Featured
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Article
| Open AccessMonkeypox virus genomic accordion strategies
The 2023 monkeypox outbreak was caused by a subclade IIb monkeypox virus (MPXV). Here, using advanced sequencing techniques, the authors identify variations on low-complexity regions of the MPXV genome and describe their potential as evolutionary drivers.
- Sara Monzón
- , Sarai Varona
- & Gustavo Palacios
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Article
| Open AccessThe genetic landscape of a metabolic interaction
Reynolds and colleagues examine a biochemically-mediated epistatic interaction between metabolic enzymes involved in folate metabolism and show that biochemical coupling shapes the range of enzyme activities sufficient to rescue cell growth.
- Thuy N. Nguyen
- , Christine Ingle
- & Kimberly A. Reynolds
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Article
| Open AccessRapid evolutionary change in trait correlations of single proteins
Trait correlations impact evolvability as selection on one trait can influence others. Here, the authors examine trait correlation in two proteins, a fluorescent protein & an antibiotic resistance enzyme, observing rapid evolution of trait correlations through changes in the biophysical properties of these proteins.
- Pouria Dasmeh
- , Jia Zheng
- & Andreas Wagner
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Article
| Open AccessPhylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages
Grasses share a whole-genome duplication called rho, but the adaptive implications are unclear. Here, the authors conduct phylogenomic and phylotranscriptomic analyses of 363 grasses, identifying additional whole-genome duplications and finding that duplicates are implicated in environmental adaptations or morphogenesis.
- Taikui Zhang
- , Weichen Huang
- & Hong Ma
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Matters Arising
| Open AccessPopulation genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data
- Vivak Soni
- , John W. Terbot II
- & Jeffrey D. Jensen
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Article
| Open AccessUnexpectedly uneven distribution of functional trade-offs explains cranial morphological diversity in carnivores
Functional trade-offs can affect phenotypic variation. Here, the authors examine trade-offs between bite force and speed in 132 carnivore species, finding that optimising for velocity can be obtained in more ways than optimising for force, and this may impact morphological variability.
- Gabriele Sansalone
- , Stephen Wroe
- & Carmelo Fruciano
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Matters Arising
| Open AccessReply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data
- Chase W. Nelson
- , Leo L. M. Poon
- & Haogao Gu
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Article
| Open AccessPositive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution
SARS-CoV-2 constantly evolves but the roles of resulting mutations are not always clear. In this study, the authors report that ORF8 knockout confers a fitness advantage to SARS-CoV-2 using genomic surveillance data, highlighting how different types of adaptations across the SARS-CoV-2 genome can drive variant fitness.
- Cassia Wagner
- , Kathryn E. Kistler
- & Trevor Bedford
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Article
| Open AccessAnnelid adult cell type diversity and their pluripotent cellular origins
The cellular atlas of Pristina leidyi reveals cell type diversity in adult annelids by single cell transcriptomics, discovering several novel cell types and suggesting a pluripotent stem cell signature associated with adult cell type differentiation
- Patricia Álvarez-Campos
- , Helena García-Castro
- & Jordi Solana
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Article
| Open AccessIntrogression and disruption of migration routes have shaped the genetic integrity of wildebeest populations
The evolutionary genetics of a keystone savannah species the blue wildebeest, and the related black wildebeest, remain largely unexplored. This study finds evidence for archaic introgression of black wildebeest to blue wildebeest and detrimental effects of human activities on migratory populations.
- Xiaodong Liu
- , Long Lin
- & Rasmus Heller
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Article
| Open AccessTumor phylogeography reveals block-shaped spatial heterogeneity and the mode of evolution in Hepatocellular Carcinoma
Hepatocellular carcinomas (HCC) present spatial intratumour heterogeneity (sITH). Here, the authors perform a genomic and phylogenetic analysis of spatially-sampled HCC tumour sections, observe block-shaped sITH, and find ongoing natural selection where ancestral and derived clones spatially compete in the same tumor.
- Xiaodong Liu
- , Ke Zhang
- & Weiwei Zhai
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Article
| Open AccessEvolution of T cells in the cancer-resistant naked mole-rat
Naked mole-rats are long-lived rodents with remarkable resistance to cancer. Here authors show that their T-cell compartment is different from that of mice in that they have a large population of circulating cytotoxic γδ T cells harboring a dominant clonotype, and the clonotypic diversity of their conventional cytotoxic αβ T cells is more modest than that of mice.
- Tzuhua D. Lin
- , Nimrod D. Rubinstein
- & Rochelle Buffenstein
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Article
| Open AccessAdaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events
Endogenous retroviruses (ERVs) are remnants of ancient viruses embedded in animal DNA. This study found that the solitary long terminal repeats of ERVs in birds, particularly Passeriformes, have evolved to influence gene expression, potentially contributing to adaptive diversification of species.
- Guangji Chen
- , Dan Yu
- & Shaohong Feng
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Article
| Open AccessDynamics of collective cooperation under personalised strategy updates
Collective cooperation is found across many social and biological systems. Here, the authors find that infrequent hub updates promote the emergence of collective cooperation and develop an algorithm that optimises collective cooperation with update rates.
- Yao Meng
- , Sean P. Cornelius
- & Aming Li
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Article
| Open AccessAn adaptive biomolecular condensation response is conserved across environmentally divergent species
Cells must respond to environmental changes. In three fungal species adapted to different temperatures, cellular responses are conserved yet tuned to each organism’s thermal niche, including the formation of adaptive biomolecular condensates.
- Samantha Keyport Kik
- , Dana Christopher
- & D. Allan Drummond
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Article
| Open AccessThe genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus
This study on respiratory syncytial virus (RSV) reveals global genomic gaps. Using INFORM-RSV data, it uncovers selection’s impact on RSVA and RSVB diversity. Analysing full genomes, it highlights non-neutral epidemic processes. The research emphasises air travel’s influence on global spread, underscoring the need for comprehensive RSV genomic surveillance.
- Annefleur C. Langedijk
- , Bram Vrancken
- & Shabir A. Madhi
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Article
| Open AccessAllopolyploid origin and diversification of the Hawaiian endemic mints
Hawaiian endemic mints represent the second largest plant radiation in the archipelago. Here, the authors present a reference genome and numerous resequenced individuals to uncover evidence for polyploidy, geographic speciation and localized hybridization underlying diversification in this lineage
- Crystal M. Tomlin
- , Sitaram Rajaraman
- & Charlotte Lindqvist
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Article
| Open AccessA chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution
Modern sugarcane cultivars have complicated genome due to interspecific crosses and multiple backcrossing. Here, the authors report the haplotype-resolved, chromosome-level genome assembly of a modern hybrid sugarcane cultivar and reveal the expansion of genes related to sugar accumulation and smut resistance.
- Yixue Bao
- , Qing Zhang
- & Muqing Zhang
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Article
| Open AccessCis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona
The notochord is an essential hallmark of the chordate phylum. Here, Negrón-Piñeiro et al. study the notochord gene regulatory network in Ciona, and their findings illustrate how notochord transcription factors are coordinated by Brachyury and Foxa2.
- Lenny J. Negrón-Piñeiro
- , Yushi Wu
- & Anna Di Gregorio
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Article
| Open AccessExtracellular DNA traps in a ctenophore demonstrate immune cell behaviors in a non-bilaterian
Identifying core mechanisms of immune cells is critical for understanding the evolution of animal immune function. Here, Vandepas et al. report that ctenophore immune-like cells release extracellular DNA traps when exposed to microbes.
- Lauren E. Vandepas
- , Caroline Stefani
- & Adam Lacy-Hulbert
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Article
| Open AccessGlobal latitudinal gradients and the evolution of body size in dinosaurs and mammals
Bergmann’s Rule predicts larger body sizes in colder climates. Here, the authors examine extinct and extant dinosaurs (birds) and mammaliaforms, finding no evidence of body size variation with latitude in any group, but a small variation with temperature in extant birds.
- Lauren N. Wilson
- , Jacob D. Gardner
- & Chris L. Organ
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Article
| Open AccessOrigin and dispersal history of Hepatitis B virus in Eastern Eurasia
Hepatitis B virus is an ancient human pathogen that dates back more than 10,000 years. Here, the authors investigate the evolutionary history of the virus in Eastern Eurasia by sequencing 34 genomes dating from approximately 400–5,000 years ago and comparing them with other contemporary sequences.
- Bing Sun
- , Aida Andrades Valtueña
- & Yinqiu Cui
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Article
| Open AccessEarly detection of emerging viral variants through analysis of community structure of coordinated substitution networks
Rise of new viral strains is a major public health challenge, demanding advanced detection and forecasting methods. This study shows how examining communities within networks of viral mutations enables early detection of emerging strains.
- Fatemeh Mohebbi
- , Alex Zelikovsky
- & Pavel Skums
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Article
| Open AccessThe Miocene primate Pliobates is a pliopithecoid
Pliobates cataloniae is a small-bodied Miocene catarrhine primate with unclear systematic status. Here, the authors present additional dental remains from this species, conducting cladistic analyses that indicate it is a pliopithecoid convergent with apes in elbow and wrist morphology.
- Florian Bouchet
- , Clément Zanolli
- & David M. Alba
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Article
| Open AccessHigh temperature delays and low temperature accelerates evolution of a new protein phenotype
The effect of temperature fluctuations on the evolution of new phenotypes is largely unknown. Using experimental evolution of fluorescent protein in E. coli, this study shows that a cooling environment can accelerate, and a warming environment decelerate, the evolution of a new protein phenotype.
- Jia Zheng
- , Ning Guo
- & Andreas Wagner
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Article
| Open AccessAnaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution
Here, Pratt et al identify a community of deep-branching anaerobic fungi in tortoise feces. Multiple characteristics underpinning their success in tortoise, as opposed to scarcity in mammalian alimentary tracts, are presented.
- Carrie J. Pratt
- , Casey H. Meili
- & Noha H. Youssef
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Article
| Open AccessMethyl transfer in psilocybin biosynthesis
The natural hallucinogen psilocybin — produced by so-called magic mushrooms — holds promise for the treatment of depression and other mental health conditions. Here, the authors provide a structural and biochemical analysis of the Psilocybe methyl transferase PsiM that provides mechanistic insight into the last step of psilocybin biosynthesis.
- Jesse Hudspeth
- , Kai Rogge
- & Sebastiaan Werten
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Article
| Open AccessBee-pollination promotes rapid divergent evolution in plants growing in different soils
In nature, soil, pollinators, and herbivores are the main drivers of plant adaptation and diversification. This study reveals that the interaction between soil and biotic pollination causes divergent evolution where pollinators play a key role, leading to strong divergence among plants in different soils.
- Thomas Dorey
- & Florian P. Schiestl
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Article
| Open AccessNaked mole-rats have distinctive cardiometabolic and genetic adaptations to their underground low-oxygen lifestyles
The naked mole-rat exhibits extreme longevity, resistance to hypoxia and absence of cardiovascular disease. Here, Faulkes et al. identify mechanisms behind these traits by comparing cardiac metabolomes and transcriptomes of naked more-rats to other African mole-rat genera and evolutionary divergent mammals.
- Chris G. Faulkes
- , Thomas R. Eykyn
- & Dunja Aksentijevic
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Article
| Open AccessTrade-offs shaping transmission of sylvatic dengue and Zika viruses in monkey hosts
Hanley et al show that transmission of dengue and Zika virus from Old and New World monkeys is shaped by an immunologically-mediated trade-off between magnitude and duration of replication. Patterns of Zika transmission suggests high risk of spillback into neotropical monkeys.
- Kathryn A. Hanley
- , Hélène Cecilia
- & Shannan L. Rossi
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Article
| Open AccessMacroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages
Correspondence between genome and organismal complexity over macroevolutionary time is poorly understood. Here the authors show that multicellular eukaryotes increasingly simplify their genomes and suggest that the concept of functional outsourcing, via ecological interactions, could explain this paradoxical complexity decoupling.
- Mirjana Domazet-Lošo
- , Tin Široki
- & Tomislav Domazet-Lošo
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Article
| Open AccessSynthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Pseudomonas putida is becoming a host of choice for the valorization of lignocellulosic substrates. Here, the authors provide insight into the adaptation of this bacterium to the non-native substrate D-xylose, enabled by metabolic engineering and adaptive laboratory evolution.
- Pavel Dvořák
- , Barbora Burýšková
- & Martin Benešík
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Article
| Open AccessThe Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal
The timing and chronology of the movement of Homo sapiens after migration out of Africa remains unclear. Here, the authors combine a genetic approach with a palaeoecological model to estimate that the Persian Plateau could have been a hub for migration out of Africa, suggesting the environment may have been suitable for population maintenance.
- Leonardo Vallini
- , Carlo Zampieri
- & Luca Pagani
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Article
| Open AccessPlasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria
In this work, authors combine computational models with single-cell and population-level data showing the variability in plasmid copy number within bacterial populations leads to phenotypic diversity. They reveal how multicopy plasmids contribute to bacterial transient antibiotic resistance.
- J. Carlos R. Hernandez-Beltran
- , Jerónimo Rodríguez-Beltrán
- & Rafael Peña-Miller
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Article
| Open AccessPredictive evolutionary modelling for influenza virus by site-based dynamics of mutations
Seasonal influenza vaccine effectiveness depends on including virus strains in the vaccine that closely match those circulating in the upcoming season. In this study, the authors develop a computational model of influenza virus evolution to predict future circulating strains and therefore support vaccine strain selection.
- Jingzhi Lou
- , Weiwen Liang
- & Maggie Haitian Wang
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Article
| Open AccessAn evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway
Unmet expectations, a previously uncharacterized fly protein, is a SAM sensor for the mTORC1 pathway. Tracing the evolution of Unmet reveals that the pathway uses the GATOR2 complex to capture and repurpose ancestral enzymes as nutrient sensors.
- Grace Y. Liu
- , Patrick Jouandin
- & David M. Sabatini
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Article
| Open AccessDynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry
Subgenome dominance is widely observed in allopolyploid species, but the molecular mechanisms remain unclear. Here, the authors generate genome-wide map of accessible chromatin regions (ACRs) in allo-octoploid cultivated strawberry and reveal that dynamics of the ACRs play an important role in its subgenome dominance.
- Chao Fang
- , Ning Jiang
- & Jiming Jiang
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Article
| Open AccessThe evolutionary origin of naturally occurring intermolecular Diels-Alderases from Morus alba
Diels-Alderases (DAs), enzymes catalyzing [4 + 2] cycloaddition reactions, are of high interest, but insights into their evolution are lacking. Here, the authors investigate the evolutionary origins of the intermolecular DAs in the biosynthesis of Moraceae plant-derived Diels-Alder-type secondary metabolites, suggesting they evolved from an ancestor functioning as a flavin adenine dinucleotide-dependent oxidocyclase.
- Qi Ding
- , Nianxin Guo
- & Xiaoguang Lei
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Article
| Open AccessSingle cell atlas of Xenoturbella bocki highlights limited cell-type complexity
Recent phylogenetic analyses have identified orphan clades, including Xenacoelomorphs, that can offer insights into bilaterian evolution. Here they generate a cell type atlas of Xenoturbella bockithat highlights cellular diversity in the nervous system and other tissues, reinforcing the idea of parallel evolution of cell types across animals.
- Helen E. Robertson
- , Arnau Sebé-Pedrós
- & Heather Marlow
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Article
| Open AccessEvolutionary origin of Hoxc13-dependent skin appendages in amphibians
Hair is the main skin appendage of mammals. Here, the authors show that claws of clawed frogs and hair contain homologous keratins and depend on the same transcription factor, Hoxc13, suggesting a common evolutionary origin of these skin appendages.
- Marjolein Carron
- , Attila Placido Sachslehner
- & Leopold Eckhart
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Article
| Open AccessTemporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids
Wei et al. report a unique interspecific ascidian hybrid system and single-cell RNA sequencing to reveal the temporal hierarchy, spatial heterogeneity, and allele-specific expression of zygotic genome activation in urochordates.
- Jiankai Wei
- , Wei Zhang
- & Bo Dong
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Article
| Open AccessClearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation
There is limited data on immune factors contributing to SARS-CoV-2 viral clearance in people living with HIV. Here, the authors show that re-emergence of the neutralizing antibody response may be key to clearing persistent SARS-CoV-2 infection in ART-mediated recovery from immunosuppression in advanced HIV disease.
- Farina Karim
- , Catherine Riou
- & Alex Sigal
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Article
| Open AccessDivergent dynamics of sexual and habitat isolation at the transition between stick insect populations and species
Speciation may not be a mechanistically or temporally uniform process. We show divergent evolution of sexual versus habitat isolation and flat versus linear accumulation of the latter for within- versus between-species comparisons, revealing a critical role for species.
- Patrik Nosil
- , Zachariah Gompert
- & Daniel J. Funk
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Article
| Open AccessInter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis
Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection closely related to Streptococcus pyogenes. Here the authors investigate the degree of genomic similarity between the two species and assess implications for development of vaccines.
- Ouli Xie
- , Jacqueline M. Morris
- & Mark R. Davies
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Article
| Open AccessNew estimates indicate that males are not larger than females in most mammal species
The narrative that larger males are the norm in mammals has predominated for over a century. An analysis of body mass dimorphism across mammals, sampling families by their species richness, indicates that males are not larger than females in most mammals and that monomorphism is almost as prevalent.
- Kaia J. Tombak
- , Severine B. S. W. Hex
- & Daniel I. Rubenstein
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Article
| Open AccessDependency on host vitamin B12 has shaped Mycobacterium tuberculosis Complex evolution
Campos-Pardos et al show that the virulence of Mycobacterium tuberculosis is dependent on sufficient uptake of exogenous vitamin B12 from host serum and this phenotype is not conserved in environmental, opportunistic and ancestral lineages.
- Elena Campos-Pardos
- , Santiago Uranga
- & Jesús Gonzalo-Asensio
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Article
| Open AccessThe global speciation continuum of the cyanobacterium Microcoleus
The relative importance of the various mechanisms that can drive microbial speciation is poorly understood. Here, Stanojković et al. explore the diversification of the soil cyanobacterium Microcoleus, showing that this genus represents a global speciation continuum of at least 12 lineages, with lineage divergence driven by selection, geographical distance, and the environment.
- Aleksandar Stanojković
- , Svatopluk Skoupý
- & Petr Dvořák
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Article
| Open AccessBet hedging in a unicellular microalga
Bet hedging is an evolutionary strategy facilitating survival in randomly fluctuating environments. Here, the authors report bet hedging in the unicellular microalga Haematococcus pluvialis, undergoing reversible diversification into mobile and non-mobile cells.
- Si Tang
- , Yaqing Liu
- & Zhonghua Cai
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Article
| Open AccessBiosensor and machine learning-aided engineering of an amaryllidaceae enzyme
Amaryllidaceae alkaloids, such as the Alzheimer’s medication galantamine, are currently extracted from low-yielding daffodils. Here, authors pair biosensor-assisted screening with machine learning-guided protein design to rapidly engineer an improved Amaryllidaceae enzyme in a microbial host.
- Simon d’Oelsnitz
- , Daniel J. Diaz
- & Andrew D. Ellington
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