每日专业名词 | 通俗解释
2024年01月18日
什么是纳米颗粒靶向静脉递送系统？
脂质纳米颗粒（Lipid nanoparticle, LNP）
2024年01月18日
抗体本来属于免疫学的内容，但因为应用过于广泛，所以必须学习。
大家都知道抗体就是与抗原特异结合的大蛋白，也知道抗体的Y型结构，那具体结构是如何呢？
几个问题：
- 抗体（Antibody），又称免疫球蛋白（immunoglobulins ,Ig）IgG只是其中的一种
- 抗体的两种主要功能是什么？抗原结合和生物活性介导
- 抗体有几条肽链，几条重链和轻链？四条多肽链构成——两条重链和两条轻链
- 抗体有几种类型？IgG、IgM、IgA、IgE和IgD，通过重链类型进行区分。
- 可变区和恒定区的作用？
- 靶蛋白抗体制作流程？
- 单克隆抗体是什么？
- 如何理解Fc介导的效应功能（ADCC、ADCP、CDC）？
IgG并不能特异性的与任何蛋白结合，那么IgG所带下来的蛋白都是非特异性的与IgG结合的蛋白，得到的东西就是背景。
IgG较其他类Ig更易扩散到血管外的间隙内，因而在结合补体、增强免疫细胞吞噬病原微生物和中和细菌毒素的能力方面，具有重要作用，能有效地抗感染
IgG抗体由Fab区和Fc区组成，Fab区主要作用是特异性识别抗原，发挥免疫功能。Fc区可以识别并结合表达Fc受体的免疫细胞及血液中补体进而发挥抗体依赖的细胞介导的细胞毒性作用（ADCC），抗体依赖的细胞介导的细胞吞噬作用（ADCP）以及补体依赖的细胞毒作用（CDC）（表1）等效应功能；Fc还可以结合新生IgG转运受体（FcRn）从而使抗体在体内不被轻易清除而延长了其在机体内的半衰期
大多数上市的ADC选择IgG1骨架，但全身给药时抗体的异质性是个长期且重大的问题。抗体形式的改进和创新有望增强靶标特异性、改善组织渗透性，调动免疫系统和降低全身毒性。
ADC相关概念的文献分布和趋势：ADC联合免疫疗法占文献数量最多（图9）；ADC最常见的递送系统是纳米颗粒靶向静脉递送系统（图10）；ADC采用的payload主要是auristatins和calicheamicins（图11）；HER2和EGFR仍然是实体瘤中最广泛探索的靶抗原，Trop-2和Nectin-4抗原在过去5年中持续稳定增长（图12）；癌症免疫治疗中最常用的IgG亚型是IgG1和IgG4，文献中IgG2和IgG3在ADC中的应用比IgG1增长得更快（图13）；治疗性ADC中首选的连接子类型为可裂解连接子（图14）。
2023年12月14日
vehicle control，vehicle就是载体的意思，通常DMSO就是药物的载体，为了严格起见，对照都是等量的DMSO，而不是空白！
Hopefully, you were already planning on including a no drug treatment control, where you have cells that have not been treated with your drug. Another important control is the vehicle control. The vehicle is the solvent used to dissolve the drug (e.g. DMSO). Unless the solvent is media, this type of control is necessary so that you can be confident that any observed effects are due to the drug alone and not the solvent. The same volume of vehicle and vehicle + drug should be added to their respective wells since the only difference between these conditions is the inclusion of the drug.
参考：6 Steps for Successful in vitro Drug Treatment
2023年12月11日
Agonist和Antagonist，还是容易搞混。
Agonist兴奋剂，类似普通ligand的作用，激活功能。
Antagonist多了三个字母-nta-，拮抗剂，抑制活性。
Agonist: A chemical substance that binds to and activates certain receptors on cells, causing a biological response. Oxycodone, morphine, heroin, fentanyl, methadone, and endorphins are all examples of opioid receptor agonists.
Antagonist: A chemical substance that binds to and blocks the activation of certain receptors on cells, preventing a biological response. Naloxone is an example of an opioid receptor antagonist
2023年07月19日
Luminescence：化学发光，这种形式的光，来自于酶学反应提供的能量，所以如果你的试剂盒中，提供了底物，而你的样品可以表达荧光素酶，则需要用这个模块进行检测。因为这种模式下，没有任何外源的光信号，完全是靠样品和检测试剂的反应发光，所以这个检测模式下，仪器的检测灵敏度更高。Luciferase是通过这个部分检测的。
Fluorescence：这是荧光。这种可检测的光是来自于外源光提供的能量。所以通常试剂盒中会有荧光染料，并会要求调节仪器的激发光和发射光。如果试剂盒里面根本没提激发波长和发射波长的信息，多半不需要这个检测模块。GFP，RFP是用这个模块检测的。
2023年01月28日
阿霉素（Dox）是一种广泛的肿瘤化学治疗药物，具有很高的心脏毒性。【经常会在cancer的paper里看到Dox- +处理】
2023年01月02日
Histology, also known as microscopic anatomy or microanatomy, is the branch of biology which studies the microscopic anatomy of biological tissues.
组织学，通常也是临床的金标准技术，直接看相关的tissue的情况，也可以结合IHC（immunohistochemistry），直接看相关marker的表达。
这也是reviewer惯问的问题，如果你做了病人样品，但是提供的信息不全，则会摆出这一点。
但我们做的是冷门的HSCR，而且是用iPSC来做，因为消化道是个非常复杂的连续性器官体，我们无法提供这些信息。
常识：Histology通常是针对有tissue结构的mouse和human，以及organoid，至于简单的cell line则没有意义。
临床和病理的区别【一个对人、一个对样本】
Clinical and pathological
我居然一直都以为这是一个东西，直到看到审稿回复才知道，这两个可以说是差别非常大的。
Clinical stage is based on all of the available information obtained before a surgery to remove the tumor, while pathologic stage adds additional information gained by examination of the tumor microscopically after surgery expressing the stage before therapy only (Lucas 2006).
临床好理解，就是医生，在不做手术前，可以通过一切仪器和检测报告对病人作出一个诊断；
病理怎像是医院的researcher，一定是在做了手术或者取样后，对样本进行分析。
最后会综合对病人作出一个诊断，我们真正的researcher则是相当于高级病理专家，运用各种先进技术，来负责诊断和治疗。
2022年03月01日
HSCR文章的一些科普
progenitor和precursor的区别
The main difference between progenitor and precursor cells is that progenitor cells are mainly multipotent cells that can differentiate into many types of cells, whereas precursor cells are unipotent cells that can only differentiate into a particular type of cells.
糖酵解glycolysis
糖酵解（英语：glycolysis，又称糖解）是把葡萄糖（C6H12O6）转化成丙酮酸（CH3COCOO− + H+）的代谢途径。在这个过程中所释放的自由能被用于形成高能量化合物ATP和NADH。糖酵解作用及其各种变化形式发生在几乎所有的生物中，无论是有氧和厌氧。糖酵解的广泛发生显示它是最古老的已知的代谢途径之一。糖酵解作用是所有生物细胞糖代谢过程的第一步。糖酵解作用是一共有10个步骤酶促反应的确定序列。在该过程中，一分子葡萄糖会经过十步酶促反应转变成两分子丙酮酸。糖酵解作用发生在大多数生物体中的细胞的胞质溶胶。
脂肪酸分解Fatty acid catabolism
脂肪酸的氧化作用發生在粒線體（mitochondria）內，脂肪酸必須先和ATP反應，轉變為活化的中間產物，才能與其他酵素作更進一步的代謝，長鏈的Fatty acyl-CoA不能穿過粒線體內膜進入粒線體基質，需藉肉酸素（carnitine）運送機制，脂肪酸氧化(Fatty acid oxidation)。
氧化磷酸化（英语：oxidative phosphorylation，缩写作 OXPHOS）是细胞的一种代谢途径，该过程在真核生物的线粒体内膜或原核生物的细胞膜上发生，使用其中的酶及氧化各类营养素所释放的能量来合成三磷酸腺苷（ATP）。与其他的代谢途径，特别是糖酵解之类的无氧发酵途径相比，它能更高效地释放能量。
Glycolysis and FAO are essential metabolic pathways for producing pyruvate and acetyl-CoA, respectively, to fuel the tricarboxylic acid (TCA) cycle for ATP generation under an energy-demanding condition.
三羧酸循环（tricarboxylic acid cycle） 可简称为TCA cycle，亦作柠檬酸循环（citric acid cycle），是有氧呼吸的第三阶段。该循环以循环中一个重要中间体柠檬酸命名，又因为柠檬酸是一种三元羧酸，该反应又称为三羧酸循环。丙酮酸在经过丙酮酸脱氢酶系氧化，生成乙酰辅酶A（acetyl-CoA）后，与四碳二元羧酸草酰乙酸化合，生成柠檬酸，进入柠檬酸循环。
卡尔文循环（英语：Calvin cycle，或简称卡氏循环，又译作开尔文循环），卡尔文循环是光合作用里碳反应的一部分，反应场所为叶绿体内的底物，分为三个阶段：羧化、还原和二磷酸核酮糖的再生。
SAG - agonist
SAG (Smoothened Agonist) is a chlorobenzothiophene-containing compound which acts as an activator of the G protein-coupled receptor Smoothened (SMO, EC₅₀ = 3 nM; Chen et al.) SMO is a component of the Hedgehog signaling pathway, which is translocated to the primary cilium after stimulation of the Patched receptor by Hedgehog family ligands, leading to pathway activation. SAG activates SMO via direct binding to the heptahelical bundle (Kd = 59 nM), stabilizing a specific conformation of SMO in cilia and leading to increased downstream gene expression (Rohatgi et al.). SAG abrogates cyclopamine inhibition of SMO, indicating that it acts downstream of cyclopamine (Frank-Kamenetsky et al.; Chen et al.; Lewis & Krieg).
Cyclow - antagonist
Cyclopamine-KAAD, CAS 306387-90-6, is a cell-permeable potent analog of Cyclopamine (Cat. No. 239803) that specifically inhibits Hedgehog (Hh) signaling with similar or lower toxicity. Suppresses both the ShhNp-induced pathway activity and SmoA1-induced reporter activity.
2021年06月08日
能量代谢
Glycolysis 糖酵解
Fatty acid metabolism 脂肪酸代谢
Pentose phosphate pathway - PPP - 磷酸戊糖途径
tricarboxylic acid cycle - TCA - 三羧酸循环
一句话总结：
参考：糖酵解TCA
干细胞领域专有名词
S/L ESCs, conventional ESCs cultured in serum/LIF (SL) 血清和白血病抑制因子
ground-state ESCs【不同paper叫法不同，S/L and 2i ESCs，CSC paper】
naive, primed and ground state pluripotency
Mouse embryonic stem cells (mESCs) are derived from the inner cell mass (ICM) of pre-implantation stage embryos1,2. mESCs derived in leukemia inhibitory factor (LIF) and serum are representatives of the naive state of pluripotency. The combination of LIF + serum (LS) is used as a “conventional” culture condition for mESCs derivation.【在SL里培养的就是naive，也是conventional】
Until 2008, the derivation of germ-line competent mESCs from non-permissive mice was not possible. However, using the combination of two small molecule inhibitors PD0325901 (PD) and Chir99021 (CH), referred to as “2i”, ESCs could also be derived from non-permissive mouse strains at a higher efficiency5,6. PD and CH are inhibitors of the fibroblast growth factor (FGF) and the glycogen synthase kinase 3 beta (GSK3β) signaling pathways respectively. In mice, pluripotent stem cells can also be derived from the epiblast of post-implantation stage embryos, commonly referred to as epiblast stem cells (EpiSCs). These pluripotent stem cells display primed characteristics and are dependent upon activation of FGF and Activin signaling for their self-renewal7,8. Thus, three distinct pluripotent states, namely naive, primed and ground pluripotency states have been defined in mouse.【用2个抑制剂培养的就是ground state，primed就是用的比较迟的细胞】
参考：
The many faces of Pluripotency: in vitro adaptations of a continuum of in vivo states
Ex vivo (Latin: "out of the living") literally means that which takes place outside an organism. In science, ex vivo refers to experimentation or measurements done in or on tissue from an organism in an external environment with minimal alteration of natural conditions.
Ex vivo means that something is experimented on or investigated outside its natural in vivo environment while in vitro means in the test tube.
2021年05月31日
GO分析后，会出现很多的term，以negative regulation开头，这是什么意思呢？
negative regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
这表明了方向性，说明这些基因可以抑制某些生物过程。
2021年05月20日
细胞clone
A clone is a group of identical cells that share a common ancestry, meaning they are derived from the same cell.
Broad peaks and Narrow peaks of Histone modifications区别
Different histone mods have very different distributions. For example, "active" marks like H3K4me3 and H3K9ac form sharp peaks at transcription start sites while heterochromatin marks like H3K27me3 can cover blocks of many kb. So which peaks you use for analysis would depend on the modification you're looking at and the questions you're asking. In my experience, the narrow peaks of active marks can be analysed much like the standard analysis of transcription factor binding while you have to be a bit more inventive in analysing marks with broader distributions. I would be very cautious about combining the different peaks though as different distributions may well represent different epigenetic functions.
narrowpeaks can be generally called for TF, since the region bound is pretty much limited. broadpeaks are better for histone modifications or histone modifiers since the regions can be much wider.
TF binding affinity 就是TF结合到DNA序列的一个score 【参考】
massively-parallel reporter assays (MPRA) 大规模平行报告基因分析，利用合成生物学，直接在试管里模拟GWAS，找eQTL。
2021年05月18日
karyotypes 核型，就是染色后直接去看没有分裂的染色体，是否完整，是否有缺失或三体等。
photographs of chromosomes are taken in order to determine the chromosome complement of an individual, including the number of chromosomes and any abnormalities.
Phased And Unphased Genotypes
phase即分型，在genetic领域特指分出haplotype，双倍体
Phased data are ordered along one chromosome and so from these data you know the haplotype. Unphased data are simply the genotypes without regard to which one of the pair of chromosomes holds that allele.
A biallelic genotype comes from two chromosomes. Phased means I know not only the genotypes but which chromosome each genotype call came from. This lets you interpret which sets of genotypes are being inherited together
区分：sequencing、genotyping、phasing，先后承接
haplotype frequency：约定N个碱基，理论上有2的N次方种haplotypes，但实际很少，只有几种。参考：Statistical Genetics – Part I - CSE Home
GWAS conditional analysis 已经有一个lead SNP，再看其他周边的SNP在它的条件下是否显著
I want to test if the SNPs in chr 19 are independent of my top SNP rs2075650.
Conditional analysis to identify the independently associated SNPs, can be done just with the summary statistics using GCTA software.
https://cnsgenomics.com/software/gcta/#Overview
allele-specific expression 很有意思的话题，同一个位点，为什么两个allele的表达情况不同，显隐性
Allele-specific expression (ASE) analysis, which quantifies the relative expression of two alleles in a diploid individual, is a powerful tool for identifying cis-regulated gene expression variations that underlie phenotypic differences among individuals.
拓展：Allele-Specific Enhancer Activities，variant也会影响到enhancer的活性
2021年05月12日
干细胞领域
根据全能性的强弱来划分：
- totipotent / omnipotent
- pluripotent
- multipotent
- bipotent
- oligopotent
- unipotent
IPSC - 诱导性多能干细胞【优点：可以从病人的组织重编程得到IPSC，携带其全部遗传物质；缺点：全能性不够】
Totipotent cells can form all the cell types in a body, plus the extraembryonic, or placental, cells. Embryonic cells within the first couple of cell divisions after fertilization are the only cells that are totipotent. Pluripotent cells can give rise to all of the cell types that make up the body; embryonic stem cells are considered pluripotent. Multipotent cells can develop into more than one cell type, but are more limited than pluripotent cells; adult stem cells and cord blood stem cells are considered multipotent.
EPSC - Expanded Potential Stem Cell - 超潜能干细胞【类似ESC的细胞，这两个E不是一个意思，不能重编程，只能从受精卵获取】
We sought to establish cultures of new stem cells from cleavage stage mouse embryos. Under such a culture condition, we speculated that the self renewing stem cell population might have expanded potential as the cells of 4-cell (4C) or 8-cell (8C) embryos or the individual blastomeres retain the potential to differentiate to both the trophoectoderm (TE) and the inner cell mass (ICM)
参考：
基因操作选择【找不到更好的词】
Cre-LOX：多用于老鼠模型，可以conditional编辑基因，诱导型。
CRISPR：多用于细胞系，对操作环境和材料要求高，相对简单的细胞系更容易成功。
2021年04月27日
碰到陌生pathway不要怕，查一下就行了。
membrane potential 膜电势 - 神经元之间的信号传导
Neuromuscular junction 肌肉神经接点
Single-cell isolation 单细胞分离技术【认真区分这些技术，不要一团浆糊】
Serial dilution 连续稀释 - 拿不同的培养液连续稀释，得到单细胞悬浮液。优点：convenient operation, low cost，in vitro里应用广泛；缺点：time-consuming，无法精准得到target cells
Micromanipulation 显微操纵 - 直接在显微镜下人工分离，缺点：low throughput
fluorescence-activated cell sorting (FACS) 荧光激活细胞分选术 - 基于flow cytometry【刚科普过】，优点：高通量自动分选；缺点：requires a large number of cell suspensions，不适合分离low-abundance cells，mechanical damage
immunomagnetic separation (IMS) 免疫磁化分离 - magnetic beads磁珠结合到细胞表面的抗体，缺点：操作相对复杂，优点：tumor samples已经应用
laser capture microdissection (LCM) 激光捕获显微切割 - 直接在显微镜下用激光切割target部位，优点：cancer里广泛应用；缺点：high cost, low flux, lack of automation, and limited accuracy
microfluidic platforms 微流体平台 - 现在的商业化的标准单细胞分离技术，优点：污染少、试剂便宜；缺点：装置复杂，门槛较高
参考：Progress and applications of single-cell sequencing techniques
2021年04月20日
Flow cytometry 流式细胞术
用特定的带荧光的抗体标记细胞，然后用类似单细胞的flow技术来一个一个检测细胞的信号，一般会选择两个维度，最后就画出了一个二维的散点图（颜色代表了密度density）。
对于我们的ENCC，则用了 HNK1 和 p75NTR 两个抗体
The HNK-1 antibody known to define a subpopulation of human lymphocytes with natural killer and killer cell activities was shown to detect a common neuroectodermal antigen. monoclonal antibody HNK-1 is a marker for neural crest cells from the entire rostrocaudal axis.
most caudal neural crest-derived cells co-expressed p75(NTR)-, Phox2b- and Ret-immunoreactivity
用途：
- 从混合细胞中筛选出目标细胞FACS；
- 从相对细胞计数到绝对细胞计数
- 从相对定量到绝对定量分析
- 从单色到多色荧光分析
- 从细胞膜成份到细胞内成份分析
- 液体中可溶性成分的流式细胞分析
- 分子表型分析
参考：
flow cytometry : basic principles - YT - 推荐
immunocytochemistry ICC 免疫细胞化学 - 对象是细胞
immunohistochemistry IHC 免疫组织化学 - 对象是组织
Immunofluorescence IF 免疫荧光 - 泛指
都是用抗体来检测蛋白的丰度、分布和定位。abundance, distribution, and localization
非常常用的荧光染色剂及其标记物：
- DAPI (blue) - nuclear acid
- SOX10 - dividing ENS progenitor cells
- HUC/D+ immature neurons
- 5-HT+ mature neurons
参考：
ICC vs IHC vs IF – Do You Know the Difference?
2021年04月08日
双同源重组系统 - 周斌是该领域的大佬
Sox10CreERT2 x R26ReYFP embryos
Wnt1Cre x R26ReYFP embryos
As SOX10 specifically marks dividing ENS progenitor cells, we could retrieve this subpopulation by inducing reporter expression in Sox10CreERT2 x R26ReYFP embryos【这部分是细胞和发育生物学的核心技术手段，门槛极高，必须搞懂。】
Cre-loxP系统有lineage tracing的功能，只要表达过就会一直mark。而直接敲进报告基因则比较局限，只有表达的时候才会mark。
Cre-loxP的几个核心成分
Cre是recombinase enzymes重组酶，lox是序列位点locus，Cre可以切掉两个lox之间的DNA序列，这些DNA序列可以很灵活，可以是gene、stop、reporter gene或其他。
Wildly used recombination systems: Cre-loxP, FLP-FRT, Dre-Rox
Cre recombinase is expressed under the control of a tissue- or cell-specific promoter in one mouse line.
Sox10-Cre: Cre gene is knocked into Sox10 locus, after Sox10 promoter, so Cre expression is controlled by Sox10 promoter. Cells with Sox10 expression will also express Cre.reporter gene 报告基因，用法非常灵活，即可以研究特定调控序列的功能，也可以与目标基因耦合，研究基因功能。较常用的报告基因有黄/红/绿色荧光蛋白（YFP/RFP/GFP）。
Reporter proteins: tdTomato is one of the brightest fluorescent proteins currently available. Other common fluorescent proteins include GFP, EGFP, YFP, EYFP, RFP, CFP etc. as well as non-fluorescent proteins LacZ. The protein product of LacZ gene is β-galactosidase which will react with its substrate X-galactose and generate blue color, can be visualized without fluorescent microscope.
不同的model有不同的用途，主要看marker基因的功能。
The Wnt1-Cre transgenic mouse line is extensively used in the study of the development of the neural crest and its derivatives and the midbrain.
animal model 动物模型，实验的材料，比如reporter Knockin mouse，fluorescent, bioluminescent proteins or biochemical tags are inserted into the genome. The reporter can replace a gene, be fused to a protein or inserted into the 3' UTR.
参考：
Overview of the reporter genes and reporter mouse models
Dual genetic approaches for deciphering cell fate plasticity in vivo: more than double, 2019 Current Opinion in Cell Biology
Lineage Tracing, primer. 2012 cell - Lineage Tracing through Genetic Recombination
Unravelling cellular relationships during development and regeneration using genetic lineage tracing, 2019 Nature Reviews Molecular Cell Biology
ISH, in situ hybridization 原位杂交
For all ISH analysis, we used Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org) and GenePaint (http://www.GenePaint.org).
The Allen Developing Mouse Brain Atlas offers colorimetric In Situ Hybridization data at cellular resolution at seven stages of mouse development.
IHC, immunohistochemistry 免疫组织化学
Immunohistochemistry (IHC) is the most common application of immunostaining. It involves the process of selectively identifying antigens (proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues.
2021年03月10日
Chromosome banding 染色体条带
【现在还在用，主要是保证历史延续性，让现在的人能看懂古人的研究】
用特定的染色剂处理后的染色体会出现明暗交替的区域，这就是条带【banding，条带，名词】。【染色技术是鼻祖，所以条带也是一个非常原始的发现，远远早于functional annotation】
染色体是细胞内具有遗传性质的遗传物质深度压缩形成的聚合体，易被碱性染料染成深色，所以叫染色体（由染色质组成）。（英语：chromosome；希腊语：chroma=颜色，希腊语：soma=体）
核小体是染色体结构的最基本单位。核小体的核心是由4对组织蛋白（H2A、H2B、H3和H4）各两个分子构成的扁球状8聚体。【与组蛋白修饰密切相关，为什么没有H1？】在相邻的连接线之间结合着一个第5种组蛋白（H1）的分子。从染色体的一级结构到四级结构，脱氧核糖核酸分子一共被压缩了7×6×40×5=8400倍。
1970年后陆续问世的各种显带技术对染色体的识别作出了很大贡献。中期染色体经过DNA变性、胰酶消化或荧光染色等处理，可出现沿纵轴排列的明暗相间的带纹。按照染色体上特征性的标志可将每一个臂从内到外分为若干区，每个区又可分为若干条带，每条带又再分为若干个亚带，例如“9q34.1”即表示9号染色体长臂第3区第4条带的第1个亚带。由于每条染色体带纹的数目和宽度是相对恒定的，根据带型的不同可识别每条染色体及其片段。
条带出现的本质原因？
locus 基因座
一个典型的基因座可能写成“6p21.3”，解释如下
6 = 6号染色体
p = 短臂
21 = 2区, 1带
3 = 子带3
染色体上的短臂（p）或长臂（q）位置。p来自法文petit (小)；q则是选定p的下一个字母，也有来自法文queue (尾巴)一说。
染色体带经过适当染色之后，可于显微镜底下观察。每个带皆有编号，最靠近着丝粒（centromere）的为1号。
着丝粒
端粒
