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1.
Genome Biol Evol ; 16(7)2024 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-38976568

RESUMO

Comparative analyses of gene birth-death dynamics have the potential to reveal gene families that played an important role in the evolution of morphological, behavioral, or physiological variation. Here, we used whole genomes of 30 species of butterflies and moths to identify gene birth-death dynamics among the Lepidoptera that are associated with specialist or generalist feeding strategies. Our work advances this field using a uniform set of annotated proteins for all genomes, investigating associations while correcting for phylogeny, and assessing all gene families rather than a priori subsets. We discovered that the sizes of several important gene families (e.g. those associated with pesticide resistance, xenobiotic detoxification, and/or protein digestion) are significantly correlated with diet breadth. We also found 22 gene families showing significant shifts in gene birth-death dynamics at the butterfly (Papilionoidea) crown node, the most notable of which was a family of pheromone receptors that underwent a contraction potentially linked with a shift to visual-based mate recognition. Our findings highlight the importance of uniform annotations, phylogenetic corrections, and unbiased gene family analyses in generating a list of candidate genes that warrant further exploration.


Assuntos
Borboletas , Genoma de Inseto , Filogenia , Animais , Borboletas/genética , Dieta , Mariposas/genética , Lepidópteros/genética , Evolução Molecular
2.
Soc Networks ; 76: 174-190, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-39006096

RESUMO

Social relations are embedded in material, cultural, and institutional settings that affect network dynamics and the resulting topologies. For example, romantic entanglements are subject to social and cultural norms, interfirm alliances are constrained by country-specific legislation, and adolescent friendships are conditioned by classroom settings and neighborhood effects. In short, social contexts shape social relations and the networks they give rise to. However, how and when they do so remain to be established. This paper presents network ecology as a general framework for identifying how the proximal environment shapes social networks by focusing interactions and social relations, and how these interactions and relations in turn shape the environment in which social networks form. Tie fitness is introduced as a metric that quantifies how well particular dyadic social relations would align with the setting. Using longitudinal networks collected on two cohorts each in 18 North American schools, i.e., 36 settings, we develop five generalizable observations about the time-varying fitness of adolescent friendship. Across all 252 analyzed networks, tie fitness predicted new tie formation, tie longevity, and tie survival. Dormant fit ties cluster in relational niches, thereby establishing a resource base for social identities competing for increased representation in the relational system.

3.
Ecol Evol ; 14(7): e11719, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-39011130

RESUMO

Herbarium specimens are increasingly being used as sources of information to understand the ecology and evolution of plants and their associated microbes. Most studies have used specimens as a source of genetic material using culture-independent approaches. We demonstrate that herbarium specimens can also be used to culture nodule-associated bacteria, opening the possibility of using specimens to understand plant-microbe interactions at new spatiotemporal scales. We used historic and contemporary nodules of a common legume, Medicago lupulina, to create a culture collection. We were able to recover historic bacteria in 15 genera from three specimens (collected in 1950, 2004, and 2015). This work is the first of its kind to isolate historic bacteria from herbarium specimens. Future work should include inoculating plants with historic strains to see if they produce nodules and if they affect plant phenotype and fitness. Although we were unable to recover any Ensifer, the main symbiont of Medicago lupulina, we recovered some other potential nodulating species, as well as many putative growth-promoting bacteria.

4.
Sci Rep ; 14(1): 15413, 2024 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-38965341

RESUMO

Feature selection is a hot problem in machine learning. Swarm intelligence algorithms play an essential role in feature selection due to their excellent optimisation ability. The Chimp Optimisation Algorithm (CHoA) is a new type of swarm intelligence algorithm. It has quickly won widespread attention in the academic community due to its fast convergence speed and easy implementation. However, CHoA has specific challenges in balancing local and global search, limiting its optimisation accuracy and leading to premature convergence, thus affecting the algorithm's performance on feature selection tasks. This study proposes Social coevolution and Sine chaotic opposition learning Chimp Optimization Algorithm (SOSCHoA). SOSCHoA enhances inter-population interaction through social coevolution, improving local search. Additionally, it introduces sine chaotic opposition learning to increase population diversity and prevent local optima. Extensive experiments on 12 high-dimensional classification datasets demonstrate that SOSCHoA outperforms existing algorithms in classification accuracy, convergence, and stability. Although SOSCHoA shows advantages in handling high-dimensional datasets, there is room for future research and optimization, particularly concerning feature dimensionality reduction.

5.
J Exp Bot ; 2024 Jul 19.
Artigo em Inglês | MEDLINE | ID: mdl-39028613

RESUMO

Plants are unique organisms that have developed ingenious strategies to cope with environmental challenges, such as herbivorous insects. One of these strategies is the synthesis of a vast array of chemical compounds, known as specialized metabolites, that serve many ecological functions. Among the most fascinating and diverse groups of specialized metabolites are the alkaloids, which are characterized by the presence of a nitrogen atom within a heterocyclic ring. While some have medicinal and recreational applications, others are highly unpalatable and/or toxic. The effects of alkaloids on both humans and insects can be very diverse, affecting their physiology and behavior. Insects that feed on alkaloid-containing plants have evolved diverse mechanisms to cope with the consequences of these toxins. These include sequestration, where insects store alkaloids in specialized tissues or organs, enzymatic detoxification through enzymes such as cytochrome P450 monooxygenases and glutathione S-transferases, and behavioral adaptations such as selective feeding. In this review, we explore the relationships between plant alkaloids and the evolutionary adaptations that enable insects to exploit alkaloid-rich plants as food sources and ecological niches minimizing the harmful effects of these natural compounds. We aim to provide a comprehensive and updated overview of this fascinating and complex ecological interaction.

6.
Am Nat ; 204(2): 121-132, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39008840

RESUMO

AbstractClimate change will alter interactions between parasites and their hosts. Warming may affect patterns of local adaptation, shifting the environment to favor the parasite or host and thus changing the prevalence of disease. We assessed local adaptation to hosts and temperature in the facultative ciliate parasite Lambornella clarki, which infects the western tree hole mosquito Aedes sierrensis. We conducted laboratory infection experiments with mosquito larvae and parasites collected from across a climate gradient, pairing sympatric or allopatric populations across three temperatures that were either matched or mismatched to the source environment. Lambornella clarki parasites were locally adapted to their hosts, with 2.6 times higher infection rates on sympatric populations compared with allopatric populations, but they were not locally adapted to temperature. Infection peaked at the intermediate temperature of 12.5°C, notably lower than the optimum temperature for free-living L. clarki growth, suggesting that the host's immune response can play a significant role in mediating the outcome of infection. Our results highlight the importance of host selective pressure on parasites, despite the impact of temperature on infection success.


Assuntos
Aedes , Interações Hospedeiro-Parasita , Larva , Temperatura , Animais , Aedes/parasitologia , Larva/parasitologia , Larva/crescimento & desenvolvimento , Adaptação Fisiológica , Apicomplexa/fisiologia
7.
Proc Biol Sci ; 291(2024): 20240446, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38835275

RESUMO

Many genes and signalling pathways within plant and animal taxa drive the expression of multiple organismal traits. This form of genetic pleiotropy instigates trade-offs among life-history traits if a mutation in the pleiotropic gene improves the fitness contribution of one trait at the expense of another. Whether or not pleiotropy gives rise to conflict among traits, however, likely depends on the resource costs and timing of trait deployment during organismal development. To investigate factors that could influence the evolutionary maintenance of pleiotropy in gene networks, we developed an agent-based model of co-evolution between parasites and hosts. Hosts comprise signalling networks that must faithfully complete a developmental programme while also defending against parasites, and trait signalling networks could be independent or share a pleiotropic component as they evolved to improve host fitness. We found that hosts with independent developmental and immune networks were significantly more fit than hosts with pleiotropic networks when traits were deployed asynchronously during development. When host genotypes directly competed against each other, however, pleiotropic hosts were victorious regardless of trait synchrony because the pleiotropic networks were more robust to parasite manipulation, potentially explaining the abundance of pleiotropy in immune systems despite its contribution to life history trade-offs.


Assuntos
Pleiotropia Genética , Transdução de Sinais , Animais , Evolução Biológica , Interações Hospedeiro-Parasita , Aptidão Genética , Alocação de Recursos
8.
Curr Issues Mol Biol ; 46(6): 5744-5776, 2024 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-38921015

RESUMO

In the SARS-CoV-2 lineage, RNA elements essential for its viral life cycle, including genome replication and gene expression, have been identified. Still, the precise structures and functions of these RNA regions in coronaviruses remain poorly understood. This lack of knowledge points out the need for further research to better understand these crucial aspects of viral biology and, in time, prepare for future outbreaks. In this research, the in silico analysis of the cis RNA structures that act in the alpha-, beta-, gamma-, and deltacoronavirus genera has provided a detailed view of the presence and adaptation of the structures of these elements in coronaviruses. The results emphasize the importance of these cis elements in viral biology and their variability between different viral variants. Some coronavirus variants in some groups, depending on the cis element (stem-loop1 and -2; pseudoknot stem-loop1 and -2, and s2m), exhibited functional adaptation. Additionally, the conformation flexibility of the s2m element in the SARS variants was determined, suggesting a coevolution of this element in this viral group. The variability in secondary structures suggests genomic adaptations that may be related to replication processes, genetic regulation, as well as the specific pathogenicity of each variant. The results suggest that RNA structures in coronaviruses can adapt and evolve toward different viral variants, which has important implications for viral adaptation, pathogenicity, and future therapeutic strategies.

9.
Insects ; 15(6)2024 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-38921172

RESUMO

Insect pheromones have been intensively studied with respect to their role in insect communication. However, scarce knowledge is available on the impact of pheromones on plant responses, and how these in turn affect herbivorous insects. A previous study showed that exposure of pine (Pinus sylvestris) to the sex pheromones of the pine sawfly Diprion pini results in enhanced defenses against the eggs of this sawfly; the egg survival rate on pheromone-exposed pine needles was lower than that on unexposed pine. The long-lasting common evolutionary history of D. pini and P. sylvestris suggests that D. pini has developed counter-adaptations to these pine responses. Here, we investigated by behavioral assays how D. pini copes with the defenses of pheromone-exposed pine. The sawfly females did not discriminate between the odor of pheromone-exposed and unexposed pine. However, when they had the chance to contact the trees, more unexposed than pheromone-exposed trees received eggs. The exposure of pine to the pheromones did not affect the performance of larvae and their pupation success. Our findings indicate that the effects that responses of pine to D. pini sex pheromones exert on the sawfly eggs and sawfly oviposition behavior do not extend to effects on the larvae.

10.
Mol Ecol ; 33(14): e17443, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38943372

RESUMO

The iconic Monarch butterfly is probably the best-known example of chemical defence against predation, as pictures of vomiting naive blue jays in countless textbooks vividly illustrate. Larvae of the butterfly take up toxic cardiac glycosides from their milkweed hostplants and carry them over to the adult stage. These compounds (cardiotonic steroids, including cardenolides and bufadienolides) inhibit the animal transmembrane sodium-potassium ATPase (Na,K-ATPase), but the Monarch enzyme resists this inhibition thanks to amino acid substitutions in its catalytic alpha-subunit. Some birds also have substitutions and can feast on cardiac glycoside-sequestering insects with impunity. A flurry of recent work has shown how the alpha-subunit gene has been duplicated multiple times in separate insect lineages specializing in cardiac glycoside-producing plants. In this issue of Molecular Ecology, Herbertz et al. toss the beta-subunit into the mix, by expressing all nine combinations of three alpha- and three beta-subunits of the milkweed bug Na,K-ATPase and testing their response to a cardenolide from the hostplant. The findings suggest that the diversification and subfunctionalization of genes allow milkweed bugs to balance trade-offs between resistance towards sequestered host plant toxins that protect the bugs from predators, and physiological costs in terms of Na,K-ATPase activity.


Assuntos
Asclepias , Borboletas , ATPase Trocadora de Sódio-Potássio , Animais , Borboletas/genética , ATPase Trocadora de Sódio-Potássio/genética , ATPase Trocadora de Sódio-Potássio/metabolismo , Asclepias/genética , Asclepias/química , Cardenolídeos , Duplicação Gênica , Glicosídeos Cardíacos/farmacologia , Larva
11.
Proc Natl Acad Sci U S A ; 121(27): e2311887121, 2024 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-38913900

RESUMO

Predicting which proteins interact together from amino acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments (MSAs), such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called Differentiable Pairing using Alignment-based Language Models (DiffPALM) that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids within protein chains. It also captures inter-chain coevolution, despite being trained on single-chain data. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. Starting from sequences paired by DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer. It also achieves competitive performance with using orthology-based pairing.


Assuntos
Proteínas , Alinhamento de Sequência , Alinhamento de Sequência/métodos , Proteínas/química , Proteínas/metabolismo , Sequência de Aminoácidos , Algoritmos , Análise de Sequência de Proteína/métodos , Biologia Computacional/métodos , Bases de Dados de Proteínas
12.
Front Microbiol ; 15: 1424489, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38939190

RESUMO

The expansion of betel palm cultivation is driven by rising demand for betel nut, yet this growth is accompanied by challenges such as decreased agricultural biodiversity and the spread of infectious pathogens. Among these, Yellow Leaf Disease (YLD) emerges as a prominent threat to betel palm plantation. Areca Palm Velarivirus 1 (APV1) has been identified as a primary causative agent of YLD, precipitating leaf yellowing, stunted growth, and diminished yield. However, the precise mechanisms underlying APV1-induced damage remain elusive. Our study elucidates that APV1 infiltrates chloroplasts, instigating severe damage and consequential reductions in chlorophyll a/b and carotene levels, alongside notable declines in photosynthetic efficiency. Moreover, APV1 infection exerts broad regulatory effects on gene expression, particularly suppressing key genes implicated in chloroplast function and photosynthesis. These disruptions correlate with growth retardation, yield diminishment, and compromised nut quality. Intriguingly, the paradoxical destruction of the host's photosynthetic machinery by APV1 prompts inquiry into its evolutionary rationale, given the virus's dependence on host resources for replication and proliferation. Our findings reveal that APV1-induced leaf yellowing acts as a beacon for transmission vectors, hinting at a nuanced "host-pathogen-vector co-evolutionary" dynamic.

13.
Genome Biol Evol ; 16(7)2024 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-38941482

RESUMO

Male seminal fluid proteins often show signs of positive selection and divergent evolution, believed to reflect male-female coevolution. Yet, our understanding of the predicted concerted evolution of seminal fluid proteins and female reproductive proteins is limited. We sequenced, assembled, and annotated the genome of two species of seed beetles allowing a comparative analysis of four closely related species of these herbivorous insects. We compare the general pattern of evolution in genes encoding seminal fluid proteins and female reproductive proteins with those in digestive protein genes and well-conserved reference genes. We found that female reproductive proteins showed an overall ratio of nonsynonymous to synonymous substitutions (ω) similar to that of conserved genes, while seminal fluid proteins and digestive proteins exhibited higher overall ω values. Further, seminal fluid proteins and digestive proteins showed a higher proportion of sites putatively under positive selection, and explicit tests showed no difference in relaxed selection between protein types. Evolutionary rate covariation analyses showed that evolutionary rates among seminal fluid proteins were on average more closely correlated with those in female reproductive proteins than with either digestive or conserved genes. Gene expression showed the expected negative covariation with ω values, except for male-biased genes where this negative relationship was reversed. In conclusion, seminal fluid proteins showed relatively rapid evolution and signs of positive selection. In contrast, female reproductive proteins evolved at a lower rate under selective constraints, on par with genes known to be well conserved. Although our findings provide support for concerted evolution of seminal fluid proteins and female reproductive proteins, they also suggest that these two classes of proteins evolve under partly distinct selective regimes.


Assuntos
Besouros , Evolução Molecular , Seleção Genética , Animais , Besouros/genética , Masculino , Feminino , Proteínas de Insetos/genética , Filogenia , Genoma de Inseto , Proteínas de Plasma Seminal/genética , Genômica , Reprodução/genética
14.
Plant Sci ; 346: 112165, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-38925477

RESUMO

Agriculture and global food security encounter significant challenges due to viral threats. In the following decades, several molecular studies have focused on discovering biosynthetic pathways of numerous defensive and signaling compounds, as key regulators of plant interactions, either with viruses or their associated vectors. Nevertheless, the complexities of specialized metabolites mediated plant-virus-vector tripartite viewpoint and the identification of their co-evolutionary crossroads toward antiviral defense system, remain elusive. The current study reviews the various roles of plant-specialized metabolites (PSMs) and how plants use these metabolites to defend against viruses. It discusses recent examples of specialized metabolites that have broad-spectrum antiviral properties. Additionally, the study presents the co-evolutionary basis of metabolite-mediated plant-virus-insect interactions as a potential bioinspired approach to combat viral threats. The prospects also show promising metabolic engineering strategies aimed at discovering a wide range of PSMs that are effective in fending off viruses and their related vectors. These advances in understanding the potential role of PSMs in plant-virus interactions not only serve as a cornerstone for developing plant antiviral systems, but also highlight essential principles of biological control.


Assuntos
Doenças das Plantas , Vírus de Plantas , Plantas , Vírus de Plantas/fisiologia , Plantas/virologia , Plantas/metabolismo , Doenças das Plantas/virologia , Animais , Interações Hospedeiro-Patógeno , Evolução Biológica
15.
Mol Biol Evol ; 41(6)2024 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-38865490

RESUMO

Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins ("DNA-protein crosslink repair"). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA-protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.


Assuntos
Reparo do DNA , Proteínas de Drosophila , Evolução Molecular , Duplicação Gênica , Animais , Proteínas de Drosophila/genética , Filogenia , Drosophila melanogaster/genética , Drosophila/genética , Família Multigênica , Seleção Genética , DNA Satélite/genética
16.
Mol Cell ; 84(12): 2223-2237.e4, 2024 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-38870937

RESUMO

In Saccharomyces cerevisiae (S. cerevisiae), Mre11-Rad50-Xrs2 (MRX)-Sae2 nuclease activity is required for the resection of DNA breaks with secondary structures or protein blocks, while in humans, the MRE11-RAD50-NBS1 (MRN) homolog with CtIP is needed to initiate DNA end resection of all breaks. Phosphorylated Sae2/CtIP stimulates the endonuclease activity of MRX/N. Structural insights into the activation of the Mre11 nuclease are available only for organisms lacking Sae2/CtIP, so little is known about how Sae2/CtIP activates the nuclease ensemble. Here, we uncover the mechanism of Mre11 activation by Sae2 using a combination of AlphaFold2 structural modeling of biochemical and genetic assays. We show that Sae2 stabilizes the Mre11 nuclease in a conformation poised to cleave substrate DNA. Several designs of compensatory mutations establish how Sae2 activates MRX in vitro and in vivo, supporting the structural model. Finally, our study uncovers how human CtIP, despite considerable sequence divergence, employs a similar mechanism to activate MRN.


Assuntos
Proteínas de Ligação a DNA , Endodesoxirribonucleases , Endonucleases , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/enzimologia , Saccharomyces cerevisiae/metabolismo , Endonucleases/metabolismo , Endonucleases/genética , Proteínas de Ligação a DNA/metabolismo , Proteínas de Ligação a DNA/genética , Endodesoxirribonucleases/metabolismo , Endodesoxirribonucleases/genética , Endodesoxirribonucleases/química , Humanos , Exodesoxirribonucleases/metabolismo , Exodesoxirribonucleases/genética , Modelos Moleculares , Fosforilação , Enzimas Reparadoras do DNA/metabolismo , Enzimas Reparadoras do DNA/genética , Quebras de DNA de Cadeia Dupla , Hidrolases Anidrido Ácido/metabolismo , Hidrolases Anidrido Ácido/genética , Mutação , Proteína Homóloga a MRE11/metabolismo , Proteína Homóloga a MRE11/genética , Reparo do DNA , Ativação Enzimática
17.
J Transl Med ; 22(1): 559, 2024 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-38863033

RESUMO

BACKGROUND: Exploration of adaptive evolutionary changes at the genetic level in vaginal microbial communities during different stages of cervical cancer remains limited. This study aimed to elucidate the mutational profile of the vaginal microbiota throughout the progression of cervical disease and subsequently establish diagnostic models. METHODS: This study utilized a metagenomic dataset consisting of 151 subjects classified into four categories: invasive cervical cancer (CC) (n = 42), cervical intraepithelial neoplasia (CIN) (n = 43), HPV-infected (HPVi) patients without cervical lesions (n = 34), and healthy controls (n = 32). The analysis focused on changes in microbiome abundance and extracted information on genetic variation. Consequently, comprehensive multimodal microbial signatures associated with CC, encompassing taxonomic alterations, mutation signatures, and enriched metabolic functional pathways, were identified. Diagnostic models for predicting CC were established considering gene characteristics based on single nucleotide variants (SNVs). RESULTS: In this study, we screened and analyzed the abundances of 18 key microbial strains during CC progression. Additionally, 71,6358 non-redundant mutations were identified, predominantly consisting of SNVs that were further annotated into 25,773 genes. Altered abundances of SNVs and mutation types were observed across the four groups. Specifically, there were 9847 SNVs in the HPV-infected group and 14,892 in the CC group. Furthermore, two distinct mutation signatures corresponding to the benign and malignant groups were identified. The enriched metabolic pathways showed limited similarity with only two overlapping pathways among the four groups. HPVi patients exhibited active nucleotide biosynthesis, whereas patients with CC demonstrated a significantly higher abundance of signaling and cellular-associated protein families. In contrast, healthy controls showed a distinct enrichment in sugar metabolism. Moreover, biomarkers based on microbial SNV abundance displayed stronger diagnostic capability (cc.AUC = 0.87) than the species-level biomarkers (cc.AUC = 0.78). Ultimately, the integration of multimodal biomarkers demonstrated optimal performance for accurately identifying different cervical statuses (cc.AUC = 0.86), with an acceptable performance (AUC = 0.79) in the external testing set. CONCLUSIONS: The vaginal microbiome exhibits specific SNV evolution in conjunction with the progression of CC, and serves as a specific biomarker for distinguishing between different statuses of cervical disease.


Assuntos
Microbiota , Neoplasias do Colo do Útero , Vagina , Humanos , Feminino , Neoplasias do Colo do Útero/microbiologia , Neoplasias do Colo do Útero/virologia , Neoplasias do Colo do Útero/genética , Vagina/microbiologia , Microbiota/genética , Mutação/genética , Pessoa de Meia-Idade , Adulto , Polimorfismo de Nucleotídeo Único/genética , Estudos de Casos e Controles , Progressão da Doença
18.
Integr Zool ; 2024 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-38872359

RESUMO

Chytridiomycosis, an infectious skin disease caused by the chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans, poses a significant threat to amphibian biodiversity worldwide. Antifungal bacteria found on the skin of chytrid-resistant amphibians could potentially provide defense against chytridiomycosis and lower mortality rates among resistant individuals. The Hong Kong newt (Paramesotriton hongkongensis) is native to East Asia, a region suspected to be the origin of chytrids, and has exhibited asymptomatic infection, suggesting a long-term coexistence with the chytrids. Therefore, the skin microbiota of this resistant species warrant investigation, along with other factors that can affect the microbiota. Among the 149 newts sampled in their natural habitats in Hong Kong, China, putative antifungal bacteria were found in all individuals. There were 314 amplicon sequence variants distributed over 25 genera of putative antifungal bacteria; abundant ones included Acinetobacter, Flavobacterium, and Novosphingobium spp. The skin microbiota compositions were strongly influenced by the inter-site geographical distances. Despite inter-site differences, we identified some core skin microbes across sites that could be vital to P. hongkongensis. The dominant cores included the family Comamonadaceae, family Chitinophagaceae, and class Betaproteobacteria. Moreover, habitat elevation and host sex also exhibited significant effects on skin microbiota compositions. The antifungal bacteria found on these newts offer an important resource for conservation against chytridiomycosis, such as developing probiotic treatments for susceptible species.

19.
J Chem Ecol ; 2024 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-38842636

RESUMO

Animals that consume toxic diets provide models for understanding the molecular and physiological adaptations to ecological challenges. Garter snakes (Thamnophis) in western North America prey on Pacific newts (Taricha), which employ tetrodotoxin (TTX) as an antipredator defense. These snakes possess mutations in voltage-gated sodium channels (Nav), the molecular targets of TTX, that decrease the binding ability of TTX to sodium channels (target-site resistance). However, genetic variation at these loci that cannot explain all the phenotypic variation in TTX resistance in Thamnophis. We explored a separate means of resistance, toxin metabolism, to determine if TTX-resistant snakes either rapidly remove TTX or sequester TTX. We examined the metabolism and distribution of TTX in the body (toxicokinetics), to determine differences between TTX-resistant and TTX-sensitive snakes in the rates at which TTX is eliminated from organs and the whole body (using TTX half-life as our metric). We assayed TTX half-life in snakes from TTX-resistant and TTX-sensitive populations of three garter snake species with a coevolutionary history with newts (T. atratus, T. couchii, T. sirtalis), as well as two non-resistant "outgroup" species (T. elegans, Pituophis catenifer) that seldom (if ever) engage newts. We found TTX half-life varied across species, populations, and tissues. Interestingly, TTX half-life was shortest in T. elegans and P. catenifer compared to all other snakes. Furthermore, TTX-resistant populations of T. couchii and T. sirtalis eliminated TTX faster (shorter TTX half-life) than their TTX-sensitive counterparts, while populations of TTX-resistant and TTX-sensitive T. atratus showed no difference rates of TTX removal (same TTX half-life). The ability to rapidly eliminate TTX may have permitted increased prey consumption, which may have promoted the evolution of additional resistance mechanisms. Finally, snakes still retain substantial amounts of TTX, and we projected that snakes could be dangerous to their own predators days to weeks following the ingestion of a single newt. Thus, aspects of toxin metabolism may have been key in driving predator-prey relationships, and important in determining other ecological interactions.

20.
Zoology (Jena) ; 165: 126181, 2024 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-38833995

RESUMO

Climbing animals such as geckos and arthropods developed astonishing adhesive mechanisms which are fundamental for their survival and represent valuable models for biomimetic purposes. A firm adhesion to the host surface, in order to successfully lay eggs is necessary for the reproduction of most parasitoid insects. In the present study, we performed a comparative investigation on the attachment ability of four parasitoid species (the egg parasitoid Anastatus bifasciatus (Eupelmidae), the aphid parasitoid Aphidius ervi (Braconidae), the fly pupal ectoparasitoid Muscidifurax raptorellus (Pteromalidae) and the pupal parasitoid of Drosophila Trichopria drosophilae (Diapriidae)) with hosts characterized by a surface having different wettability properties. The friction force measurements were performed on smooth artificial (glass) surfaces showing different contact angles of water. We found that attachment systems of parasitoid insects are tuned to match the wettability of the host surface. Sexual dimorphism in the attachment ability of some tested species has been also observed. The obtained results are probably related to different microstructure and chemical composition of the host surfaces and to different chemical composition of the parasitoid adhesive fluid. The data here presented can be interpreted as an adaptation, especially in the female, to the physicochemical properties of the host surface and contribute to shed light on the coevolutionary processes of parasitoid insects and their hosts.

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