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1.
Nat Commun ; 15(1): 5796, 2024 Jul 10.
Artículo en Inglés | MEDLINE | ID: mdl-38987243

RESUMEN

Metabolite extraction is the critical first-step in metabolomics experiments, where it is generally regarded to inactivate and remove proteins. Here, arising from efforts to improve extraction conditions for polar metabolomics, we discover a proteomic landscape of over 1000 proteins within metabolite extracts. This is a ubiquitous feature across several common extraction and sample types. By combining post-resuspension stable isotope addition and enzyme inhibitors, we demonstrate in-extract metabolite interconversions due to residual transaminase activity. We extend these findings with untargeted metabolomics where we observe extensive protein-mediated metabolite changes, including in-extract formation of glutamate dipeptide and depletion of total glutathione. Finally, we present a simple extraction workflow that integrates 3 kDa filtration for protein removal as a superior method for polar metabolomics. In this work, we uncover a previously unrecognized, protein-mediated source of observer effects in metabolomics experiments with broad-reaching implications across all research fields using metabolomics and molecular metabolism.


Asunto(s)
Metabolómica , Proteoma , Proteómica , Proteoma/metabolismo , Metabolómica/métodos , Proteómica/métodos , Humanos , Animales , Glutatión/metabolismo , Metaboloma , Transaminasas/metabolismo
2.
Cell Metab ; 2024 Jun 27.
Artículo en Inglés | MEDLINE | ID: mdl-38964323

RESUMEN

Mature red blood cells (RBCs) lack mitochondria and thus exclusively rely on glycolysis to generate adenosine triphosphate (ATP) during aging in vivo or storage in blood banks. Here, we leveraged 13,029 volunteers from the Recipient Epidemiology and Donor Evaluation Study to identify associations between end-of-storage levels of glycolytic metabolites and donor age, sex, and ancestry-specific genetic polymorphisms in regions encoding phosphofructokinase 1, platelet (detected in mature RBCs); hexokinase 1 (HK1); and ADP-ribosyl cyclase 1 and 2 (CD38/BST1). Gene-metabolite associations were validated in fresh and stored RBCs from 525 Diversity Outbred mice and via multi-omics characterization of 1,929 samples from 643 human RBC units during storage. ATP and hypoxanthine (HYPX) levels-and the genetic traits linked to them-were associated with hemolysis in vitro and in vivo, both in healthy autologous transfusion recipients and in 5,816 critically ill patients receiving heterologous transfusions, suggesting their potential as markers to improve transfusion outcomes.

3.
Hortic Res ; 11(6): uhae126, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38919555

RESUMEN

Stem cell homeostasis is pivotal for continuous and programmed formation of organs in plants. The precise control of meristem proliferation is mediated by the evolutionarily conserved signaling that encompasses complex interactions among multiple peptide ligands and their receptor-like kinases. Here, we identified compensation mechanisms involving the CLAVATA1 (CLV1) receptor and its paralogs, BARELY ANY MERISTEMs (BAMs), for stem cell proliferation in two Solanaceae species, tomato and groundcherry. Genetic analyses of higher-order mutants deficient in multiple receptor genes, generated via CRISPR-Cas9 genome editing, reveal that tomato SlBAM1 and SlBAM2 compensate for slclv1 mutations. Unlike the compensatory responses between orthologous receptors observed in Arabidopsis, tomato slclv1 mutations do not trigger transcriptional upregulation of four SlBAM genes. The compensation mechanisms within receptors are also conserved in groundcherry, and critical amino acid residues of the receptors associated with the physical interaction with peptide ligands are highly conserved in Solanaceae plants. Our findings demonstrate that the evolutionary conservation of both compensation mechanisms and critical coding sequences between receptor-like kinases provides a strong buffering capacity during stem cell homeostasis in tomato and groundcherry.

4.
Biomedicines ; 12(6)2024 Jun 18.
Artículo en Inglés | MEDLINE | ID: mdl-38927553

RESUMEN

Kilohertz high-frequency spinal cord stimulation (kHF-SCS) is a rapidly advancing neuromodulatory technique in the clinical management of chronic pain. However, the precise cellular mechanisms underlying kHF-SCS-induced paresthesia-free pain relief, as well as the neural responses within spinal pain circuits, remain largely unexplored. In this study, using a novel preparation, we investigated the impact of varying kilohertz frequency SCS on dorsal horn neuron activation. Employing calcium imaging on isolated spinal cord slices, we found that extracellular electric fields at kilohertz frequencies (1, 3, 5, 8, and 10 kHz) induce distinct patterns of activation in dorsal horn neurons. Notably, as the frequency of extracellular electric fields increased, there was a clear and significant monotonic escalation in neuronal activity. This phenomenon was observed not only in superficial dorsal horn neurons, but also in those located deeper within the dorsal horn. Our study demonstrates the unique patterns of dorsal horn neuron activation in response to varying kilohertz frequencies of extracellular electric fields, and we contribute to a deeper understanding of how kHF-SCS induces paresthesia-free pain relief. Furthermore, our study highlights the potential for kHF-SCS to modulate sensory information processing within spinal pain circuits. These insights pave the way for future research aimed at optimizing kHF-SCS parameters and refining its therapeutic applications in the clinical management of chronic pain.

5.
J Stroke Cerebrovasc Dis ; 33(8): 107807, 2024 Jun 06.
Artículo en Inglés | MEDLINE | ID: mdl-38851548

RESUMEN

INTRODUCTION: There are sex-based differences in stroke epidemiology, treatment, and outcomes. In this manuscript, we discuss the differences that exist in the clinical presentation of acute stroke among sexes. DISCUSSION: We present the differences in stroke presentation among sexes including age at the time of presentation, severity of stroke on presentation, and stroke type and location. We discuss the atypical clinical presentations, explore the radiographic findings on presentation (including location, infarct core volume, the impact of collateral circulation, hematoma location in intracranial hemorrhage), and discuss differences in time elapsed between symptom onset and management amongst sexes. CONCLUSION: Differences exist in stroke clinical presentation amongst sexes. These disparities have public health implications, and as they become better understood, impact awareness campaigns in both the public and healthcare communities.

6.
Curr Opin Plant Biol ; 81: 102595, 2024 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-38943829

RESUMEN

Studying morphological novelties offers special insights into developmental biology and evolution. The inflated calyx syndrome (ICS) is a largely unrecognized but fascinating feature of flower development, where sepals form balloon-like husks that encapsulate fruits. Despite its independent emergence in many lineages of flowering plants, the genetic and molecular mechanisms of ICS remain unknown. Early studies in the Solanaceae genus Physalis put forth key roles of MADS-box genes in ICS. However, recent work suggests these classical floral identity transcription factors were false leads. With newfound capabilities that allow rapid development of genetic systems through genomics and genome editing, Physalis has re-emerged as the most tractable model species for dissecting ICS. This review revisits current understanding of ICS and highlights how recent advancements enable a reset in the search for genetic and molecular mechanisms using unbiased, systematic approaches.

7.
Genetics ; 2024 Jun 11.
Artículo en Inglés | MEDLINE | ID: mdl-38861403

RESUMEN

Spatially continuous patterns of genetic differentiation, which are common in nature, are often poorly described by existing population genetic theory or methods that assume either panmixia or discrete, clearly definable populations. There is therefore a need for statistical approaches in population genetics that can accommodate continuous geographic structure, and that ideally use georeferenced individuals as the unit of analysis, rather than populations or subpopulations. In addition, researchers are often interested in describing the diversity of a population distributed continuously in space; this diversity is intimately linked to both the dispersal potential and the population density of the organism. A statistical model that leverages information from patterns of isolation-by-distance to jointly infer parameters that control local demography (such as Wright's neighborhood size), and the long-term effective size (Ne) of a population would be useful. Here, we introduce such a model that uses individual-level pairwise genetic and geographic distances to infer Wright's neighborhood size and long-term Ne. We demonstrate the utility of our model by applying it to complex, forward-time demographic simulations as well as an empirical dataset of the two-form bumblebee (Bombus bifarius). The model performed well on simulated data relative to alternative approaches and produced reasonable empirical results given the natural history of bumblebees. The resulting inferences provide important insights into the population genetic dynamics of spatially structured populations.

8.
PLoS One ; 19(6): e0300358, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38848330

RESUMEN

Clustering is an important task in biomedical science, and it is widely believed that different data sets are best clustered using different algorithms. When choosing between clustering algorithms on the same data set, reseachers typically rely on global measures of quality, such as the mean silhouette width, and overlook the fine details of clustering. However, the silhouette width actually computes scores that describe how well each individual element is clustered. Inspired by this observation, we developed a novel clustering method, called SillyPutty. Unlike existing methods, SillyPutty uses the silhouette width for individual elements as a tool to optimize the mean silhouette width. This shift in perspective allows for a more granular evaluation of clustering quality, potentially addressing limitations in current methodologies. To test the SillyPutty algorithm, we first simulated a series of data sets using the Umpire R package and then used real-workd data from The Cancer Genome Atlas. Using these data sets, we compared SillyPutty to several existing algorithms using multiple metrics (Silhouette Width, Adjusted Rand Index, Entropy, Normalized Within-group Sum of Square errors, and Perfect Classification Count). Our findings revealed that SillyPutty is a valid standalone clustering method, comparable in accuracy to the best existing methods. We also found that the combination of hierarchical clustering followed by SillyPutty has the best overall performance in terms of both accuracy and speed. Availability: The SillyPutty R package can be downloaded from the Comprehensive R Archive Network (CRAN).


Asunto(s)
Algoritmos , Análisis por Conglomerados , Humanos , Neoplasias/patología , Programas Informáticos
9.
Int J Drug Policy ; 128: 104450, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38749214

RESUMEN

BACKGROUND: As cannabis policy trends toward liberalization, assessing cannabis health warning effects becomes increasingly important. This study investigated underlying mechanisms accounting for the effectiveness of cannabis health warnings on protective health intentions. METHOD: A sample of 1,095 adults (21+) living in legal recreational US states who reported using cannabis in the past 12 months participated in an online experiment. Participants were randomly assigned to view cannabis health warnings that described risks of impaired driving, mental health, and smoke exposure and varied pictures and text (vs. text-only) attributes in warnings. Outcomes were message reactions (cognitive elaboration, fear, and hope), attitudes and beliefs (perceived severity of cannabis harms and perceived susceptibility to cannabis harms, and perceived response and self-efficacy to prevent cannabis harms), and protective health intentions (information-seeking about cannabis health effects and having interpersonal discussions about cannabis harms with family, friends, and medical professionals). RESULTS: MANCOVA results showed no significant differences between text-only vs. pictorial attributes on protective health intentions; thus, warning conditions were controlled and analyzed using structural equation modeling (SEM). SEM results showed that attention to cannabis health warnings (text-only or pictorial) elicited higher cognitive elaboration, fear, and hope-an emotion associated with coping actions that motivate positive expectations of future events. These outcomes, in turn, were associated with greater perceived severity and susceptibility and greater perceived response efficacy, respectively. Hope, perceived severity, and perceived response and self-efficacy were independently associated with greater intentions to seek information about cannabis health effects and to discuss cannabis health harms. CONCLUSION: Attention to warnings impacted emotions, attitudes, and protective health intentions. Fear is commonly associated with health warning effects, and our results suggest that hope is also an important factor. This research contributes to understanding the effects of cannabis health warnings and can inform regulatory agencies that mandate warnings on cannabis products.


Asunto(s)
Intención , Humanos , Masculino , Femenino , Adulto , Estados Unidos , Adulto Joven , Persona de Mediana Edad , Conocimientos, Actitudes y Práctica en Salud , Cannabis , Etiquetado de Productos/legislación & jurisprudencia , Autoeficacia , Fumar Marihuana/psicología , Fumar Marihuana/legislación & jurisprudencia , Miedo , Uso de la Marihuana/legislación & jurisprudencia , Uso de la Marihuana/psicología
10.
bioRxiv ; 2024 May 14.
Artículo en Inglés | MEDLINE | ID: mdl-38798560

RESUMEN

The mechanisms underlying the pathophysiology of endometriosis, characterized by the presence of endometrium-like tissue outside the uterus, remain poorly understood. This study aimed to identify cell type-specific gene expression changes in superficial peritoneal endometriotic lesions and elucidate the crosstalk among the stroma, epithelium, and macrophages compared to patient-matched eutopic endometrium. Surprisingly, comparison between lesions and eutopic endometrium revealed transcriptional similarities, indicating minimal alterations in the sub-epithelial stroma and epithelium of lesions. Spatial transcriptomics highlighted increased signaling between the lesion epithelium and macrophages, emphasizing the role of the epithelium in driving lesion inflammation. We propose that the superficial endometriotic lesion epithelium orchestrates inflammatory signaling and promotes a pro-repair phenotype in macrophages, providing a new role for Complement 3 in lesion pathobiology. This study underscores the significance of considering spatial context and cellular interactions in uncovering mechanisms governing disease in endometriotic lesions.

11.
Water Environ Res ; 96(5): e11036, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38740567

RESUMEN

The cheese making and vegetable processing industries generate immense volumes of high-nitrogen wastewater that is often treated at rural facilities using land applications. Laboratory incubation results showed denitrification decreased with temperature in industry facility soils but remained high in soils from agricultural sites (75% at 2.1°C). 16S rRNA, phospholipid fatty acid (PLFA), and soil respiration analyses were conducted to investigate potential soil microbiome impacts. Biotic and abiotic system factor correlations showed no clear patterns explaining the divergent denitrification rates. In all three soil types at the phylum level, Actinobacteria, Proteobacteria, and Acidobacteria dominated, whereas at the class level, Nitrososphaeria and Alphaproteobacteria dominated, similar to denitrifying systems such as wetlands, wastewater resource recovery facilities, and wastewater-irrigated agricultural systems. Results show that potential denitrification drivers vary but lay the foundation to develop a better understanding of the key factors regulating denitrification in land application systems and protect local groundwater supplies. PRACTITIONER POINTS: Incubation study denitrification rates decreased as temperatures decreased, potentially leading to groundwater contamination issues during colder months. The three most dominant phyla for all systems are Actinobacteria, Proteobacteria, and Acidobacteria. The dominant class for all systems is Nitrosphaeria (phyla Crenarchaeota). No correlation patterns between denitrification rates and system biotic and abiotic factors were observed that explained system efficiency differences.


Asunto(s)
Queso , Desnitrificación , Microbiología del Suelo , Verduras , Bacterias/clasificación , Bacterias/metabolismo , Bacterias/genética , Aguas Residuales/química , Eliminación de Residuos Líquidos/métodos , Suelo/química
12.
J Math Biol ; 88(5): 54, 2024 Apr 03.
Artículo en Inglés | MEDLINE | ID: mdl-38568223

RESUMEN

Fisher's fundamental theorem of natural selection has haunted theoretical population genetic literature since it was proposed in 1930, leading to numerous interpretations. Most of the confusion stemmed from Fisher's own obscure presentation. By the 1970s, a clearer view of Fisher's theorem had been achieved and it was found that, regardless of its utility or significance, it represents a general theorem of evolutionary biology. Basener and Sanford (J Math Biol 76:1589-1622, 2018) writing in JOMB, however, paint a different picture of the fundamental theorem as one hindered by its assumptions and incomplete due to its failure to explicitly incorporate mutational effects. They argue that Fisher saw his theorem as a "mathematical proof of Darwinian evolution". In this reply, we show that, contrary to Basener and Sanford, Fisher's theorem is a general theorem that applies to any evolving population, and that, far from their assertion that it needed to be expanded, the theorem already implicitly incorporates ancestor-descendant variation. We also show that their numerical simulations produce unrealistic results. Lastly, we argue that Basener and Sanford's motivations were in undermining not merely Fisher's theorem, but the concept of universal common descent itself.


Asunto(s)
Páncreas , Mutación
13.
J Magn Reson Imaging ; 2024 Apr 25.
Artículo en Inglés | MEDLINE | ID: mdl-38662966

RESUMEN

BACKGROUND: Standard Cartesian time-of-flight (TOF) head magnetic resonance angiography (MRA) is routinely used to evaluate the intracranial arteries, but does not provide quantitative hemodynamic information that is useful for patient risk stratification as well as for monitoring treatment and tracking changes in blood flow over time. Quantitative TOF (qTOF) MRA represents a new and efficient method for simultaneous evaluating the intracranial arteries and quantifying blood flow velocity, but it has not yet been evaluated in patients with cerebrovascular disease. PURPOSE: To evaluate qTOF for simultaneously evaluating the intracranial arteries and quantifying intracranial blood flow velocity in patients with cerebrovascular disease, without the need for a phase contrast (PC) scan. STUDY TYPE: Prospective. SUBJECTS: Twenty-four patients (18 female, 6 male) with cerebrovascular disease. FIELD STRENGTH/SEQUENCES: Head MRA at 3 T using gradient-echo 3D qTOF, standard Cartesian TOF, and PC protocols. ASSESSMENT: Three independent readers assessed arterial image quality using a 4-point scale (1: non-diagnostic, 4: excellent) and artifact presence. Total and component flow velocities obtained with qTOF and PC were measured. STATISTICAL TESTS: Wilcoxon signed-rank tests, Gwet's AC2, intraclass correlation coefficients (ICC) for absolute agreement, Bland-Altman analyses, tests of equal proportions. P values <0.05 were considered statistically significant. RESULTS: Averaged across readers and compared to standard Cartesian TOF, qTOF significantly improved overall arterial image quality (3.8 ± 0.2 vs. 3.6 ± 0.5), image quality at locations of pathology (3.7 ± 0.5 vs. 3.4 ± 0.7), and increased the proportion of evaluations rated without artifacts (63.9% [46/72] vs. 37.5% [27/72]). qTOF significantly agreed with PC for total flow velocity (ICC = 0.71) and component flow velocity (ICC = 0.89). DATA CONCLUSION: qTOF angiography of the head matched or improved upon the image quality of standard Cartesian TOF, reduced image artifacts, and provided quantitative hemodynamic data, without the need for a PC scan. EVIDENCE LEVEL: 2 TECHNICAL EFFICACY: Stage 2.

14.
J Mol Med (Berl) ; 102(6): 751-760, 2024 06.
Artículo en Inglés | MEDLINE | ID: mdl-38639785

RESUMEN

Annexins, a group of Ca2+-dependent phospholipid-binding proteins, exert diverse roles in neuronal development, normal central nervous system (CNS) functioning, neurological disorders, and CNS tumors. This paper reviews the roles of individual annexins (A1-A13) in these contexts. Annexins possess unique structural and functional features, such as Ca2+-dependent binding to phospholipids, participating in membrane organization, and modulating cell signaling. They are implicated in various CNS processes, including endocytosis, exocytosis, and stabilization of plasma membranes. Annexins exhibit dynamic roles in neuronal development, influencing differentiation, proliferation, and synaptic formation in CNS tissues. Notably, annexins such as ANXA1 and ANXA2 play roles in apoptosis and blood-brain barrier (BBB) integrity. Neurological disorders, including Alzheimer's disease, multiple sclerosis, and depression, involve annexin dysregulation, influencing neuroinflammation, blood-brain barrier integrity, and stress responses. Moreover, annexins contribute to the pathogenesis of CNS tumors, either promoting or suppressing tumor growth, angiogenesis, and invasion. Annexin expression patterns vary across different CNS tumor types, providing potential prognostic markers and therapeutic targets. This review underscores the multifaceted roles of annexins in the CNS, highlighting their importance in normal functioning, disease progression, and potential therapeutic interventions.


Asunto(s)
Anexinas , Sistema Nervioso Central , Humanos , Anexinas/metabolismo , Animales , Sistema Nervioso Central/metabolismo , Barrera Hematoencefálica/metabolismo , Enfermedades del Sistema Nervioso Central/metabolismo , Enfermedades del Sistema Nervioso Central/patología , Neoplasias del Sistema Nervioso Central/metabolismo , Neoplasias del Sistema Nervioso Central/patología
15.
Brain Behav Immun ; 119: 146-153, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38555986

RESUMEN

BACKGROUND: Perinatal depression (including antenatal-, postnatal-, and depression that spans both timepoints) is a prevalent disorder with high morbidity that affects both mother and child. Even though the full biological blueprints of perinatal depression remain incomplete, multiple studies indicate that, at least for antenatal depression, the disorder has an inflammatory component likely linked to a dysregulation of the enzymatic kynurenine pathway. The production of neuroactive metabolites in this pathway, including quinolinic acid (QUIN), is upregulated in the placenta due to the multiple immunological roles of the metabolites during pregnancy. Since neuroactive metabolites produced by the pathway also may affect mood by directly affecting glutamate neurotransmission, we sought to investigate whether the placental expression of kynurenine pathway enzymes controlling QUIN production was associated with both peripheral inflammation and depressive symptoms during pregnancy. METHODS: 68 placentas obtained at birth were analyzed using qPCR to determine the expression of kynurenine pathway enzymes. Cytokines and metabolites were quantified in plasma using high-sensitivity electroluminescence and ultra-performance liquid chromatography, respectively. Maternal depressive symptoms were assessed using the Edinburgh Postnatal Depression Scale (EPDS) throughout pregnancy and the post-partum. Associations between these factors were assessed using robust linear regression with ranked enzymes. RESULTS: Low placental quinolinate phosphoribosyl transferase (QPRT), the enzyme responsible for degrading QUIN, was associated with higher IL-6 and higher QUIN/kynurenic acid ratios at the 3rd trimester. Moreover, women with severe depressive symptoms in the 3rd trimester had significantly lower placental expression of both QPRT and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (ACMSD); impaired activity of these two enzymes leads to QUIN accumulation. CONCLUSION: Overall, our data support that a compromised placental environment, featuring low expression of critical kynurenine pathway enzymes is associated with increased levels of plasma cytokines and the dysregulated kynurenine metabolite pattern observed in depressed women during pregnancy.


Asunto(s)
Depresión , Inflamación , Quinurenina , Placenta , Ácido Quinolínico , Humanos , Femenino , Embarazo , Quinurenina/metabolismo , Quinurenina/sangre , Placenta/metabolismo , Adulto , Inflamación/metabolismo , Depresión/metabolismo , Ácido Quinolínico/metabolismo , Ácido Quinolínico/sangre , Citocinas/metabolismo , Complicaciones del Embarazo/metabolismo , Carboxiliasas/metabolismo , Pentosiltransferasa
16.
Clin Cancer Res ; 2024 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-38506712

RESUMEN

PURPOSE: The importance of cellular context to the synergy of DNA Damage Response (DDR) targeted agents is important for tumors with mutations in DDR pathways, but less well-established for tumors driven by oncogenic transcription factors. In this study, we exploit the widespread transcriptional dysregulation of the EWS-FLI1 transcription factor to identify an effective DDR targeted combination therapy for Ewing Sarcoma (ES). EXPERIMENTAL DESIGN: We used matrix drug screening to evaluate synergy between a DNA-PK inhibitor (M9831) or an ATR inhibitor (berzosertib) and chemotherapy. The combination of berzosertib and cisplatin was selected for broad synergy, mechanistically evaluated for ES selectivity, and optimized for in vivo schedule. RESULTS: Berzosertib combined with cisplatin demonstrates profound synergy in multiple ES cell lines at clinically achievable concentrations. The synergy is due to loss of expression of the ATR downstream target CHEK1, loss of cell cycle checkpoints, and mitotic catastrophe. Consistent with the goals of the project, EWS-FLI1 drives the expression of CHEK1 and five other ATR pathway members. The loss of CHEK1 expression is not due to transcriptional repression and instead caused by degradation coupled with suppression of protein translation. The profound synergy is realized in vivo with a novel optimized schedule of this combination in subsets of ES models leading to durable complete responses in 50% of animals bearing two different ES xenografts. CONCLUSION: These data exploit EWS-FLI1 driven alterations in cell context to broaden the therapeutic window of berzosertib and cisplatin to establish a promising combination therapy and a novel in vivo schedule.

17.
Microbiol Resour Announc ; 13(4): e0129923, 2024 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-38526097

RESUMEN

Pediococcus acidilactici is a well-studied fermentative bacterium reported to have potential probiotic properties. Here, we report the draft genome of P. acidilactici 3G3 previously isolated from burong babi, a Philippine fermented pork dish. The 3G3 draft genome has 1,886,498 bp, a GC content of 42.27%, and a completeness of 99.38%.

18.
PLoS Genet ; 20(3): e1011174, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38437180

RESUMEN

A striking paradox is that genes with conserved protein sequence, function and expression pattern over deep time often exhibit extremely divergent cis-regulatory sequences. It remains unclear how such drastic cis-regulatory evolution across species allows preservation of gene function, and to what extent these differences influence how cis-regulatory variation arising within species impacts phenotypic change. Here, we investigated these questions using a plant stem cell regulator conserved in expression pattern and function over ~125 million years. Using in-vivo genome editing in two distantly related models, Arabidopsis thaliana (Arabidopsis) and Solanum lycopersicum (tomato), we generated over 70 deletion alleles in the upstream and downstream regions of the stem cell repressor gene CLAVATA3 (CLV3) and compared their individual and combined effects on a shared phenotype, the number of carpels that make fruits. We found that sequences upstream of tomato CLV3 are highly sensitive to even small perturbations compared to its downstream region. In contrast, Arabidopsis CLV3 function is tolerant to severe disruptions both upstream and downstream of the coding sequence. Combining upstream and downstream deletions also revealed a different regulatory outcome. Whereas phenotypic enhancement from adding downstream mutations was predominantly weak and additive in tomato, mutating both regions of Arabidopsis CLV3 caused substantial and synergistic effects, demonstrating distinct distribution and redundancy of functional cis-regulatory sequences. Our results demonstrate remarkable malleability in cis-regulatory structural organization of a deeply conserved plant stem cell regulator and suggest that major reconfiguration of cis-regulatory sequence space is a common yet cryptic evolutionary force altering genotype-to-phenotype relationships from regulatory variation in conserved genes. Finally, our findings underscore the need for lineage-specific dissection of the spatial architecture of cis-regulation to effectively engineer trait variation from conserved productivity genes in crops.


Asunto(s)
Arabidopsis , Arabidopsis/genética , Secuencias Reguladoras de Ácidos Nucleicos/genética , Productos Agrícolas , Alelos , Secuencia de Aminoácidos
19.
Elife ; 132024 Feb 06.
Artículo en Inglés | MEDLINE | ID: mdl-38319148

RESUMEN

Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized 'codes' that are read by specialized regions (reader domains) in chromatin-associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP: histone PTM] specificities, and thus decipher the histone code and guide epigenetic therapies. However, this has largely been done using the reductive approach of isolated reader domains and histone peptides, which cannot account for any higher-order factors. Here, we show that the [BPTF PHD finger and bromodomain: histone PTM] interaction is dependent on nucleosome context. The tandem reader selectively associates with nucleosomal H3K4me3 and H3K14ac or H3K18ac, a combinatorial engagement that despite being in cis is not predicted by peptides. This in vitro specificity of the BPTF tandem reader for PTM-defined nucleosomes is recapitulated in a cellular context. We propose that regulatable histone tail accessibility and its impact on the binding potential of reader domains necessitates we refine the 'histone code' concept and interrogate it at the nucleosome level.


Asunto(s)
Histonas , Nucleosomas , Histonas/metabolismo , Código de Histonas , Cromatina , Procesamiento Proteico-Postraduccional , Péptidos/metabolismo
20.
Annu Rev Public Health ; 45(1): 425-442, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38166502

RESUMEN

Warning labels help consumers understand product risks, enabling informed decisions. Since the 1966 introduction of cigarette warning labels in the United States, research has determined the most effective message content (health effects information) and format (brand-free packaging with pictures). However, new challenges have emerged. This article reviews the current state of tobacco warning labels in the United States, where legal battles have stalled pictorial cigarette warnings and new products such as electronic cigarettes and synthetic nicotine products pose unknown health risks. This article describes the emerging research on cannabis warnings; as more places legalize recreational cannabis, they are adopting lessons from tobacco warnings. However, its uncertain legal status and widespread underestimation of harms impede strict warning standards. The article also reviews opioid medication warning labels, suggesting that lessons from tobacco could help in the development of effective and culturally appropriate FDA-compliant opioid warning labels that promote safe medication use and increased co-dispensing of naloxone.


Asunto(s)
Analgésicos Opioides , Etiquetado de Productos , Humanos , Estados Unidos , Etiquetado de Productos/normas , Analgésicos Opioides/efectos adversos , Salud Pública , Etiquetado de Medicamentos/normas , United States Food and Drug Administration , Productos de Tabaco/efectos adversos
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