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Photoreceptor metabolic reprogramming: current understanding and therapeutic implications Commun. Biol. (IF 4.165) Pub Date : 2021-02-24 Warren W. Pan; Thomas J. Wubben; Cagri G. Besirli
Acquired and inherited retinal disorders are responsible for vision loss in an increasing proportion of individuals worldwide. Photoreceptor (PR) death is central to the vision loss individuals experience in these various retinal diseases. Unfortunately, there is a lack of treatment options to prevent PR loss, so an urgent unmet need exists for therapies that improve PR survival and ultimately, vision
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Universal probabilistic programming offers a powerful approach to statistical phylogenetics Commun. Biol. (IF 4.165) Pub Date : 2021-02-24 Fredrik Ronquist; Jan Kudlicka; Viktor Senderov; Johannes Borgström; Nicolas Lartillot; Daniel Lundén; Lawrence Murray; Thomas B. Schön; David Broman
Statistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabilistic graphical models, but this formalism can only partly express phylogenetic problems. Here, we show that universal probabilistic programming languages
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βA1-crystallin regulates glucose metabolism and mitochondrial function in mouse retinal astrocytes by modulating PTP1B activity Commun. Biol. (IF 4.165) Pub Date : 2021-02-24 Sayan Ghosh; Haitao Liu; Meysam Yazdankhah; Nadezda Stepicheva; Peng Shang; Tanuja Vaidya; Stacey Hose; Urvi Gupta; Michael Joseph Calderon; Ming-Wen Hu; Archana Padmanabhan Nair; Joseph Weiss; Christopher S. Fitting; Imran A. Bhutto; Santosh Gopi Krishna Gadde; Naveen Kumar Naik; Chaitra Jaydev; Gerard A. Lutty; James T. Handa; Ashwath Jayagopal; Jiang Qian; José-Alain Sahel; Dhivyaa Rajasundaram;
βA3/A1-crystallin, a lens protein that is also expressed in astrocytes, is produced as βA3 and βA1-crystallin isoforms by leaky ribosomal scanning. In a previous human proteome high-throughput array, we found that βA3/A1-crystallin interacts with protein tyrosine phosphatase 1B (PTP1B), a key regulator of glucose metabolism. This prompted us to explore possible roles of βA3/A1-crystallin in metabolism
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Limited window for donation of convalescent plasma with high live-virus neutralizing antibody titers for COVID-19 immunotherapy Commun. Biol. (IF 4.165) Pub Date : 2021-02-24 Abhinay Gontu; Sreenidhi Srinivasan; Eric Salazar; Meera Surendran Nair; Ruth H. Nissly; Denver Greenawalt; Ian M. Bird; Catherine M. Herzog; Matthew J. Ferrari; Indira Poojary; Robab Katani; Scott E. Lindner; Allen M. Minns; Randall Rossi; Paul A. Christensen; Brian Castillo; Jian Chen; Todd N. Eagar; Xin Yi; Picheng Zhao; Christopher Leveque; Randall J. Olsen; David W. Bernard; Jimmy Gollihar; Suresh
Millions of individuals who have recovered from SARS-CoV-2 infection may be eligible to participate in convalescent plasma donor programs, yet the optimal window for donating high neutralizing titer convalescent plasma for COVID-19 immunotherapy remains unknown. Here we studied the response trajectories of antibodies directed to the SARS-CoV-2 surface spike glycoprotein and in vitro SARS-CoV-2 live
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Specific residues in the cytoplasmic domain modulate photocurrent kinetics of channelrhodopsin from Klebsormidium nitens Commun. Biol. (IF 4.165) Pub Date : 2021-02-23 Rintaro Tashiro; Kumari Sushmita; Shoko Hososhima; Sunita Sharma; Suneel Kateriya; Hideki Kandori; Satoshi P. Tsunoda
Channelrhodopsins (ChRs) are light-gated ion channels extensively applied as optogenetics tools for manipulating neuronal activity. All currently known ChRs comprise a large cytoplasmic domain, whose function is elusive. Here, we report the cation channel properties of KnChR, one of the photoreceptors from a filamentous terrestrial alga Klebsormidium nitens, and demonstrate that the cytoplasmic domain
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Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations Commun. Biol. (IF 4.165) Pub Date : 2021-02-23 Utsab R. Shrestha; Jeremy C. Smith; Loukas Petridis
Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three
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Presynaptic endoplasmic reticulum regulates short-term plasticity in hippocampal synapses Commun. Biol. (IF 4.165) Pub Date : 2021-02-23 Nishant Singh; Thomas Bartol; Herbert Levine; Terrence Sejnowski; Suhita Nadkarni
Short-term plasticity preserves a brief history of synaptic activity that is communicated to the postsynaptic neuron. This is primarily regulated by a calcium signal initiated by voltage dependent calcium channels in the presynaptic terminal. Imaging studies of CA3-CA1 synapses reveal the presence of another source of calcium, the endoplasmic reticulum (ER) in all presynaptic terminals. However, the
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Jaw shape and mechanical advantage are indicative of diet in Mesozoic mammals Commun. Biol. (IF 4.165) Pub Date : 2021-02-23 Nuria Melisa Morales-García; Pamela G. Gill; Christine M. Janis; Emily J. Rayfield
Jaw morphology is closely linked to both diet and biomechanical performance, and jaws are one of the most common Mesozoic mammal fossil elements. Knowledge of the dietary and functional diversity of early mammals informs on the ecological structure of palaeocommunities throughout the longest era of mammalian evolution: the Mesozoic. Here, we analyse how jaw shape and mechanical advantage of the masseter
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Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation Commun. Biol. (IF 4.165) Pub Date : 2021-02-22 Travis T. Sims; Molly B. El Alam; Tatiana V. Karpinets; Stephanie Dorta-Estremera; Venkatesh L. Hegde; Sita Nookala; Kyoko Yoshida-Court; Xiaogang Wu; Greyson W. G. Biegert; Andrea Y. Delgado Medrano; Travis Solley; Mustapha Ahmed-Kaddar; Bhavana V. Chapman; K. Jagannadha Sastry; Melissa P. Mezzari; Joseph F. Petrosino; Lilie L. Lin; Lois Ramondetta; Anuja Jhingran; Kathleen M. Schmeler; Nadim J. Ajami;
Diversity of the gut microbiome is associated with higher response rates for cancer patients receiving immunotherapy but has not been investigated in patients receiving radiation therapy. Additionally, current studies investigating the gut microbiome and outcomes in cancer patients may not have adjusted for established risk factors. Here, we sought to determine if diversity and composition of the gut
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Passive eDNA collection enhances aquatic biodiversity analysis Commun. Biol. (IF 4.165) Pub Date : 2021-02-22 Bessey Cindy; Jarman Simon Neil; Simpson Tiffany; Miller Haylea; Stewart Todd; Keesing John Kenneth; Berry Oliver
Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach for species detection and biodiversity assessment. The most common eDNA collection method in aquatic systems is actively filtering water through a membrane, which is time consuming and requires specialized equipment. Ecological studies investigating species abundance or distribution often require more samples than can be
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Annotation of chromatin states in 66 complete mouse epigenomes during development Commun. Biol. (IF 4.165) Pub Date : 2021-02-22 Arjan van der Velde; Kaili Fan; Junko Tsuji; Jill E. Moore; Michael J. Purcaro; Henry E. Pratt; Zhiping Weng
The morphologically and functionally distinct cell types of a multicellular organism are maintained by their unique epigenomes and gene expression programs. Phase III of the ENCODE Project profiled 66 mouse epigenomes across twelve tissues at daily intervals from embryonic day 11.5 to birth. Applying the ChromHMM algorithm to these epigenomes, we annotated eighteen chromatin states with characteristics
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High-throughput screening and validation of antibodies against synaptic proteins to explore opioid signaling dynamics Commun. Biol. (IF 4.165) Pub Date : 2021-02-22 Mariana Lemos Duarte; Nikita A. Trimbake; Achla Gupta; Christine Tumanut; Xiaomin Fan; Catherine Woods; Akila Ram; Ivone Gomes; Erin N. Bobeck; Deborah Schechtman; Lakshmi A. Devi
Antibodies represent powerful tools to examine signal transduction pathways. Here, we present a strategy integrating multiple state-of-the-art methods to produce, validate, and utilize antibodies. Focusing on understudied synaptic proteins, we generated 137 recombinant antibodies. We used yeast display antibody libraries from the B cells of immunized rabbits, followed by FACS sorting under stringent
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Looking forward in 2021 Commun. Biol. (IF 4.165) Pub Date : 2021-02-19
A new year symbolizes new hope for the future, especially this year as we start to see the first wave of vaccines administered against COVID-19. Here, we take stock of the year behind us and look forward to seeing where science takes us in 2021.
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Ex vivo visualization of RNA polymerase III-specific gene activity with electron microscopy Commun. Biol. (IF 4.165) Pub Date : 2021-02-19 Sina Manger; Utz H. Ermel; Achilleas S. Frangakis
The direct study of transcription or DNA–protein-binding events, requires imaging of individual genes at molecular resolution. Electron microscopy (EM) can show local detail of the genome. However, direct visualization and analysis of specific individual genes is currently not feasible as they cannot be unambiguously localized in the crowded, landmark-free environment of the nucleus. Here, we present
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Engineering multifunctional bactericidal nanofibers for abdominal hernia repair Commun. Biol. (IF 4.165) Pub Date : 2021-02-19 Samson Afewerki; Nicole Bassous; Samarah Vargas Harb; Marcus Alexandre F. Corat; Sushila Maharjan; Guillermo U. Ruiz-Esparza; Mirian M. M. de Paula; Thomas J. Webster; Carla Roberta Tim; Bartolomeu Cruz Viana; Danquan Wang; Xichi Wang; Fernanda Roberta Marciano; Anderson Oliveira Lobo
The engineering of multifunctional surgical bactericidal nanofibers with inherent suitable mechanical and biological properties, through facile and cheap fabrication technology, is a great challenge. Moreover, hernia, which is when organ is pushed through an opening in the muscle or adjacent tissue due to damage of tissue structure or function, is a dire clinical challenge that currently needs surgery
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Development of an α-synuclein knockdown peptide and evaluation of its efficacy in Parkinson’s disease models Commun. Biol. (IF 4.165) Pub Date : 2021-02-19 Jack Wuyang Jin; Xuelai Fan; Esther del Cid-Pellitero; Xing-Xing Liu; Limin Zhou; Chunfang Dai; Ebrima Gibbs; Wenting He; Hongjie Li; Xiaobin Wu; Austin Hill; Blair R. Leavitt; Neil Cashman; Lidong Liu; Jie Lu; Thomas M. Durcan; Zhifang Dong; Edward A. Fon; Yu Tian Wang
Convincing evidence supports the premise that reducing α-synuclein levels may be an effective therapy for Parkinson’s disease (PD); however, there has been lack of a clinically applicable α-synuclein reducing therapeutic strategy. This study was undertaken to develop a blood-brain barrier and plasma membrane-permeable α-synuclein knockdown peptide, Tat-βsyn-degron, that may have therapeutic potential
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Spermidine-induced recovery of human dermal structure and barrier function by skin microbiome Commun. Biol. (IF 4.165) Pub Date : 2021-02-19 Gihyeon Kim; Misun Kim; Minji Kim; Changho Park; Youngmin Yoon; Doo-Hyeon Lim; Hyeonju Yeo; Seunghyun Kang; Yeong-Geun Lee; Nam-In Beak; Jongsung Lee; Sujeong Kim; Jee Young Kwon; Won Woo Choi; Charles Lee; Kyoung Wan Yoon; Hansoo Park; Dong-Geol Lee
An unbalanced microbial ecosystem on the human skin is closely related to skin diseases and has been associated with inflammation and immune responses. However, little is known about the role of the skin microbiome on skin aging. Here, we report that the Streptococcus species improved the skin structure and barrier function, thereby contributing to anti-aging. Metagenomic analyses showed the abundance
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Quercetin 3,5,7,3′,4′-pentamethyl ether from Kaempferia parviflora directly and effectively activates human SIRT1 Commun. Biol. (IF 4.165) Pub Date : 2021-02-19 Mimin Zhang; Peng Lu; Tohru Terada; Miaomiao Sui; Haruka Furuta; Kilico Iida; Yukie Katayama; Yi Lu; Ken Okamoto; Michio Suzuki; Tomiko Asakura; Kentaro Shimizu; Fumihiko Hakuno; Shin-Ichiro Takahashi; Norimoto Shimada; Jinwei Yang; Tsutomu Ishikawa; Jin Tatsuzaki; Koji Nagata
Sirtuin 1 (SIRT1), an NAD+-dependent deacetylase, is a crucial regulator that produces multiple physiological benefits, such as the prevention of cancer and age-related diseases. SIRT1 is activated by sirtuin-activating compounds (STACs). Here, we report that quercetin 3,5,7,3′,4′-pentamethyl ether (KPMF-8), a natural STAC from Thai black ginger Kaempferia parviflora, interacts with SIRT1 directly
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Thank you to all of our reviewers in 2020 Commun. Biol. (IF 4.165) Pub Date : 2021-02-19
5314 individual reviewers contributed to the peer review process at Communications Biology in 2020. We acknowledge and thank each of them here.
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Endosomal TLR3 co-receptor CLEC18A enhances host immune response to viral infection Commun. Biol. (IF 4.165) Pub Date : 2021-02-18 Ya-Lang Huang; Ming-Ting Huang; Pei-Shan Sung; Teh-Ying Chou; Ruey-Bing Yang; An-Suei Yang; Chung-Ming Yu; Yu-Wen Hsu; Wei-Chiao Chang; Shie-Liang Hsieh
Human C-type lectin member 18A (CLEC18A) is ubiquitously expressed in human, and highest expression levels are found in human myeloid cells and liver. In contrast, mouse CLEC18A (mCLEC18A) is only expressed in brain, kidney and heart. However, the biological functions of CLEC18A are still unclear. We have shown that a single amino acid change (S339 →R339) in CTLD domain has profound effect in their
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Climate change threatens Chinook salmon throughout their life cycle Commun. Biol. (IF 4.165) Pub Date : 2021-02-18 Lisa G. Crozier; Brian J. Burke; Brandon E. Chasco; Daniel L. Widener; Richard W. Zabel
Widespread declines in Atlantic and Pacific salmon (Salmo salar and Oncorhynchus spp.) have tracked recent climate changes, but managers still lack quantitative projections of the viability of any individual population in response to future climate change. To address this gap, we assembled a vast database of survival and other data for eight wild populations of threatened Chinook salmon (O. tshawytscha)
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Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults Commun. Biol. (IF 4.165) Pub Date : 2021-02-18 Rong Xu; Renfei Lu; Tao Zhang; Qunfu Wu; Weihua Cai; Xudong Han; Zhenzhou Wan; Xia Jin; Zhigang Zhang; Chiyu Zhang
SARS-CoV-2 is the cause of COVID-19. It infects multiple organs including the respiratory tract and gut. Dynamic changes of regional microbiomes in infected adults are largely unknown. Here, we performed longitudinal analyses of throat and anal swabs from 35 COVID-19 and 19 healthy adult controls, as well as 10 non-COVID-19 patients with other diseases, by 16 S rRNA gene sequencing. The results showed
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PANDAA intentionally violates conventional qPCR design to enable durable, mismatch-agnostic detection of highly polymorphic pathogens Commun. Biol. (IF 4.165) Pub Date : 2021-02-18 Iain J. MacLeod; Christopher F. Rowley; M. Essex
Sensitive and reproducible diagnostics are fundamental to containing the spread of existing and emerging pathogens. Despite the reliance of clinical virology on qPCR, technical challenges persist that compromise their reliability for sustainable epidemic containment as sequence instability in probe-binding regions produces false-negative results. We systematically violated canonical qPCR design principles
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Fossil evidence for vampire squid inhabiting oxygen-depleted ocean zones since at least the Oligocene Commun. Biol. (IF 4.165) Pub Date : 2021-02-18 Martin Košťák; Ján Schlögl; Dirk Fuchs; Katarína Holcová; Natalia Hudáčková; Adam Culka; István Fözy; Adam Tomašových; Rastislav Milovský; Juraj Šurka; Martin Mazuch
A marked 120 My gap in the fossil record of vampire squids separates the only extant species (Vampyroteuthis infernalis) from its Early Cretaceous, morphologically-similar ancestors. While the extant species possesses unique physiological adaptations to bathyal environments with low oxygen concentrations, Mesozoic vampyromorphs inhabited epicontinental shelves. However, the timing of their retreat
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RSPO4-CRISPR alleviates liver injury and restores gut microbiota in a rat model of liver fibrosis Commun. Biol. (IF 4.165) Pub Date : 2021-02-18 Linghua Yu; Linlin Wang; Xiaojun Wu; Huixing Yi
Wnt signaling dysfunction and gut dysbiosis may lead to liver fibrosis, yet the underlying mechanisms are not well elucidated. This study demonstrated the role of RSPO4, a Wnt signaling agonist, in liver fibrogenesis and its impact on the gut microbiome. RSPO4 gene in CCl4-induced fibrotic-liver rats was knockout by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system, with healthy
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The structural basis of function and regulation of neuronal cotransporters NKCC1 and KCC2 Commun. Biol. (IF 4.165) Pub Date : 2021-02-17 Sensen Zhang; Jun Zhou; Yuebin Zhang; Tianya Liu; Perrine Friedel; Wei Zhuo; Suma Somasekharan; Kasturi Roy; Laixing Zhang; Yang Liu; Xianbin Meng; Haiteng Deng; Wenwen Zeng; Guohui Li; Biff Forbush; Maojun Yang
NKCC and KCC transporters mediate coupled transport of Na++K++Cl− and K++Cl− across the plasma membrane, thus regulating cell Cl− concentration and cell volume and playing critical roles in transepithelial salt and water transport and in neuronal excitability. The function of these transporters has been intensively studied, but a mechanistic understanding has awaited structural studies of the transporters
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Bioinformatics-aided identification, characterization and applications of mushroom linalool synthases Commun. Biol. (IF 4.165) Pub Date : 2021-02-17 Congqiang Zhang; Xixian Chen; Raphael Tze Chuen Lee; Rehka T; Sebastian Maurer-Stroh; Martin Rühl
Enzymes empower chemical industries and are the keystone for metabolic engineering. For example, linalool synthases are indispensable for the biosynthesis of linalool, an important fragrance used in 60–80% cosmetic and personal care products. However, plant linalool synthases have low activities while expressed in microbes. Aided by bioinformatics analysis, four linalool/nerolidol synthases (LNSs)
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Rapid whole cell imaging reveals a calcium-APPL1-dynein nexus that regulates cohort trafficking of stimulated EGF receptors Commun. Biol. (IF 4.165) Pub Date : 2021-02-17 H. M. York; A. Patil; U. K. Moorthi; A. Kaur; A. Bhowmik; G. J. Hyde; H. Gandhi; A. Fulcher; K. Gaus; S. Arumugam
The endosomal system provides rich signal processing capabilities for responses elicited by growth factor receptors and their ligands. At the single cell level, endosomal trafficking becomes a critical component of signal processing, as exemplified by the epidermal growth factor (EGF) receptors. Activated EGFRs are trafficked to the phosphatase-enriched peri-nuclear region (PNR), where they are dephosphorylated
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1 °C warming increases spatial competition frequency and complexity in Antarctic marine macrofauna Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 David K. A. Barnes; Gail V. Ashton; Simon A. Morley; Lloyd S. Peck
Environmental conditions of the Southern Ocean around Antarctica have varied little for >5 million years but are now changing. Here, we investigated how warming affects competition for space. Little considered in the polar regions, this is a critical component of biodiversity response. Change in competition in response to environment forcing might be detectable earlier than individual species presence/absence
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Pairwise maximum entropy model explains the role of white matter structure in shaping emergent co-activation states Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Arian Ashourvan; Preya Shah; Adam Pines; Shi Gu; Christopher W. Lynn; Danielle S. Bassett; Kathryn A. Davis; Brian Litt
A major challenge in neuroscience is determining a quantitative relationship between the brain’s white matter structural connectivity and emergent activity. We seek to uncover the intrinsic relationship among brain regions fundamental to their functional activity by constructing a pairwise maximum entropy model (MEM) of the inter-ictal activation patterns of five patients with medically refractory
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Environmental palaeogenomic reconstruction of an Ice Age algal population Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Youri Lammers; Peter D. Heintzman; Inger Greve Alsos
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment
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Structure–function studies of ultrahigh molecular weight isoprenes provide key insights into their biosynthesis Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Hiroyuki Kajiura; Takuya Yoshizawa; Yuji Tokumoto; Nobuaki Suzuki; Shinya Takeno; Kanokwan Jumtee Takeno; Takuya Yamashita; Shun-ichi Tanaka; Yoshinobu Kaneko; Kazuhito Fujiyama; Hiroyoshi Matsumura; Yoshihisa Nakazawa
Some plant trans-1,4-prenyltransferases (TPTs) produce ultrahigh molecular weight trans-1,4-polyisoprene (TPI) with a molecular weight of over 1.0 million. Although plant-derived TPI has been utilized in various industries, its biosynthesis and physiological function(s) are unclear. Here, we identified three novel Eucommia ulmoides TPT isoforms—EuTPT1, 3, and 5, which synthesized TPI in vitro without
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Biocompatible nucleus-targeted graphene quantum dots for selective killing of cancer cells via DNA damage Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Lei Qi; Tonghe Pan; Liling Ou; Zhiqiang Ye; Chunlei Yu; Bijun Bao; Zixia Wu; Dayong Cao; Liming Dai
Graphene quantum dots (GQDs) are nano-sized graphene slices. With their small size, lamellar and aromatic-ring structure, GQDs tend to enter into the cell nucleus and interfere with DNA activity. Thus, GQD alone is expected to be an anticancer reagent. Herein, we developed GQDs that suppress the growth of tumor by selectively damaging the DNA of cancer cells. The amine-functionalized GQDs were modified
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Intertissue small RNA communication mediates the acquisition and inheritance of hormesis in Caenorhabditis elegans Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Emiko Okabe; Masaharu Uno; Saya Kishimoto; Eisuke Nishida
Environmental conditions can cause phenotypic changes, part of which can be inherited by subsequent generations via soma-to-germline communication. However, the signaling molecules or pathways that mediate intertissue communication remain unclear. Here, we show that intertissue small RNA communication systems play a key role in the acquisition and inheritance of hormesis effects – stress-induced stress
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A hexokinase isoenzyme switch in human liver cancer cells promotes lipogenesis and enhances innate immunity Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Laure Perrin-Cocon; Pierre-Olivier Vidalain; Clémence Jacquemin; Anne Aublin-Gex; Keedrian Olmstead; Baptiste Panthu; Gilles Jeans Philippe Rautureau; Patrice André; Piotr Nyczka; Marc-Thorsten Hütt; Nivea Amoedo; Rodrigue Rossignol; Fabian Volker Filipp; Vincent Lotteau; Olivier Diaz
During the cancerous transformation of normal hepatocytes into hepatocellular carcinoma (HCC), the enzyme catalyzing the first rate-limiting step of glycolysis, namely the glucokinase (GCK), is replaced by the higher affinity isoenzyme, hexokinase 2 (HK2). Here, we show that in HCC tumors the highest expression level of HK2 is inversely correlated to GCK expression, and is associated to poor prognosis
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Recovery of tropical marine benthos after a trawl ban demonstrates linkage between abiotic and biotic changes Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Zhi Wang; Kenneth M. Y. Leung; Yik-Hei Sung; David Dudgeon; Jian-Wen Qiu
Bottom trawling, which is highly detrimental to seabed habitats, has been banned in some jurisdictions to mitigate the problems of habitat destruction and overfishing. However, most reports of ecosystem responses to trawling impacts originate from temperate latitudes, focusing on commercial species, and recovery of invertebrate macrobenthos from trawl ban has hardly ever been studied in the tropics
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Lipidomic and in-gel analysis of maleic acid co-polymer nanodiscs reveals differences in composition of solubilized membranes Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Marta Barniol-Xicota; Steven H. L. Verhelst
Membrane proteins are key in a large number of physiological and pathological processes. Their study often involves a prior detergent solubilization step, which strips away the membrane and can jeopardize membrane protein integrity. A recent alternative to detergents encompasses maleic acid based copolymers (xMAs), which disrupt the lipid bilayer and form lipid protein nanodiscs (xMALPs) soluble in
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Macrophage-derived EDA-A2 inhibits intestinal stem cells by targeting miR-494/EDA2R/β-catenin signaling in mice Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Lele Song; Renxu Chang; Xia Sun; Liying Lu; Han Gao; Huiying Lu; Ritian Lin; Xiaorong Xu; Zhanju Liu; Lixing Zhan
The mucosa microenvironment is critical for intestinal stem cell self-renewal and reconstruction of the epithelial barrier in inflammatory bowel disease (IBD), where the mechanisms underlying cross-talk between intestinal crypts and the microenvironment remain unclear. Here, we firstly identified miR-494-3p as an important protector in colitis. miR-494-3p levels were decreased and negatively correlated
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A high-throughput Galectin-9 imaging assay for quantifying nanoparticle uptake, endosomal escape and functional RNA delivery Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Michael J. Munson; Gwen O’Driscoll; Andreia M. Silva; Elisa Lázaro-Ibáñez; Audrey Gallud; John T. Wilson; Anna Collén; Elin K. Esbjörner; Alan Sabirsh
RNA-based therapies have great potential to treat many undruggable human diseases. However, their efficacy, in particular for mRNA, remains hampered by poor cellular delivery and limited endosomal escape. Development and optimisation of delivery vectors, such as lipid nanoparticles (LNPs), are impeded by limited screening methods to probe the intracellular processing of LNPs in sufficient detail. We
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Zn 2+ -dependent DNAzymes that cleave all combinations of ribonucleotides Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Rika Inomata; Jing Zhao; Makoto Miyagishi
Although several DNAzymes are known, their utility is limited by a narrow range of substrate specificity. Here, we report the isolation of two zinc-dependent DNAzymes, ZincDz1 and ZincDz2, which exhibit compact catalytic core sequences with highly versatile hydrolysis activity. They were selected through in vitro selection followed by deep sequencing analysis. Despite their sequence similarity, each
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Feedback mechanisms stabilise degraded turf algal systems at a CO 2 seep site Commun. Biol. (IF 4.165) Pub Date : 2021-02-16 Ben P. Harvey; Ro Allen; Sylvain Agostini; Linn J. Hoffmann; Koetsu Kon; Tina C. Summerfield; Shigeki Wada; Jason M. Hall-Spencer
Human activities are rapidly changing the structure and function of coastal marine ecosystems. Large-scale replacement of kelp forests and coral reefs with turf algal mats is resulting in homogenous habitats that have less ecological and human value. Ocean acidification has strong potential to substantially favour turf algae growth, which led us to examine the mechanisms that stabilise turf algal states
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Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi Commun. Biol. (IF 4.165) Pub Date : 2021-02-15 Cheng Li; Zejian Guo; Shanyue Zhou; Qingyue Han; Manman Zhang; Youliang Peng; Tom Hsiang; Xujun Chen
The basidiomycetous fungal genus, Rhizoctonia, can cause severe damage to many plants and is composed of multinucleate, binucleate, and uninucleate species differing in pathogenicity. Here we generated chromosome-scale genome assemblies of the three nuclear types of Rhizoctonia isolates. The genomic comparisons revealed that the uninucleate JN strain likely arose by somatic hybridization of two binucleate
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High-throughput behavioral screen in C. elegans reveals Parkinson’s disease drug candidates Commun. Biol. (IF 4.165) Pub Date : 2021-02-15 Salman Sohrabi; Danielle E. Mor; Rachel Kaletsky; William Keyes; Coleen T. Murphy
We recently linked branched-chain amino acid transferase 1 (BCAT1) dysfunction with the movement disorder Parkinson’s disease (PD), and found that RNAi-mediated knockdown of neuronal bcat-1 in C. elegans causes abnormal spasm-like ‘curling’ behavior with age. Here we report the development of a machine learning-based workflow and its application to the discovery of potentially new therapeutics for
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Insulin-like 3 affects zebrafish spermatogenic cells directly and via Sertoli cells Commun. Biol. (IF 4.165) Pub Date : 2021-02-15 Diego Crespo; Luiz H. C. Assis; Yu Ting Zhang; Diego Safian; Tomasz Furmanek; Kai Ove Skaftnesmo; Birgitta Norberg; Wei Ge; Yung-Ching Choi; Marjo J. den Broeder; Juliette Legler; Jan Bogerd; Rüdiger W. Schulz
Pituitary hormones can use local signaling molecules to regulate target tissue functions. In adult zebrafish testes, follicle-stimulating hormone (Fsh) strongly increases the production of insulin-like 3 (Insl3), a Leydig cell-derived growth factor found in all vertebrates. Little information is available regarding Insl3 function in adult spermatogenesis. The Insl3 receptors Rxfp2a and 2b were expressed
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Depth-dependent parental effects create invisible barriers to coral dispersal Commun. Biol. (IF 4.165) Pub Date : 2021-02-15 Tom Shlesinger; Yossi Loya
Historically, marine populations were considered to be interconnected across large geographic regions due to the lack of apparent physical barriers to dispersal, coupled with a potentially widely dispersive pelagic larval stage. Recent studies, however, are providing increasing evidence of small-scale genetic segregation of populations across habitats and depths, separated in some cases by only a few
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HDXmodeller: an online webserver for high-resolution HDX-MS with auto-validation Commun. Biol. (IF 4.165) Pub Date : 2021-02-15 Ramin Ekhteiari Salmas; Antoni James Borysik
The extent to which proteins are protected from hydrogen deuterium exchange (HDX) provides valuable insight into their folding, dynamics and interactions. Characterised by mass spectrometry (MS), HDX benefits from negligible mass restrictions and exceptional throughput and sensitivity but at the expense of resolution. Exchange mechanisms which naturally transpire for individual residues cannot be accurately
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CASSPER is a semantic segmentation-based particle picking algorithm for single-particle cryo-electron microscopy Commun. Biol. (IF 4.165) Pub Date : 2021-02-15 Blesson George; Anshul Assaiya; Robin J. Roy; Ajit Kembhavi; Radha Chauhan; Geetha Paul; Janesh Kumar; Ninan S. Philip
Particle identification and selection, which is a prerequisite for high-resolution structure determination of biological macromolecules via single-particle cryo-electron microscopy poses a major bottleneck for automating the steps of structure determination. Here, we present a generalized deep learning tool, CASSPER, for the automated detection and isolation of protein particles in transmission microscope
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Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants Commun. Biol. (IF 4.165) Pub Date : 2021-02-15 Rui Wang; Jiahui Chen; Kaifu Gao; Yuta Hozumi; Changchuan Yin; Guo-Wei Wei
SARS-CoV-2 has been mutating since it was first sequenced in early January 2020. Here, we analyze 45,494 complete SARS-CoV-2 geneome sequences in the world to understand their mutations. Among them, 12,754 sequences are from the United States. Our analysis suggests the presence of four substrains and eleven top mutations in the United States. These eleven top mutations belong to 3 disconnected groups
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Identification of efficient prokaryotic cell-penetrating peptides with applications in bacterial biotechnology Commun. Biol. (IF 4.165) Pub Date : 2021-02-15 Hyang-Mi Lee; Jun Ren; Kha Mong Tran; Byeong-Min Jeon; Won-Ung Park; Hyunjoo Kim; Kyung Eun Lee; Yuna Oh; Myungback Choi; Dae-Sung Kim; Dokyun Na
In bacterial biotechnology, instead of producing functional proteins from plasmids, it is often necessary to deliver functional proteins directly into live cells for genetic manipulation or physiological modification. We constructed a library of cell-penetrating peptides (CPPs) capable of delivering protein cargo into bacteria and developed an efficient delivery method for CPP-conjugated proteins.
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Function of histone H2B monoubiquitination in transcriptional regulation of auxin biosynthesis in Arabidopsis Commun. Biol. (IF 4.165) Pub Date : 2021-02-15 Li Zhang; Pan Luo; Jie Bai; Lei Wu; Dong-Wei Di; Hai-Qing Liu; Jing-Jing Li; Ya-Li Liu; Allah Jurio Khaskheli; Chang-Ming Zhao; Guang-Qin Guo
The auxin IAA is a vital plant hormone in controlling growth and development, but our knowledge about its complicated biosynthetic pathways and molecular regulation are still limited and fragmentary. cytokinin induced root waving 2 (ckrw2) was isolated as one of the auxin-deficient mutants in a large-scale forward genetic screen aiming to find more genes functioning in auxin homeostasis and/or its
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Efficient manipulation of gene dosage in human iPSCs using CRISPR/Cas9 nickases Commun. Biol. (IF 4.165) Pub Date : 2021-02-12 Tao Ye; Yangyang Duan; Hayley W. S. Tsang; He Xu; Yuewen Chen; Han Cao; Yu Chen; Amy K. Y. Fu; Nancy Y. Ip
The dysregulation of gene dosage due to duplication or haploinsufficiency is a major cause of autosomal dominant diseases such as Alzheimer’s disease. However, there is currently no rapid and efficient method for manipulating gene dosage in a human model system such as human induced pluripotent stem cells (iPSCs). Here, we demonstrate a simple and precise method to simultaneously generate iPSC lines
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Human ACE2 peptide-mimics block SARS-CoV-2 pulmonary cells infection Commun. Biol. (IF 4.165) Pub Date : 2021-02-12 Philippe Karoyan; Vincent Vieillard; Luis Gómez-Morales; Estelle Odile; Amélie Guihot; Charles-Edouard Luyt; Alexis Denis; Pascal Grondin; Olivier Lequin
In light of the recent accumulated knowledge on SARS-CoV-2 and its mode of human cells invasion, the binding of viral spike glycoprotein to human Angiotensin Converting Enzyme 2 (hACE2) receptor plays a central role in cell entry. We designed a series of peptides mimicking the N-terminal helix of hACE2 protein which contains most of the contacting residues at the binding site, exhibiting a high helical
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Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools Commun. Biol. (IF 4.165) Pub Date : 2021-02-12 Alexey Bondar; Olga Rybakova; Josef Melcr; Jan Dohnálek; Petro Khoroshyy; Ondřej Ticháček; Štěpán Timr; Paul Miclea; Alina Sakhi; Vendula Marková; Josef Lazar
Fluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such information can provide insights into protein structure, aid in development of genetically encoded probes, and allow determinations of lipid membrane properties. However
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Immunoreactive peptide maps of SARS-CoV-2 Commun. Biol. (IF 4.165) Pub Date : 2021-02-12 Nischay Mishra; Xi Huang; Shreyas Joshi; Cheng Guo; James Ng; Riddhi Thakkar; Yongjian Wu; Xin Dong; Qianlin Li; Richard S. Pinapati; Eric Sullivan; Adrian Caciula; Rafal Tokarz; Thomas Briese; Jiahai Lu; W. Ian Lipkin
Serodiagnosis of SARS-CoV-2 infection is impeded by immunological cross-reactivity among the human coronaviruses (HCoVs): SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. Here we report the identification of humoral immune responses to SARS-CoV-2 peptides that may enable discrimination between exposure to SARS-CoV-2 and other HCoVs. We used a high-density peptide microarray and plasma
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Mitochondrial ubiquitin ligase alleviates Alzheimer’s disease pathology via blocking the toxic amyloid-β oligomer generation Commun. Biol. (IF 4.165) Pub Date : 2021-02-12 Keisuke Takeda; Aoi Uda; Mikihiro Mitsubori; Shun Nagashima; Hiroko Iwasaki; Naoki Ito; Isshin Shiiba; Satoshi Ishido; Masaaki Matsuoka; Ryoko Inatome; Shigeru Yanagi
Mitochondrial pathophysiology is implicated in the development of Alzheimer’s disease (AD). An integrative database of gene dysregulation suggests that the mitochondrial ubiquitin ligase MITOL/MARCH5, a fine-tuner of mitochondrial dynamics and functions, is downregulated in patients with AD. Here, we report that the perturbation of mitochondrial dynamics by MITOL deletion triggers mitochondrial impairments
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Bridgehead effect and multiple introductions shape the global invasion history of a termite Commun. Biol. (IF 4.165) Pub Date : 2021-02-12 Alexander J. Blumenfeld; Pierre-André Eyer; Claudia Husseneder; Jianchu Mo; Laura N. L. Johnson; Changlu Wang; J. Kenneth Grace; Thomas Chouvenc; Shichen Wang; Edward L. Vargo
Native to eastern Asia, the Formosan subterranean termite Coptotermes formosanus (Shiraki) is recognized as one of the 100 worst invasive pests in the world, with established populations in Japan, Hawaii and the southeastern United States. Despite its importance, the native source(s) of C. formosanus introductions and their invasive pathway out of Asia remain elusive. Using ~22,000 SNPs, we retraced
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pH-dependent and dynamic interactions of cystatin C with heparan sulfate Commun. Biol. (IF 4.165) Pub Date : 2021-02-12 Xiaoxiao Zhang; Xinyue Liu; Guowei Su; Miaomiao Li; Jian Liu; Chunyu Wang; Ding Xu
Cystatin C (Cst-3) is a potent inhibitor of cysteine proteases with diverse biological functions. As a secreted protein, the potential interaction between Cst-3 and extracellular matrix components has not been well studied. Here we investigated the interaction between Cst-3 and heparan sulfate (HS), a major component of extracellular matrix. We discovered that Cst-3 is a HS-binding protein only at