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1.
Cancer Res Commun ; 4(6): 1581-1596, 2024 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-38722600

RESUMO

Immune checkpoint therapy (ICB) has conferred significant and durable clinical benefit to some patients with cancer. However, most patients do not respond to ICB, and reliable biomarkers of ICB response are needed to improve patient stratification. Here, we performed a transcriptome-wide meta-analysis across 1,486 tumors from ICB-treated patients and tumors with expected ICB outcomes based on microsatellite status. Using a robust transcriptome deconvolution approach, we inferred cancer- and stroma-specific gene expression differences and identified cell-type specific features of ICB response across cancer types. Consistent with current knowledge, stromal expression of CXCL9, CXCL13, and IFNG were the top determinants of favorable ICB response. In addition, we identified a group of potential immune-suppressive genes, including FCER1A, associated with poor response to ICB. Strikingly, PD-L1 expression in stromal cells, but not cancer cells, is correlated with ICB response across cancer types. Furthermore, the unbiased transcriptome-wide analysis failed to identify cancer-cell intrinsic expression signatures of ICB response conserved across tumor types, suggesting that cancer cells lack tissue-agnostic transcriptomic features of ICB response. SIGNIFICANCE: Our results challenge the prevailing dogma that cancer cells present tissue-agnostic molecular markers that modulate immune activity and ICB response, which has implications on the development of improved ICB diagnostics and treatments.


Assuntos
Inibidores de Checkpoint Imunológico , Neoplasias , Transcriptoma , Humanos , Inibidores de Checkpoint Imunológico/uso terapêutico , Inibidores de Checkpoint Imunológico/farmacologia , Neoplasias/genética , Neoplasias/imunologia , Neoplasias/tratamento farmacológico , Perfilação da Expressão Gênica , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Regulação Neoplásica da Expressão Gênica , Microambiente Tumoral/imunologia , Microambiente Tumoral/genética , Antígeno B7-H1/genética , Antígeno B7-H1/metabolismo
2.
Genome Res ; 34(5): 680-695, 2024 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-38777607

RESUMO

Gastric cancer (GC) is the fifth most common cancer worldwide and is a heterogeneous disease. Among GC subtypes, the mesenchymal phenotype (Mes-like) is more invasive than the epithelial phenotype (Epi-like). Although gene expression of the epithelial-to-mesenchymal transition (EMT) has been studied, the regulatory landscape shaping this process is not fully understood. Here we use ATAC-seq and RNA-seq data from a compendium of GC cell lines and primary tumors to detect drivers of regulatory state changes and their transcriptional responses. Using the ATAC-seq data, we developed a machine learning approach to determine the transcription factors (TFs) regulating the subtypes of GC. We identified TFs driving the mesenchymal (RUNX2, ZEB1, SNAI2, AP-1 dimer) and the epithelial (GATA4, GATA6, KLF5, HNF4A, FOXA2, GRHL2) states in GC. We identified DNA copy number alterations associated with dysregulation of these TFs, specifically deletion of GATA4 and amplification of MAPK9 Comparisons with bulk and single-cell RNA-seq data sets identified activation toward fibroblast-like epigenomic and expression signatures in Mes-like GC. The activation of this mesenchymal fibrotic program is associated with differentially accessible DNA cis-regulatory elements flanking upregulated mesenchymal genes. These findings establish a map of TF activity in GC and highlight the role of copy number driven alterations in shaping epigenomic regulatory programs as potential drivers of GC heterogeneity and progression.


Assuntos
Transição Epitelial-Mesenquimal , Regulação Neoplásica da Expressão Gênica , Aprendizado de Máquina , Neoplasias Gástricas , Humanos , Neoplasias Gástricas/genética , Neoplasias Gástricas/patologia , Neoplasias Gástricas/metabolismo , Transição Epitelial-Mesenquimal/genética , Fator de Transcrição AP-1/metabolismo , Fator de Transcrição AP-1/genética , Linhagem Celular Tumoral , Fibrose/genética , Subunidade alfa 1 de Fator de Ligação ao Core/genética , Subunidade alfa 1 de Fator de Ligação ao Core/metabolismo , Variações do Número de Cópias de DNA , Subunidade alfa 2 de Fator de Ligação ao Core
3.
bioRxiv ; 2024 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-38798522

RESUMO

Background: NK cells are being extensively studied as a cell therapy for cancer. Their effector functions are induced by the recognition of ligands on tumor cells and by various cytokines. IL-15 is broadly used to stimulate endogenous and adoptively transferred NK cells in cancer patients. These stimuli activate the membrane protease ADAM17, which then cleaves assorted receptors on the surface of NK cells as a negative feedback loop to limit their activation and function. We have shown that ADAM17 inhibition can enhance IL-15-mediated NK cell proliferation in vitro and in vivo . In this study, we investigated the underlying mechanism of this process. Methods: PBMCs or enriched NK cells from human peripheral blood, either unlabeled or labeled with a cell proliferation dye, were cultured for up to 7 days in the presence of rhIL-15 +/- an ADAM17 function-blocking antibody. Different versions of the antibody were generated; Medi-1 (IgG1), Medi-4 (IgG4), Medi-PGLALA, Medi-F(ab') 2 , and TAB16 (anti-ADAM17 and anti-CD16 bispecific) to modulate CD16A engagement on NK cells. Flow cytometry was used to assess NK cell proliferation and phenotypic markers, immunoblotting to examine CD16A signaling, and IncuCyte-based live cell imaging to measure NK cell anti-tumor activity. Results: The ADAM17 function-blocking mAb Medi-1 markedly increased initial NK cell activation by IL-15. Using different engineered versions of the antibody revealed that the activating Fcγ receptor CD16A, a well-described ADAM17 substrate, was critical for enhancing IL-15 stimulation. Hence, Medi-1 bound to ADAM17 on NK cells can be engaged by CD16A and block its shedding, inducing and prolonging its signaling. This process did not promote evident NK cell fratricide, phagocytosis, or dysfunction. Synergistic activity by Medi-1 and IL-15 enhanced the upregulation of CD137 on CD16A + NK cells and augmented their proliferation in the presence of PBMC accessory cells. Conclusions: Our data reveal for the first time that CD16A and CD137 underpin Medi-1 enhancement of IL-15-driven NK cell activation and proliferation, respectively. The use of Medi-1 represents a novel strategy to enhance IL-15-driven NK cell proliferation, and it may be of therapeutic importance by increasing the anti-tumor activity of NK cells in cancer patients. What is already known on this topic: NK cell therapies are being broadly investigated to treat cancer. NK cell stimulation by IL-15 prolongs their survival in cancer patients. Various stimuli including IL-15 activate ADAM17 in NK cells, a membrane protease that regulates the cell surface density of various receptors as a negative feedback mechanism. What this study adds: Treating NK cells with the ADAM17 function-blocking mAb Medi-1 markedly enhanced their activation and proliferation. Our study reveals that the Fc and Fab regions of Medi-1 function synergistically with IL-15 in NK cell activation. Medi-1 treatment augments the upregulation of CD137 by NK cells, which enhances their proliferation in the presence of PBMC accessory cells. How this study might affect research practice or policy: Our study is of translational importance as Medi-1 treatment in combination with IL-15 could potentially augment the proliferation and function of endogenous or adoptively transferred NK cells in cancer patients.

4.
Nature ; 629(8014): 1062-1068, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38720082

RESUMO

Most chemistry and biology occurs in solution, in which conformational dynamics and complexation underlie behaviour and function. Single-molecule techniques1 are uniquely suited to resolving molecular diversity and new label-free approaches are reshaping the power of single-molecule measurements. A label-free single-molecule method2-16 capable of revealing details of molecular conformation in solution17,18 would allow a new microscopic perspective of unprecedented detail. Here we use the enhanced light-molecule interactions in high-finesse fibre-based Fabry-Pérot microcavities19-21 to detect individual biomolecules as small as 1.2 kDa, a ten-amino-acid peptide, with signal-to-noise ratios (SNRs) >100, even as the molecules are unlabelled and freely diffusing in solution. Our method delivers 2D intensity and temporal profiles, enabling the distinction of subpopulations in mixed samples. Notably, we observe a linear relationship between passage time and molecular radius, unlocking the potential to gather crucial information about diffusion and solution-phase conformation. Furthermore, mixtures of biomolecule isomers of the same molecular weight and composition but different conformation can also be resolved. Detection is based on the creation of a new molecular velocity filter window and a dynamic thermal priming mechanism that make use of the interplay between optical and thermal dynamics22,23 and Pound-Drever-Hall (PDH) cavity locking24 to reveal molecular motion even while suppressing environmental noise. New in vitro ways of revealing molecular conformation, diversity and dynamics can find broad potential for applications in the life and chemical sciences.


Assuntos
Peptídeos , Imagem Individual de Molécula , Difusão , Isomerismo , Luz , Peptídeos/análise , Peptídeos/química , Peptídeos/efeitos da radiação , Razão Sinal-Ruído , Imagem Individual de Molécula/métodos , Soluções , Conformação Proteica , Peso Molecular , Movimento (Física)
5.
J Integr Neurosci ; 23(4): 84, 2024 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-38682230

RESUMO

BACKGROUND: Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is a well-established treatment for the motor symptoms of Parkinson's disease (PD). While PD is primarily characterized by motor symptoms such as tremor, rigidity, and bradykinesia, it also involves a range of non-motor symptoms, and anxiety is one of the most common. The relationship between PD and anxiety is complex and can be a result of both pathological neural changes and the psychological and emotional impacts of living with a chronic progressive condition. Managing anxiety in PD is critical for improving the patients' quality of life. However, patients undergoing STN DBS can occasionally experience increased anxiety. METHODS: This study investigates changes in risk-avoidant behavior following STN DBS in a pre-motor animal model of PD under chronic and acute unilateral high frequency stimulation. RESULTS: No significant changes in risk-avoidant behaviors were observed in rats who underwent STN DBS compared with sham stimulation controls. Chronic stimulation prevented sensitization in the elevated zero maze. CONCLUSIONS: These results suggest that unilateral stimulation of the STN may have minimal effects on risk-avoidant behaviors in PD. However, additional research is required to fully understand the mechanisms responsible for changes in anxiety during STN DBS for PD.


Assuntos
Estimulação Encefálica Profunda , Modelos Animais de Doenças , Oxidopamina , Núcleo Subtalâmico , Animais , Oxidopamina/farmacologia , Masculino , Comportamento Animal/fisiologia , Transtornos Parkinsonianos/terapia , Transtornos Parkinsonianos/fisiopatologia , Ansiedade/etiologia , Ansiedade/fisiopatologia , Ratos , Ratos Sprague-Dawley , Aprendizagem da Esquiva/fisiologia , Doença de Parkinson/terapia , Doença de Parkinson/fisiopatologia
6.
Cancer Res ; 84(8): 1195-1198, 2024 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-38616656

RESUMO

The 15th annual Frontiers in Cancer Science (FCS) conference gathered scientific experts who shared the latest research converging upon several themes of cancer biology. These themes included the dysregulation of metabolism, cell death, and other signaling processes in cancer cells; using patient "omics" datasets and single-cell and spatial approaches to investigate heterogeneity, understand therapy resistance, and identify targets; innovative strategies for inhibiting tumors, including rational drug combinations and improved drug delivery mechanisms; and advances in models that can facilitate screening for cancer vulnerabilities and drug testing. We hope the insights from this meeting will stimulate further progress in the field.


Assuntos
Neoplasias , Pesquisa , Humanos , Morte Celular , Sistemas de Liberação de Medicamentos , Neoplasias/terapia
7.
Cancer Discov ; 14(4): 573-578, 2024 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-38571432

RESUMO

SUMMARY: Traditional endpoints such as progression-free survival and overall survival do not fully capture the pharmacologic and pharmacodynamic effects of a therapeutic intervention. Incorporating mechanism-driven biomarkers and validated surrogate proximal endpoints can provide orthogonal readouts of anti-tumor activity and delineate the relative contribution of treatment components on an individual level, highlighting the limitation of solely relying on aggregated readouts from clinical trials to facilitate go/no-go decisions for precision therapies.


Assuntos
Neoplasias , Humanos , Neoplasias/tratamento farmacológico , Neoplasias/genética , Medicina de Precisão , Biomarcadores , Oncologia , Intervalo Livre de Progressão
8.
Cancer Res ; 84(12): 2009-2020, 2024 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-38587551

RESUMO

Non-small cell lung cancers (NSCLC) in nonsmokers are mostly driven by mutations in the oncogenes EGFR, ERBB2, and MET and fusions involving ALK and RET. In addition to occurring in nonsmokers, alterations in these "nonsmoking-related oncogenes" (NSRO) also occur in smokers. To better understand the clonal architecture and genomic landscape of NSRO-driven tumors in smokers compared with typical-smoking NSCLCs, we investigated genomic and transcriptomic alterations in 173 tumor sectors from 48 NSCLC patients. NSRO-driven NSCLCs in smokers and nonsmokers had similar genomic landscapes. Surprisingly, even in patients with prominent smoking histories, the mutational signature caused by tobacco smoking was essentially absent in NSRO-driven NSCLCs, which was confirmed in two large NSCLC data sets from other geographic regions. However, NSRO-driven NSCLCs in smokers had higher transcriptomic activities related to the regulation of the cell cycle. These findings suggest that, whereas the genomic landscape is similar between NSRO-driven NSCLC in smokers and nonsmokers, smoking still affects the tumor phenotype independently of genomic alterations. SIGNIFICANCE: Non-small cell lung cancers driven by nonsmoking-related oncogenes do not harbor genomic scars caused by smoking regardless of smoking history, indicating that the impact of smoking on these tumors is mainly nongenomic.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , Neoplasias Pulmonares , Mutação , Oncogenes , Fumar , Humanos , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/patologia , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Masculino , Feminino , Oncogenes/genética , Fumar/efeitos adversos , Fumar/genética , Pessoa de Meia-Idade , Idoso , Adulto
9.
Nat Metab ; 6(4): 764-777, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38429390

RESUMO

Surviving long periods without food has shaped human evolution. In ancient and modern societies, prolonged fasting was/is practiced by billions of people globally for religious purposes, used to treat diseases such as epilepsy, and recently gained popularity as weight loss intervention, but we still have a very limited understanding of the systemic adaptions in humans to extreme caloric restriction of different durations. Here we show that a 7-day water-only fast leads to an average weight loss of 5.7 kg (±0.8 kg) among 12 volunteers (5 women, 7 men). We demonstrate nine distinct proteomic response profiles, with systemic changes evident only after 3 days of complete calorie restriction based on in-depth characterization of the temporal trajectories of ~3,000 plasma proteins measured before, daily during, and after fasting. The multi-organ response to complete caloric restriction shows distinct effects of fasting duration and weight loss and is remarkably conserved across volunteers with >1,000 significantly responding proteins. The fasting signature is strongly enriched for extracellular matrix proteins from various body sites, demonstrating profound non-metabolic adaptions, including extreme changes in the brain-specific extracellular matrix protein tenascin-R. Using proteogenomic approaches, we estimate the health consequences for 212 proteins that change during fasting across ~500 outcomes and identified putative beneficial (SWAP70 and rheumatoid arthritis or HYOU1 and heart disease), as well as adverse effects. Our results advance our understanding of prolonged fasting in humans beyond a merely energy-centric adaptions towards a systemic response that can inform targeted therapeutic modulation.


Assuntos
Restrição Calórica , Jejum , Proteoma , Humanos , Proteoma/metabolismo , Feminino , Masculino , Adulto , Redução de Peso , Proteômica/métodos , Adaptação Fisiológica
10.
J Integr Plant Biol ; 66(6): 1170-1191, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38477647

RESUMO

The evolution of the latitudinal diversity gradient (LDG), characterized by a peak in diversity toward the tropics, has captured significant attention in evolutionary biology and ecology. However, the inverse LDG (i-LDG) mechanism, wherein species richness increases toward the poles, remains inadequately explored. Cycads are among one of the oldest lineages of extant seed plants and have undergone extensive diversification in the tropics. Intriguingly, the extant cycad abundance exhibits an i-LDG pattern, and the underlying causes for this phenomenon remain largely elusive. Here, using 1,843 nuclear genes from a nearly complete sampling, we conducted comprehensive phylogenomic analyses to establish a robust species-level phylogeny for Cycas, the largest genus within cycads. We then reconstructed the spatial-temporal dynamics and integrated global environmental data to evaluate the roles of species ages, diversification rates, contemporary environment, and conservatism to ancestral niches in shaping the i-LDG pattern. We found Cycas experienced decreased diversification rates, coupled with the cooling temperature since its origin in the Eocene from continental Asia. Different regions have distinctively contributed to the formation of i-LDG for Cycas, with the northern hemisphere acting as evolutionary museums and the southern hemisphere serving as cradles. Moreover, water-related climate variables, specifically precipitation seasonality and potential evapotranspiration, were identified as paramount factors constraining Cycas species richness in the rainforest biome near the equator. Notably, the adherence to ancestral monsoonal climates emerges as a critical factor in sustaining the diversity pattern. This study underscores the imperative of integrating both evolutionary and ecological approaches to comprehensively unravel the mechanisms underpinning global biodiversity patterns.


Assuntos
Biodiversidade , Evolução Biológica , Cycas , Filogenia , Cycas/genética
11.
ERJ Open Res ; 10(2)2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38529345

RESUMO

Background: Breathlessness is a troublesome and prevalent symptom in the population, but knowledge of related factors is scarce. The aim of this study was to identify the factors most strongly associated with breathlessness in the general population and to describe the shapes of the associations between the main factors and breathlessness. Methods: A cross-sectional analysis was carried out of the multicentre population-based Swedish CArdioPulmonary bioImage Study (SCAPIS) of adults aged 50 to 64 years. Breathlessness was defined as a modified Medical Research Council breathlessness rating ≥2. The machine learning algorithm extreme gradient boosting (XGBoost) was used to classify participants as either breathless or nonbreathless using 449 factors, including physiological measurements, blood samples, computed tomography cardiac and lung measurements, lifestyle, health conditions and socioeconomics. The strength of the associations between the factors and breathlessness were measured by SHapley Additive exPlanations (SHAP), with higher scores reflecting stronger associations. Results: A total of 28 730 participants (52% women) were included in the study. The strongest associated factors for breathlessness were (in order of magnitude): body mass index ( SHAP score 0.39), forced expiratory volume in 1 s (0.32), physical activity measured by accelerometery (0.27), sleep apnoea (0.22), diffusing lung capacity for carbon monoxide (0.21), self-reported physical activity (0.17), chest pain when hurrying (0.17), high-sensitivity C-reactive protein (0.17), recent weight change (0.14) and cough (0.13). Conclusion: This large population-based study of men and women aged 50-64 years identified the main factors related to breathlessness that may be prevented or amenable to public health interventions.

12.
IEEE Trans Biomed Eng ; 71(7): 2170-2179, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38335073

RESUMO

OBJECTIVE: The purpose of this paper is to investigate the persistence of nerve blockade beyond the duration of applying high frequency alternating current (HFAC) to thinly myelinated and non-myelinated fibers, also termed a "carry-over effect". METHODS: In this study, we used electrically-evoked compound action potentials from isolated rat vagus nerves to assess the influence of 5 kHz HFAC amplitude and duration on the degree of the carry-over effect. Current amplitudes from 1-10 mA and 5 kHz durations from 10-120 seconds were tested. RESULTS: By testing 20 different combinations of 5 kHz amplitude and duration, we found a significant interaction between 5 kHz amplitude and duration on influencing the carry-over effect. CONCLUSION: The degree of carry-over effect was dependent on 5 kHz amplitude, as well as duration. SIGNIFICANCE: Utilizing the carry-over effect may be useful in designing energy efficient nerve blocking algorithms for the treatment of diseases influenced by nerve activity.


Assuntos
Condução Nervosa , Ratos Sprague-Dawley , Animais , Ratos , Condução Nervosa/fisiologia , Potenciais de Ação/fisiologia , Nervo Vago/fisiologia , Bloqueio Nervoso/métodos , Masculino
13.
Cancer ; 130(10): 1758-1765, 2024 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-38422026

RESUMO

BACKGROUND: In early-stage non-small cell lung cancer (NSCLC), recurrence is frequently observed. Circulating tumor DNA (ctDNA) has emerged as a noninvasive tool to risk stratify patients for recurrence after curative intent therapy. This study aimed to risk stratify patients with early-stage NSCLC via a personalized, tumor-informed multiplex polymerase chain reaction (mPCR) next-generation sequencing assay. METHODS: This retrospective cohort study included patients with stage I-III NSCLC. Recruited patients received standard-of-care management (surgical resection with or without adjuvant chemotherapy, followed by surveillance). Whole-exome sequencing of NSCLC resected tissue and matched germline DNA was used to design patient-specific mPCR assays (Signatera, Natera, Inc) to track up to 16 single-nucleotide variants in plasma samples. RESULTS: The overall cohort with analyzed plasma samples consisted of 57 patients. Stage distribution was 68% for stage I and 16% each for stages II and III. Presurgery (i.e., at baseline), ctDNA was detected in 15 of 57 patients (26%). ctDNA detection presurgery was significantly associated with shorter recurrence-free survival (RFS; hazard ratio [HR], 3.54; 95% confidence interval [CI], 1.00-12.62; p = .009). In the postsurgery setting, ctDNA was detected in seven patients, of whom 100% experienced radiological recurrence. ctDNA positivity preceded radiological findings by a median lead time of 2.8 months (range, 0-12.9 months). Longitudinally, ctDNA detection at any time point was associated with shorter RFS (HR, 16.1; 95% CI, 1.63-158.9; p < .0001). CONCLUSIONS: ctDNA detection before surgical resection was strongly associated with a high risk of relapse in early-stage NSCLC in a large unique Asian cohort. Prospective studies are needed to assess the clinical utility of ctDNA status in this setting.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , DNA Tumoral Circulante , Sequenciamento de Nucleotídeos em Larga Escala , Neoplasias Pulmonares , Recidiva Local de Neoplasia , Estadiamento de Neoplasias , Neoplasia Residual , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/sangue , Neoplasias Pulmonares/patologia , Masculino , DNA Tumoral Circulante/sangue , DNA Tumoral Circulante/genética , Feminino , Pessoa de Meia-Idade , Idoso , Estudos Retrospectivos , Recidiva Local de Neoplasia/genética , Recidiva Local de Neoplasia/diagnóstico , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/sangue , Carcinoma Pulmonar de Células não Pequenas/patologia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Neoplasia Residual/genética , Neoplasia Residual/diagnóstico , Detecção Precoce de Câncer/métodos , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/sangue , Adulto , Idoso de 80 Anos ou mais , Reação em Cadeia da Polimerase Multiplex/métodos
14.
Am J Bot ; 111(2): e16280, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38334273

RESUMO

PREMISE: Cultivation and naturalization of plants beyond their natural range can bring previously geographically isolated taxa together, increasing the opportunity for hybridization, the outcomes of which are not predictable. Here, we explored the phenotypic and genomic effects of interspecific gene flow following the widespread cultivation of Mentha spicata (spearmint), M. longifolia, and M. suaveolens. METHODS: We morphologically evaluated 155 herbarium specimens of three Mentha species and sequenced the genomes of a subset of 93 specimens. We analyzed the whole genomes in a population and the phylogenetic framework and associated genomic classifications in conjunction with the morphological assessments. RESULTS: The allopolyploid M. spicata, which likely evolved in cultivation, had altered trichome characters, that is possibly a product of human selection for a more palatable plant or a byproduct of selection for essential oils. There were signs of genetic admixture between mints, including allopolyploids, indicating that the reproductive barriers between Mentha species with differences in ploidy are likely incomplete. Still, despite gene flow between species, we found that genetic variants associated with the cultivated trichome morphology continue to segregate. CONCLUSIONS: Although hybridization, allopolyploidization, and human selection during cultivation can increase species richness (e.g., by forming hybrid taxa), we showed that unless reproductive barriers are strong, these processes can also result in mixing of genes between species and the potential loss of natural biodiversity.


Assuntos
Mentha , Óleos Voláteis , Humanos , Mentha/genética , Fluxo Gênico , Filogenia , Óleos Voláteis/farmacologia , Hibridização Genética
15.
ACS Omega ; 9(7): 8503-8509, 2024 Feb 20.
Artigo em Inglês | MEDLINE | ID: mdl-38405521

RESUMO

Natural fiber-welded (NFW) biopolymer composites are rapidly garnering industrial and commercial attention in the textile sector, and a recent disclosure demonstrating the production of mesoporous NFW materials suggests a bright future as sorbents, filters, and nanoparticle scaffolds. A significant roadblock in the mass production of mesoporous NFW composites for research and development is their lengthy preparation time: 24 h of water rinses to remove the ionic liquid (IL) serving as a welding medium and then 72 h of solvent exchanges (polar to nonpolar), followed by oven drying to attain a mesoporous composite. In this work, the rinsing procedure is systematically truncated using the solution conductivity as a yardstick to monitor IL removal. The traditional water immersion rinses are replaced by a flow-through system (i.e., infinite dilution) using a peristaltic pump, reducing the required water rinse time for the maximum removal of IL to 30 min. This procedure also allows for easy in-line monitoring of solution conductivity and reclamation of an expensive welding solvent. Further, the organic solvent exchange is minimized to 10 min per solvent (from 24 h), resulting in a total combined rinse time of 1 h. This process acceleration reduces the overall solvent exposure time from 96 to 1 h, an almost 99% temporal improvement.

16.
Nature ; 625(7994): 301-311, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38200295

RESUMO

Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.


Assuntos
Genética Populacional , Genoma Humano , Migração Humana , Metagenômica , Humanos , Agricultura/história , Ásia Ocidental , Mar Negro , Diploide , Europa (Continente)/etnologia , Genótipo , História Antiga , Migração Humana/história , Caça/história , Camada de Gelo
17.
bioRxiv ; 2024 Jan 12.
Artigo em Inglês | MEDLINE | ID: mdl-38260520

RESUMO

Heritability of regional subcortical brain volumes (rSBVs) describes the role of genetics in middle and inner brain development. rSBVs are highly heritable in adults but are not characterized well in adolescents. The Adolescent Brain Cognitive Development study (ABCD), taken over 22 US sites, provides data to characterize the heritability of subcortical structures in adolescence. In ABCD, site-specific effects co-occur with genetic effects which can bias heritability estimates. Existing methods adjusting for site effects require additional steps to adjust for site effects and can lead to inconsistent estimation. We propose a random-effect model-based method of moments approach that is a single step estimator and is a theoretically consistent estimator even when sites are imbalanced and performs well under simulations. We compare methods on rSBVs from ABCD. The proposed approach yielded heritability estimates similar to previous results derived from single-site studies. The cerebellum cortex and hippocampus were the most heritable regions (> 50%).

19.
J Chem Theory Comput ; 20(1): 385-395, 2024 Jan 09.
Artigo em Inglês | MEDLINE | ID: mdl-38150288

RESUMO

The tunable design of protein redox potentials promises to open a range of applications in biotechnology and catalysis. Here, we introduce a method to calculate redox potential changes by combining fluctuation relations with molecular dynamics simulations. It involves the simulation of reduced and oxidized states, followed by the instantaneous conversion between them. Energy differences introduced by the perturbations are obtained using the Kubo-Onsager approach. Using a detailed fluctuation relation coupled with Bayesian inference, these are postprocessed into estimates for the redox potentials in an efficient manner. This new method, denoted MD + CB, is tested on a de novo four-helix bundle heme protein (the m4D2 "maquette") and five designed mutants, including some mutants characterized experimentally in this work. The MD + CB approach is found to perform reliably, giving redox potential shifts with reasonably good correlation (0.85) to the experimental values for the mutants. The MD + CB approach also compares well with redox potential shift predictions using a continuum electrostatic method. The estimation method employed within the MD + CB approach is straightforwardly transferable to standard equilibrium MD simulations and holds promise for redox protein engineering and design applications.


Assuntos
Heme , Simulação de Dinâmica Molecular , Sequência de Aminoácidos , Teorema de Bayes , Estrutura Secundária de Proteína , Heme/química , Proteínas/química , Oxirredução
20.
ACS Macro Lett ; 12(12): 1654-1658, 2023 Dec 19.
Artigo em Inglês | MEDLINE | ID: mdl-38104265

RESUMO

Seemingly nonporous biopolymer composites prepared by natural fiber welding (NFW) possess latent pores that can be exfoliated by conscientious solvation. We present a seminal demonstration of this concept for cellulose and explore the impact of latent pores on the manufacture and commercialization of NFW products.

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