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1.
bioRxiv ; 2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38746265

RESUMO

Animals use a small number of morphogens to pattern tissues, but it is unclear how evolution modulates morphogen signaling range to match tissues of varying sizes. Here, we used single molecule imaging in reconstituted morphogen gradients and in tissue explants to determine that Hedgehog diffused extra-cellularly as a monomer, and rapidly transitioned between membrane-confined and -unconfined states. Unexpectedly, the vertebrate-specific protein SCUBE1 expanded Hedgehog gradients by accelerating the transition rates between states without affecting the relative abundance of molecules in each state. This observation could not be explained under existing models of morphogen diffusion. Instead, we developed a topology-limited diffusion model in which cell-cell gaps create diffusion barriers, and morphogens can only overcome the barrier by passing through a membrane-unconfined state. Under this model, SCUBE1 promotes Hedgehog secretion and diffusion by allowing it to transiently overcome diffusion barriers. This multiscale understanding of morphogen gradient formation unified prior models and discovered novel knobs that nature can use to tune morphogen gradient sizes across tissues and organisms.

2.
Nat Struct Mol Biol ; 2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38698207

RESUMO

Vortioxetine (VTX) is a recently approved antidepressant that targets a variety of serotonin receptors. Here, we investigate the drug's molecular mechanism of operation at the serotonin 5-HT3 receptor (5-HT3R), which features two properties: VTX acts differently on rodent and human 5-HT3R, and VTX appears to suppress any subsequent response to agonists. Using a combination of cryo-EM, electrophysiology, voltage-clamp fluorometry and molecular dynamics, we show that VTX stabilizes a resting inhibited state of the mouse 5-HT3R and an agonist-bound-like state of human 5-HT3R, in line with the functional profile of the drug. We report four human 5-HT3R structures and show that the human receptor transmembrane domain is intrinsically fragile. We also explain the lack of recovery after VTX administration via a membrane partition mechanism.

3.
Cancer Treat Res Commun ; 40: 100820, 2024 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-38761787

RESUMO

BACKGROUND: Several studies have analyzed the effect of anticoagulants on cancer survival, with varying results. This study aimed to assess the effect of warfarin on survival in patients with colorectal cancer (CRC) in relation to timing of warfarin initiation. METHODS: Data on 10,051 individuals aged ≥45 years in the Västra Götaland Region of Sweden, and diagnosed with CRC between 2000 and 2009, were obtained from the Swedish National Cancer Register. Those who received warfarin treatment (n= 1,216) during the study period were labeled cases and those who did not (n= 8,873) were labeled controls. For statistical analysis, National Cancer Register data were merged with mortality data from the Swedish National Cause of Death register and data from the regional warfarin treatment register. RESULTS: Hazard rates for CRC-specific mortality were lower in cases than in controls. When warfarin was used for any reason at any time, cases had a significantly lower CRC-specific mortality than controls among both women (hazard ratio [HR] 0.71; 95 % confidence interval [CI] 0.59-0.85; p= 0.0002) and men (HR 0.61; 95 % CI 0.52-0.72; p < 0001). Warfarin treatment after CRC diagnosis reduced CRC-specific mortality by 80 %; however, when warfarin was given before or ≥5 years after diagnosis, CRC-specific mortality did not significantly decrease. The number needed to treat to avoid one death was four. CONCLUSION: Use of warfarin early after diagnosis in patients with CRC was associated with improved survival.

4.
Artigo em Inglês | MEDLINE | ID: mdl-38629348

RESUMO

BACKGROUND: Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly recommended for perioperative opioid-sparing multimodal analgesic treatments. Concerns regarding the potential for serious adverse events (SAEs) associated with perioperative NSAID treatment are especially relevant following gastrointestinal surgery. We assessed the risks of SAEs with perioperative NSAID treatment in patients undergoing gastrointestinal surgery. METHODS: We conducted a systematic review of randomised clinical trials assessing the harmful effects of NSAIDs versus placebo, usual care or no intervention in patients undergoing gastrointestinal surgery. The primary outcome was an incidence of SAEs. We systematically searched for eligible trials in five major databases up to January 2024. We performed risk of bias assessments to account for systematic errors, trial sequential analysis (TSA) to account for the risks of random errors, performed meta-analyses using R and used the Grading of Recommendations Assessment, Development and Evaluation framework to describe the certainty of evidence. RESULTS: We included 22 trials enrolling 1622 patients for our primary analyses. Most trials were at high risk of bias. Meta-analyses (risk ratio 0.78; 95% confidence interval [CI] 0.51-1.19; I2 = 4%; p = .24; very low certainty of evidence) and TSA indicated a lack of information on the effects of NSAIDs compared to placebo on the risks of SAEs. Post-hoc beta-binomial regression sensitivity analyses including trials with zero events showed a reduction in SAEs with NSAIDs versus placebo (odds ratio 0.73; CI 0.54-0.99; p = .042). CONCLUSION: In adult patients undergoing gastrointestinal surgery, there was insufficient information to draw firm conclusions on the effects of NSAIDs on SAEs. The certainty of the evidence was very low.

5.
Mol Cell ; 84(7): 1365-1376.e7, 2024 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-38452764

RESUMO

Enhancer-gene communication is dependent on topologically associating domains (TADs) and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying structures and mechanisms remain controversial. Here, we investigate a boundary that typically insulates fibroblast growth factor (FGF) oncogenes but is disrupted by DNA hypermethylation in gastrointestinal stromal tumors (GISTs). The boundary contains an array of CTCF sites that enforce adjacent TADs, one containing FGF genes and the other containing ANO1 and its putative enhancers, which are specifically active in GIST and its likely cell of origin. We show that coordinate disruption of four CTCF motifs in the boundary fuses the adjacent TADs, allows the ANO1 enhancer to contact FGF3, and causes its robust induction. High-resolution micro-C maps reveal specific contact between transcription initiation sites in the ANO1 enhancer and FGF3 promoter that quantitatively scales with FGF3 induction such that modest changes in contact frequency result in strong changes in expression, consistent with a causal relationship.


Assuntos
Cromatina , Elementos Facilitadores Genéticos , Fator de Ligação a CCCTC/genética , Fator de Ligação a CCCTC/metabolismo , Cromatina/genética , Oncogenes , DNA/química
6.
Mol Plant ; 17(4): 552-578, 2024 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-38475993

RESUMO

Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP-theoretically reaching one when using the Pearson's correlation as a metric-is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.


Assuntos
Genoma de Planta , Melhoramento Vegetal , Humanos , Genoma de Planta/genética , Seleção Genética , Genômica , Fenótipo , Genótipo , Plantas , Polimorfismo de Nucleotídeo Único/genética
7.
J Zoo Wildl Med ; 55(1): 195-199, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38453502

RESUMO

Heart disease in birds contributes to premature death and is usually detected postmortem. Echocardiography is a sensitive and noninvasive diagnostic modality but reported standard values for many species of birds, including American flamingos (Phoenicopterus ruber), are unavailable. Echocardiography was opportunistically performed on 30 unsedated American flamingos during their annual routine health examination. Structural heart disease was not found in any of the examined birds. However, 18 birds showed varying degrees of dynamic intraventricular obstruction. Echocardiographic parameters are reported. Benign neurocardiogenic weakness or syncopal events during handling were suspected in three birds. Stress combined with an intraventricular obstruction is believed to have triggered a cascade of parasympathetic innervation and sympathetic inhibition, similar to neurally mediated reflex syncope in humans.


Assuntos
Aves , Síncope , Animais , Síncope/veterinária
8.
J Rheumatol ; 51(4): 350-359, 2024 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-38302173

RESUMO

OBJECTIVE: This study aimed to compare the prevalence and incidence of polyautoimmunity between anticyclic citrullinated peptide antibody (anti-CCP)-positive and anti-CCP-negative patients with rheumatoid arthritis (RA). METHODS: In a nationwide register-based cohort study, patients with RA (disease duration ≤ 2 yrs) in the DANBIO rheumatology register with an available anti-CCP test in the Register of Laboratory Results for Research were identified. The polyautoimmunity outcome included 21 nonrheumatic autoimmune diseases identified by linkage between the Danish Patient Registry and Prescription Registry. The age- and sex-adjusted prevalence ratio (PR) was calculated by modified Poisson regression to estimate the prevalence at diagnosis in anti-CCP-positive vs anti-CCP-negative patients. The hazard ratio (HR) of polyautoimmunity within 5 years of entry into DANBIO was estimated in cause-specific Cox regression models. RESULTS: The study included 5839 anti-CCP-positive and 3799 anti-CCP-negative patients with RA. At first visit, the prevalence of prespecified polyautoimmune diseases in the Danish registers was 11.1% and 11.9% in anti-CCP-positive and anti-CCP-negative patients, respectively (PR 0.93, 95% CI 0.84-1.05). The most frequent autoimmune diseases were autoimmune thyroid disease, inflammatory bowel disease, and type 1 diabetes mellitus. During a mean follow-up of 3.5 years, only a few (n = 210) patients developed polyautoimmunity (HR 0.6, 95% CI 0.46-0.79). CONCLUSION: Polyautoimmunity as captured through the Danish National Patient Registry occurred in approximately 1 in 10 patients with RA at time of diagnosis regardless of anti-CCP status. In the years subsequent to the RA diagnosis, only a few and mainly anti-CCP-negative patients developed autoimmune disease.


Assuntos
Anticorpos Antiproteína Citrulinada , Artrite Reumatoide , Humanos , Estudos de Coortes , Artrite Reumatoide/diagnóstico , Artrite Reumatoide/epidemiologia , Autoanticorpos , Dinamarca/epidemiologia , Peptídeos , Peptídeos Cíclicos
9.
Artigo em Inglês | MEDLINE | ID: mdl-38413840

RESUMO

The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at promoters in an orientation-independent and distance-independent manner. Despite being crucial for gene regulation in animals, what mechanisms underlie enhancer selectivity for promoters, and more fundamentally, how enhancers interact with promoters and activate transcription, remain poorly understood. In this Review, we first discuss current models of enhancer-promoter interactions in space and time and how enhancers affect transcription activation. Next, we discuss different mechanisms that mediate enhancer selectivity, including repression, biochemical compatibility and regulation of 3D genome structure. Through 3D polymer simulations, we illustrate how the ability of 3D genome folding mechanisms to mediate enhancer selectivity strongly varies for different enhancer-promoter interaction mechanisms. Finally, we discuss how recent technical advances may provide new insights into mechanisms of enhancer-promoter interactions and how technical biases in methods such as Hi-C and Micro-C and imaging techniques may affect their interpretation.

10.
bioRxiv ; 2024 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-38370764

RESUMO

Although only a fraction of CTCF motifs are bound in any cell type, and few occupied sites overlap cohesin, the mechanisms underlying cell-type specific attachment and ability to function as a chromatin organizer remain unknown. To investigate the relationship between CTCF and chromatin we applied a combination of imaging, structural and molecular approaches, using a series of brain and cancer associated CTCF mutations that act as CTCF perturbations. We demonstrate that binding and the functional impact of WT and mutant CTCF depend not only on the unique binding properties of each protein, but also on the genomic context of bound sites and enrichment of motifs for expressed TFs abutting these sites. Our studies also highlight the reciprocal relationship between CTCF and chromatin, demonstrating that the unique binding properties of WT and mutant proteins have a distinct impact on accessibility, TF binding, cohesin overlap, chromatin interactivity and gene expression programs, providing insight into their cancer and brain related effects.

11.
FEBS J ; 291(7): 1506-1529, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38145505

RESUMO

The kainate receptors GluK1-3 (glutamate receptor ionotropic, kainate receptors 1-3) belong to the family of ionotropic glutamate receptors and are essential for fast excitatory neurotransmission in the brain, and are associated with neurological and psychiatric diseases. How these receptors can be modulated by small-molecule agents is not well understood, especially for GluK3. We show that the positive allosteric modulator BPAM344 can be used to establish robust calcium-sensitive fluorescence-based assays to test agonists, antagonists, and positive allosteric modulators of GluK1-3. The half-maximal effective concentration (EC50) of BPAM344 for potentiating the response of 100 µm kainate was determined to be 26.3 µm for GluK1, 75.4 µm for GluK2, and 639 µm for GluK3. Domoate was found to be a potent agonist for GluK1 and GluK2, with an EC50 of 0.77 and 1.33 µm, respectively, upon co-application of 150 µm BPAM344. At GluK3, domoate acts as a very weak agonist or antagonist with a half-maximal inhibitory concentration (IC50) of 14.5 µm, in presence of 500 µm BPAM344 and 100 µm kainate for competition binding. Using H523A-mutated GluK3, we determined the first dimeric structure of the ligand-binding domain by X-ray crystallography, allowing location of BPAM344, as well as zinc-, sodium-, and chloride-ion binding sites at the dimer interface. Molecular dynamics simulations support the stability of the ion sites as well as the involvement of Asp761, Asp790, and Glu797 in the binding of zinc ions. Using electron microscopy, we show that, in presence of glutamate and BPAM344, full-length GluK3 adopts a dimer-of-dimers arrangement.


Assuntos
Ácido Caínico , Receptores de Ácido Caínico , Tiazinas , Receptores de Ácido Caínico/genética , Receptores de Ácido Caínico/agonistas , Ácido Caínico/farmacologia , Óxidos S-Cíclicos , Zinco/metabolismo
12.
bioRxiv ; 2023 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-37961446

RESUMO

DNA looping is vital for establishing many enhancer-promoter interactions. While CTCF is known to anchor many cohesin-mediated loops, the looped chromatin fiber appears to predominantly exist in a poorly characterized actively extruding state. To better characterize extruding chromatin loop structures, we used CTCF MNase HiChIP data to determine both CTCF binding at high resolution and 3D contact information. Here we present FactorFinder, a tool that identifies CTCF binding sites at near base-pair resolution. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics, and find that active enhancers and RNA Pol II impede cohesin extrusion, facilitating an enrichment of enhancer-promoter contacts in the partially extruded loop state. We propose a model of topological regulation whereby the transient, partially extruded states play active roles in transcription.

13.
bioRxiv ; 2023 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-37786671

RESUMO

Enhancers possess both structural elements mediating promoter looping and functional elements mediating gene expression. Traditional models of enhancer-mediated gene regulation imply genomic overlap or immediate adjacency of these elements. We test this model by combining densely-tiled CRISPRa screening with nucleosome-resolution Region Capture Micro-C topology analysis. Using this integrated approach, we comprehensively define the cis-regulatory landscape for the tumor suppressor PTEN, identifying and validating 10 distinct enhancers and defining their 3D spatial organization. Unexpectedly, we identify several long-range functional enhancers whose promoter proximity is facilitated by chromatin loop anchors several kilobases away, and demonstrate that accounting for this spatial separation improves the computational prediction of validated enhancers. Thus, we propose a new model of enhancer organization incorporating spatial separation of essential functional and structural components.

14.
Chem Sci ; 14(41): 11447-11455, 2023 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-37886102

RESUMO

Polyamorphism has been a controversial and highly debated solid-state phenomenon in both material and pharmaceutical communities. Although some evidence of this fascinating phenomenon has been reported for several inorganic systems, and more recently also for a few organic compounds, the occurrence of polyamorphism is poorly understood and the molecular-level organization of polyamorphic forms is still unknown. Here we have investigated the occurrence of polyamorphism and polyamorphic interconversions in hydrochlorothiazide (HCT), using both experimental and computational methods. Three distinct HCT polyamorphs, presenting distinct physical and thermal stabilities as well as distinct relaxation properties, were systematically prepared using spray-drying (SD), quench-cooling (QC) and ball milling (BM) methods. HCT polyamorph II (obtained by QC) was found to be more physically stable than polyamorphs I and III (obtained by SD and BM, respectively). Furthermore, polyamorphs I and III could be converted into polyamorph II after QC, while polyamorph II did not convert to any other polyamorph after SD or BM. Molecular dynamics simulations show that HCT dihedral angle distributions are significantly different for polyamorphs I and II, which is postulated as a possible explanation for their different physicochemical properties.

15.
Eur Urol Open Sci ; 56: 15-24, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37822514

RESUMO

Background: Adverse events induced by intravesical bacillus Calmette-Guérin (BCG) to treat high-grade non-muscle-invasive bladder cancer (NMIBC) often lead to treatment discontinuation. The EAU-RF NIMBUS trial found a reduced number of standard-dose BCG instillations to be inferior with the standard regimen. Nonetheless, it remains important to evaluate whether patients in the reduced BCG treatment arm had better quality of life (QoL) due to a possible reduction in toxicity or burden. Objective: To evaluate whether patients in the EAU-RF NIMBUS trial experienced better QoL after a reduced BCG instillation frequency. Design setting and participants: A total of 359 patients from 51 European sites were randomized to one of two treatment arms between December 2013 and July 2019. The standard frequency arm (n = 182) was 6 weeks of BCG induction followed by 3 weeks of maintenance at months 3, 6, and 12. The reduced frequency arm (n = 177) was BCG induction at weeks 1, 2, and 6, followed by maintenance instillations at weeks 1 and 3 of months 3, 6, and 12. Outcome measurements and statistical analysis: Analyses were performed using an intention-to-treat analysis and a per-protocol analysis. QoL was measured using the European Organization for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire Core 30 version 3.0 (QLQ-C30 v.03) prior to the first and last instillations of each BCG cycle. Group differences were determined using linear regression corrected for QoL at baseline. Differences in QoL over time were tested for significance using a linear mixed model. Side effects were recorded by the treating physician using a standardized form. Chi-square tests were used to compare the side-effect frequency between the arms. Results and limitations: There were no significant differences in the means of each QoL scale between the two arms. There were also no significant changes over time in all QoL domains for both arms. However, differences in the incidence of general malaise at T1 (before the last induction instillation), frequency, urgency, and dysuria at T7 (before the last maintenance instillation) were detected in favor of the reduced frequency arm. Conclusions: Reducing the BCG instillation frequency does not improve the QoL in NMIBC patients despite lower storage symptoms. Patient summary: In this study, we evaluated whether a reduction in the number of received bacillus Calmette-Guérin instillations led to better quality of life in patients with high-grade non-muscle-invasive bladder cancer. We found no difference in the quality of life between the standard and the reduced bacillus Calmette-Guérin instillation frequency. We conclude that reducing the number of instillations does not lead to better quality of life in patients with high-grade non-muscle-invasive bladder cancer.

16.
Phys Rev Lett ; 131(3): 033607, 2023 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-37540885

RESUMO

The emergence of photonic quantum correlations is typically associated with emitters strongly coupled to a photonic mode. Here, we show that semiconductor Rydberg excitons, which are only weakly coupled to a free-space light mode can produce strongly antibunched fields, i.e., quantum light. This effect is fueled by a micron-scale excitation blockade between Rydberg excitons inducing pair-wise polariton scattering events. Photons incident on an exciton resonance are scattered into blue- and red-detuned pairs, which enjoy relative protection from absorption and thus dominate the transmitted light. We demonstrate that this effect persists in the presence of additional phonon coupling, strong nonradiative decay, and across a wide range of experimental parameters. Our results pave the way for the observation of quantum statistics from weakly coupled semiconductor excitons.

17.
PLoS Biol ; 21(8): e3002217, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37535677

RESUMO

Animal venom peptides represent valuable compounds for biomedical exploration. The venoms of marine cone snails constitute a particularly rich source of peptide toxins, known as conotoxins. Here, we identify the sequence of an unusually large conotoxin, Mu8.1, which defines a new class of conotoxins evolutionarily related to the well-known con-ikot-ikots and 2 additional conotoxin classes not previously described. The crystal structure of recombinant Mu8.1 displays a saposin-like fold and shows structural similarity with con-ikot-ikot. Functional studies demonstrate that Mu8.1 curtails calcium influx in defined classes of murine somatosensory dorsal root ganglion (DRG) neurons. When tested on a variety of recombinantly expressed voltage-gated ion channels, Mu8.1 displayed the highest potency against the R-type (Cav2.3) calcium channel. Ca2+ signals from Mu8.1-sensitive DRG neurons were also inhibited by SNX-482, a known spider peptide modulator of Cav2.3 and voltage-gated K+ (Kv4) channels. Our findings highlight the potential of Mu8.1 as a molecular tool to identify and study neuronal subclasses expressing Cav2.3. Importantly, this multidisciplinary study showcases the potential of uncovering novel structures and bioactivities within the largely unexplored group of macro-conotoxins.


Assuntos
Conotoxinas , Camundongos , Animais , Conotoxinas/farmacologia , Conotoxinas/química , Canais de Cálcio , Peptídeos/química , Células Receptoras Sensoriais/metabolismo , Caramujos
18.
Mol Cell ; 83(15): 2624-2640, 2023 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-37419111

RESUMO

The four-dimensional nucleome (4DN) consortium studies the architecture of the genome and the nucleus in space and time. We summarize progress by the consortium and highlight the development of technologies for (1) mapping genome folding and identifying roles of nuclear components and bodies, proteins, and RNA, (2) characterizing nuclear organization with time or single-cell resolution, and (3) imaging of nuclear organization. With these tools, the consortium has provided over 2,000 public datasets. Integrative computational models based on these data are starting to reveal connections between genome structure and function. We then present a forward-looking perspective and outline current aims to (1) delineate dynamics of nuclear architecture at different timescales, from minutes to weeks as cells differentiate, in populations and in single cells, (2) characterize cis-determinants and trans-modulators of genome organization, (3) test functional consequences of changes in cis- and trans-regulators, and (4) develop predictive models of genome structure and function.


Assuntos
Núcleo Celular , Genoma , Genoma/genética , Núcleo Celular/genética , Núcleo Celular/metabolismo , Cromatina/metabolismo
19.
Nat Genet ; 55(6): 1048-1056, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-37157000

RESUMO

Although enhancers are central regulators of mammalian gene expression, the mechanisms underlying enhancer-promoter (E-P) interactions remain unclear. Chromosome conformation capture (3C) methods effectively capture large-scale three-dimensional (3D) genome structure but struggle to achieve the depth necessary to resolve fine-scale E-P interactions. Here, we develop Region Capture Micro-C (RCMC) by combining micrococcal nuclease (MNase)-based 3C with a tiling region-capture approach and generate the deepest 3D genome maps reported with only modest sequencing. By applying RCMC in mouse embryonic stem cells and reaching the genome-wide equivalent of ~317 billion unique contacts, RCMC reveals previously unresolvable patterns of highly nested and focal 3D interactions, which we term microcompartments. Microcompartments frequently connect enhancers and promoters, and although loss of loop extrusion and inhibition of transcription disrupts some microcompartments, most are largely unaffected. We therefore propose that many E-P interactions form through a compartmentalization mechanism, which may partially explain why acute cohesin depletion only modestly affects global gene expression.


Assuntos
Cromatina , Elementos Facilitadores Genéticos , Animais , Camundongos , Regiões Promotoras Genéticas , Cromossomos , Mapeamento Cromossômico , Mamíferos/genética
20.
J Econ Entomol ; 116(4): 1423-1431, 2023 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-37208312

RESUMO

Corn wireworm, Melanotus communis Gyllenhal (Coleoptera: Elateridae), is an economically important larval pest of root and tuber crops in the United States. Previous work to estimate field-level abundance of M. communis has focused on grain-based larval baits placed in soil. However, this sampling method is labor intensive and may not estimate population size accurately. Recent discovery of the M. communis sex pheromone, 13-tetradecenyl acetate, provides a new method to monitor this pest during the adult stage. Early studies with this pheromone showed that different trapping methods might enhance catch and improve trap servicing. We hypothesized that placing lures on elevated traps would increase M. communis capture relative to the in-ground pitfall trapping that is currently used. We had 2 objectives for this study: (a) to compare pheromone captures among in-ground pitfall traps, on-ground pitfalls, elevated pitfalls (1 m), or elevated sticky cards (1 m) and (b) test lure longevity by aging the lures outdoors at 8-, 6-, 4-, 2-, and 0-wk intervals prior to trap deployment in the field. Experiments were conducted in North Carolina, Virginia, South Carolina, and Florida during the 2021 and 2022 field seasons. Results highlight large variation in M. communis abundance across the 4 states. We showed that 1 m elevated pheromone traps caught the most beetles. The age of the lure prior to deployment had a significant effect on trap catch. The lures that were aged for fewer weeks attracted significantly more beetles, with 0- and 2-wk-old lures capturing the greatest numbers.


Assuntos
Besouros , Atrativos Sexuais , Animais , Atrativos Sexuais/farmacologia , Feromônios/farmacologia , Larva , Acetatos , Controle de Insetos/métodos
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