Article
Multidisciplinary Sciences
Hannah Schmidbaur, Akane Kawaguchi, Tereza Clarence, Xiao Fu, Oi Pui Hoang, Bob Zimmermann, Elena A. Ritschard, Anton Weissenbacher, Jamie S. Foster, Spencer Nyholm, Paul A. Bates, Caroline B. Albertin, Elly Tanaka, Oleg Simakov
Summary: This study reveals the unique genomic, topological, and regulatory organization of cephalopod genomes, identifies microsyntenies associated with cephalopod nervous system evolution, and suggests that microsyntenic profiling will be central to understanding cephalopod innovations.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
Yang Liu, Zhiyuan Huang, Honghe Liu, Zhicheng Ji, Amit Arora, Danfeng Cai, Hongjin Wang, Mingming Liu, Eric A. J. Simko, Yanjun Zhang, Goran Periz, Zhe Liu, Jiou Wang
Summary: The C9orf72 HRE DNA binds to DAXX and promotes its liquid-liquid phase separation, resulting in chromatin remodeling and epigenetic changes. DAXX regulates global gene expression and suppresses the expression of C9orf72 through chromatin remodeling and epigenetic modifications. Modulating DAXX or rebalancing epigenetic modifications can mitigate the stress-induced sensitivity of C9orf72-patient-derived motor neurons.
Article
Multidisciplinary Sciences
Philippe J. Batut, Xin Yang Bing, Zachary Sisco, Joao Raimundo, Michal Levo, Michael S. Levine
Summary: Past studies have provided contradictory claims about the role of genome organization in gene activity regulation. This study demonstrates that the Drosophila genome is organized by two independent classes of regulatory sequences, tethering elements and insulators. These two levels of genome organization operate independently to ensure precise transcriptional dynamics and reliable complex patterning processes.
Article
Biochemistry & Molecular Biology
Jordi Bernues, Andrea Izquierdo-Boulstridge, Oscar Reina, Lucia Castejon, Elena Fernandez-Castaner, Nuria Leal, Nancy Guerrero-Pepinosa, Carles Bonet-Costa, Olivera Vujatovic, Paula Climent-Canto, Fernando Azorin
Summary: Post-translational modifications of core histones, such as dH1K27me2, play crucial roles in epigenetic regulation of chromatin. In Drosophila, dH1K27me2 is a major modification of heterochromatin and contributes to heterochromatin organization independently of H3K9 methylation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Hsiang-Chen Chou, Kuhulika Bhalla, Osama El Demerdesh, Olaf Klingbeil, Kaarina Hanington, Sergey Aganezov, Peter Andrews, Habeeb Alsudani, Kenneth Chang, Christopher R. Vakoc, Michael C. Schatz, W. Richard McCombie, Bruce Stillman
Summary: Each subunit of ORC and CDC6 is essential in human cells, with their deficiency leading to difficulties in DNA replication initiation and cell division cycle progression, as well as abnormal nuclear and cell morphology.
Article
Biochemistry & Molecular Biology
Xianguo Zhao, Yahong Li, Zhangwu Zhao, Juan Du
Summary: Global warming has serious impacts on insect sleep, which is critical for animals due to its important physiological functions. Understanding the regulation mechanism of sleep changes is essential for studying the impact of global warming, and can provide insights into improving sleep quality. This study found that extra sex combs (ESC) act as a regulatory factor in buffering sleep-related stresses through regulating Heat shock proteins (Hsps).
Article
Genetics & Heredity
Daniela Torres-Campana, Beatrice Horard, Sandrine Denaud, Gerard Benoit, Benjamin Loppin, Guillermo A. Orsi
Summary: This study identifies regulators and mechanisms involved in the expression of the dhd gene, shedding light on the complex regulation of gene expression in multicellular development. The researchers demonstrate the critical role of multiple epigenomic effectors in tissue-specific gene activation.
Article
Biology
Neta Erez, Lena Israitel, Eliya Bitman-Lotan, Wing H. Wong, Gal Raz, Dayanne Cornelio-Parra, Salwa Danial, Na'ama Flint Brodsly, Elena Belova, Oksana Maksimenko, Pavel Georgiev, Todd Druley, Ryan D. Mohan, Amir Orian
Summary: The study reveals that the deubiquitinase Non-stop and Non-stop identity complex (NIC) play crucial roles in regulating the identity of Drosophila midgut enterocytes (ECs), protecting cells from premature aging effects.
Article
Cell Biology
Danyan Li, David H. Taylor, Josien C. van Wolfswinkel
Summary: PIWI proteins play a crucial role in regeneration and cell differentiation in animals, with a complex interplay between transposons and cell differentiation. They control the activation of transposons during cell differentiation, and the absence of specific PIWI proteins results in transposon derepression and defective cell differentiation.
Article
Multidisciplinary Sciences
Anjali Kaushal, Julien Dorier, Bihan Wang, Giriram Mohana, Michael Taschner, Pascal Cousin, Patrice Waridel, Christian Iseli, Anastasiia Semenova, Simon Restrepo, Nicolas Guex, Erez Lieberman Aiden, Maria Cristina Gambetta
Summary: Boundaries in animal genomes play a crucial role in limiting regulatory cross-talk and guiding enhancers to target promoters. This study reveals that the formation and function of boundaries in flies are different from mammals. Unlike mammalian boundaries, most Drosophila boundaries form independently of CTCF and are recruited by Cp190. These boundaries are essential for early development and prevent regulatory cross-talk between specific gene loci, but are dispensable for long-range enhancer-promoter communication.
Article
Multidisciplinary Sciences
Nhu Nguyen, Kristbjorn O. Gudmundsson, Anthony R. Soltis, Kevin Oakley, Kartik R. Roy, Yufen Han, Carmelo Gurnari, Jaroslaw P. Maciejewski, Gary Crouch, Patricia Ernst, Clifton L. Dalgard, Yang Du
Summary: Abnormal activation of SETBP1 is frequently found in myeloid neoplasms and is associated with poor prognosis. The direct interaction between SETBP1 and histone methyltransferase MLL1 plays a critical role in SETBP1-induced transcriptional activation and transformation, and represents a promising target for treating myeloid neoplasms with SETBP1 activation.
Article
Biochemistry & Molecular Biology
Karen Jule Nieken, Kathryn O'Brien, Alexander McDonnell, Liudmila Zhaunova, Hiroyuki Ohkura
Summary: During the prophase of the first meiotic division, chromatin forms a compact spherical cluster called the karyosome in the nucleus of the oocyte in Drosophila melanogaster. This phenomenon is also observed in oocytes of various species, including humans. A large-scale cytological screen was conducted to identify genes involved in karyosome formation using Drosophila melanogaster oocytes, leading to the discovery of 106 genes that triggered reproducible karyosome defects. These defects were found to be related to DNA repair, piRNA processing, chromatin, nuclear envelope, actin, and mitochondrial dysfunction. The study provides new insights into the formation and maintenance of the karyosome, and its implications in chromatin organization in oocytes.
Article
Multidisciplinary Sciences
Shumpei Morita, Nathalie Oulhen, Stephany Foster, Gary M. Wessel
Summary: By comparing single cell RNA sequencing data of primordial germ cells (PGCs) from two sea urchin species, it was found that there were differences in the expression of the germline gene Nanos2 (Nan2) between the two species. Further analysis revealed that the difference was due to the regulatory element in the 3'UTR region of Nan2 mRNA in one species, which was lacking in the other species. This study highlights the importance of post-transcriptional regulation in germline specification.
Article
Multidisciplinary Sciences
Harmony R. Salzler, Vasudha Vandadi, Benjamin D. McMichael, John C. Brown, Sally A. Boerma, Mary P. Leatham-Jensen, Kirsten M. Adams, Michael P. Meers, Jeremy M. Simon, Robert J. Duronio, Daniel J. McKay, A. Gregory Matera
Summary: Polycomb complexes regulate cell type-specific gene expression programs through heritable silencing. H3K27me3 is essential for this process, while disruption of H3K36 interferes with H3K27me3. Mutants of Drosophila replication-dependent or replication-independent histone H3 genes maintain Polycomb silencing and reach later stages of development, but combined mutants display widespread Hox gene misexpression and fail to develop past the first larval stage. Chromatin profiling revealed that the H3.2K36R mutation disrupts H3K27me3 levels broadly, while H3.3K36R animals are mostly unaffected. Analysis of H3.3 distributions showed the enrichment of H3.3 at presumptive Polycomb response elements located outside of silenced domains.
Article
Multidisciplinary Sciences
Nan Pan, Muhammad Zeeshan Bhatti, Wen Zhang, Bing Ni, Xinpeng Fan, Jiwu Chen
Summary: This study investigated the expression profiles of long non-coding RNAs (lncRNAs) in dormant cysts and vegetative cells of the hypotrich ciliate Pseudourostyla cristata, identifying 853 differentially expressed lncRNAs. Three lncRNAs, DN12058, DN20924 and DN30855, were found to play roles in encystment by regulating various physiological activities essential for the process. The findings provide new insight into the molecular mechanisms regulating encystment in ciliated protozoa.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Antonino Asaro, Rishabhdev Sinha, Magda Bakun, Oleksandra Kalnytska, Anne-Sophie Carlo-Spiewok, Tymon Rubel, Annemieke Rozeboom, Michal Dadlez, Bozena Kaminska, Eleonora Aronica, Anna R. Malik, Thomas E. Willnow
Summary: Sortilin is a neuronal receptor for apoE that plays a crucial role in anti-inflammatory gene expression in the brain. The presence of apoE4 disrupts the interaction between Sortilin and FABP7, leading to impaired lipid signaling and loss of neuroprotective lipid metabolism. This study provides a mechanistic explanation for the impact of these interactions on neuronal lipid homeostasis in Alzheimer's disease.
JOURNAL OF CELL SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Dominique-Maurice Kehlenbeck, Daouda A. K. Traore, Inokentijs Josts, Simon Sander, Martine Moulin, Michael Haertlein, Sylvain Prevost, V. Trevor Forsyth, Henning Tidow
Summary: Researchers have reconstituted MsbA in saposin A-lipoprotein nanoparticles and determined the structure of ADP-vanadate-bound MsbA using single-particle cryo-electron microscopy, resulting in improved resolution and detailed modeling of nucleotide interactions. This approach may be applicable to other dynamic membrane proteins as well.
Article
Cell Biology
Margaux R. Audett, Erin L. Johnson, Jessica M. McGory, Dylan M. Barcelos, Evelin Oroszne Szalai, Marcin R. Przewloka, Thomas J. Maresca
Summary: The N-terminal region (NTR) of KNL1 binds microtubules (MTs) and recruits PP1-87B, while the central disordered region binds SAC proteins through Aurora B kinase phosphorylation, providing a regulatory mechanism for SAC signaling during cell division in Drosophila melanogaster.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Multidisciplinary Sciences
Lukas Gajdos, Matthew P. Blakeley, Michael Haertlein, V. Trevor Forsyth, Juliette M. Devos, Anne Imberty
Summary: The study investigates the interaction mechanism between Pseudomonas aeruginosa lectin and host cells through neutron crystallography, providing insights for designing anti-adhesive compounds against multi-resistance bacterial infections.
NATURE COMMUNICATIONS
(2022)
Article
Medicine, General & Internal
Aleksandra Turek-Jakubowska, Janusz Debski, Maciej Jakubowski, Ewa Szahidewicz-Krupska, Jakub Gawrys, Karolina Gawrys, Agnieszka Janus, Malgorzata Trocha, Adrian Doroszko
Summary: This study used dynamic LC/MS technology to analyze the changes in serum proteome of patients with acute ischemic stroke, and compared them with a control group. The results identified 10 proteins with significantly different serum concentrations between the two groups of volunteers.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Medicine, General & Internal
Karolina Gawrys, Aleksandra Turek-Jakubowska, Jakub Gawrys, Maciej Jakubowski, Janusz Debski, Ewa Szahidewicz-Krupska, Malgorzata Trocha, Arkadiusz Derkacz, Adrian Doroszko
Summary: The aim of this dynamic LC-MS proteomic study in human platelets was to identify potential protein candidates for biomarkers of acute ischemic stroke (AIS), assess their changes during the acute phase of stroke, and define new drug targets. The study found differences in platelet proteins between AIS patients and healthy controls, and identified Thymidine Phosphorylase 4 (TYMP-4) as a promising drug target for the management or prevention of ischemic stroke.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Aleksandra Robak, Michal Kistowski, Grzegorz Wojtas, Anna Perzanowska, Tomasz Targowski, Agata Michalak, Grzegorz Krasowski, Michal Dadlez, Dominik Domanski
Summary: This study developed a mass spectrometry-based multiple reaction monitoring-protein panel assay to determine the cause of pleural effusion (PE) and discriminate between different types of PE. The study identified specific infection/inflammation markers for different types of infectious PEs and cancer markers for cancerous PEs. The approach and markers have the potential to assist in clinical diagnosis and guide therapy decisions in the future.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Aniruddha Das, Pankaj Thapa, Ulises Santiago, Nilesh Shanmugam, Katarzyna Banasiak, Katarzyna Dabrowska, Hendrik Nolte, Natalia A. Szulc, Rose M. Gathungu, Dominik Cysewski, Marcus Krueger, Michal Dadlez, Marcin Nowotny, Carlos J. Camacho, Thorsten Hoppe, Wojciech Pokrzywa
Summary: The study revealed that UFD-2 binding enhances cooperation between CHN-1 and ubiquitin-conjugating E2 enzymes, while HSP70/HSP-1 chaperone protein restricts this cooperation, leading CHN-1 to an autoinhibited state. This finding elucidates the molecular mechanism underlying the synergistic cooperation of CHN-1 and UFD-2 in substrate ubiquitylation.
Article
Biochemistry & Molecular Biology
Tetiana Bondarchuk, Vyacheslav F. Shalak, Dmytro M. Lozhko, Agnieszka Fatalska, Roman H. Szczepanowski, Vladyslava Liudkovska, Oleksandr Yu Tsuvariev, Michal Dadlez, Anna El'skaya, Boris S. Negrutskii
Summary: Protein synthesis in eukaryotic cells is compartmentalized, ensuring high efficiency. Higher eukaryotes have stable multi-protein complexes of aminoacyl-tRNA synthetases and translation elongation factors. The human guanine-nucleotide exchange factor (GEF) complex eEF1B is organized in a quaternary structure, with alpha, beta, and gamma subunits forming a heterotrimeric form eEF1B(alpha beta gamma)(3). This unique assembly of GEFs within a stable complex serves as a "GEF hub" that maintains the translationally active GTP-bound conformation of eEF1A in higher eukaryotes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Tatiana N. Murugova, Oleksandr I. Ivankov, Yury L. Ryzhykau, Dmytro V. Soloviov, Kirill V. Kovalev, Daria V. Skachkova, Adam Round, Christian Baeken, Andrii V. Ishchenko, Oleksandr A. Volkov, Andrey V. Rogachev, Alexey V. Vlasov, Alexander I. Kuklin, Valentin I. Gordeliy
Summary: Despite remarkable progress in LCP and 'bicelle' crystallization, the lack of structural information remains a bottleneck in membrane protein research. This study uses small-angle scattering to investigate the evolution of the bicelle crystallization matrix during MP crystal growth and reveals the mechanisms of bicelle MP crystallization, providing support for rational design of crystallization.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Jaydeep Patel, Adam Round, Johan Bielecki, Katerina Doerner, Henry Kirkwood, Romain Letrun, Joachim Schulz, Marcin Sikorski, Mohammad Vakili, Raphael de Wijn, Andrew Peele, Adrian P. Mancuso, Brian Abbey
Summary: This article explores the application of liquid sample delivery systems in XFEL experiments and proposes an algorithm that uses machine vision to automatically align the X-ray beam and liquid jet. The performance of the algorithm is evaluated by comparing it with manual analysis, and it achieves a success rate of 0.98 in identifying hits among four different nozzle designs.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2022)
Article
Biochemistry & Molecular Biology
Iwona Maria Pranke, Benoit Chevalier, Aiswarya Premchandar, Nesrine Baatallah, Kamil F. Tomaszewski, Sara Bitam, Danielle Tondelier, Anita Golec, Jan Stolk, Gergely L. Lukacs, Pieter S. Hiemstra, Michal Dadlez, David A. Lomas, James A. Irving, Agnes Delaunay-Moisan, Eelco van Anken, Alexandre Hinzpeter, Isabelle Sermet-Gaudelus, Aleksander Edelman
Summary: Early recognition and enhanced degradation of misfolded proteins by the endoplasmic reticulum (ER) quality control and ER-associated degradation (ERAD) are important mechanisms. This study found that decreasing Keratin 8 (K8) expression increased the secretion of misfolded Z-alpha-1-antitrypsin (Z-A1AT) protein and F508del-CFTR protein. K8 was shown to regulate the Hrd1-governed ERAD pathway and may act as a scaffolding protein in ERAD complexes. Targeting K8-containing ERAD complexes could be a promising strategy for the treatment of alpha-1-antitrypsin deficiency (A1ATD).
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Gianluca Amadei, David M. M. Glover
Summary: Studies have found that stem cells can self-assemble in the culture dish to mimic early embryonic development. These stem cell-derived models can imitate cell movements and gene expression patterns of gastrulation, and even develop into different organs and tissues. This article explores the journey of discovering and understanding these stem cell capabilities.
Article
Biology
Levente Kovacs, Agnieszka Fatalska, David M. Glover
Summary: In this study, a 24-amino-acid sequence from the tail anchor domain of the Drosophila proapoptotic protein Hid was used to target exogenous proteins to the mitochondria in Drosophila cells. It was found that Drosophila Sas6 can bind both Drosophila Gorab and its human GORAB ortholog, whereas human SAS6 is unable to bind either GORAB or Gorab. These findings are discussed in relation to the evolutionary conservation of Gorab and the divergence of Sas6.
Review
Biology
A. L. Sperling, D. M. Glover
Summary: Parthenogenesis is widely observed in animals, but remains understudied. In dipterans, it is of particular importance due to the presence of parthenogenetic species that are disease vectors and agricultural pests. This study presents a catalog of parthenogenetic dipterans, explores the genetic basis of parthenogenesis, and discusses the evolutionary significance of parthenogenesis in this order.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)