合成生物学論文メモ (Nov 2022)
読み流した論文のメモ。黒色はメモ、緑色は感想、赤色は特に面白いと思ったもの。23報
Synthetic Biology
Cell-free / Reconstruction
無細胞系、再構成など- Fitness Landscape-Guided Engineering of Locally Supercharged Virus-like Particles with Enhanced Cell Uptake Properties
- Authors: Pistono, Paige E; Huang, Paul; Brauer, Daniel D; Francis, Matthew B
- Journal: ACS chemical biology
- Year: 2022
- DOI: 10.1021/acschembio.2c00318
- Institution: UC Berkeley, USA
Optogenetics
光駆動型ツール、蛍光イメージング、光受容体など、その他〇〇genetics系- Extension of the short wavelength side of fluorescent proteins using hydrated chromophores, and its application
- Authors: Sugiura, Kazunori; Nagai, Takeharu
- Journal: Communications Biology
- Year: 2022
- DOI: 10.1038/s42003-022-04153-7
- Institution: Osaka University, Japan
発色団周りの変異導入ステップが丁寧。
- Chemically stable fluorescent proteins for advanced microscopy
- Authors: Campbell, Benjamin C; Paez-Segala, Maria G; Looger, Loren L; Petsko, Gregory A; Liu, Ce Feng
- Journal: Nature methods
- Year: 2022
- DOI: 10.1038/s41592-022-01660-7
- Institution: Weill Cornell Medicine, USA
比較のグラフが一つだけ異次元で笑ってしまった。
Protein Engineering
タンパク質工学- Logistic Regression-Guided Identification of Cofactor Specificity-Contributing Residues in Enzyme with Sequence Datasets Partitioned by Catalytic Properties
- Authors: Sugiki, Sou; Niide, Teppei; Toya, Yoshihiro; Shimizu, Hiroshi
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00315
- Institution: Osaka University, Japan
そもそものモデルの予測精度がかなり高いので、他のタンパク質の転用できるかどうかは配列データや予測の難易度次第な気もする。
- Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity
- Authors: Neugebauer, Monica E; Hsu, Alvin; Arbab, Mandana; Krasnow, Nicholas A; McElroy, Amber N; Pandey, Smriti; Doman, Jordan L; Huang, Tony P; Raguram, Aditya; Banskota, Samagya; Newby, Gregory A; Tolar, Jakub; Osborn, Mark J; Liu, David R
- Journal: Nature biotechnology
- Year: 2022
- DOI: 10.1038/s41587-022-01533-6
- Institution: Broad Institute, USA
不活性な変異体を見れないのが難点ではあるが、Continuous directed evolution強い。Non-continuous版とも並行して実験していて一部の変異は両方で見られている。
- Re-engineering the adenine deaminase TadA-8e for efficient and specific CRISPR-based cytosine base editing
- Authors: Chen, Liang; Zhu, Biyun; Ru, Gaomeng; Meng, Haowei; Yan, Yongchang; Hong, Mengjia; Zhang, Dan; Luan, Changming; Zhang, Shun; Wu, Hao; Gao, Hongyi; Bai, Sijia; Li, Changqing; Ding, Ruoyi; Xue, Niannian; Lei, Zhixin; Chen, Yuting; Guan, Yuting; Siwko, Stefan; Cheng, Yiyun; Song, Gaojie; Wang, Liren; Yi, Chengqi; Liu, Mingyao; Li, Dali
- Journal: Nature biotechnology
- Year: 2022
- DOI: 10.1038/s41587-022-01532-7
- Institution: East China Normal University, China
構造ベースとdirected evolutionで同じ変異と違う変異が両方あって面白い。
- Computationally designed GPCR quaternary structures bias signaling pathway activation
- Authors: Paradis, Justine S; Feng, Xiang; Murat, Brigitte; Jefferson, Robert E; Sokrat, Badr; Szpakowska, Martyna; Hogue, Mireille; Bergkamp, Nick D; Heydenreich, Franziska M; Smit, Martine J; Chevign{\'e}, Andy; Bouvier, Michel; Barth, Patrick
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-34382-7
- Institution: Université de Montréal, Canada
膜タンパクでかつコンフォメーションも複数あって中々難しそう。
- PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries
- Authors: Henson, Sierra N; Elko, Evan A; Swiderski, Piotr M; Liang, Yong; Engelbrektson, Anna L; Pi{\~n}a, Alejandra; Boyle, Annalee S; Fink, Zane; Facista, Salvatore J; Martinez, Vidal; Rahee, Fatima; Brown, Annabelle; Kelley, Erin J; Nelson, Georgia A; Raspet, Isaiah; Mead, Heather L; Altin, John A; Ladner, Jason T
- Journal: Nature protocols
- Year: 2022
- DOI: 10.1038/s41596-022-00766-8
- Institution: Translational Genomics Research Institute, USA
CRISPR/Cas
クリスパー系- Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering
- Authors: Esquerra-Ruvira, Belen; Baquedano, Ignacio; Ruiz, Raul; Fernandez, Almudena; Montoliu, Lluis; Mojica, Francisco J M
- Journal: bioRxiv
- Year: 2022
- DOI: 10.1101/2022.10.31.514646
- Institution: University of Alicante, Spain
- RNA-activated protein cleavage with a CRISPR-associated endopeptidase
- Authors: Strecker, Jonathan; Demircioglu, F Esra; Li, David; Faure, Guilhem; Wilkinson, Max E; Gootenberg, Jonathan S; Abudayyeh, Omar O; Nishimasu, Hiroshi; Macrae, Rhiannon K; Zhang, Feng
- Journal: Science
- Year: 2022
- DOI: 10.1126/science.add7450
- Institution: MIT, USA
実験量が多い上に、DiCASPの機能としても面白い&応用先が広そう。
- RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease
- Authors: Kato, Kazuki; Okazaki, Sae; Schmitt-Ulms, Cian; Jiang, Kaiyi; Zhou, Wenyuan; Ishikawa, Junichiro; Isayama, Yukari; Adachi, Shungo; Nishizawa, Tomohiro; Makarova, Kira S; Koonin, Eugene V; Abudayyeh, Omar O; Gootenberg, Jonathan S; Nishimasu, Hiroshi
- Journal: Science
- Year: 2022
- DOI: 10.1126/science.add7347
- Institution: University of Tokyo, Japan
もう一方のScienceと同時に出た論文。構造や生化学活性の示唆を与えている。
- Expanding the Scope of Bacterial CRISPR Activation with PAM-Flexible dCas9 Variants
- Authors: Kiattisewee, Cholpisit; Karanjia, Ava V; Legut, Mateusz; Daniloski, Zharko; Koplik, Samantha E; Nelson, Joely; Kleinstiver, Benjamin P; Sanjana, Neville E; Carothers, James M; Zalatan, Jesse G
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00405
- Institution: University of Washington, Seattle, USA
SpCas9以外についても知りたいところ。
Cell / Tissue Engineering
細胞設計、組織工学など- speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing
- Authors: Castellanos-Rueda, Roc{\'\i}o; Di Roberto, Rapha{\e}l B; Bieberich, Florian; Schlatter, Fabrice S; Palianina, Darya; Nguyen, Oanh T P; Kapetanovic, Edo; L{\a}ubli, Heinz; Hierlemann, Andreas; Khanna, Nina; Reddy, Sai T
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-34141-8
- Institution: ETH Zurich, Switzerland
- Directed assembly of genetically engineered eukaryotic cells into living functional materials via ultrahigh-affinity protein interactions
- Authors: Yi, Qikun; Dai, Xin; Park, Byung Min; Gu, Junhao; Luo, Jiren; Wang, Ri; Yu, Cong; Kou, Songzi; Huang, Jinqing; Lakerveld, Richard; Sun, Fei
- Journal: Science advances
- Year: 2022
- DOI: 10.1126/sciadv.ade0073
- Institution: Hong Kong University of Science and Technology, Hong Kong
PEGが必要ではあるが細胞凝集を整列させるアイデアが面白かった。
- Programming cell-surface signaling by phase-separation-controlled compartmentalization
- Authors: Li, Ru; Li, Tiantian; Lu, Genzhe; Cao, Zhi; Chen, Bowen; Wang, Yalong; Du, Juanjuan; Li, Pilong
- Journal: Nature chemical biology
- Year: 2022
- DOI: 10.1038/s41589-022-01192-3
- Institution: Tsinghua University, China
実験量がすごい。細胞接着関連のタンパク質とも組み合わせられたりすると工学的なレイヤーが増えて更に面白そう。
Alternative Hosts / Strain Engineering
宿主や系統株の開発- Host Cell Transcriptional Tuning with CRISPR/dCas9 to Mitigate the Effects of Toxin Exposure
- Authors: Metzger, David; Miller, Kennedy; Lyon, Wanda; Migliozzi, Rebecca; Pangburn, Heather A; Saldanha, Roland
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00214
- Institution: Air Force Research Laboratory, USA
抗生物質耐性菌のメカニズムを埋め込んでいる様な感じで面白かった。論文で空軍研究所はじめて見た。
Computational Biology / Bioinformatics
- Training self-supervised peptide sequence models on artificially chopped proteins
- Authors: Sadeh, Gil; Wang, Zichen; Grewal, Jasleen; Rangwala, Huzefa; Price, Layne
- Journal: arXiv
- Year: 2022
- DOI: 10.48550/arXiv.2211.06428
- Institution: Amazon Devices, USA
応用の結果を見ると単純に長さを制限してMLMを解く恩恵が大きそう。
Generative Model
生成モデル- De novo PROTAC design using graph-based deep generative models
- Authors: Nori, Divya; Coley, Connor W; Mercado, Roc{\'\i}o
- Journal: arXiv
- Year: 2022
- DOI: 10.48550/arXiv.2211.02660
- Institution: MIT, USA
- Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design
- Authors: Gao, Kaiyuan; Wu, Lijun; Zhu, Jinhua; Peng, Tianbo; Xia, Yingce; He, Liang; Xie, Shufang; Qin, Tao; Liu, Haiguang; He, Kun; Liu, Tie-Yan
- Journal: arXiv
- Year: 2022
- DOI: 10.48550/arXiv.2211.08406
- Institution: Huazhong University of Science and Technology, China
デザイン対象ごとにBERTの事前学習をする様な流れがくると、計算量も多くなっていよいよドメイン知識の応用の仕方が問われそう。
- HelixMO: Sample-Efficient Molecular Optimization in Scene-Sensitive Latent Space
- Authors: Chen, Zhiyuan; Fang, Xiaomin; Hua, Zixu; Huang, Yueyang; Wang, Fan; Wu, Hua
- Journal: arXiv
- Year: 2021
- DOI: 10.48550/arXiv.2112.00905
- Institution: Baidu Inc., China
MLPで明示的に潜在空間を変形させるのは損失関数の設計が中々難しそう。
Deep Learning
深層学習を使ったバイオインフォ系のタスク- Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks
- Authors: Guo, Zhiye; Liu, Jian; Skolnick, Jeffrey; Cheng, Jianlin
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-34600-2
- Institution: University of Missouri, USA
変異体デザインなんかには良さそう。
- Deep learning to decompose macromolecules into independent Markovian domains
- Authors: Mardt, Andreas; Hempel, Tim; Clementi, Cecilia; No{\'e}, Frank
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-34603-z
- Institution: Freie Universität Berlin, Germany
ドメイン数を明示的に与える必要があるのが難しいところ。
Biology in general
- High-throughput retrieval of target sequences from complex clone libraries using CRISPRi
- Authors: Burian, J{\'a}n; Libis, Vincent K; Hernandez, Yozen A; Guerrero-Porras, Liliana; Ternei, Melinda A; Brady, Sean F
- Journal: Nature biotechnology
- Year: 2022
- DOI: 10.1038/s41587-022-01531-8
- Institution: Rockefeller University, USA
分野は遠かったが面白かった。メタゲノム解析と同定が進めばゲノムマイニングやMLモデルの訓練で扱えるの対象も増えて助かる。
合成生物学論文メモ (Oct 2022)
読み流した論文のメモ。黒色はメモ、緑色は感想、赤色は特に面白いと思ったもの。12報。
Synthetic Biology
Transcription/Translation Control
遺伝子回路、転写翻訳制御など- Modular, Synthetic Boolean Logic Gates Enabled in Saccharomyces cerevisiae through T7 Polymerases/CRISPR dCas9 Designs
- Authors: Presnell, Kristin V; Melhem, Omar; Morse, Nicholas J; Alper, Hal S
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00327
- Institution: University of Texas at Austin, USA
Cell-free / Reconstruction
無細胞系、再構成など- Control of Enzyme Reaction Initiation inside Giant Unilamellar Vesicles by the Cell-Penetrating Peptide-Mediated Translocation of Cargo Proteins
- Authors: Miwa, Akari; Kamiya, Koki
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00413
- Institution: Gunma University, Japan
細胞透過ペプチド以外にも細胞膜と物理的に相互作用する機能をGUVで試せそう。
Optogenetics
光駆動型ツール、蛍光イメージング、光受容体など、その他〇〇genetics系- Analysis of Slow-Cycling Variants of the Light-Inducible Nuclear Protein Export System LEXY in Mammalian Cells
- Authors: Forlani, Giada; Antwi, Enoch B; Weis, Daniel; Ozturk, Mehmet A; Queck, Bastian A W; Brecht, Dominik; Di Ventura, Barbara
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00232
- Institution: Albert Ludwigs University of Freiburg, Germany
定常状態の局在度合いについては、輸送シグナルの配列組成でも制御出来そう。
Protein Engineering
タンパク質工学- De novo design of immunoglobulin-like domains
- Authors: Chidyausiku, Tamuka M; Mendes, Soraia R; Klima, Jason C; Nadal, Marta; Eckhard, Ulrich; Roel-Touris, Jorge; Houliston, Scott; Guevara, Tibisay; Haddox, Hugh K; Moyer, Adam; Arrowsmith, Cheryl H; Gomis-R{\u}th, F Xavier; Baker, David; Marcos, Enrique
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-33004-6
- Institution: University of Washington, USA
職人芸っぽい
CRISPR/Cas
クリスパー系- G-Quadruplex DNAzyme-Substrated CRISPR/Cas12 Assay for Label-Free Detection of Single-Celled Parasitic Infection
- Authors: Gao, Hua; Feng, Miaomiao; Li, Feng; Zhang, Kaixiang; Zhang, Ting; Zhang, Zifang; Yang, Chengyun; Deng, Ruijie; Zhang, Junrong; Jiang, Peng
- Journal: ACS sensors
- Year: 2022
- DOI: 10.1021/acssensors.2c01104
- Institution: Zhengzhou University, China
G4部分が配列レベルで調整されていて面白かった。
- Engineered Protein Nanocages for Concurrent RNA and Protein Packaging In Vivo
- Authors: Kwon, Seokmu; Giessen, Tobias W
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00391
- Institution: University of Michigan, Ann Arbor, USA
オリゴマー形成自体を誘導可能な形にしたり出来ると、ヌクレアーゼに頑健な反応場を可逆的に制御できたりして面白そう。
Alternative Hosts / Strain Engineering
宿主や系統株の開発- Construction of an rAAV Producer Cell Line through Synthetic Biology
- Authors: Lee, Zion; Lu, Min; Irfanullah, Eesha; Soukup, Morgan; Hu, Wei-Shou
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00207
- Institution: University of Minnesota, USA
プロモーターやプラスミドの配列レベルでの設計や、長期の安定発現可能性など、色々改善出来そう。
- Organellar Glue: A Molecular Tool to Artificially Control Chloroplast-Chloroplast Interactions
- Authors: Ichikawa, Shintaro; Kato, Shota; Fujii, Yuta; Ishikawa, Kazuya; Numata, Keiji; Kodama, Yutaka
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00367
- Institution: Utsunomiya University, Japan
植物細胞での発現難易度が分からないが、E.coli等で使われる誘導性のヘテロ結合ツールも応用出来そう。split-mVenusだとツールとしては凝集が起きないと観察ができなくなってしまうのが扱いづらい気がした。
- Engineering Endosymbiotic Growth of E. coli in Mammalian Cells
- Authors: Gabelein, Christoph G; Reiter, Michael A; Ernst, Chantal; Giger, Gabriel H; Vorholt, Julia A
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00292
- Institution: ETH Zurich, Switzerland
発想はシンプルだが面白かった。
Computational Biology / Bioinformatics
- Deciphering microbial gene function using natural language processing
- Authors: Miller, Danielle; Stern, Adi; Burstein, David
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-33397-4
- Institution: Tel-Aviv University, Israel
予測の域を出ないので実証が難しそう。データベースの古いバージョンの情報で訓練したモデルで最近のアノテーションが予測できる、的な事が出来れば検証にはなるかも?
- Single-sequence protein structure prediction using a language model and deep learning
- Authors: Chowdhury, Ratul; Bouatta, Nazim; Biswas, Surojit; Floristean, Christina; Kharkare, Anant; Roye, Koushik; Rochereau, Charlotte; Ahdritz, Gustaf; Zhang, Joanna; Church, George M; Sorger, Peter K; AlQuraishi, Mohammed
- Journal: Nature biotechnology
- Year: 2022
- DOI: 10.1038/s41587-022-01432-w
- Institution: Harvard Medical School, USA
Deep Learning
深層学習を使ったバイオインフォ系のタスク- AlphaFold Distillation for Improved Inverse Protein Folding
- Authors: Melnyk, Igor; Lozano, Aurelie; Das, Payel; Chenthamarakshan, Vijil
- Journal: arXiv
- Year: 2022
- DOI: 10.48550/arXiv.2210.03488
- Institution: IBM Research, USA
合成生物学論文メモ (Jul 2022)
読み流した論文のメモ。黒色はメモ、緑色は感想、赤色は特に面白いと思ったもの。19報。
Synthetic Biology
Transcription/Translation Control
遺伝子回路、転写翻訳制御など- Deciphering the Rules of Ribosome Binding Site Differentiation in Context Dependence
- Authors: Duan, Yanting; Zhang, Xiaojuan; Zhai, Weiji; Zhang, Jinpeng; Zhang, Xiaomei; Xu, Guoqiang; Li, Hui; Deng, Zhaohong; Shi, Jinsong; Xu, Zhenghong
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00139
- Institution: Jiangnan University, China
GFP発現量の比較が難しいからだとは思うが、36ntの付加でCDSの異なるコンテクストとして妥当かは少し疑問。
- Developing cyanobacterial quorum sensing toolkits: towards interspecies coordination in mixed autotroph/heterotroph communities
- Authors: Kokarakis, Emmanuel J; Rillema, Rees; Ducat, Daniel C; Sakkos, Jonathan K
- Journal: bioRxiv
- Year: 2022
- DOI: 10.1101/2022.07.20.500858
- Institution: Michigan State University, USA
OFFの時の発現漏れは他のシステムの導入で工夫出来そう。
Cell-free / Reconstruction
無細胞系、再構成など- Rapid Assembly and Prototyping of Biocatalytic Virus-like Particle Nanoreactors
- Authors: Esquirol, Lygie; McNeale, Donna; Douglas, Trevor; Vickers, Claudia E; Sainsbury, Frank
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00117
- Institution: Griffith University, Australia
Optogenetics
光駆動型ツール、蛍光イメージング、光受容体など、その他〇〇genetics系- Light-activated mitochondrial fission through optogenetic control of mitochondria-lysosome contacts
- Authors: Qiu, Kangqiang; Zou, Weiwei; Fang, Hongbao; Hao, Mingang; Mehta, Kritika; Tian, Zhiqi; Guan, Jun-Lin; Zhang, Kai; Huang, Taosheng; Diao, Jiajie
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-31970-5
- Institution: University of Cincinnati College of Medicine, USA
ミトコンドリアの再結合の方のメカニズムは知らないが、こちらも誘導出来たら面白そう。
Protein Engineering
タンパク質工学- Rotamer-free protein sequence design based on deep learning and self-consistency
- Authors: Liu, Yufeng; Zhang, Lu; Wang, Weilun; Zhu, Min; Wang, Chenchen; Li, Fudong; Zhang, Jiahai; Li, Houqiang; Chen, Quan; Liu, Haiyan
- Journal: Nature Computational Science
- Year: 2022
- DOI: 10.1038/s43588-022-00273-6
- Institution: University of Science and Technology of China, China
事前学習法の工夫が面白かった。デザインの構造->配列ステップは続々と出てきている感じがある。
- De novo design of protein homodimers containing tunable symmetric protein pockets
- Authors: Hicks, Derrick R; Kennedy, Madison A; Thompson, Kirsten A; DeWitt, Michelle; Coventry, Brian; Kang, Alex; Bera, Asim K; Brunette, T J; Sankaran, Banumathi; Stoddard, Barry; Baker, David
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2113400119
- Institution: University of Washington, USA
デザインの各ステップが明快だった。水溶性の時点で大分サンプルが削れてしまったのでその点を考慮すればより良さそう。
- Logic-gated antibody pairs that selectively act on cells co-expressing two antigens
- Authors: Oostindie, Simone C; Rinaldi, Derek A; Zom, Gijs G; Wester, Michael J; Paulet, Desiree; Al-Tamimi, Kusai; van der Meijden, Els; Scheick, Jennifer R; Wilpshaar, Tessa; de Jong, Bart; Hoff-van den Broek, Marloes; Grattan, Rachel M; Oosterhoff, Janita J; Vignau, Julie; Verploegen, Sandra; Boross, Peter; Beurskens, Frank J; Lidke, Diane S; Schuurman, Janine; de Jong, Rob N
- Journal: Nature biotechnology
- Year: 2022
- DOI: 10.1038/s41587-022-01384-1
- Institution: Leiden University Medical Center, Netherlands
二段階でオリゴマーの嗜好性を制御している点が面白かった。
- Natural Evolution Provides Strong Hints about Laboratory Evolution of Designer Enzymes
- Authors: Xie, Wen Jun; Warshel, Arieh
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2207904119
- Institution: University of Southern California, USA
事前学習モデルがこれらの特徴をどれ位捉えられているか調べたら面白そう。酵素活性以外の特性にも当てはまるかは検証できると面白い。
CRISPR/Cas
クリスパー系- Recording gene expression order in DNA by CRISPR addition of retron barcodes
- Authors: Bhattarai-Kline, Santi; Lear, Sierra K; Fishman, Chloe B; Lopez, Santiago C; Lockshin, Elana R; Schubert, Max G; Nivala, Jeff; Church, George M; Shipman, Seth L
- Journal: Nature
- Year: 2022
- DOI: 10.1038/s41586-022-04994-6
- Institution: Gladstone Institute of Data Science and Biotechnology, USA
転写の計測に新たな次元が加わった感じで発展性がすごい。色々と最適化の余地はありそうなので期待。
- Engineering Metabolic Pathways for Cofactor Self-Sufficiency and Serotonin Production in Escherichia coli
- Authors: Shen, Peijie; Gu, Suyi; Jin, Dou; Su, Yu; Wu, Hongxuan; Li, Qingchen; Yang, Jinhua; He, Wenjin; Huang, Jianzhong; Qi, Feng
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00298
- Institution: Fujian Normal University, China
- A modular spring-loaded actuator for mechanical activation of membrane proteins
- Authors: Mills, A; Aissaoui, N; Maurel, D; Elezgaray, J; Morvan, F; Vasseur, J J; Margeat, E; Quast, R B; Lai Kee-Him, J; Saint, N; Benistant, C; Nord, A; Pedaci, F; Bellot, G
- Journal: Nature communications
- Year: 2022
- DOI: s41467-022-30745-2
- Institution: Université de Montpellier, France
シンプルにすごい。現状はコレステロールで細胞膜に接着させているが、nanobody等で特異性を持たせることも出来るかもしれないとのこと。
Alternative Hosts / Strain Engineering
宿主や系統株の開発- Engineering Agrobacterium tumefaciens Adhesion to Target Cells
- Authors: Pierrat, Xavier; Pham, Alix; Wong, Jeremy P H; Al-Mayyah, Zainebe; Persat, Alexandre
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00069
- Institution: Ecole Polytechnique Fédérale de Lausanne, Switzerland
autotransporterのデザインからするのが大変そう、面白かった。
Miscellany
その他- A Modified Yeast Two-Hybrid Platform Enables Dynamic Control of Expression Intensities to Unmask Properties of Protein-Protein Interactions
- Authors: Feuer, Erez; Zimran, Gil; Shpilman, Michal; Mosquna, Assaf
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00192
- Institution: The Hebrew University of Jerusalem, Israel
Computational Biology / Bioinformatics
- Self-supervised deep learning encodes high-resolution features of protein subcellular localization
- Authors: Kobayashi, Hirofumi; Cheveralls, Keith C; Leonetti, Manuel D; Royer, Loic A
- Journal: Nature methods
- Year: 2022
- DOI: 10.1038/s41592-022-01541-z
- Institution: Chan Zuckerberg Biohub, USA
階層的な表現学習は配列に対しても二次構造やIDR予測等で応用できそう。
- ProtGPT2 is a deep unsupervised language model for protein design
- Authors: Ferruz, Noelia; Schmidt, Steffen; H{\o}cker, Birte
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-32007-7
- Institution: University of Bayreuth, Germany
ドライ側では難しいが、今後の実証実験でどの程度の性能が出るか楽しみ。
- Deep self-supervised learning for biosynthetic gene cluster detection and product classification
- Authors: Rios-Martinez, Carolina; Bhattacharya, Nicholas; Amini, Ava P; Crawford, Lorin; Yang, Kevin K
- Journal: bioRxiv
- Year: 2022
- DOI: 10.1101/2022.07.22.500861
- Institution: Microsoft Research New England, USA
Fine-tuning後の性能が振るわなかったのは残念だが、事前学習後の性能が良いのでdiscussionにもある様にマイニングに良さそう。
- iACVP: markedly enhanced identification of anti-coronavirus peptides using a dataset-specific word2vec model
- Authors: Kurata, Hiroyuki; Tsukiyama, Sho; Manavalan, Balachandran
- Journal: Briefings in bioinformatics
- Year: 2022
- DOI: 10.1093/bib/bbac265
- Institution: Kyushu Institute of Technology, Japan
データセットが小さいとやはり潜在表現を使う方向性の方が良さそう。タンパク質言語モデルの潜在表現は精度が出なかったのかは気になる。
- Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval
- Authors: Notin, Pascal; Dias, Mafalda; Frazer, Jonathan; Marchena-Hurtado, Javier; Gomez, Aidan; Marks, Debora S; Gal, Yarin
- Journal: arxiv
- Year: 2022
- DOI: 2205.13760
- Institution: University of Oxford, UK
Deep Learning
深層学習を使ったバイオインフォ系のタスク- HelixFold-Single: MSA-free Protein Structure Prediction by Using Protein Language Model as an Alternative
- Authors: Fang, Xiaomin; Wang, Fan; Liu, Lihang; He, Jingzhou; Lin, Dayong; Xiang, Yingfei; Zhang, Xiaonan; Wu, Hua; Li, Hui; Song, Le
- Journal: arxiv
- Year: 2022
- DOI: 2207.13921
- Institution: Baidu Inc., China
合成生物学論文メモ (Jun 2022)
読み流した論文のメモ。黒色はメモ、緑色は感想、赤色は特に面白いと思ったもの。
Synthetic Biology
Transcription/Translation Control
遺伝子回路、転写翻訳制御など- CRISPR-mediated protein-tagging signal amplification systems for efficient transcriptional activation and repression in Saccharomyces cerevisiae
- Authors: Zhai, Haotian; Cui, Li; Xiong, Zhen; Qi, Qingsheng; Hou, Jin
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac463
- Institution: Shandong University, China
パーツが増えてくると細胞の代謝負荷がどれくらいなのか気になる。
- A genetic mammalian proportional-integral feedback control circuit for robust and precise gene regulation
- Authors: Frei, Timothy; Chang, Ching-Hsiang; Filo, Maurice; Arampatzis, Asterios; Khammash, Mustafa
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2122132119
- Institution: ETH Zurich, Switzerland
とんでもない量の最適化をしていそう。シンプルにすごい。
- Machine Learning Guided Batched Design of a Bacterial Ribosome Binding Site
- Authors: Zhang, Mengyan; Holowko, Maciej Bartosz; Hayman Zumpe, Huw; Ong, Cheng Soon
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00015
- Institution: Australian National University, Australia
最大値は向上しているが集団としてはもう少しラウンド数が必要そう。
RNA Synthetic Biology
アプタマー、リボザイムなど- Utilizing RNA origami scaffolds in Saccharomyces cerevisiae for dCas9-mediated transcriptional control
- Authors: Pothoulakis, Georgios; Nguyen, Michael T A; Andersen, Ebbe S
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac470
- Institution: Aarhus University, Denmark
RNA折り紙を使ったツール最近よく見る。
- Directed evolution and selection of biostable l-DNA aptamers with a mirror-image DNA polymerase
- Authors: Chen, Ji; Chen, Mengyin; Zhu, Ting F
- Journal: Nature biotechnology
- Year: 2022
- DOI: 10.1038/s41587-022-01337-8
- Institution: Tsinghua University, China
アイデアも結果もかなり面白い。結構な数のPAGEシーケンシングで大変そう。
Cell-free / Reconstruction
無細胞系、再構成など- Noncanonical amino acid mutagenesis in response to recoding signal-enhanced quadruplet codons
- Authors: Chen, Yan; He, Xinyuan; Ma, Bin; Liu, Kun; Gao, Tianyu; Niu, Wei; Guo, Jiantao
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac474/6601289
- Institution: University of Nebraska-Lincoln, USA
対応するtRNAやaaRS次第で可能性が広がりそうで面白い。
Optogenetics
光駆動型ツール、蛍光イメージング、光受容体など、その他〇〇genetics系- Controlling synthetic membraneless organelles by a red-light-dependent singlet oxygen-generating protein
- Authors: Li, Manjia; Park, Byung Min; Dai, Xin; Xu, Yingjie; Huang, Jinqing; Sun, Fei
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30933-0
- Institution: The Hong Kong University of Science and Technology, Hong Kong/China
色々なシステムの実装をしていて盛り沢山だった。
- An Optogenetic Toolkit for Light-Inducible Antibiotic Resistance
- Authors: Sheets, Michael B; Dunlop, Mary J
- Journal: bioRxiv
- Year: 2022
- DOI: 10.1101/2022.06.10.495621
- Institution: Boston University, USA
オプトジェネティックな制御を厳密にしたい場合は有効そう。でも代謝荷重を考えると抗生物質自体を光ケージで修飾する様な方が(あれば)使い勝手は良いのかも。
Protein Engineering
タンパク質工学- BacPROTACs mediate targeted protein degradation in bacteria
- Authors: Morreale, Francesca E; Kleine, Stefan; Leodolter, Julia; Junker, Sabryna; Hoi, David M; Ovchinnikov, Stepan; Okun, Anastasia; Kley, Juliane; Kurzbauer, Robert; Junk, Lukas; Guha, Somraj; Podlesainski, David; Kazmaier, Uli; Boehmelt, Guido; Weinstabl, Harald; Rumpel, Klaus; Schmiedel, Volker M; Hartl, Markus; Haselbach, David; Meinhart, Anton; Kaiser, Markus; Clausen, Tim
- Journal: Cell
- Year: 2022
- DOI: 10.1016/j.cell.2022.05.009
- Institution: Reseaarch Institute of Molecular Pathology, Austria
化学的なデザイン部分は良くわからないが、手順が面白かった。
- Repurposing Peptide Nanomaterials as Synthetic Biomolecular Condensates in Bacteria
- Authors: Tomares, Dylan T; Whitlock, Sara; Mann, Matthew; DiBernardo, Emma; Childers, W Seth
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00078
- Institution: University of Pittsburgh, USA
現象自体も面白かったし、細胞内反応の場を人工的に作れそう。
- Cell-Free Mutant Analysis Combined with Structure Prediction of a Lasso Peptide Biosynthetic Protease B2
- Authors: Alfi, Almasul; Popov, Aleksandr; Kumar, Ashutosh; Zhang, Kam Y J; Dubiley, Svetlana; Severinov, Konstantin; Tagami, Shunsuke
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00176
- Institution: RIKEN, Japan
AF2の予測構造で十分な証拠として認められる様になってすごい。
- Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders
- Authors: Wamhoff, Eike-Christian; Romanov, Anna; Huang, Hellen; Read, Benjamin J; Ginsburg, Eric; Knappe, Grant A; Kim, Hyun Min; Farrell, Nicholas P; Irvine, Darrell J; Bathe, Mark
- Journal: ACS nano
- Year: 2022
- DOI: 10.1021/acsnano.1c11575
- Institution: MIT, USA
- Light-activated molecular machines are fast-acting broad-spectrum antibacterials that target the membrane
- Authors: Santos, Ana L; Liu, Dongdong; Reed, Anna K; Wyderka, Aaron M; van Venrooy, Alexis; Li, John T; Li, Victor D; Misiura, Mikita; Samoylova, Olga; Beckham, Jacob L; Ayala-Orozco, Ciceron; Kolomeisky, Anatoly B; Alemany, Lawrence B; Oliver, Antonio; Tegos, George P; Tour, James M
- Journal: Science advances
- Year: 2022
- DOI: 10.1126/sciadv.abm2055
- Institution: Rice University, USA
- Graph Computation Using Algorithmic Self-Assembly of DNA Molecules
- Authors: Xu, Jin; Chen, Congzhou; Shi, Xiaolong
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00120
- Institution: Peking University, China
グラフを作る発想は見た事がなかったので面白かったし、相性が良さそう。大規模にするには直交性の確保が大変そうではある。
Alternative Hosts / Strain Engineering
宿主や系統株の開発- A streamlined strain engineering workflow with genome-wide screening detects enhanced protein secretion in Komagataella phaffii
- Authors: Ito, Yoichiro; Ishigami, Misa; Terai, Goro; Nakamura, Yasuyuki; Hashiba, Noriko; Nishi, Teruyuki; Nakazawa, Hikaru; Hasunuma, Tomohisa; Asai, Kiyoshi; Umetsu, Mitsuo; Ishii, Jun; Kondo, Akihiko
- Journal: Communications Biology
- Year: 2022
- DOI: 10.1038/s42003-022-03475-w
- Institution: Kobe University, Japan
形質転換/ゲノム編集周りの難しさが解決できれば、手広くスクリーニングが進みそう。
Computational Biology / Bioinformatics
- Generative aptamer discovery using RaptGen
- Authors: Iwano, Natsuki; Adachi, Tatsuo; Aoki, Kazuteru; Nakamura, Yoshikazu; Hamada, Michiaki
- Journal: Nature Computational Science
- Year: 2022
- DOI: 10.1038/s43588-022-00249-6
- Institution: Waseda University, Japan
- Effector-GAN: prediction of fungal effector proteins based on pretrained deep representation learning methods and generative adversarial networks
- Authors: Wang, Yansu; Luo, Ximei; Zou, Quan
- Journal: Bioinformatics
- Year: 2022
- DOI: 10.1093/bioinformatics/btac374
- Institution: University of Electronic Science and Technology of China, China
表現学習を広く使えそうな手法で面白い。
- NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning
- Authors: H{\o}ie, Magnus Haraldson; Kiehl, Erik Nicolas; Petersen, Bent; Nielsen, Morten; Winther, Ole; Nielsen, Henrik; Hallgren, Jeppe; Marcatili, Paolo
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac439
- Institution: Technical University of Denmark, Denmark
- Language models can learn complex molecular distributions
- Authors: Flam-Shepherd, Daniel; Zhu, Kevin; Aspuru-Guzik, Al{\'a}n
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30839-x
- Institution: University of Tronto, Canada
評価が難しそうだが、大まかなアイデアとしては核酸やタンパク質でも出来るかも?巨大な化合物タスクが難しいかもしれないがBERTや事前学習済みモデルについても比較があれば面白そう。
- Screening membraneless organelle participants with machine-learning models that integrate multimodal features
- Authors: Chen, Zhaoming; Hou, Chao; Wang, Liang; Yu, Chunyu; Chen, Taoyu; Shen, Boyan; Hou, Yaoyao; Li, Pilong; Li, Tingting
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2115369119
- Institution: Peking University Health Science Center, China
特徴抽出の選別から実証実験まで丁寧にされていて良かった。
Deep Learning
深層学習を使ったバイオインフォ系のタスク- Assessing sequence-based protein--protein interaction predictors for use in therapeutic peptide engineering
- Authors: Charih, Fran{\c c}ois; Biggar, Kyle K; Green, James R
- Journal: Scientific reports
- Year: 2022
- DOI: 10.1038/s41598-022-13227-9
- Institution: Carleton University, Canada
工学的に実験が必要な配列を提案する視点でのモデル比較は面白かった。一方で、AF2登場以降は配列ベースの予測に限定する必要がないように思った。
Bioinformatics in general
バイオインフォマティクス一般- Machine learning aided construction of the quorum sensing communication network for human gut microbiota
- Authors: Wu, Shengbo; Feng, Jie; Liu, Chunjiang; Wu, Hao; Qiu, Zekai; Ge, Jianjun; Sun, Shuyang; Hong, Xia; Li, Yukun; Wang, Xiaona; Yang, Aidong; Guo, Fei; Qiao, Jianjun
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30741-6
- Institution: Tianjin University, China
実験でどのくらい確度が補完されるか期待。
- AllerCatPro 2.0: a web server for predicting protein allergenicity potential
- Authors: Nguyen, Minh N; Krutz, Nora L; Limviphuvadh, Vachiranee; Lopata, Andreas L; Gerberick, G Frank; Maurer-Stroh, Sebastian
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac446
- Institution: Singapore Institute for Food and Biotechnology Innovation, Singapore
BLASTPのエピトープ類似度探索を3D構造の比較とするのはどうなのか、よく分からなかった。
Biology in general
- Characterization of ColE1 Production for Robust tolC Plate Dual-Selection in E. coli
- Authors: Baas-Thomas, Maximilien S; Oehm, Sebastian B; Ostrov, Nili; Church, George M
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00061
- Institution: Wyss Institute for Biologically Inspired Engineering, USA
lysateとはいえ細胞を混ぜるのは気持ち的に怖いなと感じてしまった。
- Binding of the transcription activator-like effector augments transcriptional regulation by another transcription factor
- Authors: Leben, Katja; Strm{\v s}ek, {\v Z}iga; Lebar, Tina; Verbi{\v c}, An{\v z}e; Dragovan, Matej; Omersa, Ne{\v z}a; Anderluh, Gregor; Jerala, Roman
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac454
- Institution: National Institute of Chemistry, Slovenia
新たな作用が明らかとなる面白い結果だった。どの様なメカニズムか実証されるのを期待。
合成生物学論文メモ (May 2022)
読み流した論文のメモ。黒色はメモ、緑色は感想、赤色は特に面白いと思ったもの。
30報
Synthetic Biology
Transcription/Translation Control
遺伝子回路、転写翻訳制御など- Modulating gene regulation function by chemically controlled transcription factor clustering
- Authors: Wu, Jiegen; Chen, Baoqiang; Liu, Yadi; Ma, Liang; Huang, Wen; Lin, Yihan
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30397-2
- Institution: Peking University, China
相分離によるタンパク質の隔離効果も組み合わせられると面白そう。
- DeepTESR: A Deep Learning Framework to Predict the Degree of Translational Elongation Short Ramp for Gene Expression Control
- Authors: Kim, Dong Jae; Kim, Jiwoo; Lee, Dong Hyun; Lee, Jongwuk; Woo, Han Min
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00202
- Institution: Sungkyunkwan University, Republic of Korea
GFPとRFPの違いで0.6程度の相関だと、他のコドン組成の影響もかなり大きそう。
- LOICA: Integrating Models with Data for Genetic Network Design Automation
- Authors: Vidal, Gonzalo; Vidal-C{\'e}spedes, Carlos; Rudge, Timothy J
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.1c00603
- Institution: Pontificia Universidad Católica de Chile, Chile
試してみたい。
- Engineering of a TrpR-Based Biosensor for Altered Dynamic Range and Ligand Preference
- Authors: Gong, Xinyu; Zhang, Ruihua; Wang, Jian; Yan, Yajun
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00134
- Institution: The University of Georgia, USA
- Complex dynamics in a synchronized cell-free genetic clock
- Authors: Aufinger, Lukas; Brenner, Johann; Simmel, Friedrich C
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30478-2
- Institution: Technical University Munich, Germany
RNA Synthetic Biology
アプタマー、リボザイムなど- SHAPE-enabled fragment-based ligand discovery for RNA
- Authors: Zeller, Meredith J; Favorov, Oleg; Li, Kelin; Nuthanakanti, Ashok; Hussein, Dina; Michaud, Aur{\'e}liane; Lafontaine, Daniel A; Busan, Steven; Serganov, Alexander; Aub{\'e}, Jeffrey; Weeks, Kevin M
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2122660119
- Institution: University of North Carolina, USA
SHAPEを使ったスクリーニングも、その後のリガンドデザインも面白かった。
Cell-free / Reconstruction
無細胞系、再構成など- Hyperaccurate Ribosomes for Improved Genetic Code Reprogramming
- Authors: Shakya, Bipasana; Joyner, Olivia G; Hartman, Matthew C T
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00150
- Institution: Virginia Commonwealth University, USA
細胞内でどの位差が出るのか気になる。
- Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures
- Authors: Val{\'e}rio, Mariana; Mendon{\c c}a, Diogo A; Morais, Jo{\~a}o; Buga, Carolina C; Cruz, Carlos H; Castanho, Miguel A R B; Melo, Manuel N; Soares, Cl{\'a}udio M; Veiga, Ana Salom{\'e}; Lousa, Diana
- Journal: ACS chemical biology
- Year: 2022
- DOI: 10.1021/acschembio.2c00208
- Institution: Universidade Nova de Lisboa, Portugal
Optogenetics
光駆動型ツール、蛍光イメージング、光受容体など、その他〇〇genetics系- Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine
- Authors: Dietler, Julia; Gelfert, Renate; Kaiser, Jennifer; Borin, Veniamin; Renzl, Christian; Pilsl, Sebastian; Ranzani, Am{\'e}rico Tavares; Garc{\'\i}a de Fuentes, Andr{\'e}s; Gleichmann, Tobias; Diensthuber, Ralph P; Weyand, Michael; Mayer, G{\u}nter; Schapiro, Igor; M{\o}glich, Andreas
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30252-4
- Institution: University of Bayreuth, Germany
Fig2bが綺麗で面白い。実はちゃんと検証されていない活性グループがLOVドメイン以外にもありそう。
- Synthetic biology and bioelectrochemical tools for electrogenetic system engineering
- Authors: Lawrence, Joshua M; Yin, Yutong; Bombelli, Paolo; Scarampi, Alberto; Storch, Marko; Wey, Laura T; Climent-Catala, Alicia; {PixCell iGEM Team}; Baldwin, Geoff S; O'Hare, Danny; Howe, Christopher J; Zhang, Jenny Z; Ouldridge, Thomas E; Ledesma-Amaro, Rodrigo
- Journal: Science advances
- Year: 2022
- DOI: 10.1126/sciadv.abm5091
- Institution: University of Cambridge, UK
生体に内在性の溶質で出来るともっと面白くなりそう。
Protein Engineering
タンパク質工学- Functional Nanopore Screen: A Versatile High-Throughput Assay to Study and Engineer Protein Nanopores in Escherichia coli
- Authors: Weber, Wadim; Roeder, Markus; Probanowski, Tobias; Yang, Jie; Abujubara, Helal; Koeppl, Heinz; Tietze, Alesia; Stein, Viktor
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.1c00635
- Institution: TU Darmstadt, Germany
スクリーニングから工学までの流れが良かった、面白い。
- Deep mutational scanning of essential bacterial proteins can guide antibiotic development
- Authors: Dewachter, Liselot; Brooks, Aaron N; Noon, Katherine; Krishnamurthy, Nandini; Versees, Wim; Vranken, Wim; Michiels, Jan
- Journal: bioRxiv
- Year: 2022
- DOI: 10.1101/2022.05.23.493065
- Institution: KU Leuven, Belgium
結果はそれ程振るわなかった感じがあるが、面白い試み。
CRISPR/Cas
クリスパー系- Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing
- Authors: McGaw, Colin; Garrity, Anthony J; Munoz, Gabrielle Z; Haswell, Jeffrey R; Sengupta, Sejuti; Keston-Smith, Elise; Hunnewell, Pratyusha; Ornstein, Alexa; Bose, Mishti; Wessells, Quinton; Jakimo, Noah; Yan, Paul; Zhang, Huaibin; Alfonse, Lauren E; Ziblat, Roy; Carte, Jason M; Lu, Wei-Cheng; Cerchione, Derek; Hilbert, Brendan; Sothiselvam, Shanmugapriya; Yan, Winston X; Cheng, David R; Scott, David A; DiTommaso, Tia; Chong, Shaorong
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30465-7
- Institution: Arbor Biotechnologies, USA
gRNAの設計難易度がどれくらい変わるのかが気になった。
- Structural basis for RNA-guided DNA cleavage by IscB-$\omega$RNA and mechanistic comparison with Cas9
- Authors: Schuler, Gabriel; Hu, Chunyi; Ke, Ailong
- Journal: Science
- Year: 2022
- DOI: 10.1126/science.abq7220
- Institution: Cornell University, USA
Cas9がトランスポゾン由来だとは知らなかった。
- Multiagent Screening Improves Directed Enzyme Evolution by Identifying Epistatic Mutations
- Authors: Yang, Tian; Ye, Zhixia; Lynch, Michael D
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00136
- Institution: Duke University, USA
やりようによっては酵素以外にも適用出来そうな面白いアイデア。配列の潜在空間を数理的に探索する場合との比較も気になる。
Alternative Hosts / Strain Engineering
宿主や系統株の開発- CRISPR-Cas Assisted Shotgun Mutagenesis Method for Evolutionary Genome Engineering
- Authors: Zhao, Ming; Gao, Miaomiao; Xiong, Liangbin; Liu, Yongjun; Tao, Xinyi; Gao, Bei; Liu, Min; Wang, Feng-Qing; Wei, Dong-Zhi
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00112
- Institution: East China University of Science and Technology, Chinaa
進化後のシーケンシングコストが大変そうだが、面白かった。
- An in vivo gene amplification system for high level expression in Saccharomyces cerevisiae
- Authors: Peng, Bingyin; Esquirol, Lygie; Lu, Zeyu; Shen, Qianyi; Cheah, Li Chen; Howard, Christopher B; Scott, Colin; Trau, Matt; Dumsday, Geoff; Vickers, Claudia E
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30529-8
- Institution: The University of Queensland, Australia
アイデアが面白かった、発展性もありそう。
Miscellany
その他Computational Biology / Bioinformatics
- iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets
- Authors: Chen, Zhen; Liu, Xuhan; Zhao, Pei; Li, Chen; Wang, Yanan; Li, Fuyi; Akutsu, Tatsuya; Bain, Chris; Gasser, Robin B; Li, Junzhou; Yang, Zuoren; Gao, Xin; Kurgan, Lukasz; Song, Jiangning
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac351
- Institution: Henan Agricultural University, China
深層学習をかけられない小規模データで特徴抽出するのに助かる。
- Prediction of protein-protein interaction using graph neural networks
- Authors: Jha, Kanchan; Saha, Sriparna; Singh, Hiteshi
- Journal: Scientific reports
- Year: 2022
- DOI: 10.1038/s41598-022-12201-9
- Institution: Indian Institute of Technology, India
ProtBERTより他のモデルの方が良いかもしれないが、配列長の制約?
- PepNN: a deep attention model for the identification of peptide binding sites
- Authors: Abdin, Osama; Nim, Satra; Wen, Han; Kim, Philip M
- Journal: Communications Biology
- Year: 2022
- DOI: 10.1038/s42003-022-03445-2
- Institution: University of Toronto, Canada
Alphafoldとの比較を色々しないとで大変そう。
Machine Learning
機械学習を使ったバイオインフォ系のタスク- A systematic evaluation of data processing and problem formulation of CRISPR off-target site prediction
- Authors: Yaish, Ofir; Asif, Maor; Orenstein, Yaron
- Journal: Briefings in bioinformatics
- Year: 2022
- DOI: 10.1093/bib/bbac157
- Institution: Ben-Gurion University of the Negev, Israel
- ToxinPred2: an improved method for predicting toxicity of proteins
- Authors: Sharma, Neelam; Naorem, Leimarembi Devi; Jain, Shipra; Raghava, Gajendra P S
- Journal: Briefings in bioinformatics
- Year: 2022
- DOI: 10.1093/bib/bbac174
- Institution: Indraprastha Institute of Information Technology, Indis
マニアックな予測タスク、嫌いじゃない
- Prediction of protein--ligand binding affinity from sequencing data with interpretable machine learning
- Authors: Rube, H Tomas; Rastogi, Chaitanya; Feng, Siqian; Kribelbauer, Judith F; Li, Allyson; Becerra, Basheer; Melo, Lucas A N; Do, Bach Viet; Li, Xiaoting; Adam, Hammaad H; Shah, Neel H; Mann, Richard S; Bussemaker, Harmen J
- Journal: Nature biotechnology
- Year: 2022
- DOI: 10.1038/s41587-022-01307-0
- Institution: University of California, Merced, USA
泥臭いデータ処理を物凄い数やっていて尊敬する。
Bioinformatics in general
バイオインフォマティクス一般- DDGun: an untrained predictor of protein stability changes upon amino acid variants
- Authors: Montanucci, Ludovica; Capriotti, Emidio; Birolo, Giovanni; Benevenuta, Silvia; Pancotti, Corrado; Lal, Dennis; Fariselli, Piero
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac325
- Institution: Lerner Research Institute, USA
重みの定数は訓練していないと主張しているが、既知データセットとの相関度合いを参考にしたらしい。それはもう訓練してるし、素直にフィッティングした方が良くない?
- Automated Leak Analysis of Nucleic Acid Circuits
- Authors: Zarubiieva, Iuliia; Spaccasassi, Carlo; Kulkarni, Vishwesh; Phillips, Andrew
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00084
- Institution: University of Warwick, UK
Biology in general
- The cyclic octapeptide antibiotic argyrin B inhibits translation by trapping EF-G on the ribosome during translocation
- Authors: Wieland, Maximiliane; Holm, Mikael; Rundlet, Emily J; Morici, Martino; Koller, Timm O; Maviza, Tinashe P; Pogorevc, Domen; Osterman, Ilya A; M{\u}ller, Rolf; Blanchard, Scott C; Wilson, Daniel N
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2114214119
- Institution: University of Hamburg, Germany
- Cellular perception of growth rate and the mechanistic origin of bacterial growth law
- Authors: Wu, Chenhao; Balakrishnan, Rohan; Braniff, Nathan; Mori, Matteo; Manzanarez, Gabriel; Zhang, Zhongge; Hwa, Terence
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2201585119
- Institution: UCSD, USA
- In vitro reconstitution of Escherichia coli divisome activation
- Authors: Radler, Philipp; Baranova, Natalia; Caldas, Paulo; Sommer, Christoph; L{\'o}pez-Pelegr{\'\i}n, Mar; Michalik, David; Loose, Martin
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30301-y
- Institution: IST Austria, Austria
- Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome
- Authors: Herzel, Lydia; Stanley, Julian A; Yao, Chun-Chen; Li, Gene-Wei
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac295
- Institution: MIT, USA
分解中のRNAに生物学的な役割があると面白そうなくらいの割合。
- Live-Cell Fluorescence Lifetime Multiplexing Using Synthetic Fluorescent Probes
- Authors: Frei, Michelle S; Koch, Birgit; Hiblot, Julien; Johnsson, Kai
- Journal: ACS chemical biology
- Year: 2022
- DOI: 10.1021/acschembio.2c00041
- Institution: Max Planck Institute, Germany
パラメータ次第では蛍光タンパクにも応用できるかも。持続時間をターゲットにした蛍光タンパクデザインも出来るかもしれない。
合成生物学論文メモ (Apr 2022)
読み流した論文のメモ。黒色はメモ、緑色は感想、赤色は特に面白いと思ったもの。
32報
Synthetic Biology
Transcription/Translation Control
遺伝子回路、転写翻訳制御など- Growth rate controls the sensitivity of gene regulatory circuits
- Authors: Julou, Thomas; Gervais, Théo; Blank, Diana; van Nimwegen, Erik
- Journal: bioRxiv
- Year: 2022
- DOI: 10.1101/2022.04.03.486858
- Institution: University of Basel, Switzerland
拡散と成長速度の両方を考慮した遺伝子回路設計が出来ると面白そう。
- DNA Input Classification by a Riboregulator-Based Cell-Free Perceptron
- Authors: van der Linden, Ardjan J; Pieters, Pascal A; Bartelds, Mart W; Nathalia, Bryan L; Yin, Peng; Huck, Wilhelm T S; Kim, Jongmin; de Greef, Tom F A
- Journal: ACS Synthetic Biology
- Year: 2022
- DOI: 10.1021/acssynbio.1c00596
- Institution: Eindhoven University of Technology, Netherlands
言葉遊びな部分はあるが、back propagation等の実装にも繋がりそうな気がするので面白そう。
- Transcriptional Interference in Toehold Switch-Based RNA Circuits
- Authors: Falgenhauer, Elisabeth; Mückl, Andrea; Schwarz-Schilling, Matthaeus; Simmel, Friedrich C
- Journal: ACS Synthetic Biology
- Year: 2022
- DOI: 10.1021/acssynbio.1c00486
- Institution: TU Munich, Germany
拡散や分解をうまく調整すれば振動やパターン形成も目指せそう。
- Redesigning regulatory components of quorum-sensing system for diverse metabolic control
- Authors: Ge, Chang; Yu, Zheng; Sheng, Huakang; Shen, Xiaolin; Sun, Xinxiao; Zhang, Yifei; Yan, Yajun; Wang, Jia; Yuan, Qipeng
- Journal: Nature Communications
- Year: 2022
- DOI: 10.1038/s41467-022-29933-x
- Institution: Beijing University of Chemical Technology, China
TF結合領域のタンデムの様な形で面白かった。
RNA Synthetic Biology
アプタマー、リボザイムなど- Fluorogenic RNA-Based Biosensor to Sense the Glycolytic Flux in Mammalian Cells
- Authors: Geraci, Ignazio; Autour, Alexis; Pietruschka, Georg; Shiian, Aleksandra; Borisova, Marina; Mayer, Christoph; Ryckelynck, Michael; Mayer, Günter
- Journal: ACS Chemical Biology
- Year: 2022
- DOI: 10.1021/acschembio.2c00100
- Institution: University of Bonn, Germany
SELEXをうまく回すためのデザインの決め方が難しそう。
- Riboswitch-inspired toehold riboregulators for gene regulation in Escherichia coli
- Authors: Wang, Tianhe; Simmel, Friedrich C
- Journal: Nucleic Acids Research
- Year: 2022
- DOI: 10.1093/nar/gkac275
- Institution: Technische Universitat Munchen, Germany
シンプルながら汎用性の高いデザインで面白い。通常のtoehold switchとのデザイン面での比較が気になるところ。
- Synthetic Translational Regulation by Protein-Binding RNA Origami Scaffolds
- Authors: Nguyen, Michael T A; Pothoulakis, Georgios; Andersen, Ebbe S
- Journal: ACS Synthetic Biology
- Year: 2022
- DOI: 10.1021/acssynbio.1c00608
- Institution: Aarhus University, Denmark
翻訳量のモデリングも出来そう。
- Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches
- Authors: Andreasson, Johan O L; Gotrik, Michael R; Wu, Michelle J; Wayment-Steele, Hannah K; Kladwang, Wipapat; Portela, Fernando; Wellington-Oguri, Roger; Eterna Participants; Das, Rhiju; Greenleaf, William J
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2112979119
- Institution: Stanford University, USA
ゲームデザインから長期で上手くやっていて強い。
Cell-free / Reconstruction
無細胞系、再構成など- Rational Design of CRISPR/Cas12a-RPA Based One-Pot COVID-19 Detection with Design of Experiments
- Authors: Malcı, Koray; Walls, Laura E; Rios-Solis, Leonardo
- Journal: ACS Synthetic Biology
- Year: 2022
- DOI: 10.1021/acssynbio.1c00617
- Institution: University of Edinburgh, UK
Optogenetics
光駆動型ツール、蛍光イメージング、光受容体など、その他〇〇genetics系- Tuning the Sensitivity of Genetically Encoded Fluorescent Potassium Indicators through Structure-Guided and Genome Mining Strategies
- Authors: Torres Cabán, Cristina C; Yang, Minghan; Lai, Cuixin; Yang, Lina; Subach, Fedor V; Smith, Brian O; Piatkevich, Kiryl D; Boyden, Edward S
- Journal: ACS Sensors
- Year: 2022
- DOI: 10.1021/acssensors.1c02201
- Institution: MIT, USA
目的とデザインの流れが綺麗だった。活性部位を同定した時点でdirected evolutionをかけた場合との比較が気になった。
- Ultrasound-controllable engineered bacteria for cancer immunotherapy
- Authors: Abedi, Mohamad H; Yao, Michael S; Mittelstein, David R; Bar-Zion, Avinoam; Swift, Margaret B; Lee-Gosselin, Audrey; Barturen-Larrea, Pierina; Buss, Marjorie T; Shapiro, Mikhail G
- Journal: Nature Communications
- Year: 2022
- DOI: 10.1038/s41467-022-29065-2
- Institution: California Institute of Technology, USA
probioticsの新たな形で面白い。
- A highly photostable and bright green fluorescent protein
- Authors: Hirano, Masahiko; Ando, Ryoko; Shimozono, Satoshi; Sugiyama, Mayu; Takeda, Noriyo; Kurokawa, Hiroshi; Deguchi, Ryusaku; Endo, Kazuki; Haga, Kei; Takai-Todaka, Reiko; Inaura, Shunsuke; Matsumura, Yuta; Hama, Hiroshi; Okada, Yasushi; Fujiwara, Takahiro; Morimoto, Takuya; Katayama, Kazuhiko; Miyawaki, Atsushi
- Journal: Nature Biotechnology
- Year: 2022
- DOI: 10.1038/s41587-022-01278-2
- Institution: RIKEN, Japan
なぜ1残基の、しかもV->Aという微妙な変異で明るくなったのか気になった。
- Synthetic cells with self-activating optogenetic proteins communicate with natural cells
- Authors: Adir, Omer; Albalak, Mia R; Abel, Ravit; Weiss, Lucien E; Chen, Gal; Gruber, Amit; Staufer, Oskar; Kurman, Yaniv; Kaminer, Ido; Shklover, Jeny; Shainsky-Roitman, Janna; Platzman, Ilia; Gepstein, Lior; Shechtman, Yoav; Horwitz, Benjamin A; Schroeder, Avi
- Journal: Nature Communications
- Year: 2022
- DOI: 10.1038/s41467-022-29871-8
- Institution: Technion, Israel
面白いけどストーリーがやや強引では。
Protein Engineering
タンパク質工学- Overcoming universal restrictions on metal selectivity by protein design
- Authors: Choi, Tae Su; Tezcan, F Akif
- Journal: Nature
- Year: 2022
- DOI: 10.1038/s41586-022-04469-8
- Institution: UCSD, USA
- Coupling a Live Cell Directed Evolution Assay with Coevolutionary Landscapes to Engineer an Improved Fluorescent Rhodopsin Chloride Sensor
- Authors: Chi, Hsichuan; Zhou, Qin; Tutol, Jasmine N; Phelps, Shelby M; Lee, Jessica; Kapadia, Paarth; Morcos, Faruck; Dodani, Sheel C.
- Journal: ACS Synthetic Biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00033
- Institution: University of Texas, Dallas, USA
理論的な変異導入手法で、MSA-Transformer等使ったらより広く使えそう。
CRISPR/Cas
クリスパー系- Reprogrammed tracrRNAs enable repurposing of RNAs as crRNAs and sequence-specific RNA biosensors
- Authors: Liu, Yang; Pinto, Filipe; Wan, Xinyi; Yang, Zhugen; Peng, Shuguang; Li, Mengxi; Cooper, Jonathan M; Xie, Zhen; French, Christopher E; Wang, Baojun
- Journal: Nature Communications
- Year: 2022
- DOI: 10.1038/s41467-022-29604-x
- Institution: Zhejiang University, China
gRNAのデザインの幅が広がって面白い。CRISPR/Cas周りだけ使った複雑な回路が出来そう。
- Inducible and reversible RNA N6-methyladenosine editing
- Authors: Shi, Huaxia; Xu, Ying; Tian, Na; Yang, Ming; Liang, Fu-Sen
- Journal: Nature Communications
- Year: 2022
- DOI: 10.1038/s41467-022-29665-y
- Institution: Case Western Reserve University, USA
- Rational guide RNA engineering for small-molecule control of CRISPR/Cas9 and gene editing
- Authors: Liu, Xingyu; Xiong, Wei; Qi, Qianqian; Zhang, Yutong; Ji, Huimin; Cui, Shuangyu; An, Jing; Sun, Xiaoming; Yin, Hao; Tian, Tian; Zhou, Xiang
- Journal: Nucleic Acids Research
- Year: 2022
- DOI: 10.1093/nar/gkac255
- Institution: Wuhan University, China
MBLというのを初めて知った。応用の展開まで丁寧に検証されていて良かった。
- Harnessing phosphonate antibiotics argolaphos biosynthesis enables a synthetic biology-based green synthesis of glyphosate
- Authors: Chu, Leixia; Luo, Xiaoxia; Zhu, Taoting; Cao, Yingying; Zhang, Lili; Deng, Zixin; Gao, Jiangtao
- Journal: Nature Communicatios
- Year: 2022
- DOI: 10.1038/s41467-022-29188-6
- Institution: Fujian Agriculture and Forestry University, China
反応経路のどの部分をどの酵素が担っているかを解析する部分に対して配列/構造解析から解釈を与えられそう。
- Peptide-Induced Fractal Assembly of Silver Nanoparticles for Visual Detection of Disease Biomarkers
- Authors: Retout, Maurice; Mantri, Yash; Jin, Zhicheng; Zhou, Jiajing; Noël, Grégoire; Donovan, Brian; Yim, Wonjun; Jokerst, Jesse V.
- Journal: ACS Nano
- Year: 2022
- DOI: 10.1021/acsnano.1c11643
- Institution: University of Liège, Belgium
Alternative Hosts / Strain Engineering
宿主や系統株の開発- Adenine Base Editing System for Pseudomonas and Prediction Workflow for Protein Dysfunction via ABE
- Authors: Abdullah; Wang, Pujie; Han, Tongren; Liu, Wei; Ren, Wenting; Wu, Yuehong; Xiao, Yi
- Journal: ACS Synthetic Biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00066
- Institution: Shanghai Jiao Tong University, China
- Engineering and validation of a dual luciferase reporter system for quantitative and systematic assessment of regulatory sequences in Chinese hamster ovary cells.
- Authors: Toktay, Yagmur; Dayanc, Bengisu; Senturk, Serif
- Journal: Scientific Reports
- Year: 2022
- DOI: 10.1038/s41598-022-09887-2
- Institution: Izmir Biomedicine and Genome Center, Turkey
CHO(Chinese Hamster ovarian)細胞において、定常発現/トランスフェクション時のプロモーターによる発現効率を比較した。デュアルレポーターシステムのFluc/Rluc比によるとウイルス由来のCMV-mlEが最も高発現。
CMVプロモーターってすごいんだなあ。
- Generation of Synthetic Shuttle Vectors Enabling Modular Genetic Engineering of Cyanobacteria
- Authors: Opel, Franz; Siebert, Nina A; Klatt, Sabine; Tüllinghoff, Adrian; Hantke, Janis G; Toepel, Jörg; Bühler, Bruno; Nürnberg, Dennis J; Klähn, Stephan
- Journal: ACS Synthetic Biology
- Year: 2022
- DOI: 10.1021/acssynbio.1c00605
- Institution: Helmholtz Centre for Environmental Research, Germany
ORF以外の部分もまとめて導入しているようなので、その辺りの最適化を他の例だとどの様にしているのか気になった。
Miscellany
その他- Successive remodeling of IgG glycans using a solid-phase enzymatic platform
- Authors: Hsu, Yen-Pang; Verma, Deeptak; Sun, Shuwen; McGregor, Caroline; Mangion, Ian; Mann, Benjamin F
- Journal: Communications Biology
- Year: 2022
- DOI: 10.1038/s42003-022-03257-4
- Institution: Merck & Co., Inc, USA
- Development of NanoLuc-targeting protein degraders and a universal reporter system to benchmark tag-targeted degradation platforms
- Authors: Grohmann, Christoph; Magtoto, Charlene M; Walker, Joel R; Chua, Ngee Kiat; Gabrielyan, Anna; Hall, Mary; Cobbold, Simon A; Mieruszynski, Stephen; Brzozowski, Martin; Simpson, Daniel S; Dong, Hao; Dorizzi, Bridget; Jacobsen, Annette V; Morrish, Emma; Silke, Natasha; Murphy, James M; Heath, Joan K; Testa, Andrea; Maniaci, Chiara; Ciulli, Alessio; Lessene, Guillaume; Silke, John; Feltham, Rebecca
- Journal: Nature Communications
- Year: 2022
- DOI: 10.1038/s41467-022-29670-1
- Institution: The Walter and Eliza Hall Institute for Medical Research, Australia
Nanolucをルシフェラーゼとしても分解タグとしても使える様になるので便利そう。基質のコストが気になるところ。
Computational Biology / Bioinformatics
- An analysis of protein language model embeddings for fold prediction
- Authors: Villegas-Morcillo, Amelia; Gomez, Angel M; Sanchez, Victoria
- Journal: Briefings in bioinformatics
- Year: 2022
- DOI: 10.1093/bib/bbac142
- Institution: University of Granada, Spain
タンパク質の事前学習済みモデル(UniRep, SeqVec, ESM-1b, ESM-MSA, ProtBERT, ProtT5)から得られる表現ベクトルがタンパク質構造予測とファミリー分類タスクにどの程度応用できるかを比較評価した。各モデルからの表現を使ってMLP, ResCNN+BGRU, LightAttentionの何れかを学習した。また、ESM-1b, ESM-MSA, ProtT5を使ってアンサンブル学習すると殆どの評価でベストスコアを出した。 単独で使う場合はProtBERT以外のBERTはそれほど変わらなさそう。下流のNN構造も軽く試す分にはMLPで十分っぽい。
- Knowledge-based BERT: a method to extract molecular features such as computational chemists
- Authors: Wu, Zhenxing; Jiang, Dejun; Wang, Jike; Zhang, Xujun; Du, Hongyan; Pan, Lurong; Hsieh, Chang-Yu; Cao, Dongsheng; Hou, Tingjun
- Journal: Briefings in bioinformatics
- Year: 2022
- DOI: 10.1093/bib/bbac131
- Institution: Zhejiang University, China
Ablation studyもしてあって、事前学習法として面白かった。
Deep Learning
深層学習を使ったバイオインフォ系のタスク- Deep learning identifies and quantifies recombination hotspot determinants
- Authors: Li, Yu; Chen, Siyuan; Rapakoulia, Trisevgeni; Kuwahara, Hiroyuki; Yip, Kevin Y; Gao, Xin
- Journal: Bioinformatics
- Year: 2022
- DOI: 10.1093/bioinformatics/btac234
- Institution: Chinese University of Honng Kong, China
Bioinformatics in general
バイオインフォマティクス一般- Designing highly multiplex PCR primer sets with Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE)
- Authors: Xie, Nina G; Wang, Michael X; Song, Ping; Mao, Shiqi; Wang, Yifan; Yang, Yuxia; Luo, Junfeng; Ren, Shengxiang; Zhang, David Yu
- Journal: Nature Communications
- Year: 2022
- DOI: 10.1038/s41467-022-29500-4
- Institution: Tongji University, China
Biology in general
- Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity
- Authors: Anand, Amitesh; Patel, Arjun; Chen, Ke; Olson, Connor A; Phaneuf, Patrick Victor; Lamoureux, Cameron; Hefner, Ying; Szubin, Richard; Feist, Adam; Palsson, Bernhard
- Journal: bioRxiv
- Year: 2022
- DOI: 10.1101/2022.04.04.487013
- Institution: UCSD, USA
テーマもアプローチも面白かった。構成的に再現できたら更に面白そう。
- Translational recoding by chemical modification of non-AUG start codon ribonucleotide bases
- Authors: Fujita, Yoshihiko; Kameda, Takeru; Singh, Chingakham Ranjit; Pepper, Whitney; Cecil, Ariana; Hilgers, Madelyn; Thornton, Mackenzie; Asano, Izumi; Moravek, Carter; Togashi, Yuichi; Saito, Hirohide; Asano, Katsura
- Journal: Science Advances
- Year: 2022
- DOI: 10.1126/sciadv.abm8501
- Institution: Kyoto University, Japan
- Elucidation of master allostery essential for circadian clock oscillation in cyanobacteria
- Authors: Furuike, Yoshihiko; Mukaiyama, Atsushi; Ouyang, Dongyan; Ito-Miwa, Kumiko; Simon, Damien; Yamashita, Eiki; Kondo, Takao; Akiyama, Shuji
- Journal: Science Advances
- Year: 2022
- DOI: 10.1126/sciadv.abm8990
- Institution: National Institutes of Natural Sciences, Japan
面白かった。
合成生物学論文メモ (Jun 2021)
読み流した論文のメモ。黒色はメモ、緑色は感想、赤色は特に面白いと思ったもの。
15報
Synthetic Biology
Transcription/Translation Control
遺伝子回路、転写翻訳制御など- Design of Synthetic Quorum Sensing Achieving Induction Timing-Independent Signal Stabilization for Dynamic Metabolic Engineering of E. coli
- Authors: Soma, Yuki; Takahashi, Masatomo; Fujiwara, Yuri; Shinohara, Tamaki; Izumi, Yoshihiro; Hanai, Taizo; Bamba, Takeshi
- Journal: ACS Synthetic Biology
- Year: 2021
- DOI: 10.1021/acssynbio.1c00008
- Institution: Kyushu University, Japan
モデルで予測すると面白そう。
RNA Synthetic Biology
アプタマー、リボザイムなど- Establishment of a Biosensor-based High-Throughput Screening Platform for Tryptophan Overproduction
- Authors: Liu, Yongfei; Yuan, Huiling; Ding, Dongqin; Dong, Huina; Wang, Qinhong; Zhang, Dawei
- Journal: ACS Synthetic Biology
- Year: 2021
- DOI: 10.1021/acssynbio.0c00647
- Institution: Chinese Academy of Sciences, China
Cell-free / Reconstruction
無細胞系、再構成などOptogenetics
光駆動型ツール、蛍光イメージング、光受容体など、その他〇〇genetics系- Smart-watch-programmed green-light-operated percutaneous control of therapeutic transgenes
- Authors: Mansouri, Maysam; Hussherr, Marie-Didiée; Strittmatter, Tobias; Buchmann, Peter; Xue, Shuai; Camenisch, Gieri; Fussenegger, Martin
- Journal: Nature Communications
- Year: 2021
- DOI: 10.1038/s41467-021-23572-4
- Institution: ETH Zurich, Switzerland
マウスがApple Watch背負っててなんかシュール。
- Spatiotemporally confined red light-controlled gene delivery at single-cell resolution using adeno-associated viral vectors
- Authors: Hörner, Maximilian; Jerez-Longres, Carolina; Hudek, Anna; Hook, Sebastian; Sascha Yousefi, O; Schamel, Wolfgang W A; Hörner, Cindy; Zurbriggen, Matias D; Ye, Haifeng; Wagner, Hanna J; Weber, Wilfried
- Journal: Science Advances
- Year: 2021
- DOI: 10.1126/sciadv.abf0797
- Institution: University of Freiburg, Germany
一細胞単位の精度でトランスフェクション出来るらしいので、細胞集団の制御が色々捗りそう。
- Engineered NIR light-responsive bacteria as anti-tumor agent for targeted and precise cancer therapy
- Authors: Pan, Huizhuo; Li, Lianyue; Pang, Gaoju; Han, Chunli; Liu, Baona; Zhang, Yingying; Shen, Yue; Sun, Tao; Liu, Jing; Chang, Jin; Wang, Hanjie
- Journal: Chemical Engineering Journal
- Year: 2021
- DOI: 10.1016/j.cej.2021.130842
- Institution: Tianjin University, China
upcomversionを知らなかった。目的の組織等に特異的に結合させるのが難しそう。
Protein Engineering
タンパク質工学- Intracellular artificial supramolecules based on de novo designed Y15 peptides
- Authors: Miki, Takayuki; Nakai, Taichi; Hashimoto, Masahiro; Kajiwara, Keigo; Tsutsumi, Hiroshi; Mihara, Hisakazu
- Journal: Nature Communications
- Year: 2021
- DOI: 10.1038/s41467-021-23794-6
- Institution: Tokyo Institute of Technology, Japan
ディスカッションにも書かれているが、凝集性IDRとの関わりを分析したりヘテロ二量体化に転換させたり、色々拡がりそう。
- Engineering the protein dynamics of an ancestral luciferase
- Authors: Schenkmayerova, Andrea; Pinto, Gaspar P; Toul, Martin; Marek, Martin; Hernychova, Lenka; Planas-Iglesias, Joan; Liskova, Veronika Daniel; Pluskal, Daniel; Vasina, Michal; Emond, Stephane; Dörr, Mark; Chaloupkova, Radka; Bednar, David; Prokop, Zbynek; Hollfelder, Florian; Bornscheuer, Uwe T; Damborsky, Jiri
- Journal: Nature Communications
- Year: 2021
- DOI: 10.1038/s41467-021-23450-z
- Institution: St. Anne’s University Hospital Brno, Czech Republic
点変異->ドメイン置換のタンパク質進化の流れを追っているようで面白い。
- Reprogramming signal transduction through a designer receptor tyrosine kinase
- Authors: Kongkrongtong, Tatphon; Sumigama, Yuka; Nagamune, Teruyuki; Kawahara, Masahiro
- Journal: Communications Biology
- Year: 2021
- DOI: 10.1038/s42003-021-02287-8
- Institution: University of Tokyo, Japan
変異導入箇所をどう選んだのか(構造等からの確証がどれくらいあったのか)気になる。
CRISPR/Cas
クリスパー系- Engineered reproductively isolated species drive reversible population replacement
- Authors: Buchman, Anna; Shriner, Isaiah; Yang, Ting; Liu, Junru; Antoshechkin, Igor; Marshall, John M; Perry, Michael W; Akbari, Omar S
- Journal: Nature Communications
- Year: 2021
- DOI: 10.1038/s41467-021-23531-z
- Institution: University of California San Diego, USA
Metabolic/Signal Pathway Engineering
シグナル経路、代謝経路、酵素工学など- Designing an irreversible metabolic switch for scalable induction of microbial chemical production
- Authors: Mannan, Ahmad A; Bates, Declan G
- Journal: Nature Communications
- Year: 2021
- DOI: 10.1038/s41467-021-23606-x
- Institution: University of Warwick, UK
面白いアイデア。細胞が死んでいく中で長期的な代謝産物産生量の制御がどのように出来るか気になる。
DNA / Biophysics
DNA、核酸論理回路、ナノスケール構造物など- Dynamic self-assembly of compartmentalized DNA nanotubes
- Authors: Agarwal, Siddharth; Klocke, Melissa A; Pungchai, Passa E; Franco, Elisa
- Journal: Nature Communications
- Year: 2021
- DOI: 10.1038/s41467-021-23850-1
- Institution: UCLA, USA
RNA発現を誘導因子で制御出来たりすると微小管をDNAで置き換えるような事にもなりそう。
- Programmable icosahedral shell system for virus trapping
- Authors: Sigl, Christian; Willner, Elena M; Engelen, Wouter; Kretzmann, Jessica A; Sachenbacher, Ken; Liedl, Anna; Kolbe, Fenna; Wilsch, Florian; Ali Aghvami, S; Protzer, Ulrike; Hagan, Michael F; Fraden, Seth; Dietz, Hendrik
- Journal: Nature Materials
- Year: 2021
- DOI: 10.1038/s41563-021-01020-4
- Institution: Technical University of Munich, Germany
感染自体を物理的に止められる可能性。
Computational Biology / Bioinformatics
Representation Learning
核酸、アミノ酸配列の表現学習- A novel antibacterial peptide recognition algorithm based on BERT
- Authors: Zhang, Yue; Lin, Jianyuan; Zhao, Lianmin; Zeng, Xiangxiang; Liu, Xiangrong
- Journal: Briefings in bioinformatics
- Year: 2021
- DOI: 10.1093/bib/bbab200
- Institution: Xiamen University, China
k個ごとに区切るk-merの作り方だと単純に情報の粒度が1/kになって、予測精度が下がるのは当たり前な気がする。
- BERTMHC: Improved MHC-peptide class II interaction prediction with transformer and multiple instance learning
- Authors: Cheng, Jun; Bendjama, Kaïdre; Rittner, Karola; Malone, Brandon
- Journal: Bioinformatics
- Year: 2021
- DOI: 10.1093/bioinformatics/btab422
- Institution: NEC Laboratories Europe GmbH, Germany
CLSトークンを使う場合との違いはどれくらいあるのかも気になる。
General Biology
- A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations
- Authors: Nguyen, Jen; Fernandez, Vicente; Pontrelli, Sammy; Sauer, Uwe; Ackermann, Martin; Stocker, Roman
- Journal: Nature Communications
- Year: 2021
- DOI: 10.1038/s41467-021-23439-8
- Institution: ETH Zurich, Switzerland