for improved catalytic efficiency or new therapeutic activities.

Microfluidic Droplets and Their Applications: Diagnosis, Drug Screening and the Discovery of Therapeutic Enzymes

Microfluidic water-in-oil emulsion droplets are becoming a mainstay of experimental biology, where they replace the classical test tube. In most applications (e.g. in ultrahigh throughput directed evolution) the droplet content is identical for all compartmentalized assay reactions. When emulsion droplets are used for kinetics or other functional assays, though, concentration dependencies (e.g. of initial rates for Michaelis-Menten plots) are required. Droplet-on-demand systems satisfy this need but extracting large amounts of data is challenging. Here we introduce a multiplexed droplet absorbance detector which, coupled to semi-automated droplet generation, forms a tubing-based droplet-on-demand system able to generate and extract quantitative datasets from defined concentration gradients across multiple series of droplets for multiple time points. The emergence of product is detected by reading the absorbance of the droplet sets at multiple, adjustable time points (reversing the flow direction after each detection, so that the droplets pass a line scan camera multiple times). Detection multiplexing allows absorbance values at twelve distinct positions to be measured and enzyme kinetics are recorded for label-free concentration gradients (composed of about 60 droplets each, covering as many concentrations). With a throughput of around 8640 data points per hour, a 10-fold improvement compared to the previously reported single point detection method is achieved. In a single experiment, twelve full datasets of high-resolution and high accuracy Michaelis-Menten kinetics were determined to demonstrate the potential for enzyme characterization for glycosidase substrates covering a range in enzymatic hydrolysis of seven orders of magnitude in kcat/KM. The straightforward set-up, high throughput, excellent data quality, wide dynamic range that allows coverage of diverse activities suggest that this system may serve as a miniaturized spectrophotometer to for detailed analysis of study clones emerging from large-scale combinatorial experiments.

High-Throughput Steady-State Enzyme Kinetics Measured in a Parallel Droplet Generation and Absorbance Detection Platform

Droplet microfluidics allows one to address the ever-increasing demand to screen large libraries of biological samples. Absorbance spectroscopy complements the golden standard of fluorescence detection by label free target identification and providing more quantifiable data. However, this is limited by speed and sensitivity. In this paper we increase the speed of sorting by including acoustofluidics, achieving sorting rates of target droplets of 1 kHz. We improved the device design for detection of absorbance using fibre-based interrogation of samples with integrated lenses in the microfluidic PDMS device for focusing and collimation of light. This optical improvement reduces the scattering and refraction artefacts, improving the signal quality and sensitivity. The novel design allows us to overcome limitations based on dielectrophoresis sorting, such as droplet size dependency, material and dielectric properties of samples. Our acoustic activated absorbance sorter removes the need for offset dyes or matching oils and sorts about a magnitude faster than current absorbance sorters.

/pdf/acoustic-sorting-of-microfluidic-droplets-at-khz-rates-using-2e1mt9a9.pdf

Acoustic sorting of microfluidic droplets at kHz rates using optical absorbance

This chapter introduces the various categories of promiscuity and their possible role in enzyme evolution It also reviews some of the well-known examples of enzymes for which the promiscuous function is industrially relevant, leading to conversions of nonnatural compounds Enzyme promiscuity is becoming an increasingly important phenomenon in the field of biocatalysis, both directly and indirectly: directly, because many desirable conversions are “unnatural,” so expansion of the existing functions of protein catalysts is necessary to convert these “promiscuous” substrates; indirectly, through the observation that promiscuous enzymes may be particularly evolvable, opening a wide range of possibilities for engineering these potentially valuable side activities Candida antarctica lipase B (CALB) is a typical representative of the α/β-hydrolase fold family of enzymes comprising not only a number of other esterases, but also haloalkane dehalogenases and epoxide hydrolases Many of these natural products have unique bioactivity and are thus of great interest to the pharmaceutical industry Halohydrin lyases or haloalcohol dehalogenases are found in various bacteria that are able to use halogenated hydrocarbons as a sole source of carbon and energy The improvement of several of the promiscuous reactions of CALB was obtained by removing the catalytic nucleophile, naturally resulting in decreased performance for the native activity

Florian Hollfelder

Papers

peri-Dimethylamino substituent effects on proton transfer at carbon in α-naphthylacetate esters: a model for mandelate racemase.

Microfluidic Droplets and Their Applications: Diagnosis, Drug Screening and the Discovery of Therapeutic Enzymes

High-Throughput Steady-State Enzyme Kinetics Measured in a Parallel Droplet Generation and Absorbance Detection Platform

Acoustic sorting of microfluidic droplets at kHz rates using optical absorbance

Enzyme Promiscuity and Evolution of New Protein Functions