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JOURNAL ARTICLE
Hong-Yu Ji, Chao Ye, Yan-Qiong Chen, Jian-Wu Li, Arief Hidayat, Jiang-Lin Miao, Jian-Hua Li, Jian-Yong Wu, Jun-Wen Zhai, Si-Ren Lan, Xiao-Hua Jin
The tribe Collabieae (Epidendroideae, Orchidaceae) comprises approximately 500 species. Generic delimitation within Collabieae are confusing and phylogenetic interrelationships within the Collabieae have not been well resolved. Plastid genomes and nuclear internal transcribed spacer (ITS) sequences were used to estimate the phylogenetic relationships, ancestral ranges, and diversification rates of Collabieae. The results showed that Collabieae was subdivided into nine clades with high support. We proposed to combine Ancistrochilus and Pachystoma into Spathoglottis, merge Collabium and Chrysoglossum into Diglyphosa, and separate Pilophyllum and Hancockia as distinctive genera...
April 28, 2024: Molecular Phylogenetics and Evolution
#2
JOURNAL ARTICLE
Hong Wu, De-Zhu Li, Peng-Fei Ma
BACKGROUND: The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. RESULTS: We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern...
April 29, 2024: BMC Biology
#3
JOURNAL ARTICLE
Joon Ho Park, Taeyeon Kang, Hyun S Ahn
Recent advances in electrosynthesis of nanomaterials expanded structural and compositional variations accessible by the electrochemical method; however, reliably synthesizable morphological variety fall shy of that available by conventional solvothermal synthesis. In this communication, electrochemical preparation of surfactant-free hollow nanoparticles is demonstrated. By anodic conversion of core-shell precursors with metastable cores, hollowed nickel nanoparticles with uniform dimensions were synthesized and characterized...
April 26, 2024: ChemSusChem
#4
REVIEW
A review on vitamin A deficiency and depleted immunity in South Asia: From deficiency to resilience.
Rahul Kumar, Maria Jose Oruna-Concha, Keshavan Niranjan, Karani S Vimaleswaran
In the developing world, the twin challenges of depleted health and growing issue of food waste management loom large, demanding simultaneous attention and innovative solutions. This review explores how these issues can be effectively mitigated while shedding light on the transformative impact of food waste valorization on health management. A spotlight is cast on vitamin A deficiency (VAD), an acute public health concern, especially prevalent in South Asia, driven by economic constraints, sociocultural factors, inadequate diets, and poor nutrient absorption...
April 3, 2024: Nutrition
#5
JOURNAL ARTICLE
Fabio Scarpa, Leonardo Sernicola, Stefania Farcomeni, Alessandra Ciccozzi, Daria Sanna, Marco Casu, Marco Vitale, Alessia Cicenia, Marta Giovanetti, Chiara Romano, Francesco Branda, Massimo Ciccozzi, Alessandra Borsetti
The influenza A(H1N1) pdm09 virus, which emerged in 2009, has been circulating seasonally since then. In this study, we conducted a comprehensive genome-based investigation to gain a detailed understanding of the genetic and evolutionary characteristics of the hemagglutinin (HA) and neuraminidase (NA) surface proteins of A/H1N1pdm09 strains circulating in Italy over a fourteen-year period from 2009 to 2023 in relation to global strains. Phylogenetic analysis revealed rapid transmission and diversification of viral variants during the early pandemic that clustered in clade 6B...
April 17, 2024: Pathogens
#6
JOURNAL ARTICLE
Leher Singh, Sarah J Rajendra
Psychological researchers have been criticized for making broad presumptions about human behavior based on limited sampling. In part, presumptive generalizability is reflected in the limited representation of sociodemographic variation in research reports. In this analysis, we examine time-trends in reporting of a key sociodemographic construct relevant to many aspects of child development-socioeconomic status (SES)-across six mainstream developmental journals (Infancy, Child Development, Developmental Science, Developmental Psychology, Infant and Child Development, and Infant Behavior & Development) between 2016 and 2022...
April 25, 2024: Developmental Science
#7
JOURNAL ARTICLE
Alexandre R Zuntini, Tom Carruthers, Olivier Maurin, Paul C Bailey, Kevin Leempoel, Grace E Brewer, Niroshini Epitawalage, Elaine Françoso, Berta Gallego-Paramo, Catherine McGinnie, Raquel Negrão, Shyamali R Roy, Lalita Simpson, Eduardo Toledo Romero, Vanessa M A Barber, Laura Botigué, James J Clarkson, Robyn S Cowan, Steven Dodsworth, Matthew G Johnson, Jan T Kim, Lisa Pokorny, Norman J Wickett, Guilherme M Antar, Lucinda DeBolt, Karime Gutierrez, Kasper P Hendriks, Alina Hoewener, Ai-Qun Hu, Elizabeth M Joyce, Izai A B S Kikuchi, Isabel Larridon, Drew A Larson, Elton John de Lírio, Jing-Xia Liu, Panagiota Malakasi, Natalia A S Przelomska, Toral Shah, Juan Viruel, Theodore R Allnutt, Gabriel K Ameka, Rose L Andrew, Marc S Appelhans, Montserrat Arista, María Jesús Ariza, Juan Arroyo, Watchara Arthan, Julien B Bachelier, C Donovan Bailey, Helen F Barnes, Matthew D Barrett, Russell L Barrett, Randall J Bayer, Michael J Bayly, Ed Biffin, Nicky Biggs, Joanne L Birch, Diego Bogarín, Renata Borosova, Alexander M C Bowles, Peter C Boyce, Gemma L C Bramley, Marie Briggs, Linda Broadhurst, Gillian K Brown, Jeremy J Bruhl, Anne Bruneau, Sven Buerki, Edie Burns, Margaret Byrne, Stuart Cable, Ainsley Calladine, Martin W Callmander, Ángela Cano, David J Cantrill, Warren M Cardinal-McTeague, Mónica M Carlsen, Abigail J A Carruthers, Alejandra de Castro Mateo, Mark W Chase, Lars W Chatrou, Martin Cheek, Shilin Chen, Maarten J M Christenhusz, Pascal-Antoine Christin, Mark A Clements, Skye C Coffey, John G Conran, Xavier Cornejo, Thomas L P Couvreur, Ian D Cowie, Laszlo Csiba, Iain Darbyshire, Gerrit Davidse, Nina M J Davies, Aaron P Davis, Kor-Jent van Dijk, Stephen R Downie, Marco F Duretto, Melvin R Duvall, Sara L Edwards, Urs Eggli, Roy H J Erkens, Marcial Escudero, Manuel de la Estrella, Federico Fabriani, Michael F Fay, Paola de L Ferreira, Sarah Z Ficinski, Rachael M Fowler, Sue Frisby, Lin Fu, Tim Fulcher, Mercè Galbany-Casals, Elliot M Gardner, Dmitry A German, Augusto Giaretta, Marc Gibernau, Lynn J Gillespie, Cynthia C González, David J Goyder, Sean W Graham, Aurélie Grall, Laura Green, Bee F Gunn, Diego G Gutiérrez, Jan Hackel, Thomas Haevermans, Anna Haigh, Jocelyn C Hall, Tony Hall, Melissa J Harrison, Sebastian A Hatt, Oriane Hidalgo, Trevor R Hodkinson, Gareth D Holmes, Helen C F Hopkins, Christopher J Jackson, Shelley A James, Richard W Jobson, Gudrun Kadereit, Imalka M Kahandawala, Kent Kainulainen, Masahiro Kato, Elizabeth A Kellogg, Graham J King, Beata Klejevskaja, Bente B Klitgaard, Ronell R Klopper, Sandra Knapp, Marcus A Koch, James H Leebens-Mack, Frederic Lens, Christine J Leon, Étienne Léveillé-Bourret, Gwilym P Lewis, De-Zhu Li, Lan Li, Sigrid Liede-Schumann, Tatyana Livshultz, David Lorence, Meng Lu, Patricia Lu-Irving, Jaquelini Luber, Eve J Lucas, Manuel Luján, Mabel Lum, Terry D Macfarlane, Carlos Magdalena, Vidal F Mansano, Lizo E Masters, Simon J Mayo, Kristina McColl, Angela J McDonnell, Andrew E McDougall, Todd G B McLay, Hannah McPherson, Rosa I Meneses, Vincent S F T Merckx, Fabián A Michelangeli, John D Mitchell, Alexandre K Monro, Michael J Moore, Taryn L Mueller, Klaus Mummenhoff, Jérôme Munzinger, Priscilla Muriel, Daniel J Murphy, Katharina Nargar, Lars Nauheimer, Francis J Nge, Reto Nyffeler, Andrés Orejuela, Edgardo M Ortiz, Luis Palazzesi, Ariane Luna Peixoto, Susan K Pell, Jaume Pellicer, Darin S Penneys, Oscar A Perez-Escobar, Claes Persson, Marc Pignal, Yohan Pillon, José R Pirani, Gregory M Plunkett, Robyn F Powell, Ghillean T Prance, Carmen Puglisi, Ming Qin, Richard K Rabeler, Paul E J Rees, Matthew Renner, Eric H Roalson, Michele Rodda, Zachary S Rogers, Saba Rokni, Rolf Rutishauser, Miguel F de Salas, Hanno Schaefer, Rowan J Schley, Alexander Schmidt-Lebuhn, Alison Shapcott, Ihsan Al-Shehbaz, Kelly A Shepherd, Mark P Simmons, André O Simões, Ana Rita G Simões, Michelle Siros, Eric C Smidt, James F Smith, Neil Snow, Douglas E Soltis, Pamela S Soltis, Robert J Soreng, Cynthia A Sothers, Julian R Starr, Peter F Stevens, Shannon C K Straub, Lena Struwe, Jennifer M Taylor, Ian R H Telford, Andrew H Thornhill, Ifeanna Tooth, Anna Trias-Blasi, Frank Udovicic, Timothy M A Utteridge, Jose C Del Valle, G Anthony Verboom, Helen P Vonow, Maria S Vorontsova, Jurriaan M de Vos, Noor Al-Wattar, Michelle Waycott, Cassiano A D Welker, Adam J White, Jan J Wieringa, Luis T Williamson, Trevor C Wilson, Sin Yeng Wong, Lisa A Woods, Roseina Woods, Stuart Worboys, Martin Xanthos, Ya Yang, Yu-Xiao Zhang, Meng-Yuan Zhou, Sue Zmarzty, Fernando O Zuloaga, Alexandre Antonelli, Sidonie Bellot, Darren M Crayn, Olwen M Grace, Paul J Kersey, Ilia J Leitch, Hervé Sauquet, Stephen A Smith, Wolf L Eiserhardt, Félix Forest, William J Baker
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2 . A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4 . Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7 . However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications...
April 24, 2024: Nature
#8
JOURNAL ARTICLE
Wenqiu Ma, Heng Yang, Guanghui Jiang, Tao Zhou, Qinglei Zhao
The rapid transition of agricultural systems substantially affects residential and industrial land use systems in rural areas, often generating spatiotemporal trade-offs between residential and industrial functions and producing considerable ecological impacts, which has thus far not been well understood. We conduct an indicator-based assessment of transitioning agriculture systems, and then links the transitioning agricultural systems to trade-offs between residential and industrial functions from 2005 to 2020 by using a case study-the metropolitan suburbs of Beijing, China...
April 23, 2024: Journal of Environmental Management
#9
JOURNAL ARTICLE
Lian Sun, Xin-Ming Wang, Qianhui Tang, Yao Xiao, Jin-Bu Xu, Tong-Tong Zhang, Yan-Jun Liu, Xiaohuan Li, Feng Gao
The first systematic acylated diversification of naturally scarce premyrsinane diterpenes, together with their biosynthetic precursors lathyrane diterpene were carried out. Two new series of premyrsinane derivates (1a-32a) and lathyrane derivates (1-32) were synthesized from the naturally abundant lathyrane diterpene Euphorbia factor L3 through a bioinspired approach. The cholinesterase inhibitory and neuroprotective activities of these diterpenes were investigated to explore potential anti-Alzheimer's disease (AD) bioactive lead compounds...
April 15, 2024: Bioorganic Chemistry
#10
JOURNAL ARTICLE
Gilles Didier, Michel Laurin
In the last decade, the Fossilized Birth-Death (FBD) process has yielded interesting clues about the evolution of biodiversity through time. To facilitate such studies, we extend our method to compute the probability density of phylogenetic trees of extant and extinct taxa in which the only temporal information is provided by the fossil ages (i.e. without the divergence times) in order to deal with the piecewise constant FBD process, known as the "skyline FBD", which allows rates to change between pre-defined time intervals, as well as modelling extinction events at the bounds of these intervals...
April 23, 2024: Cladistics
#11
JOURNAL ARTICLE
Travis Park, Gustavo Burin, Daniela Lazo-Cancino, Joseph Pierce Gary Rees, James Rule, Graham Slater, Natalie Cooper
Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these two rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to-date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history...
April 22, 2024: Evolution; International Journal of Organic Evolution
#12
JOURNAL ARTICLE
Roman Kogay, Yuri I Wolf, Eugene V Koonin
Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species...
April 2024: Environmental Microbiology
#13
JOURNAL ARTICLE
Elena G Novoselova, Sergey M Lunin, Maxim O Khrenov, Olga V Glushkova, Tatyana V Novoselova, Svetlana B Parfenyuk
Diabetes mellitus type 1 (T1D) and type 2 (T2D) develop due to dysfunction of the Langerhans islet β-cells in the pancreas, and this dysfunction is mediated by oxidative, endoplasmic reticulum (ER), and mitochondrial stresses. Although the two types of diabetes are significantly different, β-cell failure and death play a key role in the pathogenesis of both diseases, resulting in hyperglycemia due to a reduced ability to produce insulin. In T1D, β-cell apoptosis is the main event leading to hyperglycemia, while in T2D, insulin resistance results in an inability to meet insulin requirements...
April 17, 2024: Cellular Physiology and Biochemistry
#14
JOURNAL ARTICLE
Xudong Tang, Leonardo Zepeda-Nuñez, Shengwen Yang, Zelin Zhao, Claudia Solís-Lemus
MOTIVATION: Scientists world-wide are putting together massive efforts to understand how the biodiversity that we see on Earth evolved from single-cell organisms at the origin of life and this diversification process is represented through the Tree of Life. Low sampling rates and high heterogeneity in the rate of evolution across sites and lineages produce a phenomenon denoted "long branch attraction" (LBA) in which long nonsister lineages are estimated to be sisters regardless of their true evolutionary relationship...
2024: Bioinform Adv
#15
JOURNAL ARTICLE
Peter C Searle, Dennis K Shiozawa, R Paul Evans, Jonathon T Hill, Arminda Suli, Michael R Stark, Mark C Belk
Heterochrony-alteration to the rate or timing of development-is an important mechanism of trait differentiation associated with speciation. Heterochrony may explain the morphological divergence between two polyploid species, June sucker ( Chasmistes liorus ) and Utah sucker ( Catostomus ardens ). The larvae of both species have terminal mouths; however, as adults, June sucker and Utah sucker develop subterminal and ventral mouths, respectively. We document a difference in the timing of shape development and a corresponding change in the timing of gene expression, suggesting the distinctive mouth morphology in June suckers may result from paedomorphosis...
April 19, 2024: IScience
#16
JOURNAL ARTICLE
Mario Torralba Sáez, Michael Hofreiter, Nicolas Straube
Among vertebrates, sharks exhibit both large and heterogeneous genome sizes ranging from 2.86 to 17.05 pg. Aiming for a better understanding of the patterns and causalities of shark genome size evolution, we applied phylogenetic comparative methods to published genome-size estimates for 71 species representing the main phylogenetic lineages, life-histories and ecological traits. The sixfold range of genome size variation was strongly traceable throughout the phylogeny, with a major expansion preceding shark diversification during the late Paleozoic and an ancestral state (6...
April 17, 2024: Scientific Reports
#17
JOURNAL ARTICLE
Hannah Augustijnen, Livio Bätscher, Martin Cesanek, Tinatin Chkhartishvili, Vlad Dincă, Giorgi Iankoshvili, Kota Ogawa, Roger Vila, Seraina Klopfstein, Jurriaan M de Vos, Kay Lucek
The impact of large-scale chromosomal rearrangements, such as fusions and fissions, on speciation is a long-standing conundrum. We assessed whether bursts of change in chromosome numbers resulting from chromosomal fusion or fission are related to increased speciation rates in Erebia , one of the most species-rich and karyotypically variable butterfly groups. We established a genome-based phylogeny and used state-dependent birth-death models to infer trajectories of karyotype evolution. We demonstrated that rates of anagenetic chromosomal changes (i...
April 19, 2024: Science Advances
#18
JOURNAL ARTICLE
Raheyma Siddiqui, Samantha Swank, Allison Ozark, Franklin Joaquin, Matthew P Travis, Caleb D McMahan, Michael A Bell, Yoel E Stuart
Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model and 124 years of unsuccessfully sampling the fossil record for transitions...
April 30, 2024: Proceedings. Biological Sciences
#19
JOURNAL ARTICLE
Zachary M Bailey, Claudia Igler, Carolin C Wendling
Prophages, viral sequences integrated into bacterial genomes, can be beneficial and costly. Despite the risk of prophage activation and subsequent bacterial death, active prophages are present in most bacterial genomes. However, our understanding of the selective forces that maintain prophages in bacterial populations is limited. Combining experimental evolution with stochastic modeling, we show that prophage maintenance and loss are primarily determined by environmental conditions that alter the net fitness effect of a prophage on its bacterial host...
April 5, 2024: Current Biology: CB
#20
JOURNAL ARTICLE
Justine Coïs, Sylvestre P J T Bachollet, Louis Sanchez, Nicolas Pietrancosta, Vincent Vialou, Jean-Maurice Mallet, Blaise Dumat
The combination of fluorogenic probes (fluorogens) and self-labeling protein tags represent a promising tool for imaging biological processes with high specificity but it requires the adequation between the fluorogen and its target to ensure a good activation of its fluorescence. In this work, we report a strategy to develop molecular rotors that specifically target HaloTag with a strong enhancement of their fluorescence. The divergent design facilitates the diversification of the structures to tune the photophysical and cellular properties...
April 4, 2024: Chemistry: a European Journal
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