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JOURNAL ARTICLE
Joost A Stalpers, Scott A Redhead, Tom W May, Amy Y Rossman, Jo Anne Crouch, Marc A Cubeta, Yu-Cheng Dai, Roland Kirschner, Gitta Jutta Langer, Karl-Henrik Larsson, Jonathan Mack, Lorelei L Norvell, Franz Oberwinkler, Viktor Papp, Peter Roberts, Mario Rajchenberg, Keith A Seifert, R Greg Thorn
With the change to one scientific name for fungal taxa, generic names typified by species with sexual or asexual morph types are being evaluated to determine which names represent the same genus and thus compete for use. In this paper generic names of the Agaricomycotina (Basidiomycota) were evaluated to determine synonymy based on their type. Forty-seven sets of sexually and asexually typified names were determined to be congeneric and recommendations are made for which generic name to use. In most cases the principle of priority is followed...
August 11, 2021: IMA Fungus
#22
JOURNAL ARTICLE
John R Prensner, Oana M Enache, Victor Luria, Karsten Krug, Karl R Clauser, Joshua M Dempster, Amir Karger, Li Wang, Karolina Stumbraite, Vickie M Wang, Ginevra Botta, Nicholas J Lyons, Amy Goodale, Zohra Kalani, Briana Fritchman, Adam Brown, Douglas Alan, Thomas Green, Xiaoping Yang, Jacob D Jaffe, Jennifer A Roth, Federica Piccioni, Marc W Kirschner, Zhe Ji, David E Root, Todd R Golub
Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candidates selected from noncanonical ORF datasets. Of these, 57 induced viability defects when knocked out in human cancer cell lines. Following ectopic expression, 257 showed evidence of protein expression and 401 induced gene expression changes. Clustered regularly interspaced short palindromic repeat (CRISPR) tiling and start codon mutagenesis indicated that their biological effects required translation as opposed to RNA-mediated effects...
January 28, 2021: Nature Biotechnology
#23
JOURNAL ARTICLE
What makes the cell cycle tick? a celebration of the awesome power of biochemistry and the frog egg.
Marc Kirschner
The cell cycle, a 19th century discovery of cytologists, only achieved a satisfactory biochemical explanation in the last 20 years of the 20th century. This personal retrospective focuses on how biochemical studies of the frog egg helped identify the cyclin-based mitotic oscillator and how this approach quickly merged with genetic studies in yeast to establish the basic mechanism of the eukaryotic cell division cycle. The key feature that made this a cyclic process was regulated protein degradation, mediated by ubiquitin, catalyzed by a massive enzyme machine, called the Anaphase Promoting Complex...
December 15, 2020: Molecular Biology of the Cell
#24
JOURNAL ARTICLE
Nathaniel Fogel, Lauren M Shapiro, Allison Roe, Sahitya Denduluri, Marc J Richard, Robin N Kamal
BACKGROUND: Intra-articular distal radius fractures with small volar lunate facet fragments can be challenging to address with volar plate fixation alone. Volar locked plating with supplementary spring wire fixation has been previously described in a small series but has not been further described in the literature. We hypothesized that this technique can provide adequate fixation for volar lunate facet fragments smaller than 15 mm in length, which are at risk of displacement. METHODS: We completed a retrospective chart review (2015-2019) of patients who underwent volar locked plating with the addition of supplementary spring wire fixation for intra-articular distal radius fractures with a volar lunate facet fragment (<15 mm)...
December 15, 2020: Hand: Official Journal of the American Association for Hand Surgery
#25
JOURNAL ARTICLE
Xili Liu, Seungeun Oh, Leonid Peshkin, Marc W Kirschner
The fine balance of growth and division is a fundamental property of the physiology of cells, and one of the least understood. Its study has been thwarted by difficulties in the accurate measurement of cell size and the even greater challenges of measuring growth of a single cell over time. We address these limitations by demonstrating a computationally enhanced methodology for quantitative phase microscopy for adherent cells, using improved image processing algorithms and automated cell-tracking software. Accuracy has been improved more than twofold and this improvement is sufficient to establish the dynamics of cell growth and adherence to simple growth laws...
October 21, 2020: Proceedings of the National Academy of Sciences of the United States of America
#26
JOURNAL ARTICLE
Søren Brunak, Catherine Bjerre Collin, Katharina Eva Ó Cathaoir, Martin Golebiewski, Marc Kirschner, Ingrid Kockum, Heike Moser, Dagmar Waltemath
Despite the ever-progressing technological advances in producing data in health and clinical research, the generation of new knowledge for medical benefits through advanced analytics still lags behind its full potential. Reasons for this obstacle are the inherent heterogeneity of data sources and the lack of broadly accepted standards. Further hurdles are associated with legal and ethical issues surrounding the use of personal/patient data across disciplines and borders. Consequently, there is a need for broadly applicable standards compliant with legal and ethical regulations that allow interpretation of heterogeneous health data through in silico methodologies to advance personalized medicine...
July 24, 2020: Journal of Integrative Bioinformatics
#27
JOURNAL ARTICLE
Wenzhe Ma, Maorong Chen, Hong Kang, Zachary Steinhart, Stephane Angers, Xi He, Marc W Kirschner
Dvl (Dishevelled) is one of several essential nonenzymatic components of the Wnt signaling pathway. In most current models, Dvl forms complexes with Wnt ligand receptors, Fzd and LRP5/6 at the plasma membrane, which then recruits the destruction complex, eventually leading to inactivation of β-catenin degradation. Although this model is widespread, direct evidence for the individual steps is lacking. In this study, we tagged mEGFP to C terminus of dishevelled2 gene using CRISPR/Cas9-induced homologous recombination and observed its dynamics directly at the single-molecule level with total internal reflection fluorescence (TIRF) microscopy...
July 14, 2020: Proceedings of the National Academy of Sciences of the United States of America
#28
REVIEW
Leonid Peshkin, Marc W Kirschner
Cell Atlases are currently being constructed for human tissues as well as several model organisms. New technologies make creation of vast datasets in many species possible, but the value of such data crucially depends on the quality of annotation. The tools of annotating single cell data and creating knowledge representations comparable across organisms have been lagging. We argue that successfully creating Cell Atlases will require a revival of a boot-camp style forum for communal annotation combined with an intensive learning workshop, dubbed a "Jamboree"...
June 25, 2020: Genesis: the Journal of Genetics and Development
#29
JOURNAL ARTICLE
Joaquim Radua, Eduard Vieta, Russell Shinohara, Peter Kochunov, Yann Quidé, Melissa Green, Cynthia Weickert, Thomas Weickert, Jason Bruggemann, Tilo Kircher, Igor Nenadic, Murray Cairns, Marc Seal, Ulrich Schall, Frans Henskens, Janice Fullerton, Bryan Mowry, Christos Pantelis, Rhoshel Lenroot, Vanessa Cropley, Carmel Loughland, Rodney Scott, Daniel Wolf, Theodore Satterthwaite, Yunlong Tan, Kang Sim, Fabrizio Piras, Gianfranco Spalletta, Nerisa Banaj, Edith Pomarol-Clotet, Aleix Solanes, Anton Albajes-Eizagirre, Erick Canales-Rodriguez, Salvador Sarro, Annabella Di Giorgio, Alessandro Bertolino, Michael Stäblein, Viola Oertel, Christian Knöchel, Stefan Borgwardt, Stefan du Plessis, Je-Yeon Yun, Jun Soo Kwon, Udo Dannlowski, Tim Hahn, Dominik Grotegerd, Clara Alloza, Celso Arango, Joost Janssen, Covadonga Díaz-Caneja, Wenhao Jiang, Vince Calhoun, Stefan Ehrlich, Kun Yang, Nicola Cascella, Yoichiro Takayanagi, Akira Sawa, Alexander Tomyshev, Irina Lebedeva, Vasily Kaleda, Matthias Kirschner, Cyril Hoschl, David Tomecek, Antonin Skoch, Therese van Amelsvoort, Geor Bakker, Anthony James, Adrian Preda, Andrea Weideman, Dan Stein, Fleur Howells, Anne Uhlmann, Henk Temmingh, Carlos López-Jaramillo, Ana Díaz-Zuluaga, Lydia Fortea, Eloy Martinez-Heras, Elisabeth Solana, Sara Llufriu
A common limitation of neuroimaging studies is their small sample sizes. To overcome this hurdle, the Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) Consortium combines neuroimaging data from many institutions worldwide. However, this introduces heterogeneity due to different scanning devices and sequences. ENIGMA projects commonly address this heterogeneity with random-effects meta-analysis or mixed-effects mega-analysis. Here we tested whether the batch adjustment method, ComBat, can further reduce site-related heterogeneity and thus increase statistical power...
May 26, 2020: NeuroImage
#30
JOURNAL ARTICLE
Igor Cesarino, Raffaele Dello Ioio, Gwendolyn K Kirschner, Michael S Ogden, Kelsey L Picard, Madlen I Rast-Somssich, Marc Somssich
BACKGROUND: Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established...
April 9, 2020: Annals of Botany
#31
JOURNAL ARTICLE
Xijuan Liu, Jeremy M Simon, Haibiao Xie, Lianxin Hu, Jun Wang, Giada Zurlo, Cheng Fan, Travis S Ptacek, Laura Herring, Xianming Tan, Mingjie Li, Albert S Baldwin, William Y Kim, Tao Wu, Marc W Kirschner, Kan Gong, Qing Zhang
von Hippel-Lindau (VHL) is a critical tumor suppressor in clear cell renal cell carcinomas (ccRCCs). It is important to identify additional therapeutic targets in ccRCC downstream of VHL loss besides hypoxia-inducible factor 2α (HIF2α). By performing a genome-wide screen, we identified Scm-like with four malignant brain tumor domains 1 (SFMBT1) as a candidate pVHL target. SFMBT1 was considered to be a transcriptional repressor but its role in cancer remains unclear. ccRCC patients with VHL loss-of-function mutations displayed elevated SFMBT1 protein levels...
March 19, 2020: Molecular Cell
#32
JOURNAL ARTICLE
Douaa Mugahid, Marian Kalocsay, Xili Liu, Jonathan Scott Gruver, Leonid Peshkin, Marc W Kirschner
The Hippo pathway regulates organ size, regeneration, and cell growth by controlling the stability of the transcription factor, YAP (Yorkie in Drosophila ). When there is tissue damage, YAP is activated allowing the restoration of homeostatic tissue size. The exact signals by which YAP is activated are still not fully understood, but its activation is known to affect both cell size and cell number. Here we used cultured cells to examine the coordinated regulation of cell size and number under the control of YAP...
January 9, 2020: ELife
#33
JOURNAL ARTICLE
Vanessa Weyer, Máté E Maros, Andrea Kronfeld, Stefanie Kirschner, Christoph Groden, Clemens Sommer, Yasemin Tanyildizi, Martin Kramer, Marc A Brockmann
No abstract text is available yet for this article.
November 21, 2019: Journal of Cerebral Blood Flow and Metabolism
#34
JOURNAL ARTICLE
Leonid Peshkin, Myriam Boukhali, Wilhelm Haas, Marc W Kirschner, Lev Y Yampolsky
Although the microcrustacean Daphnia is becoming an organism of choice for proteomic studies, protein expression across its life cycle have not been fully characterized. We analyzed proteomes of adult females, juveniles, asexually produced embryos, and the ephippia - resting stages containing sexually produced diapausing freezing- and desiccation-resistant embryos. Overall, we were more likely to detect proteins with known molecular functions than proteins with no detectable orthology. Similarly, we could detect proteins with stronger gene model support in two independent genome assemblies, than those without such support...
November 7, 2019: Proteomics
#35
JOURNAL ARTICLE
Kaga Gomarteli, Jens Fleckenstein, Stefanie Kirschner, Vladimir Bobu, Marc A Brockmann, Thomas Henzler, Mathias Meyer, Philipp Riffel, Stefan O Schönberg, Marlon R Veldwijk, Bettina Kränzlin, Christian Hoerner, Gerhard Glatting, Frederik Wenz, Carsten Herskind, Frank A Giordano
A long-standing hypothesis in radiotherapy is that intensity-modulated radiotherapy (IMRT) increases the risk of second cancer due to low-dose exposure of large volumes of normal tissue. Therefore, young patients are still treated with conventional techniques rather than with modern IMRT. We challenged this hypothesis in first-of-its-kind experiments using an animal model. Cancer-prone Tp53+/C273X knockout rats received mediastinal irradiation with 3 × 5 or 3 × 8 Gy using volumetric-modulated arc therapy (VMAT, an advanced IMRT) or conventional anterior-posterior/posterior-anterior (AP/PA) beams using non-irradiated rats as controls (n = 15/group, ntotal = 90)...
October 29, 2019: Scientific Reports
#36
REVIEW
W Malcolm Byrnes
This year, 2019, marks the centennial of embryologist E. E. Just's discovery of what is known as the fast block to polyspermy. Just's observation of the subtle changes that occur at the egg's surface during fertilization (and in experimental parthenogenesis) led him to postulate that the egg, and indeed every cell, possesses a property he called independent irritability, which represents the cell's ability to respond in a physiologically-relevant way to a variety of signals or triggers. In this paper, I argue that Just's concept of independent irritability informed his contemporary Johannes Holtfreter as Holtfreter attempted to explain the phenomena of embryonic induction and competence and that Holtfreter, in turn, influenced Marc Kirschner and John Gerhart in their formulation of the theory of facilitated variation...
September 23, 2019: Molecular Reproduction and Development
#37
JOURNAL ARTICLE
Richard Burt, Aditi Dey, Sarah Aref, Melanie Aguiar, Ayse Akarca, Katharine Bailey, William Day, Steven Hooper, Amy Kirkwood, Kristina Kirschner, Soo-Wah Lee, Cristina Lo Celso, Jiten Manji, Marc R Mansour, Teresa Marafioti, Rachel J Mitchell, Robert C Muirhead, Kenton Cheuk Yan Ng, Constandina Pospori, Ignazio Puccio, Krisztina Zuborne-Alapi, Erik Sahai, Adele K Fielding
We investigated and modeled the mesenchymal stromal cell (MSC) niche in adult acute lymphoblastic leukemia (ALL). We used gene expression profiling, cytokine/chemokine quantification, flow cytometry, and a variety of imaging techniques to show that MSCs, directly isolated from the primary bone marrow specimens of patients with ALL, frequently adopted an activated, cancer-associated fibroblast phenotype. Normal, primary human MSCs and the MSC cell line HS27a both were activated de novo, when exposed to the reactive oxygen species (ROS)-inducing chemotherapy agents cytarabine (AraC) and daunorubicin (DNR), a phenomenon blocked by the antioxidant N-acetyl cysteine...
October 24, 2019: Blood
#38
JOURNAL ARTICLE
Sarah Heringer, Lisa Kabelitz, Martin Kramer, Omid Nikoubashman, Marc A Brockmann, Stefanie Kirschner, Martin Wiesmann
For endovascular research pigs are an established animal model. However, experiences regarding analyses of platelet inhibition in pigs using the Multiplate® Analyzer are limited. The aims of the present study were to investigate if (1) the Multiplate® Analyzer is a suitable method for examination of porcine platelet function using manufacturers' recommendations for human blood, and (2) platelet inhibition can be induced with acetylsalicylic acid (ASA) and clopidogrel in pigs reliably, and if (3) non-responders to one of the drug can be detected...
2019: PloS One
#39
JOURNAL ARTICLE
Megan E Spurgeon
Megan E. Spurgeon works in the field of viral oncology. In this mSphere of Influence article, she reflects on how the paper "Rescuing US biomedical research from its systemic flaws" by Bruce Alberts, Marc W. Kirschner, Shirley Tilghman, and Harold Varmus (Proc Natl Acad Sci U S A 111:5773-5777, 2014, https://doi.org/10.1073/pnas.1404402111) made an impact on her by influencing her research and career outlook. The way researchers think about their science is shaped by a variety of factors, and these often include research articles that influence their technical or experimental approaches and interpretations...
July 3, 2019: MSphere
#40
JOURNAL ARTICLE
Hak-Min Kim, Jessica A Weber, Nayoung Lee, Seung Gu Park, Yun Sung Cho, Youngjune Bhak, Nayun Lee, Yeonsu Jeon, Sungwon Jeon, Victor Luria, Amir Karger, Marc W Kirschner, Ye Jin Jo, Seonock Woo, Kyoungsoon Shin, Oksung Chung, Jae-Chun Ryu, Hyung-Soon Yim, Jung-Hyun Lee, Jeremy S Edwards, Andrea Manica, Jong Bhak, Seungshic Yum
BACKGROUND: Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura's jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations...
March 29, 2019: BMC Biology
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