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Celebrating 30 years of chemical biology: A toast to multidisciplinarity Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-19 Mishtu Dey, Samantha Nelson
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Advances in the cell biology of the trafficking and processing of amyloid precursor protein: impact of familial Alzheimer's disease mutations. Biochem. J. (IF 4.4) Pub Date : 2024-10-02 Jingqi Wang,Lou Fourriere,Paul A Gleeson
The production of neurotoxic amyloid-β peptides (Aβ) is central to the initiation and progression of Alzheimer's disease (AD) and involves sequential cleavage of the amyloid precursor protein (APP) by β- and γ-secretases. APP and the secretases are transmembrane proteins and their co-localisation in the same membrane-bound sub-compartment is necessary for APP cleavage. The intracellular trafficking
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Retraction: Mechanism of short-term ERK activation by electromagnetic fields at mobile phone frequencies. Biochem. J. (IF 4.4) Pub Date : 2024-10-02
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RNA and condensates: Disease implications and therapeutic opportunities Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-19 Tina W. Han, Bede Portz, Richard A. Young, Ann Boija, Isaac A. Klein
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Reflections from advisory board members and associate editors Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-19 Michelle Arkin, Sara Buhrlage, Ling-Ling Chen, Peng Chen, Jason Gestwicki, Chuan He, Gerald F. Joyce, Angela Koehler, Milka Kostic, Jun Liu, Jim Wells
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What is chemical biology? Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-19 Albert A. Antolin, Yimon Aye, Liron Bar-Peled, Elena De Vita, Natavan Dudkina, Michael C. Jewett, Hannah Kiely-Collins, Ralph Mazitschek, Zhenrun Jerry Zhang
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The next Nobel Prize in chemistry or in physiology or medicine Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-19 Cigall Kadoch, Jason M. Sheltzer, Hang Yin
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Meet the authors: Lydia P. Tsamouri and Daniel A. Bachovchin Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-19 Lydia P. Tsamouri, Daniel A. Bachovchin
In an interview with Dr. Mishtu Dey, editor-in-chief of Cell Chemical Biology, the authors of the article entitled “The hydrophobicity of the CARD8 N-terminus tunes inflammasome activation” share their perspectives on the ways chemical biology enriches immunology research, the challenges and opportunities in the field, and their scientific career paths.
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Membrane remodeling via ubiquitin-mediated pathways Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-19 Anne-Claire Jacomin, Ivan Dikic
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Ligand discovery by activity-based protein profiling Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-19 Micah J. Niphakis, Benjamin F. Cravatt
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Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-19 Lisa M. Breckels, Charlotte Hutchings, Kishor D. Ingole, Suyeon Kim, Kathryn S. Lilley, Mehul V. Makwana, Kieran J.A. McCaskie, Eneko Villanueva
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New therapies on the horizon: Targeted protein degradation in neuroscience Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-19 James A. Gregory, Christopher M. Hickey, Juan Chavez, Angela M. Cacace
This minireview explores the burgeoning field of targeted protein degradation (TPD) and its promising applications in neuroscience and clinical development. TPD offers innovative strategies for modulating protein levels, presenting a paradigm shift in small-molecule drug discovery and therapeutic interventions. Importantly, small-molecule protein degraders specifically target and remove pathogenic
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Beware of extreme calculated lipophilicity when designing cyclic peptides Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-19 Vasanthanathan Poongavanam, Duc Duy Vo, Jan Kihlberg
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A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-19 Kenjyo Miyauchi, Satoshi Kimura, Naho Akiyama, Kazuki Inoue, Kensuke Ishiguro, Thien-Son Vu, Veerasak Srisuknimit, Kenta Koyama, Gosuke Hayashi, Akiko Soma, Asuteka Nagao, Mikako Shirouzu, Akimitsu Okamoto, Matthew K. Waldor, Tsutomu Suzuki
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Compact RNA editors with natural miniature Cas13j nucleases Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-19 Guo Li, Yaxian Cheng, Jingwen Yu, Yunfei Zhu, Hongru Ma, Yuqiao Zhou, Zhongji Pu, Guanglin Zhu, Yichen Yuan, Ziyue Zhang, Xinzhi Zhou, Kairen Tian, Jianjun Qiao, Xiaoxiang Hu, Xue-xin Chen, Quanjiang Ji, Xingxu Huang, Bin Ma, Yuan Yao
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Astrocyte allocation during brain development is controlled by Tcf4-mediated fate restriction. EMBO J. (IF 9.4) Pub Date : 2024-09-19 Yandong Zhang,Dan Li,Yuqun Cai,Rui Zou,Yilan Zhang,Xin Deng,Yafei Wang,Tianxiang Tang,Yuanyuan Ma,Feizhen Wu,Yunli Xie
Astrocytes in the brain exhibit regional heterogeneity contributing to regional circuits involved in higher-order brain functions, yet the mechanisms controlling their distribution remain unclear. Here, we show that the precise allocation of astrocytes to specific brain regions during development is achieved through transcription factor 4 (Tcf4)-mediated fate restriction based on their embryonic origin
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A shorter splicing isoform antagonizes ZBP1 to modulate cell death and inflammatory responses. EMBO J. (IF 9.4) Pub Date : 2024-09-19 Masahiro Nagata,Yasmin Carvalho Schäfer,Laurens Wachsmuth,Manolis Pasparakis
Z-DNA-binding protein 1 (ZBP1) is an interferon-inducible sensor of Z-DNA and Z-RNA, which has emerged as a critical regulator of cell death and inflammation. ZBP1 binds Z-DNA and Z-RNA via its Zα domains, and signals by engaging RIPK3 and RIPK1 via its RIP homotypic interaction motifs (RHIMs). Here, we show that mice express an alternatively-spliced shorter ZBP1 isoform (ZBP1-S), which harbours the
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Breaking down taurine Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-18 Grant Miura
N-acetyltaurine is a metabolite whose levels fluctuate with diet and exercise and that undergoes hydrolysis to form taurine and acetate. However, the enzymes that facilitate this reaction were not known. In an effort to address this, Wei et al. used liquid chromatography–mass spectrometry-based activity guided analysis of mouse tissues, detecting high N-acetyltaurine hydrolysis activity in kidney and
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Anti-aggregate activity Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-18 Russell Johnson
The formation of pathological protein aggregates occurs in many neurodegenerative diseases, such as the aggregation of the protein tau in patients with Alzheimer’s disease. Removing these aggregates offers a possible route to treat these protein misfolding diseases; however, targeting the aggregated form of a protein while sparing the monomeric form, which is required for normal cellular function,
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Sweet RNA Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-18 Yiyun Song
By coupling rPAL to enzymatic glycan cleavage and sequential window acquisition of all theoretical mass spectra (SWATH-MS), the team found that acp3U was the most enriched linker (although other putative linker substrates were identified). Importantly, knocking out DTWD2, an enzyme responsible for installing acp3U in tRNAs, reduced glycoRNA levels. This study provides not only a useful tool for glycoRNA
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An allosteric cyclin E-CDK2 site mapped by paralog hopping with covalent probes Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-18 Yuanjin Zhang, Zhonglin Liu, Marscha Hirschi, Oleg Brodsky, Eric Johnson, Sang Joon Won, Asako Nagata, Divya Bezwada, Matthew D. Petroski, Jaimeen D. Majmudar, Sherry Niessen, Todd VanArsdale, Adam M. Gilbert, Matthew M. Hayward, Al E. Stewart, Andrew R. Nager, Bruno Melillo, Benjamin F. Cravatt
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Targeting double-stranded nucleic acids using the λExo–pDNA system Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-18
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A developmental route to hematopoietic stem cells Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-18 Adam C. Wilkinson, Marella F. T. R. de Bruijn
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Bacteriophage λ exonuclease and a 5′-phosphorylated DNA guide allow PAM-independent targeting of double-stranded nucleic acids Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-18 Shengnan Fu, Junjie Li, Jing Chen, Linghao Zhang, Jiajia Liu, Huiyu Liu, Xin Su
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Acetylation of TIR domains in the TLR4-Mal-MyD88 complex regulates immune responses in sepsis. EMBO J. (IF 9.4) Pub Date : 2024-09-18 Xue Li,Xiangrong Li,Pengpeng Huang,Facai Zhang,Juanjuan K Du,Ying Kong,Ziqiang Shao,Xinxing Wu,Weijiao Fan,Houquan Tao,Chuanzan Zhou,Yan Shao,Yanling Jin,Meihua Ye,Yan Chen,Jong Deng,Jimin Shao,Jicheng Yue,Xiaju Cheng,Y Eugene Chinn
Activation of the Toll-like receptor 4 (TLR4) by bacterial endotoxins in macrophages plays a crucial role in the pathogenesis of sepsis. However, the mechanism underlying TLR4 activation in macrophages is still not fully understood. Here, we reveal that upon lipopolysaccharide (LPS) stimulation, lysine acetyltransferase CBP is recruited to the TLR4 signalosome complex leading to increased acetylation
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An experimental census of retrons for DNA production and genome editing Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-17 Asim G. Khan, Matías Rojas-Montero, Alejandro González-Delgado, Santiago C. Lopez, Rebecca F. Fang, Kate D. Crawford, Seth L. Shipman
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Multicellular artificial neural network-type architectures demonstrate computational problem solving Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-16 Deepro Bonnerjee, Saswata Chakraborty, Biyas Mukherjee, Ritwika Basu, Abhishek Paul, Sangram Bagh
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Biosynthesis of peptide–nucleobase hybrids in ribosomal peptides Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-16 Zeng-Fei Pei, Natalia M. Vior, Lingyang Zhu, Andrew W. Truman, Satish K. Nair
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ER-phagy restrains inflammatory responses through its receptor UBAC2. EMBO J. (IF 9.4) Pub Date : 2024-09-16 Xing He,Haowei He,Zitong Hou,Zheyu Wang,Qinglin Shi,Tao Zhou,Yaoxing Wu,Yunfei Qin,Jun Wang,Zhe Cai,Jun Cui,Shouheng Jin
ER-phagy, a selective form of autophagic degradation of endoplasmic reticulum (ER) fragments, plays an essential role in governing ER homeostasis. Dysregulation of ER-phagy is associated with the unfolded protein response (UPR), which is a major clue for evoking inflammatory diseases. However, the molecular mechanism underpinning the connection between ER-phagy and disease remains poorly defined. Here
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Non-autophagic Golgi-LC3 lipidation facilitates TFE3 stress response against Golgi dysfunction. EMBO J. (IF 9.4) Pub Date : 2024-09-16 Jaemin Kang,Cathena Meiling Li,Namhoon Kim,Jongyeon Baek,Yong-Keun Jung
Lipidated ATG8/LC3 proteins are recruited to single membrane compartments as well as autophagosomes, supporting their functions. Although recent studies have shown that Golgi-LC3 lipidation follows Golgi damage, its molecular mechanism and function under Golgi stress remain unknown. Here, by combining DLK1 overexpression as a new strategy for induction of Golgi-specific LC3 lipidation, and the application
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Acidity suppresses CD8 + T-cell function by perturbing IL-2, mTORC1, and c-Myc signaling. EMBO J. (IF 9.4) Pub Date : 2024-09-16 Romain Vuillefroy de Silly,Laetitia Pericou,Bili Seijo,Isaac Crespo,Melita Irving
CD8 + T cells have critical roles in tumor control, but a range of factors in their microenvironment such as low pH can suppress their function. Here, we demonstrate that acidity restricts T-cell expansion mainly through impairing IL-2 responsiveness, lowers cytokine secretion upon re-activation, and reduces the cytolytic capacity of CD8 + T cells expressing low-affinity TCR. We further find decreased
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Biotech news from around the world Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13
Researchers from Kenya’s Egerton University and Makerere University in Uganda begin a pilot program to mass breed desert locusts as a sustainable, protein-rich food source for animals and humans. The locusts are grown in giant domed-shaped, temperature- and humidity-controlled greenhouses equipped with wire gauze cages to stop them escaping. The Locust4Industry project aims to enable industrial exploitation
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FDA approves first IDH-targeted glioma drug Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13
Voranigo (vorasidenib), made by French drugmaker Servier Pharmaceuticals, was approved in August by the US Food and Drug Administration. The small-molecule isocitrate dehydrogenase-1 (IDH1) and isocitrate dehydrogenase-2 (IDH2) inhibitor has the go-ahead to treat patients with grade 2 astrocytoma or oligodendroglioma with IDH1 or IDH2 mutations. The approval follows a successful phase 3 trial showing
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Engineered parasite delivers therapeutic proteins to the mouse brain Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13 Iris Marchal
Macromolecular drugs have limited applications in the brain because they cannot cross the blood–brain barrier. A parasite that does have the natural capacity to travel to the brain is Toxoplasma gondii. In a study in Nature Microbiology, Bracha et al. make use of this feature, engineering T. gondii to deliver large proteins to the brains of mice. The authors targeted several proteins with different
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Genentech, Sangamo ink Alzheimer’s deal Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13
Genentech, part of Roche, has signed an exclusive license with Sangamo Therapeutics to develop genomic treatments for two neurodegenerative diseases. Sangamo will receive $50 million up front and could earn up to $1.9 billion in development and commercial milestone payments plus tiered royalties for its proprietary zinc finger repressors directed to the gene encoding the tau protein, which is involved
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Biogenetic Blooms: it’s microbial, and it’s art Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13
Nearly a century later, in a bungalow three blocks from the sun-baked crowds of Rockaway Beach, New York, Karen Ingram meticulously paints portraits of flower blossoms in a Petri dish using a medium of yeast. She calls her series “Biogenetic Blooms”: blue roses, yellow and orange daffodils, red tulips, pink orchids, columbines, snapdragons, irises, black-eyed Susans. The process is surprisingly tricky
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Targeting fatty acid metabolism promotes a healthy vaginal microbiome Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13 Iris Marchal
Specific microbial communities in the female genital tract are linked to health outcomes; for example, a microbiome deficient in Lactobacillus is observed in bacterial vaginosis. However, available therapies may not effectively promote the growth of beneficial bacterial species that could prevent the recurrence of disease. Writing in Cell, Zhu et al. propose that targeting unsaturated long-chain fatty
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From Bench to Podcast: Nicoletta Cieri Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13
On this episode, our Associate Editor Cláudia Vilhena interviews Nicoletta Cieri, the first author of a great story on how a devised analytic framework can aid in the prevention of post-transplant disease recurrence. Join us as Nicoletta and Cláudia explore the highlights of the story, discuss the future of individualized medicine and touch base on future career opportunities following the postdoc
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Bioremediation Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13
Recent patents relating to compositions and methods for the remediation of polluted and contaminated environments.
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US selects first ten drugs for price drops Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13
A historic law that negotiates price discounts for Medicare prescription drugs has led to the selection of the first ten drugs to be covered by these negotiations. From January 2026, enrollees will pay between 38% and 79% less for the ten commonly prescribed outpatient drugs. The negotiated prices are expected to save taxpayers billions of dollars. The biopharma industry, however, argues that the prices
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Intestinal organoids with an autologous immune compartment Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13 Iris Marchal
Although stem-cell derived organoids are useful tools for studying epithelial functions in health and disease, they generally lack the immune compartment critical for modeling organ-level processes. In a paper published in Nature, Recaldin et al. now integrate tissue-resident memory T (TRM) cells into human intestinal organoids and show how this model can be used to gain insight into drug-induced intestinal
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1H24 biotech job picture Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13 Michael Francisco
A semiannual snapshot of job expansions, reductions and availability in the biotech and pharma sectors.
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Enzymes boost ‘rock weathering’ to trap CO2 in soil Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13
Spreading powdered basalt on farmland traps CO2 from the atmosphere, a technology that is cheap, requires no huge steel reactors and, with a biotech boost, may even reduce fertilizer use.
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People Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13
Recent moves of note in and around the biotech and pharma industries.
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The prevalence of post-NDA drug patents and their relationship to the timing of generic approval Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13 Jonathan J. Darrow, Victor Van de Wiele, Beatrice Brown, Aaron S. Kesselheim
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A virtual case competition approach to bridging business acumen and biomedical graduate training Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13 Kara M. Donovan, Robert S. Goldsmith, Erica V. Ely, Samridhi Garg, Lloyd P. Ruiz, Mitre Athaiya, Sophia Meyer, Michelle Sydney Smith, Ishtiaq Mawla
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Foundation models build on ChatGPT tech to learn the fundamental language of biology Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13
Scientists are using ever more sophisticated AI algorithms trained on vast, unlabeled datasets to develop models that can ‘interpret’ biological data to help guide biomolecule design.
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The Wild West of spike-in normalization Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-13 Lauren A. Patel, Yuwei Cao, Eric M. Mendenhall, Christopher Benner, Alon Goren
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Incorporation of nitrogen in antinutritional Solanum alkaloid biosynthesis Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-13 Dagny Grzech, Samuel J. Smit, Ryan M. Alam, Marianna Boccia, Yoko Nakamura, Benke Hong, Ranjit Barbole, Sarah Heinicke, Maritta Kunert, Wibke Seibt, Veit Grabe, Lorenzo Caputi, Benjamin R. Lichman, Sarah E. O’Connor, Asaph Aharoni, Prashant D. Sonawane
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Decoupled transcript and protein concentrations ensure histone homeostasis in different nutrients. EMBO J. (IF 9.4) Pub Date : 2024-09-13 Dimitra Chatzitheodoridou,Daniela Bureik,Francesco Padovani,Kalyan V Nadimpalli,Kurt M Schmoller
To maintain protein homeostasis in changing nutrient environments, cells must precisely control the amount of their proteins, despite the accompanying changes in cell growth and biosynthetic capacity. As nutrients are major regulators of cell cycle length and progression, a particular challenge arises for the nutrient-dependent regulation of 'cell cycle genes', which are periodically expressed during
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Entangling roles of cholesterol-dependent interaction and cholesterol-mediated lipid phase heterogeneity in regulating listeriolysin O pore-formation. Biochem. J. (IF 4.4) Pub Date : 2024-09-13 Kusum Lata,Gregor Anderluh,Kausik Chattopadhyay
Cholesterol-dependent cytolysins (CDCs) are the distinct class of β-barrel pore-forming toxins (β-PFTs) that attack eukaryotic cell membranes, and form large, oligomeric, transmembrane β-barrel pores. Listeriolysin O (LLO) is a prominent member in the CDC family. As documented for the other CDCs, membrane cholesterol is essential for the pore-forming functionality of LLO. However, it remains obscure
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Customizable gene sensing and response without altering endogenous coding sequences Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-12 Fabio Caliendo, Elvira Vitu, Junmin Wang, Shuo-Hsiu Kuo, Hayden Sandt, Casper Nørskov Enghuus, Jesse Tordoff, Neslly Estrada, James J. Collins, Ron Weiss
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Control of DNA demethylation by superoxide anion in plant stem cells Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-12 Shiwen Wang, Min Liu, Dongping Hu, Zhicheng Dong, Zhong Zhao
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Recoded gene circuits for multiplexed genetic code expansion Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-11
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Insights into lysophosphatidylserine recognition and Gα12/13-coupling specificity of P2Y10 Cell Chem. Bio. (IF 6.6) Pub Date : 2024-09-11 Han Yin, Nozomi Kamakura, Yu Qian, Manae Tatsumi, Tatsuya Ikuta, Jiale Liang, Zhenmei Xu, Ruixue Xia, Anqi Zhang, Changyou Guo, Asuka Inoue, Yuanzheng He
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Enriching productive mutational paths accelerates enzyme evolution Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-11 David Patsch, Thomas Schwander, Moritz Voss, Daniela Schaub, Sean Hüppi, Michael Eichenberger, Peter Stockinger, Lisa Schelbert, Sandro Giger, Francesca Peccati, Gonzalo Jiménez-Osés, Mojmír Mutný, Andreas Krause, Uwe T. Bornscheuer, Donald Hilvert, Rebecca M. Buller
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Substrate interactions guide cyclase engineering and lasso peptide diversification Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-11 Susanna E. Barrett, Song Yin, Peter Jordan, John K. Brunson, Jessica Gordon-Nunez, Gabriella Costa Machado da Cruz, Christopher Rosario, Bethany K. Okada, Kelsey Anderson, Thomas A. Pires, Ruoyang Wang, Diwakar Shukla, Mark J. Burk, Douglas A. Mitchell
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Dedifferentiating myoblasts back into a satellite cell state in vitro Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-11
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Organoid culture promotes dedifferentiation of mouse myoblasts into stem cells capable of complete muscle regeneration Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-11 Feodor D. Price, Mark N. Matyas, Andrew R. Gehrke, William Chen, Erica A. Wolin, Kristina M. Holton, Rebecca M. Gibbs, Alice Lee, Pooja S. Singu, Jeffrey S. Sakakeeny, James M. Poteracki, Kelsey Goune, Isabella T. Pfeiffer, Sarah A. Boswell, Peter K. Sorger, Mansi Srivastava, Kathleen Lindahl Pfaff, Emanuela Gussoni, Sean M. Buchanan, Lee L. Rubin
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Efficient genetic code expansion without host genome modifications Nat. Biotechnol. (IF 33.1) Pub Date : 2024-09-11 Alan Costello, Alexander A. Peterson, David L. Lanster, Zhiyi Li, Gavriela D. Carver, Ahmed H. Badran