Review
Neurosciences
Taehyun Kim, Sejin Kim, Joonyoung Kang, Minjae Kwon, Sue-Hyun Lee
Summary: Sleep deprivation adversely affects cognitive abilities, particularly memory consolidation and cognitive control functions. This review examines the consistency of previous studies on the impact of sleep deprivation on behavioral performance, considering variations in stimuli and tasks. Neural response changes associated with these behavioral changes are also examined using human fMRI studies. Additionally, the potential influence of light on sleep cycles and cognitive processes is discussed.
FRONTIERS IN NEUROSCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Hamid Ahmadi, Leili Aghebati-Maleki, Shima Rashidiani, Timea Csabai, Obodo Basil Nnaemeka, Julia Szekeres-Bartho
Summary: Assisted reproductive technologies (ART) increase the chances of successful pregnancy and live birth in infertile couples. However, concerns have been raised about the potential long-term health consequences of ART-conceived babies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Larisa Dubrovsky, Beda Brichacek, N. M. Prashant, Tatiana Pushkarsky, Nigora Mukhamedova, Andrew J. Fleetwood, Yangsong Xu, Dragana Dragoljevic, Michael Fitzgerald, Anelia Horvath, Andrew J. Murphy, Dmitri Sviridov, Michael I. Bukrinsky
Summary: A possible explanation for chronic inflammation in HIV-infected individuals treated with anti-retroviral therapy is hyperreactivity of myeloid cells due to a phenomenon called trained immunity. Here, we demonstrate that human monocyte-derived macrophages originating from monocytes initially treated with extracellular vesicles containing HIV-1 protein Nef (exNef), but differentiating in the absence of exNef, release increased levels of pro-inflammatory cytokines after lipopolysaccharide stimulation. This effect is associated with chromatin changes at the genes involved in inflammation and cholesterol metabolism pathways and upregulation of the lipid rafts and is blocked by methyl-beta-cyclodextrin, statin, and an inhibitor of the lipid raft-associated receptor IGF1R. Bone-marrow-derived macrophages from exNef-injected mice, as well as from mice trans-planted with bone marrow from exNef-injected animals, produce elevated levels of tumor necrosis factor alpha (TNF-alpha) upon stimulation. These phenomena are consistent with exNef-induced trained immunity that may contribute to persistent inflammation and associated co-morbidities in HIV-infected individuals with unde-tectable HIV load.
Article
Medicine, General & Internal
Mario Henriquez-Beltran, Ivan Benitez, Thalia Belmonte, Jorge Jorquera, Jorge Jorquera-Diaz, Igor Cigarroa, Matias Burgos, Rocio Sanhueza, Claudia Jeria, Isabel Fernandez-Bussy, Estefania Nova-Lamperti, Ferran Barbe, Adriano Targa, Gonzalo Labarca
Summary: This study evaluates the impact of ARDS on sleep and circadian rest-activity rhythm of COVID-19 survivors twelve months after hospital discharge. The findings show that the majority of survivors had poor sleep quality and a high prevalence of sleep disorders after twelve months. However, there was no significant improvement in sleep or circadian rest-activity rhythm between four and twelve months, or between the ARDS and non-ARDS groups.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Plant Sciences
Xiuxiu Yan, Jing An, Lijie Zhang, Lingyan Zhang, Xu Zhou, Shuhe Wei
Summary: In this study, the ecotoxicological effects and bioaccumulation of triclosan (TCS) in E. crassipes were investigated through 28-day exposure experiments. The results showed that TCS had different effects on chlorophyll content and soluble protein concentration in E. crassipes, and also affected the activity of antioxidant enzymes. Differentially expressed genes were observed in the roots of E. crassipes after exposure to TCS, and the TCS content in roots and leaves increased with exposure time. These findings provide experimental data to assess the ecological risk of long-term exposure to TCS in aquatic systems.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Tal Falick Michaeli, Ofra Sabag, Rimma Fok, Batia Azria, Jonathan Monin, Yuval Nevo, Yuval Gielchinsky, Benjamin P. Berman, Howard Cedar, Yehudit Bergman
Summary: Muscle injury activates stem cells and changes their methylation pattern to facilitate myocyte differentiation. This change can also occur in satellite cells from other muscles and in muscle stem cells (MuSCs) of female animals following pregnancy.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Neurosciences
Martyna Rakowska, Mahmoud E. A. Abdellahi, Paulina Bagrowska, Miguel Navarrete, Penelope A. Lewis
Summary: The effects of TMR on task performance can last for at least 10 days post-encoding, with time spent in stage 2 of NREM sleep predicting cueing benefit. In addition, there is a significant increase in spindle density and SO-spindle coupling during the cue period, highlighting their importance in procedural memory consolidation.
Article
Biochemistry & Molecular Biology
Candice Brinkmeyer-Langford, Katia Amstalden, Kranti Konganti, Andrew Hillhouse, Koedi Lawley, Aracely Perez-Gomez, Colin R. Young, C. Jane Welsh, David W. Threadgill
Summary: By infecting genetically diverse Collaborative Cross (CC) mouse strains, a broader spectrum of phenotypic outcomes were identified, and different TMEV response profiles were categorized into resistant, susceptible, and resilient groups. Each profile had a distinct gene expression signature, allowing the identification of pathways and networks specific to each TMEV response group.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Masato Okuda, Akiko Noda, Kunihiro Iwamoto, Honoka Nakashima, Kozue Takeda, Seiko Miyata, Fumihiko Yasuma, Norio Ozaki, Akito Shimouchi
Summary: Research shows that long sleep duration and irregular sleep-wake rhythm in older adults may have adverse effects on executive function and working memory.
SCIENTIFIC REPORTS
(2021)
Review
Endocrinology & Metabolism
Si-Ke He, Jia-Hao Wang, Tao Li, Shan Yin, Jian-Wei Cui, Yun-Fei Xiao, Yin Tang, Jia Wang, Yun-Jin Bai
Summary: This article reviews the relationship between circadian rhythm disturbance and kidney stone disease (KSD), summarizing the risk factors and treatment methods. The results indicate that KSD is associated with systemic disorders such as metabolic syndrome, inflammatory bowel disease, and microbiome dysbiosis, and some chronotherapies have been proven effective.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Physiology
Zikun Wang, Samantha Lincoln, Andrew D. D. Nguyen, Wanhe Li, Michael W. W. Young
Summary: Chronic sleep loss disrupts the rhythmic gene expression, and aging contributes to this disruption.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Environmental Sciences
Thomas Sol Dourdin, Guillaume Riviere, Alexandre Cormier, Carole Di Poi, Killian Guyomard, Manuella Rabiller, Farida Akcha, Thierno Bah Sadialiou, Pauline Le Monier, Rossana Sussarellu
Summary: Early exposure to an environmentally relevant pesticide mixture induces multi-scale latent effects possibly affecting life history traits in the Pacific oyster, Crassostrea gigas. The study found that exposure to a combination of 18 pesticides and metals at environmental concentrations during the embryo-larval stage resulted in disturbed swimming behavior, increased size and weight at specific time points, and altered expression of development-related genes. Additionally, DNA methylation analyses showed significant modifications in exposed larvae, marked by a demethylation trend.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biology
Carol A. Edwards, William M. D. Watkinson, Stephanie B. Telerman, Lisa C. Hulsmann, Russell S. Hamilton, Anne C. Ferguson-Smith, Deborah Bourc'his
Summary: In mice and humans, imprinting genes play important roles in development, behavior, and post-natal adaptations. Failure to properly imprint genes in humans is associated with various disorders and diseases. Researchers have used RNA-seq technologies and hybrid mouse strains to identify novel imprinted genes, leading to an increase in reported genes with parental origin-specific expression bias. However, validation experiments show that many of these genes are not genuine imprinted genes and that the mouse strain has a greater influence on expression biases than parental origin.
Review
Biochemistry & Molecular Biology
Marie Gombert, Pilar Codoner-Franch
Summary: Melatonin present in breast milk has various positive effects on infant health, such as regulating the infant's circadian rhythm, providing antioxidant properties, modulating inflammation, and shaping the gut microbiota. These actions help limit weight gain in infants and reduce the risk of obesity and related comorbidities over time.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Volker Roettgen, Lisa-Maria Tuemmler, Dirk Koczan, Alexander Rebl, Bjoern Kuhla, Jens Vanselow, Anja Baufeld
Summary: This study analyzed the effects of milk replacer feeding on the number and gene expression characteristics of granulosa cells in cattle. The results showed that the number of granulosa cells in puberty was not affected by the number of follicles in the group fed less milk replacer, while in the group fed more milk replacer, the number of granulosa cells increased with the number of follicles. The gene expression analysis revealed that feeding different milk replacers can affect immune response pathways.
Article
Microbiology
Fanny Wegner, Tim Roloff, Michael Huber, Samuel Cordey, Alban Ramette, Yannick Gerth, Claire Bertelli, Madlen Stange, Helena M. B. Seth-Smith, Alfredo Mari, Karoline Leuzinger, Lorenzo Cerutti, Keith Harshman, Ioannis Xenarios, Philippe Le Mercier, Pascal Bittel, Stefan Neuenschwander, Onya Opota, Jonas Fuchs, Marcus Panning, Charlotte Michel, Marie Hallin, Thomas Demuyser, Ricardo De Mendonca, Paul Savelkoul, Jozef Dingemans, Brian van der Veer, Stefan A. Boers, Eric C. J. Claas, Jordy P. M. Coolen, Willem J. G. Melchers, Marianne Gunell, Teemu Kallonen, Tytti Vuorinen, Antti J. Hakanen, Eva Bernhoff, Marit Andrea Klokkhammer Hetland, Hadar Golan Berman, Sheera Adar, Jacob Moran-Gilad, Dana G. Wolf, Stephen L. Leib, Oliver Nolte, Laurent Kaiser, Stefan Schmutz, Verena Kufner, Maryam Zaheri, Alexandra Trkola, Hege Vangstein Aamot, Hans H. Hirsch, Gilbert Greub, Adrian Egli
Summary: This pilot external quality assessment aimed to improve pathogen surveillance sequencing by establishing a framework between laboratories. Participating laboratories used different methods and analysis pipelines, but most were able to generate complete genomes. There was consensus on the majority of reporting criteria, although discrepancies were found in lineage and cluster assignments. The pilot program was considered successful, highlighting the high quality of participating laboratories and providing valuable feedback.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Immunology
Tiia Snaekae, Amel Bekkar, Chantal Desponds, Florence Prevel, Stephanie Claudinot, Nathalie Isorce, Filipa Teixeira, Coline Grasset, Ioannis Xenarios, Isabel C. Lopez-Mejia, Lluis Fajas, Nicolas Fasel
Summary: Mitochondria regulate steroid hormone synthesis and sex hormones regulate mitochondrial function. NLRX1 attenuates inflammation and modulates metabolic functions. NLRX1 attenuates inflammation in female mice but not in male mice.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Rick Wertenbroek, Simone Rubinacci, Ioannis Xenarios, Yann Thoma, Olivier Delaneau
Summary: In this study, a new file format called XSI is proposed, which has a smaller storage footprint and allows for computation, thus improving the efficiency of genotype data analysis.
Article
Genetics & Heredity
Clemence S. Hurni, Benjamin Weger, Cedric S. Gobet, Felix Naef
Summary: This study analyzed the temporal regulation of RNA synthesis, splicing, nuclear export, and degradation in eukaryotes, specifically focusing on the circadian cycle. The researchers found that nuclear export contributes to the modulation and generation of rhythmic profiles of 10% of the cycling nuclear mRNAs.
Article
Immunology
Amel Bekkar, Nathalie Isorce, Tiia Snaka, Stephanie Claudinot, Chantal Desponds, Dmitry Kopelyanskiy, Florence Prevel, Marta Reverte, Ioannis Xenarios, Nicolas Fasel, Filipa Teixeira
Summary: This study investigates the impact of Leishmania and LRV1 on macrophage response using RNA sequencing and gene correlation network analysis. The results reveal a strong and sustained effect of LRV1 on macrophage response and uncover several genes and regulatory networks associated with infection.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Nastassia Gobet, Maxime Jan, Paul Franken, Ioannis Xenarios
Summary: Genetic variations have an impact on behavior and disease, but understanding how these variations contribute to complex traits is still a question. One common approach is to link genetic variants to intermediate phenotypes, such as the transcriptome, using RNA-sequencing. However, the variants between samples are often ignored in the initial analysis, which can lead to biased transcriptome estimation. In this study, the researchers assessed the impact of reference-based analysis on the transcriptome and expression quantitative trait locus (eQTLs) in a mouse genetic population. They found that using custom references improved downstream analysis compared to using the classical genome reference.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Jake Yeung, Maria Florescu, Peter Zeller, Buys Anton de Barbanson, Max D. Wellenstein, Alexander Oudenaarden
Summary: scChIX-seq is a novel experimental and computational framework that allows mapping of multiple histone marks in single cells. This method enables systematic analysis of the interplay between histone modifications in individual cells.
NATURE BIOTECHNOLOGY
(2023)
Article
Genetics & Heredity
Peter Zeller, Jake Yeung, Helena Vinas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, Alexander van Oudenaarden
Summary: Post-translational histone modifications impact chromatin activity and gene expression. Lineage choice in single cells and the underlying chromatin states remain understudied. Using sortChIC, we map active and repressive histone modifications in mouse bone marrow, revealing cell-type-specific dynamic changes. Lineage choice occurs at the progenitor stage, while chromatin dynamics differentiate differentiation trajectories and lineages in hematopoiesis.
Article
Multidisciplinary Sciences
Lorenzo Talamanca, Cedric Gobet, Felix Naef
Summary: The study revealed that the circadian clock regulates human physiology, but the specific gene expression rhythms and their dependence on age and sex in humans were not well-defined. By combining data from the GTEx project and an algorithm, the researchers identified mRNA rhythms in 46 tissues and found that they varied in breadth and were affected by sex and age. The overall gene expression rhythms were more sustained in females, while rhythmic programs generally dampened with age.
Meeting Abstract
Endocrinology & Metabolism
Valerie Schwitzgebel, Ingrida Stankute, Cedric Howald, Jean-Louis Blouin, Rasa Verkauskiene, Ioannis Xenarios
HORMONE RESEARCH IN PAEDIATRICS
(2023)
Article
Genetics & Heredity
Alysha S. Taylor, Dinis Barros, Nastassia Gobet, Thierry Schuepbach, Branduff McAllister, Lorene Aeschbach, Emma L. Randall, Evgeniya Trofimenko, Eleanor R. Heuchan, Paula Barszcz, Marc Ciosi, Joanne Morgan, Nathaniel J. Hafford-Tear, Alice E. Davidson, Thomas H. Massey, Darren G. Monckton, Lesley Jones, Ioannis Xenarios, Vincent Dion
Summary: The study shows that targeted DNA sequencing methods can efficiently measure the size of short tandem repeats, which is important for diagnostic tests and preclinical studies. Researchers have developed an algorithm called Repeat Detector (RD) that accurately counts repeats in targeted sequencing data and determines repeat instability. This method does not require prior knowledge of flanking sequences and is highly versatile.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Margit Noukas, Marili Palover, Maarja Lepamets, Lucilla Pizzo, Kelli Lehto, Anu Reigo, Helene Alavere, Liis Leitsalu, Emmanouil Theophilos Dermitzakis, Ioannis Xenarios, Mait Metspalu, Alexandre Reymond, Santhosh Girirajan, Neeme Tonisson, Katrin Mannik
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Clinical Neurology
Nina Dukanovic, Francesco La Spada, Yann Emmenegger, Guy Niederhauser, Frederic Preitner, Paul Franken
Summary: The study found that sleep deprivation did not alter clock gene expression in the cortex of mice, and although food intake during sleep deprivation did not differ from baseline, mice lost weight and increased food intake during subsequent recovery. This suggests that the effects commonly attributed to sleep loss during sleep deprivation may actually be related to the resulting energy deficit from food deprivation.
Meeting Abstract
Endocrinology & Metabolism
Patrick Forny, Ximena Bonilla, David Lamparter, Wenguang Shao, Tanja Plessl, Caroline Frei, Anna Bingisser, Sandra Goetze, Audrey Van Drogen, Keith Harshman, Patrick Pedrioli, Florian Traversi, Ioannis Xenarios, Ruedi Aebersold, Nicola Zamboni, Gunnar Ratsch, Emmanouil Dermitzakis, Bernd Wollscheid, D. Sean Froese, Matthias R. Baumgartner
MOLECULAR GENETICS AND METABOLISM
(2022)