Article
Biochemical Research Methods
Jennifer Mattock, Marina Martinez-Alvaro, Matthew A. Cleveland, Rainer Roehe, Mick Watson
Summary: Accurate gene prediction is crucial for successful metagenome analysis. We introduce KOunt, a Snakemake pipeline that accurately quantifies KEGG orthologue abundance.
Article
Pharmacology & Pharmacy
Zhongyao Li, Ruoyu Chen, Yanxia Li, Qian Zhou, Huanxin Zhao, Kewu Zeng, Baobing Zhao, Zhiyuan Lu
Summary: Reversible phosphorylation of proteins is regulated by protein kinases and phosphatases, with PPM1B being a metal ion-dependent serine/threonine protein phosphatase. PPM1B regulates various biological functions by dephosphorylating substrates, including cell cycle, energy metabolism, and inflammatory responses. This review provides a summary of the current understanding of PPM1B regarding its regulation of signaling pathways, associated diseases, and potential small-molecule inhibitors, offering new insights for the development of PPM1B inhibitors and the treatment of PPM1B-related diseases.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2023)
Article
Multidisciplinary Sciences
Max Schelski, Frank Bradke
Summary: In developing vertebrate neurons, microtubules flow retrogradely within the neurites to the soma, inhibiting neurite growth. However, shortly after axon formation, microtubule retrograde flow slows down, enabling axon extension.
Editorial Material
Biochemistry & Molecular Biology
Maria Chalokh Vogel, Sandra Maday
Summary: The induction of neuronal autophagy by mTOR inhibitors is limited by myotubularin-related phosphatase 5, solving the puzzle of autophagy regulation in neurons.
Review
Biochemistry & Molecular Biology
Friederike Cuello, Friedrich W. Herberg, Konstantina Stathopoulou, Philipp Henning, Simon Diering
Summary: Pathologies such as cancer, inflammatory and cardiac diseases are often associated with long-term oxidative stress, leading to protein dysfunction and failed trials of systemic antioxidant therapy. In cardiac myocytes, cardiac contractility is mainly driven by the beta-adrenoceptor-signaling cascade activating PKA-mediated phosphorylation for positive inotropic and lusitropic effects. Both kinase and phosphatase are redox-sensitive and play crucial roles in regulating cardiac contractile function.
Article
Biochemistry & Molecular Biology
Jiarui Song, Claudia Castillo-Gonzalez, Zeyang Ma, Dorothy E. Shippen
Summary: The recent discovery of bona-fide telomerase RNA from plants has provided new insights into telomerase RNP with conserved and unique structural elements. Two highly conserved proteins in Arabidopsis, AtPOT1a and AtNAP57 (dyskerin), have been found to interact with plant telomerase. This study reveals that AtPOT1a stimulates telomerase activity by interacting with TERT, while dyskerin binds to AtTR through a plant-specific three-way junction, playing a crucial role in telomerase biogenesis and evolution.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Sidharth Bhasin, Asmita Das
Summary: SHP1 is a protein tyrosine phosphatase that plays a central role in immunity, cell growth, development, and survival. Inhibiting SHP1 can improve the prognosis of various disorders, but currently available inhibitors also inhibit SHP2, which has distinct biological functions. This study used virtual screening and molecular dynamic simulations to identify two rigidin analogues that selectively inhibit SHP1, demonstrating their potential as more effective SHP1 inhibitors compared to the commercially available inhibitor NSC-87877.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Forestry
Susanti Withaningsih, Parikesit Parikesit, Annas Dwitri Malik, Muthi'ah Aini Rahmi
Summary: This study used remote sensing techniques and geographic information systems to determine the structure and ecological functions of an extreme landscape in Rongga Sub-district, West Java. The results showed that the landscape consisted of various elements with high diversity, and the extreme topography supported landscape connectivity, making it an important refuge for protected animals.
Review
Biochemistry & Molecular Biology
Elliott M. Thompson, Andrew W. Stoker
Summary: Dual specificity phosphatases are crucial in regulating intracellular signaling pathways, with DUSP26 being an atypical member implicated in a range of human diseases, particularly cancer. DUSP26 displays both tumor-suppressive and tumor-promoting properties in cancer, depending on the context.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Shihao Su, Yawen Lei, Xuan Zhou, Takamasa Suzuki, Wei Xiao, Tetsuya Higashiyama
Summary: The shape of flowers is determined by morphogenesis along different independent axes. A shared module that regulates corolla differentiation in the proximal region axis has been discovered. The study provides insights into how petal patterns this axis of flowers.
NATURE COMMUNICATIONS
(2023)
Article
Geriatrics & Gerontology
E. Peyrusque, J. Granet, B. Pageaux, F. Buckinx, M. Aubertin-Leheudre
Summary: The study found that fast walking speed, unipodal balance, normal walking speed, and normal Timed-Up and Go test were highly reliable in remote assessment conditions, while fast Timed-Up and Go test, Sit-to-Stand function, muscle endurance, and power were extremely reliable. In terms of absolute reliability, the standard error of measurement ranged from 15.54% to 5.14%. The minimal detectable change ranged from 43.07% to 14.21%.
JOURNAL OF NUTRITION HEALTH & AGING
(2022)
Review
Sport Sciences
Andrew R. Gamble, Evangelos Pappas, Mary O'Keeffe, Giovanni Ferreira, Christopher G. Maher, Joshua R. Zadro
Summary: The study found that intensive supervised rehabilitation following ACL reconstruction did not show superiority over less supervised rehabilitation in improving self-reported function and sports participation, indicating the need for more high-quality research to confirm the conclusions.
JOURNAL OF SCIENCE AND MEDICINE IN SPORT
(2021)
Article
Biodiversity Conservation
Marcio B. Cure, Bernardo M. Flores, Caio R. C. Mattos, Rafael S. Oliveira, Marina Hirota
Summary: Vegetation types in tropical landscapes can respond differently to rainfall, and the temporal coupling between vegetation greenness and rainfall is a good indicator of ecosystem state. By studying the Brazilian Cerrado landscape, the researchers found that dry forests have the strongest coupling with rainfall, while gallery forests increase their greenness during the dry season. Savannas have a weaker response to rainfall.
ECOLOGICAL INDICATORS
(2023)
Article
Multidisciplinary Sciences
Amina Jbara, Kuan-Ting Lin, Chani Stossel, Zahava Siegfried, Haya Shqerat, Adi Amar-Schwartz, Ela Elyada, Maxim Mogilevsky, Maria Raitses-Gurevich, Jared L. Johnson, Tomer M. Yaron, Ofek Ovadia, Gun Ho Jang, Miri Danan-Gotthold, Lewis C. Cantley, Erez Y. Levanon, Steven Gallinger, Adrian R. Krainer, Talia Golan, Rotem Karni
Summary: Pancreatic ductal adenocarcinoma (PDA) is a highly lethal cancer characterized by aggressive invasion and metastasis. We identified differentially spliced events correlated with PDA progression through analysis of RNA splicing data. Overexpression of RBFOX2 in a PDA cell line reduced its metastatic potential, while depletion of RBFOX2 in primary pancreatic tumor cell lines increased their metastatic potential.
Article
Health Care Sciences & Services
Margaret A. French, Eva Keatley, Junyao Li, Aparna Balasubramanian, Nadia N. Hansel, Robert Wise, Peter Searson, Anil Singh, Preeti Raghavan, Stephen Wegener, Ryan T. Roemmich, Pablo Celnik
Summary: Remote monitoring of physical, cognitive, and psychosocial function in individuals with chronic obstructive pulmonary disease or stroke is feasible and shows high adherence, although reminders are required to maintain this level of adherence.
Article
Immunology
Kieran D. Collins, Shuai Hu, Helmut Grasberger, John Y. Kao, Karen M. Ottemann
INFECTION AND IMMUNITY
(2018)
Article
Immunology
Isabelle C. Arnold, Mariela Artola-Boran, Paulino Tallon de Lara, Andreas Kyburz, Christian Taube, Karen Ottemann, Maries van den Broek, Shida Yousefi, Hans-Uwe Simon, Anne Mueller
JOURNAL OF EXPERIMENTAL MEDICINE
(2018)
Review
Microbiology
Christina Yang, Karen M. Ottemann
CURRENT OPINION IN MICROBIOLOGY
(2019)
Article
Immunology
Hikaru Hanyu, Kristen A. Engevik, Andrea L. Matthis, Karen M. Ottemann, Marshall H. Montrose, Eitaro Aihara
INFECTION AND IMMUNITY
(2019)
Editorial Material
Immunology
Andreas J. Baumler, Anthony R. Richardson, Karen M. Ottemann
INFECTION AND IMMUNITY
(2020)
Article
Infectious Diseases
Skander Hathroubi, Julia Zerebinski, Aaron Clarke, Karen M. Ottemann
Editorial Material
Immunology
Andreas J. Baumler, Karen M. Ottemann, Anthony R. Richardson
INFECTION AND IMMUNITY
(2021)
Article
Microbiology
Kevin S. Johnson, Bassam A. Elgamoudi, Freda E-C Jen, Christopher J. Day, Emily Goers Sweeney, Megan L. Pryce, Karen Guillemin, Thomas Haselhorst, Victoria Korolik, Karen M. Ottemann
Summary: The Helicobacter pylori chemoreceptor TIpA plays a role in dampening host inflammation during chronic stomach colonization by sensing multiple attractant ligands as well as antagonist ones. This ability to regulate chemotactic responses by antagonistic chemoreceptor ligands is an emerging theme in chemotaxis systems.
Article
Multidisciplinary Sciences
Shoichi Tachiyama, Kar L. Chan, Xiaolin Liu, Skander Hathroubi, Briana Peterson, Mohammad F. Khan, Karen M. Ottemann, Jun Liu, Anna Roujeinikova
Summary: The conserved protein FliL is an assembly factor of the Helicobacter pylori flagellar motor and colocalizes with the stator. Cryogenic electron tomography reconstructions reveal that FliL forms rings integrated with the MotAB units, and FliL-C shows structural similarities to scaffolding proteins. The findings provide insights into the assembly mechanism of the FliL rings and its potential role as a scaffold.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Xiaolin Liu, Karen M. Ottemann
Summary: This study shows that the presence or absence of CheR and CheB is strongly associated with the niche of Helicobacter species, with gastric species lacking these proteins and enterohepatic species retaining them. The study also suggests that CheR and CheB can serve as markers to distinguish between gastric and enterohepatic Helicobacter species.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Immunology
Kevin S. Johnson, Christina Yang, J. Elliot Carter, Atesh K. Worthington, Elektra K. Robinson, Raymond Lopez-Magana, Frida Salgado, Isabelle Arnold, Karen M. Ottemann
Summary: Helicobacter pylori is a common bacterium that causes gastritis, ulcers, and gastric cancer. This study found that the chronic inflammation caused by H. pylori exhibits fluctuations, and a mutant strain showed different inflammation characteristics compared to the wild type.
INFECTION AND IMMUNITY
(2023)
Article
Microbiology
Xiaolin Liu, Anna Roujeinikova, Karen M. Ottemann
Summary: FliL is a protein found in the flagellar motor of bacteria. It was previously unclear what role it plays. However, through reanalyzing studies on FliL, scientists discovered that the presence or absence of different regions of the protein affects motility. The N-terminal region is found to have a negative effect on motor function, and its removal allows normal motility.
Article
Microbiology
Shuai Hu, Stefani Giacopazzi, Ryan Modlin, Kevin Karplus, David L. Bernick, Karen M. Ottemann
Summary: This paper reports an approach to improve bacterial transformation efficiency by reducing and avoiding the effects of restriction-modification (R-M) systems. Significantly higher transformation efficiency can be achieved by modifying under-represented DNA sequences in antibiotic resistance cassettes. This method is likely to be applicable to other microorganisms with sequenced genomes.
Correction
Microbiology
Xiaolin Liu, Anna Roujeinikova, Karen M. Ottemann
Article
Immunology
Daniela Keilberg, Nina Steele, Sili Fan, Christina Yang, Yana Zavros, Karen M. Ottemann, Victor J. Torres
Summary: The study revealed that the metabolomes of the corpus and antrum differ, with various secreted chemicals being depleted upon H. pylori infection, and different regions showing distinct metabolites. The corpus and antrum maintained unique metabolomic profiles over an 8-month infection period.
INFECTION AND IMMUNITY
(2021)