Article
Chemistry, Medicinal
Theresa Kircher, Tatu Pantsar, Andreas Oder, Jens Peter von Kries, Michael Juchum, Bent Pfaffenrot, Philip Kloevekorn, Wolfgang Albrecht, Roland Selig, Stefan Laufer
Summary: MKK4 plays a key role in liver regeneration, making new small molecules inhibiting MKK4 potential candidates for treating acute and chronic liver diseases. Optimization of compound design led to the selection of fluorescent compounds with high binding affinities, with compound 45 identified as a suitable tool for studying new small-molecule inhibitors of MKK4.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Editorial Material
Cell Biology
Michael X. Zhu
Summary: This study reported the cryo-EM structures of TRPC5 in complex with Ga-i3, revealing that the G protein alpha subunit directly binds to an ankyrin-like repeat domain in the periphery of TRPC5's cytosolic portion some 50 angstrom away from the membrane. This confirms that TRPC4/C5 ion channels are true effectors of Ga subunits, with channel gating dependent on the coexistence of Ca2+ and phosphatidylinositol 4,5-bisphosphate.
Article
Chemistry, Physical
Siddhartha Banerjee, Ayanjeet Ghosh
Summary: The aggregation of tau protein plays a central role in neurodegenerative diseases, with the study revealing structural heterogeneities in tau aggregates associated with different diseases, as well as multiple fibrillar polymorphs within the same tau aggregate. Additionally, mature fibrils were found to contain significant amounts of antiparallel beta sheets. The research demonstrates the promise of using nanoscale infrared spectroscopy for spatially resolved investigation of protein aggregation.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Ji-Yun Kim, Efthymia Symeonidi, Tin Yau Pang, Tom Denyer, Diana Weidauer, Margaret Bezrutczyk, Manuel Miras, Nora Zoellner, Thomas Hartwig, Michael M. Wudick, Martin Lercher, Li-Qing Chen, Marja C. P. Timmermans, Wolf B. Frommer
Summary: In this study, single-cell transcriptome analysis of leaf vasculature revealed unique metabolic patterns of phloem parenchyma cells and explored the kinship relation of vascular cell types.
Article
Chemistry, Multidisciplinary
Qiong-Qiong Yao, Jitao Wen, Sarah Perrett, Si Wu
Summary: This study reveals the mechanisms by which lipid membranes influence the amyloid formation of Tau protein. It shows that lipid membranes can induce conformational changes in Tau and either accelerate or inhibit its fibrillation process depending on the concentration of the lipid membrane.
Article
Genetics & Heredity
Artemiy S. Bakman, Aleksandra A. Kuznetsova, Lyudmila V. Yanshole, Alexander A. Ishchenko, Murat Saparbaev, Olga S. Fedorova, Nikita A. Kuznetsov
Summary: The base excision repair (BER) pathway involves a step-by-step process in which DNA glycosylases and AP endonucleases work together to repair damaged DNA. This study aimed to verify the passing-the-baton model of DNA intermediates transfer between enzymes by creating an experimental system. The findings of the study confirm that Pol beta plays a key role in coordinating the activities of APE1 and Pol beta in the initial steps of BER.
Article
Multidisciplinary Sciences
Danique M. van Bommel, Ruud F. Toonen, Matthijs Verhage
Summary: Retrograde trafficking is crucial for Golgi organization and cargo sorting, with Vti1a/b playing an important role.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Ying Wah Elizabeth Tse, Hwa Young Yun, Haley Doris Myskiw Wyatt
Summary: This article presents a protocol for generating high-quality fluorescently labeled DNA substrates for biochemical assays. The protocol involves purifying DNA oligonucleotides using polyacrylamide gel electrophoresis, annealing the oligonucleotides, and purifying the annealed substrates using anion-exchange chromatography. The protocol eliminates the need for radioisotopes, which require specialized handling and waste disposal. It is adaptable to different lengths of oligonucleotides and DNA substrates. For more details, please refer to Payliss and Tse et al. (2022).
Article
Geochemistry & Geophysics
Daniele Brandt, Marcia Ernesto, Catherine Constable
Summary: This study presents an extensive directional paleomagnetic database of the Kiaman reversed superchron, with a constant behavior of concentrated and circular distributions at latitudes higher than 10 degrees. Through Giant Gaussian Process (GGP) models, the research found a covariant type that best explains the directional distribution of the Kiaman database. The results suggest that the correlations between Gaussian coefficients are valid for the last 10 Myr and the Kiaman superchron, and that the relative variability of the Kiaman field is lower compared to the past 10 Myr.
GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS
(2021)
Article
Agriculture, Multidisciplinary
Niloofar Mosayyebi, Zahra Mehraban, Majid Siampour, Ghobad Babaei, Fabio Quaglino
Summary: During a field survey in various geographical regions of Iran, phytoplasma-like symptoms were found in peach, almond, wild almond, and GF-677 rootstock. Molecular typing revealed the presence of two subpopulations of almond witches'-broom (AlmWB) phytoplasma strains in Iran, with distinct genetic variations between Iranian and Lebanese strains. Genetic distance analysis showed significant differences between AlmWB phytoplasma strains (16SrIX-B and variants) and phytoplasmas from other 16SrIX subgroups. The study discussed the significance of genetic variation in relation to biological characteristics and geographical distinctions of 16SrIX group phytoplasmas.
ANNALS OF APPLIED BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Marta Grzechowiak, Agnieszka Ruszkowska, Joanna Sliwiak, Anna Urbanowicz, Mariusz Jaskolski, Milosz Ruszkowski
Summary: This study investigates the structure and DNA binding characteristics of AtWRKY18, a plant transcription factor, and reveals its specific structural preferences in DNA recognition, which explains how WRKY TFs precisely regulate gene expression.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Cell Biology
Marlena Herbertz, Soenke Harder, Hartmut Schlueter, Christian Lohr, Susanne Dobler
Summary: This study revealed the distribution and composition of Na,K-ATPase alpha 1/ss complexes in the nervous tissue of the milkweed bug, challenging the current understanding that the alpha 1 and ss subunits must associate to form functional complexes.
CELL AND TISSUE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Christopher J. Buehl, Noah J. Goff, Steven W. Hardwick, Martin Gellert, Tom L. Blundell, Wei Yang, Amanda K. Chaplin, Katheryn Meek
Summary: Non- homologous end joining is the main pathway for repairing double-strand breaks in mammals. DNA-PK plays a central role in orchestrating multiple steps in non- homologous end joining. Recent structural studies have revealed two distinct NHEJ complexes that mediate the synapsis of DNA ends. One complex involves a DNA-PK dimer mediated by XLF, while the other complex forms through a domain-swap mechanism involving interaction between the C terminus of Ku80 from one DNA-PK protomer and another DNA-PK protomer. The distance between the synapsed DNA ends in both complexes is the same, suggesting a conserved long-range synaptic complex. A mutational strategy has shown that these two dimers have distinct cellular functions, with one promoting fill-in end processing and the other promoting DNA end resection. The specific DNA-PK dimer formed determines the mechanism by which the ends can be ligated, and this may be influenced by the structure of the DNA ends.
Review
Chemistry, Multidisciplinary
Shai Kellner, Shai Berlin
APPLIED SCIENCES-BASEL
(2020)
Article
Biochemical Research Methods
Ronit Heinrich, Wessal Hussein, Shai Berlin
Summary: Studying the brain requires understanding both its structure and function, which has led to the development of novel tools and techniques, particularly in optical methods. The discovery of GFP and subsequent development of genetically encoded fluorescent tools now allows for functional highlighting of live cells, particularly in vivo. These photo-transformable probes, such as those undergoing photoactivation, photoconversion, or photoswitching, are particularly well-suited for studying multiple features of neurons simultaneously.
JOURNAL OF NEUROSCIENCE METHODS
(2021)
Article
Multidisciplinary Sciences
Moshe Katz, Suraj Subramaniam, Orna Chomsky-Hecht, Vladimir Tsemakhovich, Veit Flockerzi, Enno Klussmann, Joel A. Hirsch, Sharon Weiss, Nathan Dascal
Summary: CaV1.2 channels play a crucial role in regulating cardiac muscle contraction, with 0-AR increasing contraction by enhancing calcium influx through these channels via PKA activation. A recent study identified Rad as essential for PKA regulation of CaV1.2, revealing two distinct pathways of PKA modulation of CaV1.2: Rad dependent and Rad independent.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Shai Kellner, Abeer Abbasi, Ido Carmi, Ronit Heinrich, Tali Garin-Shkolnik, Tova Hershkovitz, Moshe Giladi, Yoni Haitin, Katrine M. Johannesen, Rikke Steensbjerre Moller, Shai Berlin
Summary: This study identified two toddlers with different heterozygous missense mutations in the same glycine residue of the GRIN2B gene, resulting in severely impaired glutamate binding and extreme effects on channel function. The variants exhibit dominant-negative effects on mixed channels and suppress synaptic GluNRs, pointing towards a Loss-of-Function mechanism primarily instigated by LBD mutations in GluN2B.
Article
Neurosciences
Boris Shalomov, Reem Handklo-Jamal, Haritha P. Reddy, Neta Theodor, Amal K. Bera, Nathan Dascal
Summary: GIRK4 channel mutants have different effects on K+ selectivity and inward rectification, and some mutants also lead to depolarization of zona glomerulosa cells and high aldosterone secretion.
JOURNAL OF PHYSIOLOGY-LONDON
(2022)
Article
Multidisciplinary Sciences
Kinneret Rozales, Amal Younis, Naseeb Saida, Anatoly Meller, Hodaya Goldman, Lior Kellerman, Ronit Heinrich, Shai Berlin, Reut Shalgi
Summary: This study used quantitative screens in human cells to investigate the effects of naturally-occurring DNAJ chaperone isoforms on the pathological aggregation of Huntington's disease-associated HTT-polyQ and ALS-related mutant FUS. The results showed that the aggregation of HTT-polyQ induces a cellular proteotoxic stress response, while mutant FUS aggregation leads to deteriorated proteostasis. The study also revealed complex interactions between different DNAJ isoforms and different aggregate types.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Neurosciences
Shai Berlin
BIOLOGICAL PSYCHIATRY
(2022)
Article
Biotechnology & Applied Microbiology
Shunit Olszakier, Shai Berlin
Summary: This study presents a versatile and simple method for efficient introduction of various mutation schemes using the Gibson-assembly method without the need for designing specific Gibson primers. Standard site-directed mutagenesis primers can be used with the Gibson assembly method, and an added amplification step resolves the issue of low Gibson product yield. The method also accommodates SDM primers with degenerate sequences.
Article
Biochemistry & Molecular Biology
Meng Cui, Keman Xu, Kirin D. Gada, Boris Shalomov, Michelle Ban, Giasemi C. Eptaminitaki, Takeharu Kawano, Leigh D. Plant, Nathan Dascal, Diomedes E. Logothetis
Summary: G protein-sensitive inwardly rectifying potassium (GIRK) channels are important pharmaceutical targets for neurological, cardiac, and endocrine diseases. The discovery of the highly selective small-molecule activator, 3hi2one-G4, provides a valuable tool for studying the function of GIRK4 channels and has potential applications in drug optimization for GIRK4-related diseases.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Neurosciences
Alexis G. Bavencoffe, Emily A. Spence, Michael Y. Zhu, Anibal Garza-Carbajal, Kerry E. Chu, Ona E. Bloom, Carmen W. Dessauer, Edgar T. Walters
Summary: Neuropathic pain is a major challenge for people with spinal cord injury, and the mechanisms behind it involve chronic hyperexcitability of primary nociceptors. This study found that the cytokine MIF, which is elevated in individuals with SCI, contributes to ongoing electrical activity and promotes pain. It also discovered that MIF concentrations can induce hyperactivity in nociceptors and that blocking MIF signaling can reverse hyperexcitability. Moreover, the study suggests that changes in systemic and DRG levels of MIF play a role in maintaining nociceptor hyperactivity after SCI.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Biology
Theres Friesacher, Haritha P. Reddy, Harald Bernsteiner, J. Carlo Combista, Boris Shalomov, Amal K. Bera, Eva-Maria Zangerl-Plessl, Nathan Dascal, Anna Stary-Weinzinger
Summary: This study investigates the impact of a selectivity filter mutation on the structure and function of GIRK2 channels through molecular dynamics simulations and electrophysiological experiments. It reveals an allosteric connection between the selectivity filter and a crucial activator binding site, providing insights into the mechanism of neurological disorders.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ebaston Thankarajan, Shimrit Oz, Abed Saady, Kseniya Kulbitski, Mykhail O. Kompanets, Moris S. Eisen, Shai Berlin
Summary: Magnetic resonance imaging (MRI) is a powerful imaging technique used in research and clinical applications, but it has limitations such as low signal and lack of target specificity. We developed a multimodal imaging probe that can detect targeted cells using both MRI and fluorescence microscopy. The probe consists of a SNAP-tag substrate for specific cell labeling, cyanine dyes for bright fluorescence, and a chelated Gd-III molecule for enhanced MRI contrast. Our probes showed specific and efficient labeling of genetically defined cells, as well as bright fluorescence and MRI signal. This synthetic approach provides a versatile platform for the production of multimodal imaging probes, particularly for light microscopy and MRI.
Article
Biochemistry & Molecular Biology
Reem Jada, Veronika Borisov, Eliezer Laury, Shmuel Halpert, Nina S. S. Levy, Shlomo Wagner, Shai Netser, Randall Walikonis, Ido Carmi, Shai Berlin, Andrew P. P. Levy
Summary: Researchers found that brief heat therapy can reduce seizures and restore synaptic dysfunction in neuronal cultures of A350V mice, likely mediated by Arf6-GTP.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Shaden Zoabi, Michael Andreyanov, Ronit Heinrich, Shaked Ron, Ido Carmi, Yoram Gutfreund, Shai Berlin
Summary: Researchers developed a custom-made viral vector called AAV1-T593K (AAV1*), which allows efficient transduction and manipulation of quail neurons, expanding the toolkit for avian neuroscience research. By bridging the gap in transduction efficiency between different model organisms, particularly birds, this study facilitates the use of genetically-encoded tools and methods in avian species, advancing the field of avian neuroscience research.
COMMUNICATIONS BIOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Shai Berlin