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1.
Cell ; 163(6): 1539-54, 2015 Dec 03.
Artigo em Inglês | MEDLINE | ID: mdl-26638078

RESUMO

Lifespan is a remarkably diverse trait ranging from a few days to several hundred years in nature, but the mechanisms underlying the evolution of lifespan differences remain elusive. Here we de novo assemble a reference genome for the naturally short-lived African turquoise killifish, providing a unique resource for comparative and experimental genomics. The identification of genes under positive selection in this fish reveals potential candidates to explain its compressed lifespan. Several aging genes are under positive selection in this short-lived fish and long-lived species, raising the intriguing possibility that the same gene could underlie evolution of both compressed and extended lifespans. Comparative genomics and linkage analysis identify candidate genes associated with lifespan differences between various turquoise killifish strains. Remarkably, these genes are clustered on the sex chromosome, suggesting that short lifespan might have co-evolved with sex determination. Our study provides insights into the evolutionary forces that shape lifespan in nature.


Assuntos
Evolução Biológica , Peixes Listrados/genética , Envelhecimento , Animais , DNA Helicases/genética , Genoma , Humanos , Longevidade , Anotação de Sequência Molecular , Dados de Sequência Molecular , Seleção Genética
2.
Nature ; 620(7976): 1025-1030, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-37532928

RESUMO

HIV-1 remains a global health crisis1, highlighting the need to identify new targets for therapies. Here, given the disproportionate HIV-1 burden and marked human genome diversity in Africa2, we assessed the genetic determinants of control of set-point viral load in 3,879 people of African ancestries living with HIV-1 participating in the international collaboration for the genomics of HIV3. We identify a previously undescribed association signal on chromosome 1 where the peak variant associates with an approximately 0.3 log10-transformed copies per ml lower set-point viral load per minor allele copy and is specific to populations of African descent. The top associated variant is intergenic and lies between a long intergenic non-coding RNA (LINC00624) and the coding gene CHD1L, which encodes a helicase that is involved in DNA repair4. Infection assays in iPS cell-derived macrophages and other immortalized cell lines showed increased HIV-1 replication in CHD1L-knockdown and CHD1L-knockout cells. We provide evidence from population genetic studies that Africa-specific genetic variation near CHD1L associates with HIV replication in vivo. Although experimental studies suggest that CHD1L is able to limit HIV infection in some cell types in vitro, further investigation is required to understand the mechanisms underlying our observations, including any potential indirect effects of CHD1L on HIV spread in vivo that our cell-based assays cannot recapitulate.


Assuntos
DNA Helicases , Proteínas de Ligação a DNA , Variação Genética , Infecções por HIV , HIV-1 , Carga Viral , Humanos , Linhagem Celular , DNA Helicases/genética , DNA Helicases/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Infecções por HIV/genética , HIV-1/crescimento & desenvolvimento , HIV-1/fisiologia , Carga Viral/genética , África , Cromossomos Humanos Par 1/genética , Alelos , RNA Longo não Codificante/genética , Replicação Viral
3.
Nature ; 594(7862): 207-212, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34108699

RESUMO

Chip floorplanning is the engineering task of designing the physical layout of a computer chip. Despite five decades of research1, chip floorplanning has defied automation, requiring months of intense effort by physical design engineers to produce manufacturable layouts. Here we present a deep reinforcement learning approach to chip floorplanning. In under six hours, our method automatically generates chip floorplans that are superior or comparable to those produced by humans in all key metrics, including power consumption, performance and chip area. To achieve this, we pose chip floorplanning as a reinforcement learning problem, and develop an edge-based graph convolutional neural network architecture capable of learning rich and transferable representations of the chip. As a result, our method utilizes past experience to become better and faster at solving new instances of the problem, allowing chip design to be performed by artificial agents with more experience than any human designer. Our method was used to design the next generation of Google's artificial intelligence (AI) accelerators, and has the potential to save thousands of hours of human effort for each new generation. Finally, we believe that more powerful AI-designed hardware will fuel advances in AI, creating a symbiotic relationship between the two fields.

4.
Proc Natl Acad Sci U S A ; 121(12): e2306281121, 2024 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-38466835

RESUMO

Policymakers increasingly rely on behavioral science in response to global challenges, such as climate change or global health crises. But applications of behavioral science face an important problem: Interventions often exert substantially different effects across contexts and individuals. We examine this heterogeneity for different paradigms that underlie many behavioral interventions. We study the paradigms in a series of five preregistered studies across one in-person and 10 online panels, with over 11,000 respondents in total. We find substantial heterogeneity across settings and paradigms, apply techniques for modeling the heterogeneity, and introduce a framework that measures typically omitted moderators. The framework's factors (Fluid Intelligence, Attentiveness, Crystallized Intelligence, and Experience) affect the effectiveness of many text-based interventions, producing different observed effect sizes and explaining variations across samples. Moderators are associated with effect sizes through two paths, with the intensity of the manipulation and with the effect of the manipulation directly. Our results motivate observing these moderators and provide a theoretical and empirical framework for understanding and predicting varying effect sizes in the social sciences.


Assuntos
Ciências do Comportamento , Ciências Sociais , Humanos , Atenção
5.
Proc Natl Acad Sci U S A ; 120(40): e2218385120, 2023 10 03.
Artigo em Inglês | MEDLINE | ID: mdl-37751554

RESUMO

In the months before the 2020 U.S. election, several political campaign websites added prechecked boxes (defaults), automatically making all donations into recurring weekly contributions unless donors unchecked them. Since these changes occurred at different times for different campaigns, we use a staggered difference-in-differences design to measure the causal effects of defaults on donors' behavior. We estimate that defaults increased campaign donations by over $43 million while increasing requested refunds by almost $3 million. The weekly default only impacted weekly recurring donations, and not other donations, suggesting that donors may not have intended to make weekly donations. The longer defaults were displayed, the more money campaigns raised through weekly donations. Donors did not compensate by changing the amount they donated. We found that the default had a larger impact on smaller donors and on donors who had no prior experience with defaults, causing them to start more chains and donate a larger proportion of their money through weekly recurring donations.


Assuntos
Comportamento de Escolha , Organização do Financiamento , Política , Humanos , Internet
6.
Am J Hum Genet ; 109(2): 299-310, 2022 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-35090584

RESUMO

Spontaneous clearance of acute hepatitis C virus (HCV) infection is associated with single nucleotide polymorphisms (SNPs) on the MHC class II. We fine-mapped the MHC region in European (n = 1,600; 594 HCV clearance/1,006 HCV persistence) and African (n = 1,869; 340 HCV clearance/1,529 HCV persistence) ancestry individuals and evaluated HCV peptide binding affinity of classical alleles. In both populations, HLA-DQß1Leu26 (p valueMeta = 1.24 × 10-14) located in pocket 4 was negatively associated with HCV spontaneous clearance and HLA-DQß1Pro55 (p valueMeta = 8.23 × 10-11) located in the peptide binding region was positively associated, independently of HLA-DQß1Leu26. These two amino acids are not in linkage disequilibrium (r2 < 0.1) and explain the SNPs and classical allele associations represented by rs2647011, rs9274711, HLA-DQB1∗03:01, and HLA-DRB1∗01:01. Additionally, HCV persistence classical alleles tagged by HLA-DQß1Leu26 had fewer HCV binding epitopes and lower predicted binding affinities compared to clearance alleles (geometric mean of combined IC50 nM of persistence versus clearance; 2,321 nM versus 761.7 nM, p value = 1.35 × 10-38). In summary, MHC class II fine-mapping revealed key amino acids in HLA-DQß1 explaining allelic and SNP associations with HCV outcomes. This mechanistic advance in understanding of natural recovery and immunogenetics of HCV might set the stage for much needed enhancement and design of vaccine to promote spontaneous clearance of HCV infection.


Assuntos
Cadeias beta de HLA-DQ/genética , Hepacivirus/patogenicidade , Hepatite C/genética , Interações Hospedeiro-Patógeno/genética , Polimorfismo de Nucleotídeo Único , Doença Aguda , Alelos , Substituição de Aminoácidos , População Negra , Feminino , Expressão Gênica , Estudo de Associação Genômica Ampla , Genótipo , Cadeias beta de HLA-DQ/imunologia , Hepacivirus/crescimento & desenvolvimento , Hepacivirus/imunologia , Hepatite C/etnologia , Hepatite C/imunologia , Hepatite C/virologia , Interações Hospedeiro-Patógeno/imunologia , Humanos , Leucina/imunologia , Leucina/metabolismo , Masculino , Prolina/imunologia , Prolina/metabolismo , Isoformas de Proteínas/genética , Isoformas de Proteínas/imunologia , Remissão Espontânea , População Branca
7.
Mol Psychiatry ; 2023 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-37935791

RESUMO

Cannabis is widely used worldwide, yet its links to health outcomes are not fully understood. DNA methylation can serve as a mediator to link environmental exposures to health outcomes. We conducted an epigenome-wide association study (EWAS) of peripheral blood-based DNA methylation and lifetime cannabis use (ever vs. never) in a meta-analysis including 9436 participants (7795 European and 1641 African ancestry) from seven cohorts. Accounting for effects of cigarette smoking, our trans-ancestry EWAS meta-analysis revealed four CpG sites significantly associated with lifetime cannabis use at a false discovery rate of 0.05 [Formula: see text]: cg22572071 near gene ADGRF1, cg15280358 in ADAM12, cg00813162 in ACTN1, and cg01101459 near LINC01132. Additionally, our EWAS analysis in participants who never smoked cigarettes identified another epigenome-wide significant CpG site, cg14237301 annotated to APOBR. We used a leave-one-out approach to evaluate methylation scores constructed as a weighted sum of the significant CpGs. The best model can explain 3.79% of the variance in lifetime cannabis use. These findings unravel the DNA methylation changes associated with lifetime cannabis use that are independent of cigarette smoking and may serve as a starting point for further research on the mechanisms through which cannabis exposure impacts health outcomes.

8.
Langmuir ; 40(19): 10143-10156, 2024 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-38690604

RESUMO

When placed in an ionic surfactant gradient, charged colloids will undergo diffusiophoresis at a velocity, uDP = MDP∇ ln S, where MDP is the diffusiophoretic mobility and S is the surfactant concentration. The diffusiophoretic mobility depends in part on the charges and diffusivities of the surfactants and their counterions. Since micellization decreases surfactant diffusivity and alters charge distributions in a surfactant solution, MDP of charged colloids in ionic surfactant gradients may differ significantly when surfactant concentrations are above or below the critical micelle concentration (CMC). The role of micelles in driving diffusiophoresis is unclear, and a previously published model that accounts for micellization suggests the possibility of a change in the sign of MDP above the CMC [Warren, P. B.; . Soft Matter 2019, 15, 278-288]. In the current study, microfluidic channels were used to measure the transport of negatively charged polystyrene colloids in sodium dodecyl sulfate (SDS) surfactant gradients established at SDS concentrations that are either fully above or fully below the CMC. Interpretation of diffusiophoresis was aided by measurements of the colloid electrophoretic mobility as a function of SDS concentration. A numerical transport model incorporating the prior diffusiophoretic mobility model for ionic surfactant gradients was implemented to elucidate signatures of positive and negative diffusiophoretic mobilities and compare with experiments. The theoretically predicted sign of the diffusiophoretic mobility below the CMC was determined to be particularly sensitive to uncertainty in colloid and surfactant properties, while above the CMC, the mobility was consistently predicted to be positive in the SDS concentration range considered in the experiments conducted here. In contrast, experiments only showed signatures of a negative diffusiophoretic mobility for these negatively charged colloids with no change of sign. Colloid diffusiophoretic transport measured in micellar solutions was more extensive than that below the CMC with the same ∇ ln S.

10.
Ear Hear ; 2024 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-38816900

RESUMO

OBJECTIVES: This study aimed to determine the speech-to-background ratios (SBRs) at which normal-hearing (NH) and hearing-impaired (HI) listeners can recognize both speech and environmental sounds when the two types of signals are mixed. Also examined were the effect of individual sounds on speech recognition and environmental sound recognition (ESR), and the impact of divided versus selective attention on these tasks. DESIGN: In Experiment 1 (divided attention), 11 NH and 10 HI listeners heard sentences mixed with environmental sounds at various SBRs and performed speech recognition and ESR tasks concurrently in each trial. In Experiment 2 (selective attention), 20 NH listeners performed these tasks in separate trials. Psychometric functions were generated for each task, listener group, and environmental sound. The range over which speech recognition and ESR were both high was determined, as was the optimal SBR for balancing recognition with ESR, defined as the point of intersection between each pair of normalized psychometric functions. RESULTS: The NH listeners achieved greater than 95% accuracy on concurrent speech recognition and ESR over an SBR range of approximately 20 dB or greater. The optimal SBR for maximizing both speech recognition and ESR for NH listeners was approximately +12 dB. For the HI listeners, the range over which 95% performance was observed on both tasks was far smaller (span of 1 dB), with an optimal value of +5 dB. Acoustic analyses indicated that the speech and environmental sound stimuli were similarly audible, regardless of the hearing status of the listener, but that the speech fluctuated more than the environmental sounds. Divided versus selective attention conditions produced differences in performance that were statistically significant yet only modest in magnitude. In all conditions and for both listener groups, recognition was higher for environmental sounds than for speech when presented at equal intensities (i.e., 0 dB SBR), indicating that the environmental sounds were more effective maskers of speech than the converse. Each of the 25 environmental sounds used in this study (with one exception) had a span of SBRs over which speech recognition and ESR were both higher than 95%. These ranges tended to overlap substantially. CONCLUSIONS: A range of SBRs exists over which speech and environmental sounds can be simultaneously recognized with high accuracy by NH and HI listeners, but this range is larger for NH listeners. The single optimal SBR for jointly maximizing speech recognition and ESR also differs between NH and HI listeners. The greater masking effectiveness of the environmental sounds relative to the speech may be related to the lower degree of fluctuation present in the environmental sounds as well as possibly task differences between speech recognition and ESR (open versus closed set). The observed differences between the NH and HI results may possibly be related to the HI listeners' smaller fluctuating masker benefit. As noise-reduction systems become increasingly effective, the current results could potentially guide the design of future systems that provide listeners with highly intelligible speech without depriving them of access to important environmental sounds.

11.
Pharmacoepidemiol Drug Saf ; 33(1): e5734, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38112287

RESUMO

PURPOSE: Observational studies assessing effects of medical products on suicidal behavior often rely on health record data to account for pre-existing risk. We assess whether high-dimensional models predicting suicide risk using data derived from insurance claims and electronic health records (EHRs) are superior to models using data from insurance claims alone. METHODS: Data were from seven large health systems identified outpatient mental health visits by patients aged 11 or older between 1/1/2009 and 9/30/2017. Data for the 5 years prior to each visit identified potential predictors of suicidal behavior typically available from insurance claims (e.g., mental health diagnoses, procedure codes, medication dispensings) and additional potential predictors available from EHRs (self-reported race and ethnicity, responses to Patient Health Questionnaire or PHQ-9 depression questionnaires). Nonfatal self-harm events following each visit were identified from insurance claims data and fatal self-harm events were identified by linkage to state mortality records. Random forest models predicting nonfatal or fatal self-harm over 90 days following each visit were developed in a 70% random sample of visits and validated in a held-out sample of 30%. Performance of models using linked claims and EHR data was compared to models using claims data only. RESULTS: Among 15 845 047 encounters by 1 574 612 patients, 99 098 (0.6%) were followed by a self-harm event within 90 days. Overall classification performance did not differ between the best-fitting model using all data (area under the receiver operating curve or AUC = 0.846, 95% CI 0.839-0.854) and the best-fitting model limited to data available from insurance claims (AUC = 0.846, 95% CI 0.838-0.853). Competing models showed similar classification performance across a range of cut-points and similar calibration performance across a range of risk strata. Results were similar when the sample was limited to health systems and time periods where PHQ-9 depression questionnaires were recorded more frequently. CONCLUSION: Investigators using health record data to account for pre-existing risk in observational studies of suicidal behavior need not limit that research to databases including linked EHR data.


Assuntos
Seguro , Comportamento Autodestrutivo , Humanos , Ideação Suicida , Registros Eletrônicos de Saúde , Web Semântica
12.
Antonie Van Leeuwenhoek ; 117(1): 100, 2024 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-39001997

RESUMO

An isolate of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from soil when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain was closely related to Lysinibacillus fusiformis NRRL NRS-350T (99.7%) and Lysinibacillus sphaericus NRRL B-23268T (99.2%). In phenotypic characterization, the novel strain was found to grow between 10 and 45 °C and tolerate up to 8% (w/v) NaCl. Furthermore, the strain grew in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C15: 0 (52.3%), anteiso-C15: 0 (14.8%), C16:1ω7C alcohol (11.2%), and C16: 0 (9.5%). The cell-wall peptidoglycan contained lysine-aspartic acid, the same as congeners. A draft genome was assembled and the DNA G+C content was determined to be 37.1% (mol content). A phylogenomic analysis on the core genome of the new strain and 5 closest type strains of Lysinibacillus revealed this strain formed a distinct monophyletic clade with the nearest neighbor being Lysinibacillus fusiformis. DNA-DNA relatedness studies using in silico DNA-DNA hybridizations (DDH) showed this species was below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus pinottii sp. nov. is proposed, with type strain PB211T (= NRRL B-65672T, = CCUG 77181T).


Assuntos
Bacillaceae , Composição de Bases , DNA Bacteriano , Ácidos Graxos , Filogenia , RNA Ribossômico 16S , Bacillaceae/genética , Bacillaceae/classificação , Bacillaceae/isolamento & purificação , RNA Ribossômico 16S/genética , DNA Bacteriano/genética , Ácidos Graxos/análise , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Peptidoglicano , Animais , Genoma Bacteriano , Análise de Sequência de DNA , Parede Celular/química
13.
Prenat Diagn ; 44(2): 158-166, 2024 02.
Artigo em Inglês | MEDLINE | ID: mdl-38009470

RESUMO

Fetal lower urinary tract obstruction (LUTO) is a severe malformation associated with an up to 80% mortality risk as well as significant renal and pulmonary morbidity in survivors. Fetal vesico-amniotic shunts (VAS) bypass the bladder obstruction, improve amniotic fluid volume and enhance in-utero pulmonary development. VAS has been shown to reduce respiratory morbidity and mortality in the neonatal period without proven benefit on long-term renal and bladder function. Clinically available shunts are associated with an up to 80% dislodgement rate, leading to repeat invasive procedures which increase fetal and maternal risks. We developed a novel "Vortex" shunt, which incorporates enhanced fixation to reduce dislodgement, a one-way valve to optimize in-utero bladder function, and enhanced sonographic echogenicity that optimizes the accurate deployment. Following the validation of these characteristics in initial benchtop experiments we have moved to feasibility studies in the fetal lamb model. We hope that the Vortex shunt may ultimately facilitate shunt deployment, reduce dislodgement risk, improve neonatal morbidity and mortality, and decrease the significant healthcare expenditures associated with long-term morbidity in LUTO survivors. In this manuscript, we review the natural history of LUTO, the risks and benefits of clinically available fetal shunts, and our development and early validation experiments.


Assuntos
Obstrução Uretral , Obstrução do Colo da Bexiga Urinária , Feminino , Animais , Ovinos , Gravidez , Bexiga Urinária/diagnóstico por imagem , Bexiga Urinária/cirurgia , Obstrução Uretral/cirurgia , Âmnio/cirurgia , Obstrução do Colo da Bexiga Urinária/cirurgia , Líquido Amniótico , Ultrassonografia Pré-Natal
14.
Proc Natl Acad Sci U S A ; 118(47)2021 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-34799448

RESUMO

Circadian transcriptional timekeepers in pacemaker neurons drive profound daily rhythms in sleep and wake. Here we reveal a molecular pathway that links core transcriptional oscillators to neuronal and behavioral rhythms. Using two independent genetic screens, we identified mutants of Transport and Golgi organization 10 (Tango10) with poor behavioral rhythmicity. Tango10 expression in pacemaker neurons expressing the neuropeptide PIGMENT-DISPERSING FACTOR (PDF) is required for robust rhythms. Loss of Tango10 results in elevated PDF accumulation in nerve terminals even in mutants lacking a functional core clock. TANGO10 protein itself is rhythmically expressed in PDF terminals. Mass spectrometry of TANGO10 complexes reveals interactions with the E3 ubiquitin ligase CULLIN 3 (CUL3). CUL3 depletion phenocopies Tango10 mutant effects on PDF even in the absence of the core clock gene timeless Patch clamp electrophysiology in Tango10 mutant neurons demonstrates elevated spontaneous firing potentially due to reduced voltage-gated Shaker-like potassium currents. We propose that Tango10/Cul3 transduces molecular oscillations from the core clock to neuropeptide release important for behavioral rhythms.


Assuntos
Relógios Circadianos/fisiologia , Proteínas de Drosophila/metabolismo , Neuropeptídeos/metabolismo , Ubiquitina-Proteína Ligases/metabolismo , Animais , Translocador Nuclear Receptor Aril Hidrocarboneto/genética , Translocador Nuclear Receptor Aril Hidrocarboneto/metabolismo , Proteínas Culina/genética , Proteínas Culina/metabolismo , Drosophila , Proteínas de Drosophila/genética , Neurônios/metabolismo , Neuropeptídeos/genética , Proteômica , Sono
15.
Diabetes Spectr ; 37(1): 29-38, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38385100

RESUMO

Standards of care summarized in clinical practice guidelines for nonalcoholic fatty liver disease (NAFLD) offer clinicians a streamlined diagnostic and management approach based on the best available evidence. These recommendations have changed a great deal in recent years; today, there is a clear focus on screening for the early identification and risk stratification of patients at high risk of steatohepatitis and clinically significant fibrosis to promote timely referrals to specialty care when needed. This article reviews and provides the rationale for current guidelines for NAFLD screening, diagnosis, treatment, and monitoring and addresses barriers to providing evidence-based NAFLD care and how to overcome them. The current paradigm of care calls for primary care clinicians and specialists to work together, within a multidisciplinary care team familiar with obesity and diabetes care, to provide comprehensive management of these complex patients.

16.
Wilderness Environ Med ; 35(2): 183-197, 2024 06.
Artigo em Inglês | MEDLINE | ID: mdl-38577729

RESUMO

The Wilderness Medical Society convened an expert panel to develop a set of evidence-based guidelines for the prevention and treatment of frostbite. We present a review of pertinent pathophysiology. We then discuss primary and secondary prevention measures and therapeutic management. Recommendations are made regarding each treatment and its role in management. These recommendations are graded on the basis of the quality of supporting evidence and balance between the benefits and risks or burdens for each modality according to methodology stipulated by the American College of Chest Physicians. This is an updated version of the guidelines published in 2019.


Assuntos
Congelamento das Extremidades , Sociedades Médicas , Medicina Selvagem , Congelamento das Extremidades/terapia , Congelamento das Extremidades/prevenção & controle , Medicina Selvagem/normas , Medicina Selvagem/métodos , Humanos
17.
Biophys J ; 122(15): 3117-3132, 2023 08 08.
Artigo em Inglês | MEDLINE | ID: mdl-37353934

RESUMO

Artificial proteins representing the consensus of a set of homologous sequences have attracted attention for their increased thermodynamic stability and conserved activity. Here, we applied the consensus approach to a b-type heme-binding protein to inspect the contribution of a dissociable cofactor to enhanced stability and the chemical consequences of creating a generic heme environment. We targeted the group 1 truncated hemoglobin (TrHb1) subfamily of proteins for their small size (∼120 residues) and ease of characterization. The primary structure, derived from a curated set of ∼300 representative sequences, yielded a highly soluble consensus globin (cGlbN) enriched in acidic residues. Optical and NMR spectroscopies revealed high-affinity heme binding in the expected site and in two orientations. At neutral pH, proximal and distal iron coordination was achieved with a pair of histidine residues, as observed in some natural TrHb1s, and with labile ligation on the distal side. As opposed to studied TrHb1s, which undergo additional folding upon heme binding, cGlbN displayed the same extent of secondary structure whether the heme was associated with the protein or not. Denaturation required guanidine hydrochloride and showed that apo- and holoprotein unfolded in two transitions-the first (occurring with a midpoint of ∼2 M) was shifted to higher denaturant concentration in the holoprotein (∼3.7 M) and reflected stabilization due to heme binding, while the second transition (∼6.2 M) was common to both forms. Thus, the consensus sequence stabilized the protein but exposed the existence of two separately cooperative subdomains within the globin architecture, masked as one single domain in TrHb1s with typical stabilities. The results suggested ways in which specific chemical or thermodynamic features may be controlled in artificial heme proteins.


Assuntos
Globinas , Hemeproteínas , Globinas/química , Dobramento de Proteína , Termodinâmica , Heme/metabolismo , Desnaturação Proteica
18.
J Biol Chem ; 298(5): 101909, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35398097

RESUMO

Cytochrome P450 3A4 and 3A5 catalyze the metabolic clearance of a large portion of therapeutic drugs. Azamulin is used as a selective inhibitor for 3A4 and 3A5 to define their roles in metabolism of new chemical entities during drug development. In contrast to 3A4, 3A5 exhibits homotropic cooperativity for the sequential binding of two azamulin molecules at concentrations used for inhibition. To define the underlying sites and mechanisms for cooperativity, an X-ray crystal structure of 3A5 was determined with two azamulin molecules in the active site that are stacked in an antiparallel orientation. One azamulin resides proximal to the heme in a pose similar to the 3A4-azamulin complex. Comparison to the 3A5 apo structure indicates that the distal azamulin in 3A5 ternary complex causes a significant induced fit that excludes water from the hydrophobic surfaces of binding cavity and the distal azamulin, which is augmented by the stacking interaction with the proximal azamulin. Homotropic cooperativity was not observed for the binding of related pleuromutilin antibiotics, tiamulin, retapamulin, and lefamulin, to 3A5, which are larger and unlikely to bind in the distal site in a stacked orientation. Formation of the 3A5 complex with two azamulin molecules may prevent time-dependent inhibition that is seen for 3A4 by restricting alternate product formation and/or access of reactive intermediates to vulnerable protein sites. These results also contribute to a better understanding of sites for cooperative binding and the differential structural plasticity of 3A5 and 3A4 that contribute to differential substrate and inhibitor binding.


Assuntos
Hidrocarbonetos Aromáticos com Pontes , Citocromo P-450 CYP3A , Domínio Catalítico , Citocromo P-450 CYP3A/metabolismo , Humanos , Triazóis
19.
BMC Genomics ; 24(1): 556, 2023 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-37730558

RESUMO

BACKGROUND: Cocaine use (CU) is associated with psychiatric and medical diseases. Little is known about the mechanisms of CU-related comorbidities. Findings from preclinical and clinical studies have suggested that CU is associated with aberrant DNA methylation (DNAm) that may be influenced by genetic variants [i.e., methylation quantitative trait loci (meQTLs)]. In this study, we mapped cis-meQTLs for CU-associated DNAm sites (CpGs) in an HIV-positive cohort (Ntotal = 811) and extended the meQTLs to multiple traits. RESULTS: We conducted cis-meQTL analysis for 224 candidate CpGs selected for their association with CU in blood. We identified 7,101 significant meQTLs [false discovery rate (FDR) < 0.05], which mostly mapped to genes involved in immunological functions and were enriched in immune pathways. We followed up the meQTLs using phenome-wide association study and trait enrichment analyses, which revealed 9 significant traits. We tested for causal effects of CU on these 9 traits using Mendelian Randomization and found evidence that CU plays a causal role in increasing hypertension (p-value = 2.35E-08) and decreasing heel bone mineral density (p-value = 1.92E-19). CONCLUSIONS: These findings suggest that genetic variants for CU-associated DNAm have pleiotropic effects on other relevant traits and provide new insights into the causal relationships between cocaine use and these complex traits.


Assuntos
Cocaína , Infecções por HIV , Humanos , Metilação de DNA , Fenótipo , Fenômica , Infecções por HIV/genética
20.
Hum Mol Genet ; 30(14): 1321-1336, 2021 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-33949649

RESUMO

ΔR4-R23/ΔCT micro-dystrophin (µDys) is a miniaturized version of dystrophin currently evaluated in a Duchenne muscular dystrophy (DMD) gene therapy trial to treat skeletal and cardiac muscle disease. In pre-clinical studies, µDys efficiently rescues cardiac histopathology, but only partially normalizes cardiac function. To gain insights into factors that may impact the cardiac therapeutic efficacy of µDys, we compared by mass spectrometry the composition of purified dystrophin and µDys protein complexes in the mouse heart. We report that compared to dystrophin, µDys has altered associations with α1- and ß2-syntrophins, as well as cavins, a group of caveolae-associated signaling proteins. In particular, we found that membrane localization of cavin-1 and cavin-4 in cardiomyocytes requires dystrophin and is profoundly disrupted in the heart of mdx5cv mice, a model of DMD. Following cardiac stress/damage, membrane-associated cavin-4 recruits the signaling molecule ERK to caveolae, which activates key cardio-protective responses. Evaluation of ERK signaling revealed a profound inhibition, below physiological baseline, in the mdx5cv mouse heart. Expression of µDys in mdx5cv mice prevented the development of cardiac histopathology but did not rescue membrane localization of cavins nor did it normalize ERK signaling. Our study provides the first comparative analysis of purified protein complexes assembled in vivo by full-length dystrophin and a therapeutic micro-dystrophin construct. This has revealed disruptions in cavins and ERK signaling that may contribute to DMD cardiomyopathy. This new knowledge is important for ongoing efforts to prevent and treat heart disease in DMD patients.


Assuntos
Cardiomiopatias , Distrofia Muscular de Duchenne , Animais , Cardiomiopatias/genética , Distrofina/metabolismo , Humanos , Camundongos , Camundongos Endogâmicos mdx , Distrofia Muscular de Duchenne/metabolismo , Miócitos Cardíacos/metabolismo , Proteômica
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