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JOURNAL ARTICLE
Raul de la Mata, Almudena Mollá-Morales, Belén Méndez-Vigo, Rafael Torres-Pérez, Juan Carlos Oliveros, Rocío Gómez, Arnald Marcer, Antonio R Castilla, Magnus Nordborg, Carlos Alonso-Blanco, F Xavier Picó
BACKGROUND: Despite its implications for population dynamics and evolution, the relationship between genetic and phenotypic variation in wild populations remains unclear. Here, we estimated variation and plasticity in life-history traits and fitness of the annual plant Arabidopsis thaliana in two common garden experiments that differed in environmental conditions. We used up to 306 maternal inbred lines from six Iberian populations characterized by low and high genotypic (based on whole-genome sequences) and ecological (vegetation type) diversity...
May 3, 2024: BMC ecology and evolution
#2
REVIEW
Michael Q Fitzgerald, Tiffany Chu, Francesca Puppo, Rebeca Blanch, Miguel Chillón, Shankar Subramaniam, Alysson R Muotri
Temporal development of neural electrophysiology follows genetic programming, similar to cellular maturation and organization during development. The emergent properties of this electrophysiological development, namely neural oscillations, can be used to characterize brain development. Recently, we utilized the innate programming encoded in the human genome to generate functionally mature cortical organoids. In brief, stem cells are suspended in culture via continuous shaking and naturally aggregate into embryoid bodies before being exposed to media formulations for neural induction, differentiation and maturation...
May 3, 2024: Nature Protocols
#3
JOURNAL ARTICLE
Yuexing Liu, Yao Luo, Xin Lu, Hao Gao, Ruikun He, Xin Zhang, Xuguang Zhang, Yixue Li
The relationship between genotype and fitness is fundamental to evolution, but quantitatively mapping genotypes to fitness has remained challenging. We propose the Phenotypic-Embedding theorem (P-E theorem) that bridges genotype-phenotype through an encoder-decoder deep learning framework. Inspired by this, we proposed a more general first principle for correlating genotype-phenotype, and the P-E theorem provides a computable basis for the application of first principle. As an application example of the P-E theorem, we developed the Co-attention based Transformer model to bridge Genotype and Fitness model, a Transformer-based pre-train foundation model with downstream supervised fine-tuning that can accurately simulate the neutral evolution of viruses and predict immune escape mutations...
March 27, 2024: Briefings in Bioinformatics
#4
JOURNAL ARTICLE
Hassan Farhat, Ahmed Makhlouf, Padarath Gangaram, Kawther El Aifa, Ian Howland, Fatma Babay Ep Rekik, Cyrine Abid, Mohamed Chaker Khenissi, Nicholas Castle, Loua Al-Shaikh, Moncef Khadhraoui, Imed Gargouri, James Laughton, Guillaume Alinier
BACKGROUND: The global evolution of pre-hospital care systems faces dynamic challenges, particularly in multinational settings. Machine learning (ML) techniques enable the exploration of deeply embedded data patterns for improved patient care and resource optimisation. This study's objective was to accurately predict cases that necessitated transportation versus those that did not, using ML techniques, thereby facilitating efficient resource allocation. METHODS: ML algorithms were utilised to predict patient transport decisions in a Middle Eastern national pre-hospital emergency medical care provider...
2024: PloS One
#5
JOURNAL ARTICLE
Meridia Jane Bryant, Asher M Coello, Adam M Glendening, Samuel A Hilliman, Carolina Fernanda Jara, Samuel S Pring, Aviel Rodriguez Rivera, Jennifer Santiago Membreño, Lisa Nigro, Nicole Pauloski, Matthew R Graham, Teisha King, Elizabeth L Jockusch, Rachel J O'Neill, Jill L Wegrzyn, Carlos E Santibáñez-López, Cynthia N Webster
Over 400 million years old, scorpions represent an ancient group of arachnids and one of the first animals to adapt to life on land. Presently, the lack of available genomes within scorpions hinders research on their evolution. This study leverages ultra-long nanopore sequencing and Pore-C to generate the first chromosome level assembly and annotation for the desert hairy scorpion, Hadrurus arizonensis. The assembled genome is 2.23 Gb in size with an N50 of 280 Mb. Pore-C scaffolding re-oriented 99.6% of bases into nine chromosomes and BUSCO identified 998 (98...
May 3, 2024: Genome Biology and Evolution
#6
JOURNAL ARTICLE
Jasmine A Richman, Leah R Davis, Michael P Phelps
The genomes of plant and animal species are influenced by ancestral whole genome duplication (WGD) events, which have profound impacts on the regulation and function of gene networks. To gain insight into the consequences of WGD events, we characterized the sequence conservation and expression patterns of ohnologs in the highly duplicated activin receptor signaling pathway in rainbow trout (RBT). The RBT activin receptor signaling pathway is defined by tissue-specific expression of inhibitors and ligands and broad expression of receptors and Co-Smad signaling molecules...
May 3, 2024: Genome Biology and Evolution
#7
JOURNAL ARTICLE
A D Lagorio, F R McGechie, M G Fields, J Fortner, E Mackereth, C Perez, A T Wilken, M Leal, C V Ward, K M Middleton, C M Holliday
High-resolution imaging, 3D modeling, and quantitative analyses are equipping evolutionary biologists with new approaches to understanding the variation and evolution of the musculoskeletal system. However, challenges with interpreting DiceCT data and higher order use of modeled muscles have not yet been fully explored, and the error in and accuracy of some digital methods remain unclear. West Indian Anolis lizards are a model clade for exploring patterns in functional adaptation, ecomorphology, and sexual size dimorphism in vertebrates...
2024: Integrative organismal biology
#8
Laura Torrens, Sarah Moody, Ana Carolina de Carvalho, Mariya Kazachkova, Behnoush Abedi-Ardekani, Saamin Cheema, Sergey Senkin, Thomas Cattiaux, Ricardo Cortez Cardoso Penha, Joshua R Atkins, Valérie Gaborieau, Priscilia Chopard, Christine Carreira, Ammal Abbasi, Erik N Bergstrom, Raviteja Vangara, Jingwei Wang, Stephen Fitzgerald, Calli Latimer, Marcos Diaz-Gay, David Jones, Jon Teague, Felipe Ribeiro Pinto, Luiz Paulo Kowalski, Jerry Polesel, Fabiola Giudici, José Carlos de Oliveira, Pagona Lagiou, Areti Lagiou, Marta Vilensky, Dana Mates, Ioan N Mates, Lidia Mrb Arantes, Rui Reis, Jose Roberto V Podesta, Sandra V von Zeidler, Ivana Holcatova, Maria Paula Curado, Cristina Canova, Elenora Fabianova, Paula A Rodríguez-Urrego, Laura Humphreys, Ludmil B Alexandrov, Paul Brennan, Michael R Stratton, Sandra Perdomo
Tobacco smoke, alone or combined with alcohol, is the predominant cause of head and neck cancer (HNC). Here, we further explore how tobacco exposure contributes to cancer development by mutational signature analysis of 265 whole-genome sequenced HNC from eight countries. Six tobacco-associated mutational signatures were detected, including some not previously reported. Differences in HNC incidence between countries corresponded with differences in mutation burdens of tobacco-associated signatures, consistent with the dominant role of tobacco in HNC causation...
April 17, 2024: medRxiv
#9
JOURNAL ARTICLE
Yizhen Chen, Rachita Rana, Yizhi Zhang, Adam S Hoffman, Zhennan Huang, Bo Yang, Fernando D Vila, Jorge E Perez-Aguilar, Jiyun Hong, Xu Li, Jie Zeng, Miaofang Chi, Coleman X Kronawitter, Haiyan Wang, Simon R Bare, Ambarish R Kulkarni, Bruce C Gates
Supported noble metal catalysts, ubiquitous in chemical technology, often undergo dynamic transformations between reduced and oxidized states-which influence the metal nuclearities, oxidation states, and catalytic properties. In this investigation, we report the results of in situ X-ray absorption spectroscopy, scanning transmission electron microscopy, and other physical characterization techniques, bolstered by density functional theory, to elucidate the structural transformations of a set of MgO-supported palladium catalysts under oxidative treatment conditions...
May 1, 2024: Chemical Science
#10
JOURNAL ARTICLE
Chase L Núñez, James S Clark, John R Poulsen
Understanding how tropical forests respond to abiotic environmental changes is critical for preserving biodiversity, mitigating climate change, and maintaining ecosystem services in the coming century. To evaluate the relative roles of the abiotic environment and human disturbance on Central African tree community composition, we employ tree inventory data, remotely sensed climatic data, and soil nutrient data collected from 30 1-ha plots distributed across a large-scale observational experiment in forests that had been differently impacted by logging and hunting in northern Republic of Congo...
May 2024: Ecology and Evolution
#11
JOURNAL ARTICLE
Christina H Frater, Maura R Z Ruzhnikov, Shannon Beres, Deborah Alcorn, Ann Shue, Rebecca J Levy
BACKGROUND: NGLY1 deficiency is a rare autosomal recessive disorder with core features of global developmental delay, liver enzyme abnormalities, movement disorder, polyneuropathy, and hypo- or alacrima. We characterized the full spectrum and evolution of the ocular phenotype in a prospective natural history of NGLY1 deficiency. METHODS: We collected ophthalmological data on 29 individuals with NGLY1 deficiency in a natural history study. Medical records were reviewed to confirm caregiver-reported symptoms...
April 30, 2024: Journal of AAPOS: the Official Publication of the American Association for Pediatric Ophthalmology and Strabismus
#12
JOURNAL ARTICLE
Jonathan Storkey, Chloe Maclaren, James M Bullock, Lisa R Norton, John W Redhead, Richard F Pywell
The achievements of the Green Revolution in meeting the nutritional needs of a growing global population have been won at the expense of unintended consequences for the environment. Some of these negative impacts are now threatening the sustainability of food production through the loss of pollinators and natural enemies of crop pests, the evolution of pesticide resistance, declining soil health and vulnerability to climate change. In the search for farming systems that are sustainable both agronomically and environmentally, alternative approaches have been proposed variously called 'agroecological', 'conservation agriculture', 'regenerative' and 'sustainable intensification'...
May 2, 2024: Biological Reviews of the Cambridge Philosophical Society
#13
JOURNAL ARTICLE
Thiago Gonçalves-Souza, Beatriz Milz, Nathan J Sanders, Peter B Reich, Brian Maitner, Leonardo S Chaves, Gabriel X Boldorini, Natália Ferreira, Reginaldo A F Gusmão, Phamela Bernardes Perônico, Fabrício B Teresa, María Natalia Umaña
Animal trait data are scattered across several datasets, making it challenging to compile and compare trait information across different groups. For plants, the TRY database has been an unwavering success for those ecologists interested in addressing how plant traits influence a wide variety of processes and patterns, but the same is not true for most animal taxonomic groups. Here, we introduce ZooTraits, a Shiny app designed to help users explore and obtain animal trait data for research in ecology and evolution...
May 2024: Ecology and Evolution
#14
EDITORIAL
Qinghui Shi, Jinling Xie, Jialing Wu, Shengchung Chen, Gang Sun, Juncheng Zhang
The mitochondrial genome (mitogenome) has been extensively used as molecular markers in determining the insect phylogenetic relationships. In order to resolve the relationships among tribes and subtribes of Satyrinae at the mitochondrial genomic level, we obtained the complete mitogenome of Aulocera merlina (Oberthür, 1890) (Lepidoptera: Nymphalidae: Satyrinae) with a size of 15,259 bp. The mitogenome consisted of 37 typical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region...
May 2024: Ecology and Evolution
#15
JOURNAL ARTICLE
Taiya M Jarva, Nicole M Phillips, Cory Von Eiff, Gregg R Poulakis, Gavin Naylor, Kevin A Feldheim, Alex S Flynt
Sawfishes (Pristidae) are large, highly threatened rays named for their tooth-studded rostrum, which is used for prey sensing and capture. Of all five species, the smalltooth sawfish, Pristis pectinata , has experienced the greatest decline in range, currently found in only ~20% of its historic range. To better understand the genetic underpinnings of these taxonomically and morphologically unique animals, we collected transcriptomic data from several tissue types, mapped them to the recently completed reference genome, and contrasted the patterns observed with comparable data from other elasmobranchs...
May 2024: Ecology and Evolution
#16
JOURNAL ARTICLE
G Gascoigne, J Assad, D Patterson, J Brillhart, V DiLeo, R Williams
The goal of this study was to gather information about freshwater fishes in Letchworth State Park (42.615275° N, -77.992825° W), a portion of New York State-owned land located in the Genesee River Watershed that lacks known data about its fish diversity. Fish collection took place between 2017 and 2019 in the Genesse River upstream and downstream of the falls using electrofishing, gill, hoop, and seine netting. This was the first attempt at a comprehensive survey of this portion of the river, which allowed for a baseline to be established regarding fish biodiversity in the region...
May 2024: Ecology and Evolution
#17
JOURNAL ARTICLE
Xuehuan Feng, Jinfang Zheng, Iker Irisarri, Huihui Yu, Bo Zheng, Zahin Ali, Sophie de Vries, Jean Keller, Janine M R Fürst-Jansen, Armin Dadras, Jaccoline M S Zegers, Tim P Rieseberg, Amra Dhabalia Ashok, Tatyana Darienko, Maaike J Bierenbroodspot, Lydia Gramzow, Romy Petroll, Fabian B Haas, Noe Fernandez-Pozo, Orestis Nousias, Tang Li, Elisabeth Fitzek, W Scott Grayburn, Nina Rittmeier, Charlotte Permann, Florian Rümpler, John M Archibald, Günter Theißen, Jeffrey P Mower, Maike Lorenz, Henrik Buschmann, Klaus von Schwartzenberg, Lori Boston, Richard D Hayes, Chris Daum, Kerrie Barry, Igor V Grigoriev, Xiyin Wang, Fay-Wei Li, Stefan A Rensing, Julius Ben Ari, Noa Keren, Assaf Mosquna, Andreas Holzinger, Pierre-Marc Delaux, Chi Zhang, Jinling Huang, Marek Mutwil, Jan de Vries, Yanbin Yin
Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit...
May 1, 2024: Nature Genetics
#18
JOURNAL ARTICLE
R E Ledda, S Schirò, L Leo, G Milanese, C Branchi, C Commisso, E Borgia, R Mura, C Zilioli, N Sverzellati
AIM: The comparison between chest x-ray (CXR) and computed tomography (CT) images is commonly required in clinical practice to assess the evolution of chest pathological manifestations. Intrinsic differences between the two techniques, however, limit reader confidence in such a comparison. CT average intensity projection (AIP) reconstruction allows obtaining "synthetic" CXR (s-CXR) images, which are thought to have the potential to increase the accuracy of comparison between CXR and CT imaging...
April 13, 2024: Clinical Radiology
#19
JOURNAL ARTICLE
Kishore R Kumar, Mark J Cowley, Ryan L Davis
Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements...
May 1, 2024: Seminars in Thrombosis and Hemostasis
#20
JOURNAL ARTICLE
Xianyi Xiong, Hans G Othmer, William R Harcombe
Antibiotic persistence (heterotolerance) allows a sub-population of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity...
May 1, 2024: ISME Journal
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