Article
Biology
Wellington S. Miranda, Q. Cong, A. L. Schaefer, E. K. MacLeod, A. Zimenko, D. Baker, E. P. Greenberg
Summary: Researchers have identified selectivity residues within AHL synthases and receptors using covariation methods, demonstrating their importance in the Las system. This study deepens the understanding of how communication systems evolve and diversify.
Article
Computer Science, Interdisciplinary Applications
Allan Haldane, Ronald M. Levy
Summary: Inverse Ising inference is a method used in protein physics to infer coupling parameters of a Potts/Ising model based on observed site-covariation. The Mi3-GPU software, utilizing GPU-accelerated Markov-Chain Monte Carlo sampling, solves the inverse Ising problem for protein-sequence datasets, generating models that accurately replicate observed MSA covariation patterns.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Biology
Kazumasa Oda, Takashi Nomura, Takanori Nakane, Keitaro Yamashita, Keiichi Inoue, Shota Ito, Johannes Vierock, Kunio Hirata, Andres D. Maturana, Kota Katayama, Tatsuya Ikuta, Itsuki Ishigami, Tamaki Izume, Rie Umeda, Ryuun Eguma, Satomi Oishi, Go Kasuya, Takafumi Kato, Tsukasa Kusakizako, Wataru Shihoya, Hiroto Shimada, Tomoyuki Takatsuji, Mizuki Takemoto, Reiya Taniguchi, Atsuhiro Tomita, Ryoki Nakamura, Masahiro Fukuda, Hirotake Miyauchi, Yongchan Lee, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Michihiro Sugahara, Tetsunari Kimura, Tatsuro Shimamura, Takaaki Fujiwara, Yasuaki Yamanaka, Shigeki Owada, Yasumasa Joti, Kensuke Tono, Ryuichiro Ishitani, Shigehiko Hayashi, Hideki Kandori, Peter Hegemann, So Iwata, Minoru Kubo, Tomohiro Nishizawa, Osamu Nureki
Summary: Channelrhodopsins (ChRs) are microbial light-gated ion channels used in optogenetics for controlling neural activity with light. Time-resolved crystallographic analyses revealed conformational changes in ChR following photoactivation, suggesting early changes in the pore-forming helices trigger the opening of the ion conducting pore.
Article
Biology
Jeffrey Carbillet, Benjamin Rey, Rupert Palme, Chloe Monestier, Luca Borger, Typhaine Lavabre, Marie-Line Maublanc, Nicolas Cebe, Jean-Luc Rames, Guillaume Le Loc'h, Marine Wasniewski, Benoit Rannou, Emmanuelle Gilot-Fromont, Helene Verheyden
Summary: The study found that long-term elevation of glucocorticoids may impair immune functions. However, the relationship between stress and immunity in wild animals is less clear. This study re-explored the stress-immunity relationship, considering the potential effects of behavioral profiles. The results showed that individuals with increased glucocorticoid levels exhibited increased immunity and were characterized by more reactive behavioral profiles. These findings highlight the need to consider the interplay between behavior, immunity, and glucocorticoids when studying the stress-immunity relationships in wildlife.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Shuai Sun, Christian Roedelsperger, Ralf J. Sommer
Summary: This study implemented single worm transcriptomics in the nematode Pristionchus pacificus, providing a high-resolution map of the developmental transcriptome and revealing oscillatory gene expression patterns and their potential regulatory functions. The research offers an updated protocol for SWT in nematodes and compares oscillatory gene expression dynamics between the two model organisms, P. pacificus and C. elegans.
Article
Multidisciplinary Sciences
Douglas Guilbeault, Andrea Baronchelli, Damon Centola
Summary: Individuals categorize the world differently, but large-scale communication networks can lead to the convergence of category systems, producing similar cultural patterns.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Agata Butryn, Philipp S. Simon, Pierre Aller, Philip Hinchliffe, Ramzi N. Massad, Gabriel Leen, Catherine L. Tooke, Isabel Bogacz, In-Sik Kim, Asmit Bhowmick, Aaron S. Brewster, Nicholas E. Devenish, Jurgen Brem, Jos J. A. G. Kamps, Pauline A. Lang, Patrick Rabe, Danny Axford, John H. Beale, Bradley Davy, Ali Ebrahim, Julien Orlans, Selina L. S. Storm, Tiankun Zhou, Shigeki Owada, Rie Tanaka, Kensuke Tono, Gwyndaf Evans, Robin L. Owen, Frances A. Houle, Nicholas K. Sauter, Christopher J. Schofield, James Spencer, Vittal K. Yachandra, Junko Yano, Jan F. Kern, Allen M. Orville
Summary: Serial femtosecond crystallography has provided new opportunities for studying protein dynamics with high resolution. However, the challenge lies in studying enzyme-catalyzed reactions. A drop-on-drop sample delivery system has been proposed in this study, showing potential for widespread application in studying enzyme reactions in crystallography.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
B. Thompson, B. van Opheusden, T. Sumers, T. L. Griffiths
Summary: This study found that selective social learning helps preserve rare and exceptional algorithm discoveries in a large-scale cultural evolution experiment. Participants were able to retain complex algorithms when they could choose whom to learn from, but these algorithms frequently became extinct in populations without this selection process, leading to the adoption of lower-performance algorithms.
Article
Multidisciplinary Sciences
Rachel-Ann A. Garibsingh, Elias Ndaru, Alisa A. Garaeva, Yueyue Shi, Laura Zielewicz, Paul Zakrepine, Massimiliano Bonomi, Dirk J. Slotboom, Cristina Paulino, Christof Grewer, Avner Schlessinger
Summary: ASCT2 is up-regulated in cancer and plays a crucial role in promoting cell proliferation by modulating intracellular glutamine levels; Inhibiting nutrient uptake via ASCT2 could be a potential strategy for cancer therapy; We designed a series of unique ASCT2 inhibitors using computational modeling and cryo-EM, providing a framework for the development of cancer therapeutics targeting ASCT2.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Computer Science, Artificial Intelligence
Naoki Akai, Takatsugu Hirayama, Hiroshi Murase
Summary: The study investigates the impact of neural networks based on topological insight on classification performance in order to ensure stability of their inference. Results suggest that by using persistent homology and confidence interval estimation methods, it is possible to test for the presence of outliers in datasets. Research findings with MNIST and CIFAR-10 datasets indicate that even when the transformed datasets are not topologically simple, all networks achieve test accuracies exceeding 98%.
Article
Evolutionary Biology
Maxime Courcelle, Pierre-Henri Fabre, Emmanuel J. P. Douzery
Summary: This study mined the genomes of 53 rodent species and found over 85,000 functional and pseudogene sequences of olfactory receptor (OR) genes, classifying them into phylogenetic clusters. The study showed that ecological niches strongly impacted the proportion of OR pseudogenes, and phylogenetic inertia explained the relative variations of OR gene families.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Cell Biology
Claire L. Warriner, Samaher Fageiry, Shreya Saxena, Rui M. Costa, Andrew Miri
Summary: During limb movement, spinal circuits facilitate the alternating activation of antagonistic flexor and extensor muscles. This study found that the motor cortex drives different muscle activation patterns via task-specific activity covariation.
Article
Multidisciplinary Sciences
Emily M. Carlisle, Melina Jobbins, Vanisa Pankhania, John A. Cunningham, Philip C. J. Donoghue
Summary: Experimental research on the decay of organelles in red and green algae suggests that chloroplasts are more resistant to decay than nuclei, while pyrenoids are unlikely to be preserved. This indicates potential differential organelle preservation in seed plants and prompts a reevaluation of the early eukaryotic fossil record.
Article
Multidisciplinary Sciences
Javier Ortega-Hernandez, Rudy Lerosey-Aubril, Sarah R. Losso, James C. Weaver
Summary: Recent years have seen an increase in reports of fossilized nervous tissues among Cambrian euarthropods, which provide insight into the early evolution of these animals. In this study, the authors describe the central nervous system of the chelicerate Mollisonia symmetrica from the mid-Cambrian Burgess Shale. The preserved neuroanatomy suggests that M. symmetrica represents the ancestral state of stem-group Chelicerata.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Oren Lev, Ariel D. Chipman
Summary: Research has shown fundamental differences in gene expression, timing, and interactions between the pre-gnathal segments and trunk segments in arthropods, indicating their developmental divergence and challenging the notion of serial homology. This raises important questions about the evolutionary ancestry of different regions of the arthropod head.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Genetics & Heredity
Harold Matthews, Michiel Vanneste, Kaitlin Katsura, David Aponte, Michael Patton, Peter Hammond, Gareth Baynam, Richard Spritz, Ophir D. Klein, Benedikt Hallgrimsson, Hilde Peeters, Peter Claes
Summary: This study proposed exploratory strategies for assessing facial phenotypic variation within and among clinical and molecular disease entities, and applied these techniques to samples of four RASopathies, providing insights into the direction and severity of facial effects in different syndromes.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Computer Science, Information Systems
Jordan J. Bannister, Matthias Wilms, J. David Aponte, David C. Katz, Ophir D. Klein, Francois P. J. Bernier, Richard A. Spritz, Benedikt Hallgrimsson, Nils D. Forkert
Summary: This article introduces a method for diagnosing genetic syndromes using facial features. By developing a 3D facial surface modeling approach within a deep learning framework, the model achieves a balance of interpretability and accuracy in syndrome diagnosis. The model demonstrates competitive performance in large-scale experiments.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2022)
Article
Public, Environmental & Occupational Health
Marcell D. Cadney, Ralph L. Albuquerque, Nicole E. Schwartz, Monica P. McNamara, Alberto A. Castro, Margaret P. Schmill, David A. Hillis, Theodore Garland Jr
Summary: This study investigated the long-lasting effects of early-life fructose consumption in mice and found that it increased total caloric intake, body mass, and body fat during juvenile exposure. However, it had no significant effects on adult physical activity or body weight/composition. Interestingly, mice that had early-life fructose and wheel access had reduced maximal aerobic capacity in adulthood. Overall, early-life exercise had positive long-term effects, while the effects of early-life fructose were minimal.
JOURNAL OF DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE
(2023)
Article
Evolutionary Biology
Samuel Ginot, Benedikt Hallgrimsson, Sylvie Agret, Julien Claude
Summary: Fitness-related traits have low heritabilities, while morphology tends to be highly heritable. Although many performance traits depend critically on morphology, the relationship between morphology and traits like bite force may vary within species. In this study, it was found that bite force showed undetectable additive genetic variance and heritability, suggesting it is less responsive to selection compared to its morphological determinants.
EVOLUTIONARY BIOLOGY
(2022)
Article
Biology
Monica P. McNamara, Emily M. Venable, Marcell D. Cadney, Alberto A. Castro, Margaret P. Schmill, Lawrence Kazzazi, Rachel N. Carmody, Theodore Garland
Summary: In this study, the fecal microbial community composition and diversity were compared between a group of mice selectively bred for high wheel-running activity and a control group. The results showed that the high wheel-running mice had a higher relative abundance of the bacterial family Clostridiaceae, which differed from a previous study on rats. Additionally, the replicate lines within the high wheel-running and control groups had unique microbiomes, indicating potential random genetic drift and/or multiple adaptive responses to selection.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2023)
Article
Biology
Ralph L. Albuquerque, Peter A. Zani, Theodore Garland
Summary: This study found that individual behavior is related to morphology and physiological function, which in turn indirectly affect behavior. On the other hand, parasite load has no direct effect on individual performance ability. Due to the low repeatability of field behaviors, the relationship between behavior and performance may be stronger than indicated by the results.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2023)
Article
Genetics & Heredity
Elias Aboujaoude, Janice Light, Julia E. H. Brown, W. John Boscardin, Benedikt Hallgrimsson, Ophir D. Klein
Summary: Facial recognition technology has been used in precision medicine, and geneticists hold different views on its privacy concerns. Most geneticists support the use of facial recognition technology in genetics, but are skeptical about its broader clinical application.
AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Jordan J. Bannister, Matthias Wilms, J. David Aponte, David C. Katz, Ophir D. Klein, Francois P. Bernier, Richard A. Spritz, Benedikt Hallgrimsson, Nils D. Forkert
Summary: Human genetic syndromes are difficult to diagnose clinically, and facial phenotype plays a crucial role in diagnosis. Computer-assisted facial phenotyping has shown promise in aiding diagnosis. This study compares the performance of 2D and 3D image-based approaches to syndrome diagnosis and finds that 3D surface-based classification models outperform 2D image-based models. These findings suggest that the adoption of 3D facial scanning technology and collection of syndromic 3D facial scan data can greatly improve face-based syndrome diagnosis.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Genetics & Heredity
Sahin Naqvi, Seungsoo Kim, Hanne Hoskens, Harold S. S. Matthews, Richard A. A. Spritz, Ophir D. D. Klein, Benedikt Hallgrimsson, Tomek Swigut, Peter Claes, Jonathan K. K. Pritchard, Joanna Wysocka
Summary: Transcriptional regulation is robust but sensitive to transcription factor (TF) dosage, especially in craniofacial morphology. By modulating TF levels in human facial progenitor cells, researchers found that most SOX9-dependent regulatory elements (REs) are buffered against small decreases in SOX9 dosage, while REs directly regulated by SOX9 are more sensitive and affect chondrogenesis and craniofacial shape variation associated with PRS.
Article
Multidisciplinary Sciences
Bethany N. Radford, Xiang Zhao, Tali Glazer, Malcolm Eaton, Danielle Blackwell, Shuhiba Mohammad, Lucas Daniel Lo Vercio, Jay Devine, Tali Shalom-Barak, Benedikt Hallgrimsson, James C. Cross, Henry M. Sucov, Yaacov Barak, Wendy Dean, Myriam Hemberger
Summary: This study demonstrates that the placenta might be a significant cause of congenital heart defects, using mouse genetic tools.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Nicole E. Schwartz, Monica P. McNamara, Jocelyn M. Orozco, Jaanam O. Rashid, Angie P. Thai, Theodore Garland
Summary: Selective breeding for behavioral traits can result in significant behavioral changes without proportional modifications to underlying morphological or physiological traits.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2023)
Article
Biology
Jessica L. Tingle, Brian M. Sherman, Theodore Garland Jr
Summary: Physical characteristics of the substrate have a significant impact on terrestrial locomotion of animals and machines. Snakes' gait is more influenced by the environment rather than their speed. Testing sidewinder rattlesnakes on different surfaces revealed that the body's waveform had longer wavelength on vinyl flooring and snakes lifted their bodies higher on sand.
Article
Biology
Quentin Jean-Baptiste Horta-Lacueva, Zophonias Oddur Jonsson, Dagny A. V. Thorholludottir, Benedikt Hallgrimsson, Kalina Hristova Kapralova
Summary: Transcriptomic analyses suggest that gene expression variance can rapidly diverge in sympatry and is conditioned by dominance patterns in the offspring of Arctic charr morphs and hybrids at two stages of cranial development.
COMMUNICATIONS BIOLOGY
(2023)
Article
Anthropology
Scott A. Williams, Thomas Cody Prang, Gabrielle A. Russo, Nathan M. Young, Daniel L. Gebo
Summary: Since the discovery of human fossils in the mid-19th century, the study of human origins has focused on two major subjects: our relationship to living and fossil apes, and the ancestral locomotor behaviors that preceded bipedalism. Early morphologists proposed various scenarios for the evolution of bipedalism based on limited evidence, while the rich hominin fossil record and the acceptance of chimpanzees and bonobos as our closest living relatives have made it difficult to determine the ancestral condition of hominins. The debate over these alternatives indicates that the inference of ancestral nodes and the weighing of evidence remain challenging.
AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY
(2023)
Article
Computer Science, Information Systems
Lucas D. Lo Vercio, Rebecca M. Green, Samuel Robertson, Sienna Guo, Andreas Dauter, Marta Marchini, Marta Vidal-Garcia, Xiang Zhao, Anandita Mahika, Ralph S. Marcucio, Benedikt Hallgrimsson, Nils D. Forkert
Summary: Various genetic mutations affecting cell proliferation during organism development have been found to cause structural birth defects. This study developed and evaluated automatic methods based on convolutional neural networks (CNNs) for accurate segmentation of tissue and cells in mouse embryos using Light-Sheet Microscopy (LSM) imaging. The proposed methods achieved high accuracy and consistency compared to manual segmentations, providing a useful tool for LSM image analysis.