Article
Biology
Jitka Kucerova, Alois Zdrha, Abhishek Shinde, Karel Harant, Ivan Hrdy, Jan Tachezy
Summary: This study investigated the distribution of ERMES in organisms with hydrogenosomes and used Trichomonas vaginalis as a model to estimate the cellular localization, structure, and function of ERMES.
Article
Multidisciplinary Sciences
Mattia Giacomelli, Maria Eleonora Rossi, Jesus Lozano-Fernandez, Roberto Feuda, Davide Pisani
Summary: Genomic data has helped in the understanding of the Tree of Life, but certain nodes remain unresolved. By using simulated datasets, this study found that recoding amino acid data can improve the accuracy of phylogenetic inference. The results suggest that the placement of comb jellies as sister to all other animals in phylogenies inferred from amino acid sequences is likely a tree reconstruction artifact.
Article
Biochemistry & Molecular Biology
Justyna Zitek, Zoltan Fussy, Sebastian C. Treitli, Priscila Pena-Diaz, Zuzana Vaitova, Daryna Zavadska, Karel Harant, Vladimir Hampl
Summary: The loss of mitochondria in oxymonad protists is related to the redirection of the essential Fe-S cluster assembly to the cytosol. However, as our understanding of diverse free-living protists expands, the list of functions of their mitochondrial-related organelles (MROs) also expands. By accurately analyzing the proteome of the MRO in Paratrimastix pyriformis, a close relative of oxymonads, we discovered another function, which involves the production of folate derivatives with one-carbon units and formate. These derivatives are likely to be used by the cytosolic methionine cycle.
Article
Biochemical Research Methods
Nadine Zimmann, Petr Rada, Vojtech Zarsky, Tamara Smutna, Kristina Zahonova, Joel Dacks, Karel Harant, Ivan Hrdy, Jan Tachezy
Summary: This study investigates the lysosomal proteome of the parasitic protist Trichomonas vaginalis and reveals the involvement of lysosomes in hydrolase secretion. The study also suggests that T. vaginalis utilizes glycosylation as a recognition marker for lysosomal hydrolases.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Evolutionary Biology
Peter G. Foster, Dominik Schrempf, Gergely J. Szollosi, Tom A. Williams, Cymon J. Cox, T. Martin Embley
Summary: Long branches and compositional heterogeneity in protein sequences can pose problems in phylogenetic reconstruction. Recoding alignments can help mitigate these issues, but the effectiveness depends on the specific characteristics of the data. Exchangeability-based recoding generally improves accuracy, while Chi-squared-based recoding may decrease accuracy. However, the impact of recoding on accuracy varies when dealing with alignments that exhibit different types of compositional heterogeneity. It is important to exercise caution when interpreting trees generated from recoded amino acid data sets and consider alternative models that directly account for the patterns in the data.
SYSTEMATIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Jorie Clark, Anders E. Carlson, Alberto Reyes, Elizabeth C. B. Carlson, Louise Guillaume, Glenn A. Milne, Lev Tarasov, Marc Caffee, Klaus Wilcken, Dylan H. Rood
Summary: The Clovis-first model suggests the migration of humans in the Americas occurred through the Ice-Free Corridor (IFC) between the retreating Cordilleran and Laurentide ice sheets. However, new archaeological and ancient genomic evidence suggests earlier migrations before the Clovis people, possibly through a Pacific coast route. Uncertainties in the IFC's opening age allow for the possibility of an earlier opening, consistent with a migration route around 15.5 to 16.0 ka. Using cosmogenic exposure ages, this study establishes the full opening of the IFC at 13.8 +/- 0.5 ka, proving it was not available for the initial peopling of the Americas after the Last Glacial Maximum, while supporting an earlier availability as a coastal migration route based on geochronological data from the Pacific coast.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Book Review
Multidisciplinary Sciences
Jeffrey M. Perkel
Summary: Now forgotten in drawers, handheld predecessors of modern computers marked the beginning of an era of easy calculation, achieved after 42,000 years of innovation.
Review
Immunology
Hui Yin, Na Liu, Jie Chen
Summary: The intestine plays an important role in the balance of uric acid in the body. Intestinal uric acid transporters and intestinal flora have an impact on uric acid excretion, providing new ideas for the treatment of hyperuricemia and gout.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Javier G. Serrano, Alejandra C. C. Ordonez, Jonathan Santana, Elias Sanchez-Canadillas, Matilde Arnay, Amelia Rodriguez-Rodriguez, Jacob Morales, Javier Velasco-Vazquez, Veronica Alberto-Barroso, Teresa Delgado-Darias, M. Carmen Cruz de Mercadal, Juan Carlos Hernandez, Marco A. Moreno-Benitez, Jorge Pais, Harald Ringbauer, Martin Sikora, Hugh McColl, Maria Pino-Yanes, Mariano Hernandez Ferrer, Carlos D. Bustamante, Rosa Fregel
Summary: In this study, the authors used paleogenomic data from the indigenous people of the Canary Islands to investigate the Prehistory of North Africa and how genetics were influenced by isolation and resource availability. They found that the native population of the Canary Islands showed genetic signatures related to Bronze Age expansions in Eurasia and trans-Saharan migrations, in addition to components already present in Moroccan Neolithic populations. The lack of gene flow between islands and constant or decreasing population sizes indicate isolation. The researchers also observed variations in genetic diversity among islands, with islands with fewer natural resources exhibiting greater effects of insularity and isolation. Lastly, there were consistent genetic differences between eastern and western islands, suggesting a more complex colonization process than previously thought.
NATURE COMMUNICATIONS
(2023)
Review
Environmental Sciences
Ankit Majie, Rajdeep Saha, Biswatrish Sarkar
Summary: The human monkeypox virus (MPXV) was first identified in 1959 and has experienced sporadic incidence since then. While it was originally endemic to central and western Africa, it has started spreading to non-endemic regions across North and South America, Europe, and Asia since 2017. As of May 2022, non-endemic areas have reported 62,635 cases of infection, with a mortality rate of less than 0.2%. The virus can cause various symptoms and complications, and its transmission is linked to factors such as improper handling of bushmeat, unprotected sexual intercourse, and contact with infected individuals.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Editorial Material
Medicine, General & Internal
Abraham Verghese
Summary: "The Covenant of Water" is a new novel by Abraham Verghese that tells the story of a family in South India over the 20th century. In this family, at least one member per generation is destined to die by drowning.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2023)
Review
Biology
Simona Francia, Claudia Lodovichi
Summary: This article discusses the role of odorant receptors (ORs) in the olfactory system, including their dual roles in detecting odorants in olfactory sensory neurons and guiding sensory axons to precise target locations in the brain, as well as recent findings on the mechanisms of activation and function of axonal ORs.
Review
Immunology
Weidong Zhang, Ling Gao, Wenhao Ren, Shaoming Li, Jingjing Zheng, Shasha Li, Chunmiao Jiang, Shuying Yang, Keqian Zhi
Summary: Medication-related osteonecrosis of the jaw (MRONJ) is a rare but serious adverse drug effect, with hypotheses involving reduced bone remodeling, infection, inflammation, and bisphosphonates-induced immune dysfunction. Treatment with bisphosphonates disrupts mucosal and osteo immune homeostasis, impairing the body's ability to resist infection and repair from injury, contributing to the development of MRONJ.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Donald J. Benton, Antoni G. Wrobel, Chloe Roustan, Annabel Borg, Pengqi Xu, Stephen R. Martin, Peter B. Rosenthal, John J. Skehel, Steven J. Gamblin
Summary: Studies indicate that the G614 mutant spike adopts more open conformations, which may facilitate binding to the SARS-CoV-2 receptor ACE2 and the subsequent structural rearrangements required for viral membrane fusion.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Engineering, Marine
Sergey Smirnov, Grigory Dolgikh, Igor Yaroshchuk, Alexander Lazaryuk, Alexandra Kosheleva, Alex Shvyrev, Alexander Pivovarov, Aleksandr Samchenko
Summary: This study investigates the features of resonant oscillations in the water column of the Peter the Great Gulf of the Sea of Japan. In situ measurements and numerical simulations were used to determine the characteristic spatio-temporal parameters of these oscillations. The results indicate the possibility of resonant amplification of level fluctuations by wave and periodic wind effects.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Joeri van Strien, Alexander Haupt, Uwe Schulte, Hans-Peter Braun, Alfredo Cabrera-Orefice, Jyoti S. Choudhary, Felix Evers, Erika Fernandez-Vizarra, Sergio Guerrero-Castillo, Taco W. A. Kooij, Petra Palenikova, Mercedes Pardo, Cristina Ugalde, Ilka Wittig, Lars Woehlbrand, Ulrich Brandt, Susanne Arnold, Martijn A. Huynen
Summary: Complexome profiling is a new method to study protein complexes systematically, while the CEDAR database provides an openly accessible platform for storing and exploring these data, facilitating research on protein complex composition and dynamics across biological systems.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Biochemical Research Methods
Ramiro Magno, Isabel Duarte, Ana-Teresa Maia
Summary: The PGS Catalog is an open database that contains 721 polygenic scores from over 133 publications, with the REST API being the only method for programmatic access. The quincunx R package provides a client interface to the PGS Catalog REST API, allowing users to query, retrieve, filter, and integrate metadata associated with polygenic scores in tidy table format.
Article
Endocrinology & Metabolism
Selma L. van Esveld, Richard J. Rodenburg, Fathiya Al-Murshedi, Eiman Al-Ajmi, Sana Al-Zuhaibi, Martijn A. Huynen, Johannes N. Spelbrink
Summary: In this study, two patients with a mutation in the SUPV3L1 gene were reported. They showed a neurodegenerative phenotype characterized by progressive spastic paraparesis, growth restriction, hypopigmentation, and predisposition to autoimmune disease. The mutation resulted in reduced expression of the truncated protein, decreased levels of mature mRNA, and accumulation of double-stranded RNA. Lentiviral complementation with the full-length SUPV3L1 gene partially restored the RNA abnormalities, indicating that the mutation is pathogenic and causes the disease.
JOURNAL OF INHERITED METABOLIC DISEASE
(2022)
Article
Multidisciplinary Sciences
Isabel Duarte, Gil Carraco, Nayara T. D. de Azevedo, Vladimir Benes, Raquel P. Andrade
Summary: MicroRNAs in chick embryos have been identified and shown to potentially play important roles in regulating early vertebrate embryo development. This discovery is significant for the avian research community and can lead to further experimental testing of new miRNAs.
Article
Immunology
Joshua Gillard, Bastiaan A. Blok, Daniel R. Garza, Prashanna Balaji Venkatasubramanian, Elles Simonetti, Marc J. Eleveld, Guy A. M. Berbers, Pieter G. M. van Gageldonk, Irma Joosten, Ronald de Groot, L. Charlotte J. de Bree, Reinout van Crevel, Marien de Jonge, Martijn A. Huynen, Mihai G. Netea, Dimitri A. Diavatopoulos
Summary: This study demonstrates that prior Bacille Calmette-Guerin (BCG) vaccination enhances immune responses to pertussis vaccines. Simultaneous BCG and acellular pertussis (aP) vaccinations do not show the same effect. Biomarkers of trained immunity are identified as the most reliable correlates of the enhanced immune responses.
Editorial Material
Multidisciplinary Sciences
Martijn A. Huynen, Dei M. Elurbe
Article
Medicine, General & Internal
Karolina M. Andralojc, Duaa Elmelik, Menno Rasing, Bernard Pater, Albert G. Siebers, Ruud Bekkers, Martijn A. Huynen, Johan Bulten, Diede Loopik, Willem J. G. Melchers, William P. J. Leenders
Summary: This study examined the potential of ciRNAseq-testing on cervical scrapes to identify hrHPV-positive women at risk of having or developing high-grade CIN. By detecting gene expression data and applying machine learning, the risk of CIN can be calculated. Further improvement in the model to increase specificity is warranted in larger cohorts.
Review
Biochemistry & Molecular Biology
G. A. C. Franken, M. A. Huynen, L. A. Martinez-Cruz, R. J. M. Bindels, J. H. F. de Baaij
Summary: Magnesium plays a vital role in cellular processes and disturbances in its levels can result in cell growth delay and metabolic defects. This review compares the structure and function of magnesium transporters in prokaryotes and eukaryotes, highlighting the conserved motifs and selectivity pore. It also discusses the unique features of TRP channels in eukaryotes that contribute to magnesium transport capacity.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Michele Brischigliaro, Alfredo Cabrera-Orefice, Mattia Sturlese, Dei M. Elurbe, Elena Frigo, Erika Fernandez-Vizarra, Stefano Moro, Martijn A. Huynen, Susanne Arnold, Carlo Viscomi, Massimo Zeviani
Summary: The composition of cytochrome c oxidase (COX) is functionally conserved between vertebrate and invertebrate species, despite potential differences in individual structures.
Article
Oncology
Lizelle Correia, Ramiro Magno, Joana M. Xavier, Bernardo P. de Almeida, Isabel Duarte, Filipa Esteves, Marinella Ghezzo, Matthew Eldridge, Chong Sun, Astrid Bosma, Lorenza Mittempergher, Ana Marreiros, Rene Bernards, Carlos Caldas, Suet-Feung Chin, Ana-Teresa Maia
Summary: PIK3CA mutations are common in breast cancer, and there is an allelic expression imbalance between the mutant and wild-type alleles. Preferential expression of the mutant allele is associated with poor prognosis, and ER-, PR-, and HER2+ tumors show significant preferential expression of the mutant allele.
Review
Microbiology
Mariano A. Molina, Britt A. Coenen, William P. J. Leenders, Karolina M. Andralojc, Martijn A. Huynen, Willem J. G. Melchers
Summary: Cervical cancer is the third leading cause of female cancers globally, primarily caused by persistent infections with high-risk human papillomaviruses. The composition of the cervicovaginal microenvironment plays a role in hrHPV infections, disease progression, and regression.
Article
Biotechnology & Applied Microbiology
Mariano A. Molina, Karolina M. Andralojc, Martijn A. Huynen, William P. J. Leenders, Willem J. G. Melchers
Summary: This study utilized ciRNAseq technology to analyze a large cohort of cervical smears and identified subgroups of CSTs, showing the associations between different subgroups and specific bacterial abundances as well as certain diseases. These findings are of significance for understanding women's cervical health and hrHPV-related disease progression.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Multidisciplinary Sciences
Evi van Schuppen, Janeri Froberg, Prashanna Balaji Venkatasubramanian, Pauline Versteegen, Hans de Graaf, Jana Holubova, Joshua Gillard, Pieter G. M. van Gageldonk, Irma Joosten, Ronald de Groot, Peter Sebo, Guy A. M. Berbers, Robert C. Read, Martijn A. Huynen, Marien de Jonge, Dimitri A. Diavatopoulos
Summary: This study investigates how prior exposure to Bordetella pertussis shapes the mucosal antibody response to booster vaccination using a mutant strain lacking antigens of the acellular pertussis vaccine.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Tania Barata, Isabel Duarte, Matthias E. Futschik
Summary: Stem cells possess the ability to self-renew and differentiate, making them crucial in processes like development and aging. By comparing multiple stem cell samples, a significant overlap in gene signatures was found, leading to the identification of integrated stemness signatures (ISSs). These ISSs provide a more reliable basis for research by excluding false positives.
Article
Ecology
Daniel R. Garza, F. A. Bastiaan von Meijenfeldt, Bram van Dijk, Annemarie Boleij, Martijn A. Huynen, Bas E. Dutilh
Summary: We introduce a computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics.
BMC ECOLOGY AND EVOLUTION
(2022)