Paper Reading Record

6/21
Genome-wide interrogation of gene functions through base editor screens empowered by barcoded sgRNA
2021 Nature biotechnology

CRISPR-knockout (KO) rely on double-strand breaks - leads to gene perturbation
An alternative method: a DSB-independent, genome-wide CRISPR screening method, termed iBARed cytosine base editing-mediated gene KO (BARBEKO) - perturb gene start codons or splice sites, or introduce premature termination codons
Provide efficient and accurate screening results - no longer affected by DNA cleavage-induced cytotoxicity

6/21
Phase separation in membrane biology: the interplay between membrane-bound organelles and membraneless condensates
2020 Dev Cell - review

Membraneless organelle: processing body, stress granule, paraspeckles - separated by liquid-liquid phase separation, LLPS
Interaction between membrane-bound organelles and membraneless condensates
Cell membrane provides a platform for the formation of membraneless organelles
Endoplasmic reticulum regulates the formation and dynamic changes of membraneless aggregates
Protein phase separation helps membrane organelles to form aggregates
Membrane and non-membrane organelles cooperate to complete protein transport

6/16
Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins
2016 Cell

NORAD (non-coding RNA-activated by DNA damage) - a kind of long noncoding RNAs (lncRNAs): conserved and expressed in most cell type. Will be highly expressed if the DNA is damaged. NORAD maintains genomic stability by sequestering PUMILIO proteins, which repress the stability and translation of mRNAs to which they bind. Have 500-1000 copy and each NORAD transcript has 18 pumilio response elements (PREs).
PUMILIO protein family: suppress the proteins that are responsible for stability of mitosis
NORAD suppress PUMILIO

6/12
Modular deep learning enables automated identification of monoclonal cell lines
Nature Machine Intelligence 2021
After cell sorting, help identify monoclonal from polyclonal

6/12
Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading
Science 2021

X chromosome inactivation (XCI) in mammals equalizes levels of X-linked gene expression in XX females relative to XY males. The XCI process is governed by the noncoding RNA Xist (X-inactive specific transcript), which is expressed from the inactive X chromosome elect, where it accumulates in cis and recruits factors [e.g., Xist RNA binding proteins (RBPs)-CIZ1 and SPEN and a nuclear protein scaffold] required for chromatin-based gene silencing.
The author developed a method called RNA-SPLIT (sequential pulse localization imaging over time) - can provide time-resolved imaging of individual Xist molecules in the context of cells undergoing XCI
RNA-SPLIT: fluorescence-labeled protein under 3D-SIM - previous method is using conventional diffraction-limited fluorescence microscopy which cannot observe individual Xist molecules - can understand the distinct dynamic properties of Xist RNA (expansion and steady state).
Provide insights of Xist-interaction protein: SPEN (spreading, coupling, kinetics) and CIZ1 (anchoring)

6/3
Emergent RNA-RNA interactions can promote stability in a nascent phototrophic endosymbiosis
BioRxiv 2021
endosymbiont-derived mRNA released upon endosymbiont digestion can be processed by the host RNAi system into 23-nt sRNA

6/12
Hepatic stellate cells suppress NK cell-sustained breast cancer dormancy
Nature 2021
disseminated tumour cells (DTCs) -> suppressed by NK cell with interferon-γ signalling - preventing hepatic metastases and prolonging survival
activated hepatic stellate cells (aHSCs) - CXCL12 expression and aHSC abundance - induct NK cell quiescence
interplay between NK cells and aHSCs as a master switch of cancer dormancy

6/10
Sense codon reassignment enables viral resistance and encoded polymer synthesis
Science 2021

In 2019, Jason Chin used CRISPR-Cas9 gene editing tools to create a strain named Syn61. The research team replaced 18,000 serine codons in all 40 million codon. The UCG, UCA, and the stop codon UAG were replaced with their "synonymous codons" AGC, AGU, and UAA, respectively.
This means that serine will still be integrated into the correct position of the protein produced by the Syn61 strain, but the three codons of UCG, UCA and UAG are actually "vacant" and they no longer encode anything in the protein, so Can be reused.
Stop virus infection

6/10
In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density
BioRxiv 2021
Develop a new system which can how cytoplasmic density affects other cellular processes
Use microfluidic devices to generate water-in-oil microemulsions adjusts ratios of cytoplasmic extract and extract buffer in individual droplets
density of the cytoplasm plays an important role in biochemical process
cell cycle maintains robust oscillations from the endogenous density by as low as 0.2x to more than 1.22x, otherwise it will leads to a low or high steady-state of CDK1 activity
hysteresis is supported by seeing the fact that diluting a concentrated arrested cytoplasm recovers its oscillatory behavior but requires a significantly lower concentration than 1.22x

CDK1 FRET sensor - activity ratio between CDK1-cyclin B and PP2A-B55 (antagonistic phosphatase)

6/10
Systems-Level Dissection of the Cell-Cycle Oscillator: Bypassing Positive Feedback Produces Damped Oscillations
Cell 2005

6/9
Comparison of SYBR Green and TaqMan methods in quantitative real-time polymerase chain reaction analysis of four adenosine receptor subtypes
Adv Biomed Res. 2014

6/8
Self-organization of microtubules into bipolar spindles around artificial chromosomes in Xenopus egg extracts
Nature 1996

6/7
How hair deform steel
Sicence 2021

6/7
Spatial organization of cytokinesis signaling reconstituted in a cell-free system
Sicence 2014

我这一个月在干什么……我怎么一个月没更新了？难道我一个月没看paper了吗
不应该啊

2/9
《延续香火的理想与普遍绝嗣的现实 ——基于家谱的人口数据》，陈熙。 《南方人口》 2012 年第 6 期 第 27 卷 (总 114 期)