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  • Publisher Correction: Discovery of four Noggin genes in lampreys suggests two rounds of ancient genome duplication
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-21
    Galina V. Ermakova; Alexander V. Kucheryavyy; Andrey G. Zaraisky; Andrey V. Bayramov

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-09-21
  • Author Correction: The planctomycete Stieleria maiorica Mal15 T employs stieleriacines to alter the species composition in marine biofilms
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-21
    Nicolai Kallscheuer; Olga Jeske; Birthe Sandargo; Christian Boedeker; Sandra Wiegand; Pascal Bartling; Mareike Jogler; Manfred Rohde; Jörn Petersen; Marnix H. Medema; Frank Surup; Christian Jogler

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-09-21
  • Disassociated rhamphotheca of fossil bird Confuciusornis informs early beak reconstruction, stress regime, and developmental patterns
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-21
    Case Vincent Miller; Michael Pittman; Thomas G. Kaye; Xiaoli Wang; Jen A. Bright; Xiaoting Zheng

    Soft tissue preservation in fossil birds provides a rare window into their anatomy, function, and development. Here, we present an exceptionally-preserved specimen of Confuciusornis which, through Laser-Stimulated Fluorescence imaging, is identified as preserving a disassociated rhamphotheca. Reconstruction of the in vivo position of the rhamphotheca validates the association of the rhamphotheca with

    更新日期:2020-09-21
  • Connexin26 mediates CO 2 -dependent regulation of breathing via glial cells of the medulla oblongata
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-21
    Joseph van de Wiel; Louise Meigh; Amol Bhandare; Jonathan Cook; Sarbjit Nijjar; Robert Huckstepp; Nicholas Dale

    Breathing is highly sensitive to the PCO2 of arterial blood. Although CO2 is detected via the proxy of pH, CO2 acting directly via Cx26 may also contribute to the regulation of breathing. Here we exploit our knowledge of the structural motif of CO2-binding to Cx26 to devise a dominant negative subunit (Cx26DN) that removes the CO2-sensitivity from endogenously expressed wild type Cx26. Expression of

    更新日期:2020-09-21
  • Large male proboscis monkeys have larger noses but smaller canines
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-21
    Ikki Matsuda; Danica J. Stark; Diana A. Ramirez Saldivar; Augustine Tuuga; Senthilvel K. S. S. Nathan; Benoit Goossens; Carel P. van Schaik; Hiroki Koda

    The uniquely enlarged noses of male proboscis monkeys are prominent adornments, and a sexually selected male trait. A recent study showed significant correlations among nose, body, and testis sizes and clear associations between nose size and the number of females in a male’s harem. However, to date, the analyses of other common male traits, i.e., canines, are lacking. Whereas male nose size had a

    更新日期:2020-09-21
  • A multi-scale eco-evolutionary model of cooperation reveals how microbial adaptation influences soil decomposition
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-21
    Elsa Abs; Hélène Leman; Régis Ferrière

    The decomposition of soil organic matter (SOM) is a critical process in global terrestrial ecosystems. SOM decomposition is driven by micro-organisms that cooperate by secreting costly extracellular (exo-)enzymes. This raises a fundamental puzzle: the stability of microbial decomposition in spite of its evolutionary vulnerability to “cheaters”—mutant strains that reap the benefits of cooperation while

    更新日期:2020-09-21
  • Symbiotic fouling of Vetulicola , an early Cambrian nektonic animal
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-18
    Yujing Li; Mark Williams; Thomas H. P. Harvey; Fan Wei; Yang Zhao; Jin Guo; Sarah Gabbott; Tom Fletcher; Xianguang Hou; Peiyun Cong

    Here, we report the earliest fossil record to our knowledge of surface fouling by aggregates of small vermiform, encrusting and annulated tubular organisms associated with a mobile, nektonic host, the enigmatic Cambrian animal Vetulicola. Our material is from the exceptionally preserved early Cambrian (Epoch 2, Age 3), Chengjiang biota of Yunnan Province, southwest China, a circa 518 million-year old

    更新日期:2020-09-20
  • An IMiD-induced SALL4 degron system for selective degradation of target proteins
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-18
    Satoshi Yamanaka; Yuki Shoya; Saya Matsuoka; Hisayo Nishida-Fukuda; Norio Shibata; Tatsuya Sawasaki

    Regulating the amount of proteins in living cells is a powerful approach for understanding the functions of the proteins. Immunomodulatory drugs (IMiDs) induce the degradation of neosubstrates by interacting with celebron (CRBN) in the cullin E3 ubiquitin ligase complex (CRL4CRBN). Here, we developed the IMiD-dependent Sal-like protein 4 (SALL4) degron (S4D) system for chemical protein knockdown. In

    更新日期:2020-09-20
  • A dietary anthocyanin cyanidin-3- O -glucoside binds to PPARs to regulate glucose metabolism and insulin sensitivity in mice
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-18
    Yaoyao Jia; Chunyan Wu; Young-Suk Kim; Seung Ok Yang; Yeonji Kim; Ji-Sun Kim; Mi-Young Jeong; Ji Hae Lee; Bobae Kim; Soyoung Lee; Hyun-Seok Oh; Jia Kim; Min-Young So; Ye Eun Yoon; Trung Thanh Thach; Tai Hyun Park; Sung-Joon Lee

    We demonstrate the mechanism by which C3G, a major dietary anthocyanin, regulates energy metabolism and insulin sensitivity. Oral administration of C3G reduced hepatic and plasma triglyceride levels, adiposity, and improved glucose tolerance in mice fed high-fat diet. Hepatic metabolomic analysis revealed that C3G shifted metabolite profiles towards fatty acid oxidation and ketogenesis. C3G increased

    更新日期:2020-09-20
  • Flatfishes colonised freshwater environments by acquisition of various DHA biosynthetic pathways
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-18
    Yoshiyuki Matsushita; Kaho Miyoshi; Naoki Kabeya; Shuwa Sanada; Ryosuke Yazawa; Yutaka Haga; Shuichi Satoh; Yoji Yamamoto; Carlos Augusto Strüssmann; John Adam Luckenbach; Goro Yoshizaki

    The colonisation of freshwater environments by marine fishes has historically been considered a result of adaptation to low osmolality. However, most marine fishes cannot synthesise the physiologically indispensable fatty acid, docosahexaenoic acid (DHA), due to incomplete DHA biosynthetic pathways, which must be adapted to survive in freshwater environments where DHA is poor relative to marine environments

    更新日期:2020-09-20
  • Dengue virus dominates lipid metabolism modulations in Wolbachia -coinfected Aedes aegypti
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-18
    Cassandra Koh; M. Nurul Islam; Yixin H. Ye; Nunya Chotiwan; Barbara Graham; John T. Belisle; Konstantinos A. Kouremenos; Saravanan Dayalan; Dedreia L. Tull; Stephan Klatt; Rushika Perera; Elizabeth A. McGraw

    Competition between viruses and Wolbachia for host lipids is a proposed mechanism of Wolbachia-mediated virus blocking in insects. Yet, the metabolomic interaction between virus and symbiont within the mosquito has not been clearly defined. We compare the lipid profiles of Aedes aegypti mosquitoes bearing mono- or dual-infections of the Wolbachia wMel strain and dengue virus serotype 3 (DENV3). We

    更新日期:2020-09-20
  • A novel WD40-repeat protein involved in formation of epidermal bladder cells in the halophyte quinoa
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-17
    Tomohiro Imamura; Yasuo Yasui; Hironori Koga; Hiroki Takagi; Akira Abe; Kanako Nishizawa; Nobuyuki Mizuno; Shinya Ohki; Hiroharu Mizukoshi; Masashi Mori

    Halophytes are plants that grow in high-salt environments and form characteristic epidermal bladder cells (EBCs) that are important for saline tolerance. To date, however, little has been revealed about the formation of these structures. To determine the genetic basis for their formation, we applied ethylmethanesulfonate mutagenesis and obtained two mutants with reduced levels of EBCs (rebc) and abnormal

    更新日期:2020-09-18
  • Robust estimation of bacterial cell count from optical density
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-17
    Jacob Beal; Natalie G. Farny; Traci Haddock-Angelli; Vinoo Selvarajah; Geoff S. Baldwin; Russell Buckley-Taylor; Markus Gershater; Daisuke Kiga; John Marken; Vishal Sanchania; Abigail Sison; Christopher T. Workman

    Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains

    更新日期:2020-09-18
  • Sequence specificity analysis of the SETD2 protein lysine methyltransferase and discovery of a SETD2 super-substrate
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-16
    Maren Kirstin Schuhmacher; Serap Beldar; Mina S. Khella; Alexander Bröhm; Jan Ludwig; Wolfram Tempel; Sara Weirich; Jinrong Min; Albert Jeltsch

    SETD2 catalyzes methylation at lysine 36 of histone H3 and it has many disease connections. We investigated the substrate sequence specificity of SETD2 and identified nine additional peptide and one protein (FBN1) substrates. Our data showed that SETD2 strongly prefers amino acids different from those in the H3K36 sequence at several positions of its specificity profile. Based on this, we designed

    更新日期:2020-09-16
  • The reliability and heritability of cortical folds and their genetic correlations across hemispheres
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-15
    Fabrizio Pizzagalli; Guillaume Auzias; Qifan Yang; Samuel R. Mathias; Joshua Faskowitz; Joshua D. Boyd; Armand Amini; Denis Rivière; Katie L. McMahon; Greig I. de Zubicaray; Nicholas G. Martin; Jean-François Mangin; David C. Glahn; John Blangero; Margaret J. Wright; Paul M. Thompson; Peter Kochunov; Neda Jahanshad

    Cortical folds help drive the parcellation of the human cortex into functionally specific regions. Variations in the length, depth, width, and surface area of these sulcal landmarks have been associated with disease, and may be genetically mediated. Before estimating the heritability of sulcal variation, the extent to which these metrics can be reliably extracted from in-vivo MRI must be established

    更新日期:2020-09-15
  • The origin of Rhinocerotoidea and phylogeny of Ceratomorpha (Mammalia, Perissodactyla)
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-14
    Bin Bai; Jin Meng; Chi Zhang; Yan-Xin Gong; Yuan-Qing Wang

    Rhinoceroses have been considered to have originated from tapiroids in the middle Eocene; however, the transition remains controversial, and the first unequivocal rhinocerotoids appeared about 4 Ma later than the earliest tapiroids of the Early Eocene. Here we describe 5 genera and 6 new species of rhinoceroses recently discovered from the early Eocene to the early middle Eocene deposits of the Erlian

    更新日期:2020-09-14
  • Pre-pro is a fast pre-processor for single-particle cryo-EM by enhancing 2D classification
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-11
    Szu-Chi Chung; Hsin-Hung Lin; Po-Yao Niu; Shih-Hsin Huang; I-Ping Tu; Wei-Hau Chang

    2D classification plays a pivotal role in analyzing single particle cryo-electron microscopy images. Here, we introduce a simple and loss-less pre-processor that incorporates a fast dimension-reduction (2SDR) de-noiser to enhance 2D classification. By implementing this 2SDR pre-processor prior to a representative classification algorithm like RELION and ISAC, we compare the performances with and without

    更新日期:2020-09-11
  • A flavin-dependent monooxygenase catalyzes the initial step in cyanogenic glycoside synthesis in ferns
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-11
    Sara Thodberg; Mette Sørensen; Matteo Bellucci; Christoph Crocoll; Amalie Kofoed Bendtsen; David Ralph Nelson; Mohammed Saddik Motawia; Birger Lindberg Møller; Elizabeth Heather Jakobsen Neilson

    Cyanogenic glycosides form part of a binary plant defense system that, upon catabolism, detonates a toxic hydrogen cyanide bomb. In seed plants, the initial step of cyanogenic glycoside biosynthesis—the conversion of an amino acid to the corresponding aldoxime—is catalyzed by a cytochrome P450 from the CYP79 family. An evolutionary conundrum arises, as no CYP79s have been identified in ferns, despite

    更新日期:2020-09-11
  • Analysis of single-cell transcriptomes links enrichment of olfactory receptors with cancer cell differentiation status and prognosis
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-11
    Siddhant Kalra; Aayushi Mittal; Krishan Gupta; Vrinda Singhal; Anku Gupta; Tripti Mishra; Srivatsava Naidu; Debarka Sengupta; Gaurav Ahuja

    Ectopically expressed olfactory receptors (ORs) have been linked with multiple clinically-relevant physiological processes. Previously used tissue-level expression estimation largely shadowed the potential role of ORs due to their overall low expression levels. Even after the introduction of the single-cell transcriptomics, a comprehensive delineation of expression dynamics of ORs in tumors remained

    更新日期:2020-09-11
  • An algorithm to quantify intratumor heterogeneity based on alterations of gene expression profiles
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-11
    Mengyuan Li; Zhilan Zhang; Lin Li; Xiaosheng Wang

    Intratumor heterogeneity (ITH) is a biomarker of tumor progression, metastasis, and immune evasion. Previous studies evaluated ITH mostly based on DNA alterations. Here, we developed a new algorithm (DEPTH) for quantifying ITH based on mRNA alterations in the tumor. DEPTH scores displayed significant correlations with ITH-associated features (genomic instability, tumor advancement, unfavorable prognosis

    更新日期:2020-09-11
  • Discovery of four Noggin genes in lampreys suggests two rounds of ancient genome duplication
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-10
    Galina V. Ermakova; Alexander V. Kucheryavyy; Andrey G. Zaraisky; Andrey V. Bayramov

    The secreted protein Noggin1 was the first discovered natural embryonic inducer produced by cells of the Spemann organizer. Thereafter, it was shown that vertebrates have a whole family of Noggin genes with different expression patterns and functional properties. For example, Noggin1 and Noggin2 inhibit the activity of BMP, Nodal/Activin and Wnt-beta-catenin signalling, while Noggin4 cannot suppress

    更新日期:2020-09-10
  • A neoceratopsian dinosaur from the early Cretaceous of Mongolia and the early evolution of ceratopsia
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-10
    Congyu Yu; Albert Prieto-Marquez; Tsogtbaatar Chinzorig; Zorigt Badamkhatan; Mark Norell

    Ceratopsia is a diverse dinosaur clade from the Middle Jurassic to Late Cretaceous with early diversification in East Asia. However, the phylogeny of basal ceratopsians remains unclear. Here we report a new basal neoceratopsian dinosaur Beg tse based on a partial skull from Baruunbayan, Ömnögovi aimag, Mongolia. Beg is diagnosed by a unique combination of primitive and derived characters including

    更新日期:2020-09-10
  • Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-10
    Lulu Wang; Yi Li; Xingyue Jin; Liping Liu; Xiaozhuan Dai; Yanhui Liu; Lihua Zhao; Ping Zheng; Xiaomei Wang; Yeqiang Liu; Deshu Lin; Yuan Qin

    Proper flower development is essential for sexual reproductive success and the setting of fruits and seeds. The availability of a high quality genome sequence for pineapple makes it an excellent model for studying fruit and floral organ development. In this study, we sequenced 27 different pineapple floral samples and integrated nine published RNA-seq datasets to generate tissue- and stage-specific

    更新日期:2020-09-10
  • A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-10
    Yuhua Fu; Jingya Xu; Zhenshuang Tang; Lu Wang; Dong Yin; Yu Fan; Dongdong Zhang; Fei Deng; Yanping Zhang; Haohao Zhang; Haiyan Wang; Wenhui Xing; Lilin Yin; Shilin Zhu; Mengjin Zhu; Mei Yu; Xinyun Li; Xiaolei Liu; Xiaohui Yuan; Shuhong Zhao

    The analyses of multi-omics data have revealed candidate genes for objective traits. However, they are integrated poorly, especially in non-model organisms, and they pose a great challenge for prioritizing candidate genes for follow-up experimental verification. Here, we present a general convolutional neural network model that integrates multi-omics information to prioritize the candidate genes of

    更新日期:2020-09-10
  • Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-09
    Linda J. Olson; Sandeep K. Misra; Mayumi Ishihara; Kevin P. Battaile; Oliver C. Grant; Amika Sood; Robert J. Woods; Jung-Ja P. Kim; Michael Tiemeyer; Gang Ren; Joshua S. Sharp; Nancy M. Dahms

    The cation-independent mannose 6-phosphate receptor (CI-MPR, IGF2 receptor or CD222), is a multifunctional glycoprotein required for normal development. Through the receptor’s ability to bind unrelated extracellular and intracellular ligands, it participates in numerous functions including protein trafficking, lysosomal biogenesis, and regulation of cell growth. Clinically, endogenous CI-MPR delivers

    更新日期:2020-09-10
  • Nrf2 contributes to the weight gain of mice during space travel
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-08
    Takafumi Suzuki; Akira Uruno; Akane Yumoto; Keiko Taguchi; Mikiko Suzuki; Nobuhiko Harada; Rie Ryoke; Eriko Naganuma; Nanae Osanai; Aya Goto; Hiromi Suda; Ryan Browne; Akihito Otsuki; Fumiki Katsuoka; Michael Zorzi; Takahiro Yamazaki; Daisuke Saigusa; Seizo Koshiba; Takashi Nakamura; Satoshi Fukumoto; Hironobu Ikehata; Keizo Nishikawa; Norio Suzuki; Ikuo Hirano; Ritsuko Shimizu; Tetsuya Oishi; Hozumi

    Space flight produces an extreme environment with unique stressors, but little is known about how our body responds to these stresses. While there are many intractable limitations for in-flight space research, some can be overcome by utilizing gene knockout-disease model mice. Here, we report how deletion of Nrf2, a master regulator of stress defense pathways, affects the health of mice transported

    更新日期:2020-09-08
  • L -Arginine prevents cereblon-mediated ubiquitination of glucokinase and stimulates glucose-6-phosphate production in pancreatic β-cells
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-08
    Jaeyong Cho; Yukio Horikawa; Mayumi Enya; Jun Takeda; Yoichi Imai; Yumi Imai; Hiroshi Handa; Takeshi Imai

    We sought to determine a mechanism by which L-arginine increases glucose-stimulated insulin secretion (GSIS) in β-cells by finding a protein with affinity to L-arginine using arginine-immobilized magnetic nanobeads technology. Glucokinase (GCK), the key regulator of GSIS and a disease-causing gene of maturity-onset diabetes of the young type 2 (MODY2), was found to bind L-arginine. L-Arginine stimulated

    更新日期:2020-09-08
  • Author Correction: Single-cell analysis of EphA clustering phenotypes to probe cancer cell heterogeneity
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-07
    Andrea Ravasio; Myint Z. Myaing; Shumei Chia; Aditya Arora; Aneesh Sathe; Elaine Yiqun Cao; Cristina Bertocchi; Ankur Sharma; Bakya Arasi; Vin Yee Chung; Adrianne C. Green; Tuan Zea Tan; Zhongwen Chen; Hui Ting Ong; N. Gopalakrishna Iyer; Ruby YunJu Huang; Ramanuj DasGupta; Jay T. Groves; Virgile Viasnoff

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-09-08
  • A miniaturization event in Ornithodira
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-07
    Luke R. Grinham

    The origins of Ornithodira (the last common ancestor of dinosaurs, pterosaurs, and their descendants) are yet to be resolved, and have the potential to inform on the diversification of some of the most intriguing ecologies and body forms to evolve in reptiles. A recent discovery of an extremely small ornithodiran archosaur by Christian Kammerer and colleagues is indicative of a miniaturisation event

    更新日期:2020-09-08
  • Intracellular ATP levels in mouse cortical excitatory neurons varies with sleep–wake states
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-07
    Akiyo Natsubori; Tomomi Tsunematsu; Akihiro Karashima; Hiromi Imamura; Naoya Kabe; Andrea Trevisiol; Johannes Hirrlinger; Tohru Kodama; Tomomi Sanagi; Kazuto Masamoto; Norio Takata; Klaus-Armin Nave; Ko Matsui; Kenji F. Tanaka; Makoto Honda

    Whilst the brain is assumed to exert homeostatic functions to keep the cellular energy status constant under physiological conditions, this has not been experimentally proven. Here, we conducted in vivo optical recordings of intracellular concentration of adenosine 5’-triphosphate (ATP), the major cellular energy metabolite, using a genetically encoded sensor in the mouse brain. We demonstrate that

    更新日期:2020-09-08
  • Stirred suspension bioreactors maintain naïve pluripotency of human pluripotent stem cells
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-07
    Leili Rohani; Breanna S. Borys; Golsa Razian; Pooyan Naghsh; Shiying Liu; Adiv A. Johnson; Pranav Machiraju; Heidrun Holland; Ian A. Lewis; Ryan A. Groves; Derek Toms; Paul M. K. Gordon; Joyce W. Li; Tania So; Tiffany Dang; Michael S. Kallos; Derrick E. Rancourt

    Due to their ability to standardize key physiological parameters, stirred suspension bioreactors can potentially scale the production of quality-controlled pluripotent stem cells (PSCs) for cell therapy application. Because of differences in bioreactor expansion efficiency between mouse (m) and human (h) PSCs, we investigated if conversion of hPSCs, from the conventional “primed” pluripotent state

    更新日期:2020-09-08
  • Photooxidative stress-inducible orange and pink water-soluble astaxanthin-binding proteins in eukaryotic microalga
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-07
    Shinji Kawasaki; Keita Yamazaki; Tohya Nishikata; Taichiro Ishige; Hiroki Toyoshima; Ami Miyata

    Lipid astaxanthin, a potent antioxidant known as a natural sunscreen, accumulates in eukaryotic microalgae and confers photoprotection. We previously identified a photooxidative stress-inducible water-soluble astaxanthin-binding carotenoprotein (AstaP) in a eukaryotic microalga (Coelastrella astaxanthina Ki-4) isolated from an extreme environment. The distribution in eukaryotic microalgae remains unknown

    更新日期:2020-09-08
  • Role of C 4 carbon fixation in Ulva prolifera , the macroalga responsible for the world’s largest green tides
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-07
    Dongyan Liu; Qian Ma; Ivan Valiela; Donald M. Anderson; John K. Keesing; Kunshan Gao; Yu Zhen; Xiyan Sun; Yujue Wang

    Most marine algae preferentially assimilate CO2 via the Calvin-Benson Cycle (C3) and catalyze HCO3− dehydration via carbonic anhydrase (CA) as a CO2-compensatory mechanism, but certain species utilize the Hatch-Slack Cycle (C4) to enhance photosynthesis. The occurrence and importance of the C4 pathway remains uncertain, however. Here, we demonstrate that carbon fixation in Ulva prolifera, a species

    更新日期:2020-09-08
  • Context dependent effects of ascorbic acid treatment in TET2 mutant myeloid neoplasia
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-07
    Yihong Guan; Edward F. Greenberg; Metis Hasipek; Shi Chen; Xiaochen Liu; Cassandra M. Kerr; Daniel Gackowski; Ewelina Zarakowska; Tomas Radivoyevitch; Xiaorong Gu; Belinda Willard; Valeria Visconte; Hideki Makishima; Aziz Nazha; Mridul Mukherji; Mikkael A. Sekeres; Yogen Saunthararajah; Ryszard Oliński; Mingjiang Xu; Jaroslaw P. Maciejewski; Babal K. Jha

    Loss-of-function TET2 mutations (TET2MT) are common in myeloid neoplasia. TET2, a DNA dioxygenase, requires 2-oxoglutarate and Fe(II) to oxidize 5-methylcytosine. TET2MT thus result in hypermethylation and transcriptional repression. Ascorbic acid (AA) increases dioxygenase activity by facilitating Fe(III)/Fe(II) redox reaction and may alleviate some biological consequences of TET2MT by restoring dioxygenase

    更新日期:2020-09-08
  • Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-07
    Kimberly R. Andrews; Alida Gerritsen; Arash Rashed; David W. Crowder; Silvia I. Rondon; Willem G. van Herk; Robert Vernon; Kevin W. Wanner; Cathy M. Wilson; Daniel D. New; Matthew W. Fagnan; Paul A. Hohenlohe; Samuel S. Hunter

    The larvae of click beetles (Coleoptera: Elateridae), known as “wireworms,” are agricultural pests that pose a substantial economic threat worldwide. We produced one of the first wireworm genome assemblies (Limonius californicus), and investigated population structure and phylogenetic relationships of three species (L. californicus, L. infuscatus, L. canus) across the northwest US and southwest Canada

    更新日期:2020-09-08
  • Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-04
    Hisashi Naitow,Tasuku Hamaguchi,Saori Maki-Yonekura,Masamichi Isogai,Nobuyuki Yoshikawa,Koji Yonekura

    Picorna-like plant viruses are non-enveloped RNA spherical viruses of ~30 nm. Part of the survival of these viruses depends on their capsid being stable enough to harbour the viral genome and yet malleable enough to allow its release. However, molecular mechanisms remain obscure. Here, we report a structure of a picorna-like plant virus, apple latent spherical virus, at 2.87 Å resolution by single-particle

    更新日期:2020-09-05
  • A normative modelling approach reveals age-atypical cortical thickness in a subgroup of males with autism spectrum disorder.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-04
    Richard A I Bethlehem,Jakob Seidlitz,Rafael Romero-Garcia,Stavros Trakoshis,Guillaume Dumas,Michael V Lombardo

    Understanding heterogeneity is an important goal on the path to precision medicine for autism spectrum disorders (ASD). We examined how cortical thickness (CT) in ASD can be parameterized as an individualized metric of atypicality relative to typically-developing (TD) age-related norms. Across a large sample (n = 870 per group) and wide age range (5–40 years), we applied normative modelling resulting

    更新日期:2020-09-05
  • Progesterone receptor membrane associated component 1 enhances obesity progression in mice by facilitating lipid accumulation in adipocytes.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-04
    Ryogo Furuhata,Yasuaki Kabe,Ayaka Kanai,Yuki Sugiura,Hitoshi Tsugawa,Eiji Sugiyama,Miwa Hirai,Takehiro Yamamoto,Ikko Koike,Noritada Yoshikawa,Hirotoshi Tanaka,Masahiro Koseki,Jun Nakae,Morio Matsumoto,Masaya Nakamura,Makoto Suematsu

    Progesterone receptor membrane associated component 1 (PGRMC1) exhibits haem-dependent dimerization on cell membrane and binds to EGF receptor and cytochromes P450 to regulate cancer proliferation and chemoresistance. However, its physiological functions remain unknown. Herein, we demonstrate that PGRMC1 is required for adipogenesis, and its expression is significantly enhanced by insulin or thiazolidine

    更新日期:2020-09-05
  • Genome sequence of segmented filamentous bacteria present in the human intestine.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-04
    Hans Jonsson,Luisa W Hugerth,John Sundh,Eva Lundin,Anders F Andersson

    Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host’s intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific

    更新日期:2020-09-05
  • Publisher Correction: Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-03
    Amber N Habowski,Jessica L Flesher,Jennifer M Bates,Chia-Feng Tsai,Kendall Martin,Rui Zhao,Anand K Ganesan,Robert A Edwards,Tujin Shi,H Steven Wiley,Yongsheng Shi,Klemens J Hertel,Marian L Waterman

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-09-03
  • Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-03
    Isobel C Stanton,Aimee K Murray,Lihong Zhang,Jason Snape,William H Gaze

    Determining the selective potential of antibiotics at environmental concentrations is critical for designing effective strategies to limit selection for antibiotic resistance. This study determined the minimal selective concentrations (MSCs) for macrolide and fluoroquinolone antibiotics included on the European Commissionʼs Water Framework Directive’s priority hazardous substances Watch List. The macrolides

    更新日期:2020-09-03
  • Structural basis of redox modulation on chloroplast ATP synthase.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-02
    Jay-How Yang,Dewight Williams,Eaazhisai Kandiah,Petra Fromme,Po-Lin Chiu

    In higher plants, chloroplast ATP synthase has a unique redox switch on its γ subunit that modulates enzyme activity to limit ATP hydrolysis at night. To understand the molecular details of the redox modulation, we used single-particle cryo-EM to determine the structures of spinach chloroplast ATP synthase in both reduced and oxidized states. The disulfide linkage of the oxidized γ subunit introduces

    更新日期:2020-09-02
  • Oxidation of fish oil exacerbates alcoholic liver disease by enhancing intestinal dysbiosis in mice.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-02
    Ruibing Feng,Li-Juan Ma,Meng Wang,Conghui Liu,Rujie Yang,Huanxing Su,Yan Yang,Jian-Bo Wan

    The role of n-3 polyunsaturated fatty acids (PUFAs) in alcoholic liver disease (ALD) has been controversial. N-3 PUFA oxidation in animal feeding stuffs was rarely concerned, likely contributing to inconsistent outcomes. Here, we report the impacts of oxidized fish oil (OFO) on ALD in C57BL/6 mice. Alcohol exposure increased plasma aminotransferase levels and hepatic inflammation. These deleterious

    更新日期:2020-09-02
  • Tryptophan-galactosylamine conjugates inhibit and disaggregate amyloid fibrils of Aβ42 and hIAPP peptides while reducing their toxicity.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-02
    Ashim Paul,Moran Frenkel-Pinter,Daniela Escobar Alvarez,Giulia Milordini,Ehud Gazit,Elsa Zacco,Daniel Segal

    Self-assembly of proteins into amyloid fibrils is a hallmark of various diseases, including Alzheimer’s disease (AD) and Type-2 diabetes Mellitus (T2DM). Aggregation of specific peptides, like Aβ42 in AD and hIAPP in T2DM, causes cellular dysfunction resulting in the respective pathology. While these amyloidogenic proteins lack sequence homology, they all contain aromatic amino acids in their hydrophobic

    更新日期:2020-09-02
  • Reg4 and complement factor D prevent the overgrowth of E. coli in the mouse gut.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-02
    Houbao Qi,Jianmei Wei,Yunhuan Gao,Yazheng Yang,Yuanyuan Li,Hua Zhu,Lei Su,Xiaomin Su,Yuan Zhang,Rongcun Yang

    The expansion of Enterobacteriaceae, such as E. coli is a main characteristic of gut inflammation and is related to multiple human diseases. However, how to control these E. coli overgrowth is not well understood. Here, we demonstrate that gut complement factor D (CFD) plays an important role in eliminating E. coli. Increased E. coli, which could stimulate inflammatory macrophages to induce colitis

    更新日期:2020-09-02
  • Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution.
    Commun. Biol. (IF 4.165) Pub Date : 2020-09-01
    Austin B Mudd,Jessen V Bredeson,Rachel Baum,Dirk Hockemeyer,Daniel S Rokhsar

    Closely related muntjac deer show striking karyotype differences. Here we describe chromosome-scale genome assemblies for Chinese and Indian muntjacs, Muntiacus reevesi (2n = 46) and Muntiacus muntjak vaginalis (2n = 6/7), and analyze their evolution and architecture. The genomes show extensive collinearity with each other and with other deer and cattle. We identified numerous fusion events unique

    更新日期:2020-09-01
  • Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-31
    Nicolai Kallscheuer,Olga Jeske,Birthe Sandargo,Christian Boedeker,Sandra Wiegand,Pascal Bartling,Mareike Jogler,Manfred Rohde,Jörn Petersen,Marnix H Medema,Frank Surup,Christian Jogler

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-08-31
  • Coordinated regulation of Rel expression by MAP3K4, CBP, and HDAC6 controls phenotypic switching.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-28
    Noha Ahmed Mohammed Shendy,Deepthi Raghu,Sujoy Roy,Charles Hamilton Perry,Adiba Safi,Miguel Ramos Branco,Ramin Homayouni,Amy Noel Abell

    Coordinated gene expression is required for phenotypic switching between epithelial and mesenchymal phenotypes during normal development and in disease states. Trophoblast stem (TS) cells undergo epithelial-mesenchymal transition (EMT) during implantation and placentation. Mechanisms coordinating gene expression during these processes are poorly understood. We have previously demonstrated that MAP3K4-regulated

    更新日期:2020-08-28
  • Diversity in the intrinsic apoptosis pathway of nematodes.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-28
    Neil D Young,Tiffany J Harris,Marco Evangelista,Sharon Tran,Merridee A Wouters,Tatiana P Soares da Costa,Nadia J Kershaw,Robin B Gasser,Brian J Smith,Erinna F Lee,W Douglas Fairlie

    Early studies of the free-living nematode C. elegans informed us how BCL-2-regulated apoptosis in humans is regulated. However, subsequent studies showed C. elegans apoptosis has several unique features compared with human apoptosis. To date, there has been no detailed analysis of apoptosis regulators in nematodes other than C. elegans. Here, we discovered BCL-2 orthologues in 89 free-living and parasitic

    更新日期:2020-08-28
  • Phenome-wide analyses establish a specific association between aortic valve PALMD expression and calcific aortic valve stenosis.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-28
    Zhonglin Li,Nathalie Gaudreault,Benoit J Arsenault,Patrick Mathieu,Yohan Bossé,Sébastien Thériault

    Calcific aortic valve stenosis (CAVS) is a frequent heart disease with significant morbidity and mortality. Recent genomic studies have identified a locus near the gene PALMD (palmdelphin) strongly associated with CAVS. Here, we show that genetically-determined expression of PALMD in the aortic valve is inversely associated with CAVS, with a stronger effect in women, in a meta-analysis of two large

    更新日期:2020-08-28
  • Multiple ancestral haplotypes harboring regulatory mutations cumulatively contribute to a QTL affecting chicken growth traits.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-28
    Yuzhe Wang,Xuemin Cao,Chenglong Luo,Zheya Sheng,Chunyuan Zhang,Cheng Bian,Chungang Feng,Jinxiu Li,Fei Gao,Yiqiang Zhao,Ziqin Jiang,Hao Qu,Dingming Shu,Örjan Carlborg,Xiaoxiang Hu,Ning Li

    In depth studies of quantitative trait loci (QTL) can provide insights to the genetic architectures of complex traits. A major effect QTL at the distal end of chicken chromosome 1 has been associated with growth traits in multiple populations. This locus was fine-mapped in a fifteen-generation chicken advanced intercross population including 1119 birds and explored in further detail using 222 sequenced

    更新日期:2020-08-28
  • Loss of β-cell identity and diabetic phenotype in mice caused by disruption of CNOT3-dependent mRNA deadenylation.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-28
    Dina Mostafa,Akiko Yanagiya,Eleni Georgiadou,Yibo Wu,Theodoros Stylianides,Guy A Rutter,Toru Suzuki,Tadashi Yamamoto

    Pancreatic β-cells are responsible for production and secretion of insulin in response to increasing blood glucose levels. Defects in β-cell function lead to hyperglycemia and diabetes mellitus. Here, we show that CNOT3, a CCR4–NOT deadenylase complex subunit, is dysregulated in islets in diabetic db/db mice, and that it is essential for murine β cell maturation and identity. Mice with β cell-specific

    更新日期:2020-08-28
  • Maternal dietary imbalance between omega-6 and omega-3 fatty acids triggers the offspring's overeating in mice.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-28
    Nobuyuki Sakayori,Masanori Katakura,Kei Hamazaki,Oki Higuchi,Kazuki Fujii,Ryoji Fukabori,Yoshio Iguchi,Susumu Setogawa,Keizo Takao,Teruo Miyazawa,Makoto Arita,Kazuto Kobayashi

    The increasing prevalence of obesity and its effects on our society warrant intensifying basic animal research for understanding why habitual intake of highly palatable foods has increased due to recent global environmental changes. Here, we report that pregnant mice that consume a diet high in omega-6 (n-6) polyunsaturated fatty acids (PUFAs) and low in omega-3 (n-3) PUFAs (an n-6high/n-3low diet)

    更新日期:2020-08-28
  • The archives are half-empty: an assessment of the availability of microbial community sequencing data.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-28
    Stephanie D Jurburg,Maximilian Konzack,Nico Eisenhauer,Anna Heintz-Buschart

    As DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories

    更新日期:2020-08-28
  • A spatial regime shift from predator to prey dominance in a large coastal ecosystem.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-27
    Johan S Eklöf,Göran Sundblad,Mårten Erlandsson,Serena Donadi,Joakim P Hansen,Britas Klemens Eriksson,Ulf Bergström

    Regime shifts in ecosystem structure and processes are typically studied from a temporal perspective. Yet, theory predicts that in large ecosystems with environmental gradients, shifts should start locally and gradually spread through space. Here we empirically document a spatially propagating shift in the trophic structure of a large aquatic ecosystem, from dominance of large predatory fish (perch

    更新日期:2020-08-28
  • Evidence of torpor in the tusks of Lystrosaurus from the Early Triassic of Antarctica.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-27
    Megan R Whitney,Christian A Sidor

    Antarctica has hosted a wide range of ecosystems over the past 500-million years. Early in the Mesozoic, the Antarctic portion of southern Pangaea had a more habitable climate, but its position within the polar circle imposed extreme photoperiod seasonality on its resident flora and fauna. It remains unclear to what degree physiological adaptations underpinned the ability of tetrapods to establish

    更新日期:2020-08-27
  • Molecular mechanism of mitochondrial phosphatidate transfer by Ups1.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-25
    Jiuwei Lu,Chun Chan,Leiye Yu,Jun Fan,Fei Sun,Yujia Zhai

    Cardiolipin, an essential mitochondrial physiological regulator, is synthesized from phosphatidic acid (PA) in the inner mitochondrial membrane (IMM). PA is synthesized in the endoplasmic reticulum and transferred to the IMM via the outer mitochondrial membrane (OMM) under mediation by the Ups1/Mdm35 protein family. Despite the availability of numerous crystal structures, the detailed mechanism underlying

    更新日期:2020-08-25
  • Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-25
    Takashi Gakuhari,Shigeki Nakagome,Simon Rasmussen,Morten E Allentoft,Takehiro Sato,Thorfinn Korneliussen,Blánaid Ní Chuinneagáin,Hiromi Matsumae,Kae Koganebuchi,Ryan Schmidt,Souichiro Mizushima,Osamu Kondo,Nobuo Shigehara,Minoru Yoneda,Ryosuke Kimura,Hajime Ishida,Tadayuki Masuyama,Yasuhiro Yamada,Atsushi Tajima,Hiroki Shibata,Atsushi Toyoda,Toshiyuki Tsurumoto,Tetsuaki Wakebe,Hiromi Shitara,Tsunehiko

    Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002)

    更新日期:2020-08-25
  • Author Correction: Force-exerting perpendicular lateral protrusions in fibroblastic cell contraction.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-21
    Abinash Padhi,Karanpreet Singh,Janusz Franco-Barraza,Daniel J Marston,Edna Cukierman,Klaus M Hahn,Rakesh K Kapania,Amrinder S Nain

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-08-21
  • Thinking multi-scale to advance mechanobiology.
    Commun. Biol. (IF 4.165) Pub Date : 2020-08-21
    Marco Fritzsche

    We are inviting submissions of articles on the role of mechanobiology in health and disease with the aim of publishing high quality research devoted to advance our understanding of mechanics shaping biological function. We are also happy to present a Collection of papers already published in our journal in this exciting field.

    更新日期:2020-08-21