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

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Despite the concern that has been expressed about potential method biases, and the pervasiveness of research settings with the potential to produce them, there is disagreement about whether they really are a problem for researchers in the behavioral sciences. Therefore, the purpose of this review is to explore the current state of knowledge about method biases. First, we explore the meaning of the terms “method” and “method bias” and then we examine whether method biases influence all measures equally. Next, we review the evidence of the effects that method biases have on individual measures and on the covariation between different constructs. Following this, we evaluate the procedural and statistical remedies that have been used to control method biases and provide recommendations for minimizing method bias.

Sources of Method Bias in Social Science Research and Recommendations on How to Control It

中枢神経系疾患の治療は正常細胞（ニューロン）の機能維持を目的とするが，脳血管障害のように機能障害の原因が細胞の死滅に基づくことは多い．一方，脳腫瘍の治療においては薬物療法や放射線療法といった腫瘍細胞の死滅を目標とするものが大きな位置を占める．いずれの場合にも，細胞死の機序を理解することは各種病態や治療法の理解のうえで重要である．現在のところ最も研究の進んでいる細胞死の型はアポトーシスである．そのなかで重要な位置を占めるミトコンドリアにおける反応および抗アポトーシス因子について概要を紹介する．

Neuroscience 細胞死：最近の知見

Synchronized oscillations and inhibitory interneurons have important and interconnected roles within cortical microcircuits. In particular, interneurons defined by the fast-spiking phenotype and expression of the calcium-binding protein parvalbumin have been suggested to be involved in gamma (30-80 Hz) oscillations, which are hypothesized to enhance information processing. However, because parvalbumin interneurons cannot be selectively controlled, definitive tests of their functional significance in gamma oscillations, and quantitative assessment of the impact of parvalbumin interneurons and gamma oscillations on cortical circuits, have been lacking despite potentially enormous significance (for example, abnormalities in parvalbumin interneurons may underlie altered gamma-frequency synchronization and cognition in schizophrenia and autism). Here we use a panel of optogenetic technologies in mice to selectively modulate multiple distinct circuit elements in neocortex, alone or in combination. We find that inhibiting parvalbumin interneurons suppresses gamma oscillations in vivo, whereas driving these interneurons (even by means of non-rhythmic principal cell activity) is sufficient to generate emergent gamma-frequency rhythmicity. Moreover, gamma-frequency modulation of excitatory input in turn was found to enhance signal transmission in neocortex by reducing circuit noise and amplifying circuit signals, including inputs to parvalbumin interneurons. As demonstrated here, optogenetics opens the door to a new kind of informational analysis of brain function, permitting quantitative delineation of the functional significance of individual elements in the emergent operation and function of intact neural circuitry.

https://web.stanford.edu/group/dlab/media/papers/Sohal%20Nature%202009.pdf

Parvalbumin neurons and gamma rhythms enhance cortical circuit performance

The application of recombinant Adeno-Associated Virus (rAAV) vectors as gene delivery vehicles has been limited by the modest packaging capacity (5.2kb) of rAAV. Th is limitation is imposed by the capsid size of 25nm diameter, which is determined by the capsid’s T=1 icosahedral geometry. Current methods for rAAV delivery of oversized cargo, typically involving co-delivery of dual vectors, suffer from challenges such as low efficiency in co-infection and reassembly of full-length products, indefinite ratios of the two vectors in individual cells, and necessity of re-design and re-validation for every new cargo. 

Inspired by the size polymorphism observed in natural viruses, we hypothesized that the T=1 icosahedral geometry of AAV capsids could be changed so that each capsid is built from more than 60 subunits. 

Here we present two rational design strategies that lead to eXtra Large AAV capsids (XL-AAVs). Th ese strategies involve modifying the intersubunit interactions and the assembly pathway of AAV capsids. Capsids engineered through both strategies form heterogeneous, 35nm-70nm spherical particles (Figure 1). Th e XL-AAV capsids can still package rAAV genomes, and the same protein design principles can be applied across multiple serotypes we tested (including AAV9, AAV2, AAV5, and AAVDJ). Ongoing work seeks to determine whether the XL-AAV capsids can fully protect and deliver conventionally oversized rAAV genomes. These design principles and the emerging XL-AAV capsids represent the first steps towards creating rAAV vectors with larger clone capacities, opening a path towards the delivery of disease-related genes and genetically-encoded tools with long coding sequences in single rAAV vectors.

Structure-Guided Rational Design of Adeno-Associated Viral Capsids with Expanded Sizes

Stimulation of target cells using light, e.g., in vivo or in vitro, is implemented using a variety of methods and devices. One example involves a vector for delivering a light-activated NpHR-based molecule comprising a nucleic acid sequence that codes for light-activated NpHR-based molecule and a promoter. Either a high expression of the molecule manifests a toxicity level that is less than about 75%, or the light-activated NpHR-based proteins are expressed using at least two NpHR-based molecular variants. Each of the variants characterized in being useful for expressing a light-activated NpHR-based molecule that responds to light by producing an inhibitory current to dissuade depolarization of the neuron. Other aspects and embodiments are directed to systems, methods, kits, compositions of matter and molecules for ion pumps or for controlling inhibitory currents in a cell (e.g., in in vivo and in vitro environments).

Method for optically controlling a neuron with a mammalian codon optimized nucleotide sequence that encodes a variant opsin polypeptide derived from natromonas pharaonis (NpHR)

Brain circuits are composed of vast numbers of intricately interconnected neurons with diverse molecular, anatomical and physiological properties. To allow highly specific targeting of individual neurons for structural and functional studies, we modified three site-specific DNA recombinases, Cre, Dre and Flp, by combining them with a fungal light-inducible protein, Vivid, so that their recombinase activities can be driven by blue light. We generated viral vectors to express these light-inducible recombinases and demonstrated that they can induce genomic modifications in dense or sparse populations of neurons in live mouse brains controlled by one-photon or two-photon light induction. As an important application, we showed that light-inducible recombinases can produce highly targeted, sparse and strong labeling of individual neurons thereby enabling whole-brain morphological reconstruction to identify their axonal projection specificity. In addition to targeting cortical brain areas, we applied the method in deep targets, with a demonstration of functional calcium imaging. These molecular tools enable spatiotemporally-precise, targeted genomic modifications that will greatly facilitate detailed analysis of neural circuits and linking genetic identity, morphology, connectivity and function.

https://biorxiv.org/content/biorxiv/early/2019/02/18/553271.full-text.pdf

RecV recombinase system for spatiotemporally controlled light-inducible genomic modifications.

Replying to N. K. Logothetis , 10.1038/nature09532 (2010)
 This is a welcome opportunity to discuss ofMRI, a technology for testing the causal and global impact of defined cell populations in vivo1. The accompanying Comment2 reviews well-known neuroanatomy, but does seem, in its entirety, to be founded on a suggestion that, after experiments were conducted to drive a defined circuit element and measure resulting BOLD signals1, we concluded that no other contributory circuit element was recruited by the driven population. This was not the case, however, as correctly understood by others in the fMRI community3,4,5 and as explained in the paper (for example, “contributions from additional cells and processes downstream of the defined optically triggered population are expected and indeed represent an important aspect of this approach”1). Moreover, the complexity of the brain dictates that such possible contributory mechanisms are more numerous than listed in the Comment2, including many other circuit and feedback mechanisms and classes of cells within neural circuitry6,7,8,9,10. As was discussed1, this is one of the most important and useful aspects of the ofMRI approach.
 https://www.nature.com/articles/nature09532

Viviana Gradinaru

Papers

Structure-Guided Rational Design of Adeno-Associated Viral Capsids with Expanded Sizes

Method for optically controlling a neuron with a mammalian codon optimized nucleotide sequence that encodes a variant opsin polypeptide derived from natromonas pharaonis (NpHR)

RecV recombinase system for spatiotemporally controlled light-inducible genomic modifications.

Lee et al. reply

Adeno-Associated Viral Gene Therapy Using PHP.B:NPC1 Ameliorates Disease Phenotype in Mouse Model of Niemann-Pick C1 Disease