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1.
Med Image Anal ; 90: 102967, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-37778102

RESUMEN

Any clinically-deployed image-processing pipeline must be robust to the full range of inputs it may be presented with. One popular approach to this challenge is to develop predictive models that can provide a measure of their uncertainty. Another approach is to use generative modelling to quantify the likelihood of inputs. Inputs with a low enough likelihood are deemed to be out-of-distribution and are not presented to the downstream predictive model. In this work, we evaluate several approaches to segmentation with uncertainty for the task of segmenting bleeds in 3D CT of the head. We show that these models can fail catastrophically when operating in the far out-of-distribution domain, often providing predictions that are both highly confident and wrong. We propose to instead perform out-of-distribution detection using the Latent Transformer Model: a VQ-GAN is used to provide a highly compressed latent representation of the input volume, and a transformer is then used to estimate the likelihood of this compressed representation of the input. We demonstrate this approach can identify images that are both far- and near- out-of-distribution, as well as provide spatial maps that highlight the regions considered to be out-of-distribution. Furthermore, we find a strong relationship between an image's likelihood and the quality of a model's segmentation on it, demonstrating that this approach is viable for filtering out unsuitable images.


Asunto(s)
Procesamiento de Imagen Asistido por Computador , Humanos , Probabilidad , Incertidumbre
2.
J Alzheimers Dis Rep ; 7(1): 957-972, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37849634

RESUMEN

Background: While Alzheimer's disease (AD) pathology is associated with altered brain structure, it is not clear whether gene expression changes mirror the onset and evolution of pathology in distinct brain regions. Deciphering the mechanisms which cause the differential manifestation of the disease across different regions has the potential to help early diagnosis. Objective: We aimed to identify common and unique endotypes and their regulation in tangle-free neurons in sporadic AD (SAD) across six brain regions: entorhinal cortex (EC), hippocampus (HC), medial temporal gyrus (MTG), posterior cingulate (PC), superior frontal gyrus (SFG), and visual cortex (VCX). Methods: To decipher the states of tangle-free neurons across different brain regions in human subjects afflicted with AD, we performed analysis of the neural transcriptome. We explored changes in differential gene expression, functional and transcription factor target enrichment, and co-expression gene module detection analysis to discern disease-state transcriptomic variances and characterize endotypes. Additionally, we compared our results to tangled AD neuron microarray-based study and the Allen Brain Atlas. Results: We identified impaired neuron function in EC, MTG, PC, and VCX resulting from REST activation and reversal of mature neurons to a precursor-like state in EC, MTG, and SFG linked to SOX2 activation. Additionally, decreased neuron function and increased dedifferentiation were linked to the activation of SUZ12. Energetic deficit connected to NRF1 inactivation was found in HC, PC, and VCX. Conclusions: Our findings suggest that SAD manifestation varies in scale and severity in different brain regions. We identify endotypes, such as energetic shortfalls, impaired neuronal function, and dedifferentiation.

3.
Microb Physiol ; 33(1): 49-62, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37321192

RESUMEN

Members of the Piezo family of mechanically activated cation channels are involved in multiple physiological processes in higher eukaryotes, including vascular development, cell differentiation, touch perception, hearing, and more, but they are also common in single-celled eukaryotic microorganisms. Mutations in these proteins in humans are associated with a variety of diseases, such as colorectal adenomatous polyposis, dehydrated hereditary stomatocytosis, and hereditary xerocytosis. Available 3D structures for Piezo proteins show nine regions of four transmembrane segments each that have the same fold. Despite the remarkable similarity among the nine characteristic structural repeats in the family, no significant sequence similarity among them has been reported. Using bioinformatics approaches and the Transporter Classification Database (TCDB) as reference, we reliably identified sequence similarity among repeats based on four lines of evidence: (1) hidden Markov model-profile similarities across repeats at the family level, (2) pairwise sequence similarities between different repeats across Piezo homologs, (3) Piezo-specific conserved sequence signatures that consistently identify the same regions across repeats, and (4) conserved residues that maintain the same orientation and location in 3D space.


Asunto(s)
Toxinas Bacterianas , Clostridioides difficile , Humanos , Clostridioides difficile/metabolismo , Canales Iónicos/genética , Canales Iónicos/química , Canales Iónicos/metabolismo , Mutación , Secuencia Conservada
4.
PLoS One ; 18(5): e0280841, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37235566

RESUMEN

Breast cancer claims 11,400 lives on average every year in the UK, making it one of the deadliest diseases. Mammography is the gold standard for detecting early signs of breast cancer, which can help cure the disease during its early stages. However, incorrect mammography diagnoses are common and may harm patients through unnecessary treatments and operations (or a lack of treatment). Therefore, systems that can learn to detect breast cancer on their own could help reduce the number of incorrect interpretations and missed cases. Various deep learning techniques, which can be used to implement a system that learns how to detect instances of breast cancer in mammograms, are explored throughout this paper. Convolution Neural Networks (CNNs) are used as part of a pipeline based on deep learning techniques. A divide and conquer approach is followed to analyse the effects on performance and efficiency when utilising diverse deep learning techniques such as varying network architectures (VGG19, ResNet50, InceptionV3, DenseNet121, MobileNetV2), class weights, input sizes, image ratios, pre-processing techniques, transfer learning, dropout rates, and types of mammogram projections. This approach serves as a starting point for model development of mammography classification tasks. Practitioners can benefit from this work by using the divide and conquer results to select the most suitable deep learning techniques for their case out-of-the-box, thus reducing the need for extensive exploratory experimentation. Multiple techniques are found to provide accuracy gains relative to a general baseline (VGG19 model using uncropped 512 × 512 pixels input images with a dropout rate of 0.2 and a learning rate of 1 × 10-3) on the Curated Breast Imaging Subset of DDSM (CBIS-DDSM) dataset. These techniques involve transfer learning pre-trained ImagetNet weights to a MobileNetV2 architecture, with pre-trained weights from a binarised version of the mini Mammography Image Analysis Society (mini-MIAS) dataset applied to the fully connected layers of the model, coupled with using weights to alleviate class imbalance, and splitting CBIS-DDSM samples between images of masses and calcifications. Using these techniques, a 5.6% gain in accuracy over the baseline model was accomplished. Other deep learning techniques from the divide and conquer approach, such as larger image sizes, do not yield increased accuracies without the use of image pre-processing techniques such as Gaussian filtering, histogram equalisation and input cropping.


Asunto(s)
Neoplasias de la Mama , Aprendizaje Profundo , Humanos , Femenino , Mamografía/métodos , Neoplasias de la Mama/diagnóstico por imagen , Redes Neurales de la Computación , Mama
5.
ACS Chem Biol ; 17(10): 2890-2898, 2022 10 21.
Artículo en Inglés | MEDLINE | ID: mdl-36173802

RESUMEN

Non-ribosomal peptides play a critical role in the clinic as therapeutic agents. To access more chemically diverse therapeutics, non-ribosomal peptide synthetases (NRPSs) have been targeted for engineering through combinatorial biosynthesis; however, this has been met with limited success in part due to the lack of proper protein-protein interactions between non-cognate proteins. Herein, we report our use of chemical biology to enable X-ray crystallography, molecular dynamics (MD) simulations, and biochemical studies to elucidate binding specificities between peptidyl carrier proteins (PCPs) and adenylation (A) domains. Specifically, we determined X-ray crystal structures of a type II PCP crosslinked to its cognate A domain, PigG and PigI, and of PigG crosslinked to a non-cognate PigI homologue, PltF. The crosslinked PCP-A domain structures possess large protein-protein interfaces that predominantly feature hydrophobic interactions, with specific electrostatic interactions that orient the substrate for active site delivery. MD simulations of the PCP-A domain complexes and unbound PCP structures provide a dynamical evaluation of the transient interactions formed at PCP-A domain interfaces, which confirm the previously hypothesized role of a PCP loop as a crucial recognition element. Finally, we demonstrate that the interfacial interactions at the PCP loop 1 region can be modified to control PCP binding specificity through gain-of-function mutations. This work suggests that loop conformational preferences and dynamism account for improved shape complementary in the PCP-A domain interactions. Ultimately, these studies show how crystallographic, biochemical, and computational methods can be used to rationally re-engineer NRPSs for non-cognate interactions.


Asunto(s)
Péptido Sintasas , Péptidos , Secuencia de Aminoácidos , Péptido Sintasas/metabolismo , Péptidos/química , Dominio Catalítico , Proteínas Portadoras/metabolismo
6.
Chem Sci ; 13(12): 3609, 2022 Mar 24.
Artículo en Inglés | MEDLINE | ID: mdl-35432871

RESUMEN

[This corrects the article DOI: 10.1039/D0SC02717K.].

7.
ACS Appl Mater Interfaces ; 13(36): 43489-43504, 2021 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-34468116

RESUMEN

Aluminum and its alloys are widely used in various industries. Aluminum plays an important role in heat transfer applications, where enhancing the overall system performance through surface nanostructuring is achieved. Combining optimized nanostructures with a conformal hydrophobic coating leads to superhydrophobicity, which enables coalescence induced droplet jumping, enhanced condensation heat transfer, and delayed frosting. Hence, the development of a rapid, energy-efficient, and highly scalable fabrication method for rendering aluminum superhydrophobic is crucial. Here, we employ a simple, ultrascalable fabrication method to create boehmite nanostructures on aluminum. We systematically explore the influence of fabrication conditions such as water immersion time and immersion temperature, on the created nanostructure morphology and resultant nanostructure length scale. We achieved optimized structures and fabrication procedures for best droplet jumping performance as measured by total manufacturing energy utilization, fabrication time, and total cost. The wettability of the nanostructures was studied using the modified Cassie-Baxter model. To better differentiate performance of the fabricated superhydrophobic surfaces, we quantify the role of the nanostructure morphology to corresponding condensation and antifrosting performance through study of droplet jumping behavior and frost propagation dynamics. The effect of aluminum substrate composition (alloy) on wettability, condensation and antifrosting performance was investigated, providing important directions for proper substrate selection. Our findings indicate that the presence of trace alloying elements play a previously unobserved and important role on wettability, condensation, and frosting behavior via the inclusion of defect sites on the surface that are difficult to remove and act as pinning locations to increase liquid-solid adhesion. Our work provides optimization strategies for the fabrication of ultrascalable aluminum and aluminum alloy superhydrophobic surfaces for a variety of applications.

8.
Urology ; 158: 180-183, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34186130

RESUMEN

OBJECTIVE: To compare improvement/change of hydronephrosis and hydroureter in patients with complete ureteral duplications that underwent upper and lower robotic-assisted laparoscopic uretero-ureterostomies. The hypothesis being that improvement of hydronephrosis and hydroureter between the two groups was similar. METHODS: 35 subjects met inclusion criteria and were reviewed retrospectively. 'Upper' anastomoses were defined as those being done below the lower pole of the kidney (Group 1), while 'lower' anastomoses were those done below the iliac vessels (Group 2). Primary variables analyzed were antero-posterior and diameter measurements of the renal pelvis and ureter, respectively, before and after surgery. Secondary variables included operative time, length of hospital stay, and complication rates. RESULTS: Group 1 consisted of 20 subjects while Group 2 consisted of 15 subjects. Presenting diagnoses were hydronephrosis in 31 subjects and incontinence in 4 subjects. Group 1 mean AP renal diameters decreased by 62.9% (P<.05), while Group 2 decreased by 65.4% (P<.05). Group 1 mean hydroureter diameter measurements decreased by 80.3% (P<.05), while Group 2 decreased by 83% (P<.05). The improvement in hydronephrosis and hydroureter between the two groups was not statistically different. Group 1 median operative time (271 minutes) was longer than Group 2 (201 minutes) (P<.05). There was no significant difference in hospital stay between the groups and there were no significant complications within the cohort. CONCLUSION: The improvement rate of hydronephrosis and hydroureter is similar in upper versus lower RAL UU. Operative time was significantly shorter in the lower anastomosis group.


Asunto(s)
Hidronefrosis/cirugía , Laparoscopía , Procedimientos Quirúrgicos Robotizados , Ureterostomía/métodos , Niño , Preescolar , Femenino , Humanos , Masculino , Tempo Operativo , Estudios Retrospectivos
9.
Commun Biol ; 4(1): 340, 2021 03 16.
Artículo en Inglés | MEDLINE | ID: mdl-33727677

RESUMEN

Fatty acid biosynthesis (FAB) is an essential and highly conserved metabolic pathway. In bacteria, this process is mediated by an elaborate network of protein•protein interactions (PPIs) involving a small, dynamic acyl carrier protein that interacts with dozens of other partner proteins (PPs). These PPIs have remained poorly characterized due to their dynamic and transient nature. Using a combination of solution-phase NMR spectroscopy and protein-protein docking simulations, we report a comprehensive residue-by-residue comparison of the PPIs formed during FAB in Escherichia coli. This technique describes and compares the molecular basis of six discrete binding events responsible for E. coli FAB and offers insights into a method to characterize these events and those in related carrier protein-dependent pathways.


Asunto(s)
Proteína Transportadora de Acilo/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimología , Acido Graso Sintasa Tipo II/metabolismo , Ácidos Grasos/biosíntesis , 3-Oxoacil-(Proteína Transportadora de Acil) Sintasa/metabolismo , Acetiltransferasas/metabolismo , Oxidorreductasas de Alcohol/metabolismo , Sitios de Unión , Enoil-ACP Reductasa (NADH)/metabolismo , Lisofosfolipasa/metabolismo , Simulación del Acoplamiento Molecular , Proteínas Periplasmáticas/metabolismo , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Espectroscopía de Protones por Resonancia Magnética
10.
J Pediatr Urol ; 17(2): 256.e1-256.e5, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33349560

RESUMEN

PURPOSE: There is limited evidence that prophylactic antibiotics prevent surgical site infection in stented, distal hypospadias repair. Our hypothesis is that the use of prophylactic antibiotics does not affect the rate of surgical site infection in this setting. METHODS: We conducted a retrospective study of consecutive patients over a 6-year period with distal penile hypospadias treated with urethral stenting. Variables analyzed include age, type of repair, usage of preoperative and/or postoperative antibiotics, and length of follow-up. Patients with a history of proximal or re-operative hypospadias repair were excluded. Surgical site infection was defined by the presence of postoperative penile erythema and/or purulent drainage treated with therapeutic antibiotics. Secondary outcome analysis included the presence of other hypospadias complications. RESULTS: 441 consecutive subjects met our inclusion criteria with a mean age of 13.3 months. Patients were categorized into groups: Group 1 - Preoperative antibiotics (n = 64), Group 2 - Both Preoperative & Postoperative antibiotics (n = 159), Group 3 - Postoperative antibiotics (n = 122), Group 4 - No Preoperative or Postoperative antibiotics (n = 96). Two surgical site infections were reported out of the 441 patients: 1 in Group 3 and 1 in Group 4 (p = 0.513). There was no significant difference in the total patients with a hypospadias complication between groups. In the table below, Groups 1-3 were combined (345 patients) for comparison to Group 4 (No antibiotics, 96 patients) for further analysis with no difference in SSIs (p = 0.388) or respective hypospadias complications. CONCLUSIONS: The use of perioperative prophylactic antibiotics, both before and after surgery for distal, stented hypospadias repair, have not been shown to reduce the rate of surgical site infections nor hypospadias complications. Consequently, the benefit of prophylactic antibiotics in this setting is unclear.


Asunto(s)
Hipospadias , Infección de la Herida Quirúrgica , Antibacterianos/uso terapéutico , Humanos , Hipospadias/cirugía , Lactante , Masculino , Complicaciones Posoperatorias/epidemiología , Complicaciones Posoperatorias/prevención & control , Estudios Retrospectivos , Infección de la Herida Quirúrgica/epidemiología , Infección de la Herida Quirúrgica/prevención & control , Resultado del Tratamiento , Uretra , Procedimientos Quirúrgicos Urológicos Masculinos/efectos adversos
11.
Telemed J E Health ; 27(2): 213-217, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-32539570

RESUMEN

Introduction: Telemedicine allows health care professionals to diagnose and treat patients remotely. Enuresis is one of the most common chronic problems in childhood and specialized care can be limited. Utilization of telemedicine in this setting has not been previously analyzed. Materials and Methods: This study's aim is to evaluate the feasibility and effectiveness of telemedicine follow-up treatment of enuresis compared with traditional follow-up at our institution. A retrospective review of patients treated for nocturnal enuresis with either telemedicine (Group 1) or traditional (Group2) follow-up care was conducted. Patients, aged 5-18 years, treated for enuresis between July 2016 and December 2017 were included. Patients with confounding disease were excluded. Resolution of enuresis was the primary outcome as categorized by the International Children's Continence Society standards. Results: Seventy-seven (n = 77) patients met inclusion criteria with 23 patients in Group 1 and 54 patients in Group 2. Two patients in each group were lost to follow-up and 61.9% in Group 1 and 48.1% in Group 2 responded to treatment. The average age for both groups was 9.2 years. Patients in Group 1 averaged four appointments per patient and patients in Group 2 averaged 3.04 appointments per patient. Telemedicine follow-up patients missed fewer appointments (0.14) than patients with traditional follow-up (0.5) (p-value = 0.016). Thirteen of 21 patients (61.9%) responded to treatment in Group 1 (7 partial and 6 complete responders) as compared with 25 of 52 patients (48.1%) responding to treatment in Group 2 (8 partial and 17 complete responders) (p = 0.22). Of patients in Group 1, 87% reported they would use telemedicine again. Conclusions: Telemedicine follow-up of patients with enuresis demonstrated comparable effectiveness. Most patient families demonstrate a favorable opinion of using telemedicine again for this problem. Further research to understand the efficacy and benefits of telemedicine in this setting is needed.


Asunto(s)
Enuresis Nocturna , Telemedicina , Incontinencia Urinaria , Adolescente , Niño , Preescolar , Estudios de Seguimiento , Humanos , Estudios Retrospectivos
12.
Chem Sci ; 11(26): 6907-6914, 2020 Jul 14.
Artículo en Inglés | MEDLINE | ID: mdl-33209243

RESUMEN

Bioisostere replacement is a core concept in modern medicinal chemistry and has proven an invaluable strategy to address pharmacodynamic and pharmacokinetic limitations of therapeutics. The success of bioisostere replacement is often dependent on the scaffold that is being modified (i.e., "context dependence"). The application of bioisostere replacement to a picolinic acid fragment was recently demonstrated as a means to expand a library of metal-binding pharmacophores (MBPs) to modulate their physicochemical properties, while retaining their metal binding and metalloenzyme inhibitory activity. Here, metal binding isosteres (MBIs) with different nitrogen-containing heteroarenes is explored. This resulted in a number of new MBIs that were evaluated for their physicochemical properties and metal binding features. It was observed that the coordination behavior of an MBI is dependent on the identity and arrangement of the heteroatoms within each heteroarene. To further understand the observed coordination chemistry trends, density functional theory (DFT) calculations were performed. Theory indicates that preferences in coordination geometry are largely determined by the electronic character of the heteroarene scaffold. These results provide important insights into the development of novel MBI scaffolds that can serve to broaden the scope of scaffolds for metalloenzyme inhibitor development.

13.
Proc Natl Acad Sci U S A ; 117(39): 24224-24233, 2020 09 29.
Artículo en Inglés | MEDLINE | ID: mdl-32929027

RESUMEN

Fatty acid synthases (FASs) and polyketide synthases (PKSs) iteratively elongate and often reduce two-carbon ketide units in de novo fatty acid and polyketide biosynthesis. Cycles of chain extensions in FAS and PKS are initiated by an acyltransferase (AT), which loads monomer units onto acyl carrier proteins (ACPs), small, flexible proteins that shuttle covalently linked intermediates between catalytic partners. Formation of productive ACP-AT interactions is required for catalysis and specificity within primary and secondary FAS and PKS pathways. Here, we use the Escherichia coli FAS AT, FabD, and its cognate ACP, AcpP, to interrogate type II FAS ACP-AT interactions. We utilize a covalent crosslinking probe to trap transient interactions between AcpP and FabD to elucidate the X-ray crystal structure of a type II ACP-AT complex. Our structural data are supported using a combination of mutational, crosslinking, and kinetic analyses, and long-timescale molecular dynamics (MD) simulations. Together, these complementary approaches reveal key catalytic features of FAS ACP-AT interactions. These mechanistic inferences suggest that AcpP adopts multiple, productive conformations at the AT binding interface, allowing the complex to sustain high transacylation rates. Furthermore, MD simulations support rigid body subdomain motions within the FabD structure that may play a key role in AT activity and substrate selectivity.


Asunto(s)
Proteína Transportadora de Acilo/metabolismo , S-Maloniltransferasa de la Proteína Transportadora de Grupos Acilo/metabolismo , Dominio Catalítico , Proteínas de Escherichia coli/metabolismo , Acido Graso Sintasa Tipo II/metabolismo , Cristalografía por Rayos X
14.
Sci Rep ; 10(1): 12715, 2020 07 29.
Artículo en Inglés | MEDLINE | ID: mdl-32728162

RESUMEN

Hypospadias is a common birth defect where the urethral opening forms on the ventral side of the penis. We performed integrative methylomic, genomic, and transcriptomic analyses to characterize sites of DNA methylation that influence genital development. In case-control and case-only epigenome-wide association studies (EWAS) of preputial tissue we identified 25 CpGs associated with hypospadias characteristics and used one-sample two stage least squares Mendelian randomization (2SLS MR) to show a causal relationship for 21 of the CpGs. The largest difference was 15.7% lower beta-value at cg14436889 among hypospadias cases than controls (EWAS P = 5.4e-7) and is likely causal (2SLS MR P = 9.8e-15). Integrative annotation using two-sample Mendelian randomization of these methylation regions highlight potentially causal roles of genes involved in germ layer differentiation (WDHD1, DNM1L, TULP3), beta-catenin signaling (PKP2, UBE2R2, TNKS), androgens (CYP4A11, CYP4A22, CYP4B1, CYP4X1, CYP4Z2P, EPHX1, CD33/SIGLEC3, SIGLEC5, SIGLEC7, KLK5, KLK7, KLK10, KLK13, KLK14), and reproductive traits (ACAA1, PLCD1, EFCAB4B, GMCL1, MKRN2, DNM1L, TEAD4, TSPAN9, KLK family). This study identified CpGs that remained differentially methylated after urogenital development and used the most relevant tissue sample available to study hypospadias. We identified multiple methylation sites and candidate genes that can be further evaluated for their roles in regulating urogenital development.


Asunto(s)
Metilación de ADN , Perfilación de la Expresión Génica/métodos , Redes Reguladoras de Genes , Hipospadias/genética , Estudios de Casos y Controles , Islas de CpG , Epigénesis Genética , Regulación de la Expresión Génica , Estudio de Asociación del Genoma Completo , Humanos , Lactante , Masculino
15.
Nat Commun ; 11(1): 1727, 2020 04 07.
Artículo en Inglés | MEDLINE | ID: mdl-32265440

RESUMEN

Carbon-carbon bond forming reactions are essential transformations in natural product biosynthesis. During de novo fatty acid and polyketide biosynthesis, ß-ketoacyl-acyl carrier protein (ACP) synthases (KS), catalyze this process via a decarboxylative Claisen-like condensation reaction. KSs must recognize multiple chemically distinct ACPs and choreograph a ping-pong mechanism, often in an iterative fashion. Here, we report crystal structures of substrate mimetic bearing ACPs in complex with the elongating KSs from Escherichia coli, FabF and FabB, in order to better understand the stereochemical features governing substrate discrimination by KSs. Complemented by molecular dynamics (MD) simulations and mutagenesis studies, these structures reveal conformational states accessed during KS catalysis. These data taken together support a gating mechanism that regulates acyl-ACP binding and substrate delivery to the KS active site. Two active site loops undergo large conformational excursions during this dynamic gating mechanism and are likely evolutionarily conserved features in elongating KSs.


Asunto(s)
3-Oxoacil-(Proteína Transportadora de Acil) Sintasa/química , Acetiltransferasas/química , Proteínas de Escherichia coli/química , Escherichia coli/química , Acido Graso Sintasa Tipo II/química , 3-Oxoacil-(Proteína Transportadora de Acil) Sintasa/aislamiento & purificación , 3-Oxoacil-(Proteína Transportadora de Acil) Sintasa/metabolismo , Acetiltransferasas/metabolismo , Secuencia de Aminoácidos/genética , Sitios de Unión/genética , Catálisis , Dominio Catalítico/genética , Cristalografía por Rayos X , Escherichia coli/enzimología , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Acido Graso Sintasa Tipo II/metabolismo , Enlace de Hidrógeno , Interacciones Hidrofóbicas e Hidrofílicas , Modelos Moleculares , Simulación de Dinámica Molecular , Mutagénesis , Mutación , Conformación Proteica , Proteínas Recombinantes
16.
Birth Defects Res ; 111(13): 932-937, 2019 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-31102501

RESUMEN

BACKGROUND: Recent genome-wide association studies of hypospadias have implicated the role of genetic variants in or near the diacylglycerol kinase kappa (DGKK) gene. However, these variants are largely identified among samples of mild and moderate hypospadias cases. Therefore, we evaluated previously identified DGKK variants among second- and third-degree hypospadias cases and controls recruited in Arkansas, a state characterized by a high birth prevalence of hypospadias. METHODS: Second- and third-degree hypospadias non-Hispanic white cases (n = 36 and n = 9, respectively) and controls (n = 45) were recruited at Arkansas Children's Hospital. Preputial tissue was collected on cases and controls between 2013 and 2017. Cases and controls were genotyped using the Illumina Infinium Global Screening Array. We used logistic regression models to assess the association of genotyped and imputed genetic variants mapped to the DGKK region with second- and third-degree hypospadias. RESULTS: All families self-reported as non-Hispanic white and genetic principal component analyses did not demonstrate evidence of population stratification. Five DGKK variants previously reported as associated with hypospadias were identified in the genotype data. None of the variants were associated with second- or third-degree hypospadias (range of odds ratios = 0.7-0.9, all p > .05). CONCLUSIONS: In our analyses, genetic variation in DGKK does not play a role in the development of moderate and severe hypospadias. Our findings provide support to the etiologic heterogeneity of hypospadias by all classifications of severity.


Asunto(s)
Diacilglicerol Quinasa/genética , Hipospadias/genética , Adulto , Arkansas/epidemiología , Estudios de Casos y Controles , Diacilglicerol Quinasa/metabolismo , Femenino , Predisposición Genética a la Enfermedad/genética , Variación Genética/genética , Estudio de Asociación del Genoma Completo/métodos , Genotipo , Humanos , Hipospadias/metabolismo , Lactante , Masculino , Oportunidad Relativa , Polimorfismo de Nucleótido Simple/genética , Factores de Riesgo , Población Blanca/genética
17.
Angew Chem Int Ed Engl ; 58(32): 10888-10892, 2019 08 05.
Artículo en Inglés | MEDLINE | ID: mdl-31140212

RESUMEN

At the center of many complex biosynthetic pathways, the acyl carrier protein (ACP) shuttles substrates to appropriate enzymatic partners to produce fatty acids and polyketides. Carrier proteins covalently tether their cargo via a thioester linkage to a phosphopantetheine cofactor. Due to the labile nature of this linkage, chemoenzymatic methods have been developed that involve replacement of the thioester with a more stable amide or ester bond. We explored the importance of the thioester bond to the structure of the carrier protein by using solution NMR spectroscopy and molecular dynamics simulations. Remarkably, the replacement of sulfur with other heteroatoms results in significant structural changes, thus suggesting more rigorous selections of isosteric substitutes is needed.


Asunto(s)
Proteínas Portadoras/química , Ésteres/química , Compuestos de Sulfhidrilo/química , Enlace de Hidrógeno , Espectroscopía de Resonancia Magnética , Simulación de Dinámica Molecular , Estructura Molecular
18.
J Am Chem Soc ; 141(17): 6995-7004, 2019 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-30907087

RESUMEN

In the course of a total synthesis effort directed toward the natural product curcusone C, the Stoltz group discovered an unexpected thermal rearrangement of a divinylcyclopropane to the product of a formal Cope/1,3-sigmatropic shift sequence. Since the involvement of a thermally forbidden 1,3-shift seemed unlikely, theoretical studies involving two approaches, the "trial-and-error" testing of various conceivable mechanisms (Houk group) and an "automatic" approach using the Maeda-Morokuma AFIR method (Morokuma group) were applied to explore the mechanism. Eventually, both approaches converged on a cascade mechanism shown to have some partial literature precedent: Cope rearrangement/1,5-sigmatropic silyl shift/Claisen rearrangement/retro-Claisen rearrangement/1,5-sigmatropic silyl shift, comprising a quintet of five sequential thermally allowed pericyclic rearrangements.


Asunto(s)
Diterpenos/síntesis química , Modelos Químicos , Algoritmos , Teoría Funcional de la Densidad , Isomerismo
19.
Proc Natl Acad Sci U S A ; 116(14): 6775-6783, 2019 04 02.
Artículo en Inglés | MEDLINE | ID: mdl-30872475

RESUMEN

Fatty acid biosynthesis in α- and γ-proteobacteria requires two functionally distinct dehydratases, FabA and FabZ. Here, mechanistic cross-linking facilitates the structural characterization of a stable hexameric complex of six Escherichia coli FabZ dehydratase subunits with six AcpP acyl carrier proteins. The crystal structure sheds light on the divergent substrate selectivity of FabA and FabZ by revealing distinct architectures of the binding pocket. Molecular dynamics simulations demonstrate differential biasing of substrate orientations and conformations within the active sites of FabA and FabZ such that FabZ is preorganized to catalyze only dehydration, while FabA is primed for both dehydration and isomerization.


Asunto(s)
Proteína Transportadora de Acilo/química , Proteínas de Escherichia coli/química , Escherichia coli/química , Acido Graso Sintasa Tipo II/química , Ácidos Grasos/química , Hidroliasas/química , Simulación de Dinámica Molecular , Complejos Multienzimáticos/química , Proteína Transportadora de Acilo/genética , Proteína Transportadora de Acilo/metabolismo , Catálisis , Cristalografía por Rayos X , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Acido Graso Sintasa Tipo II/genética , Acido Graso Sintasa Tipo II/metabolismo , Ácidos Grasos/biosíntesis , Ácidos Grasos/genética , Hidroliasas/genética , Hidroliasas/metabolismo , Complejos Multienzimáticos/genética , Complejos Multienzimáticos/metabolismo
20.
Can J Urol ; 26(1): 9675-9679, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30797251

RESUMEN

INTRODUCTION: 2-octyl cyanoacrylate (OC) has been shown to be a viable option for usage following standard circumcision but data on its utilization following hypospadias repair is limited. Both OC and a standard waterproof transparent dressing (WD) are used following hypospadias repair at our children's hospital. Our hypothesis is that patients with distal hypospadias repair using OC for surgical dressing have similar outcomes as compared to patients with WD. MATERIALS AND METHODS: A retrospective study was performed evaluating all patients with distal hypospadias repair during a 2 year period. OC was primarily used by one of the three physicians in the practice with the other two primarily used WD for surgical dressing. The primary endpoints evaluated include hematoma requiring surgical drainage, infection, meatal stenosis, urethrocutaneous fistula, dehiscence, and diverticulum. Standard follow up after hypospadias repair includes a 1 week follow up for patients requiring urethral stent removal and reevaluation for all patients 3-4 months after surgery. REDCap was used in order to compile the database used in this study. RESULTS: A total of 280 patients underwent distal hypospadias repair during this interval. One hundred twenty-two patients had OC used with 3 (2.4%) having complications: 2 fistulas and 1 with both meatal stenosis and fistula. One hundred fifty-eight patients were dressed with WD with 5 (3.2%) complications: 4 fistulas and 1 meatal stenosis. No patients had hematoma, wound dehiscence, diverticulum, or infection. CONCLUSION: A low rate of complication was observed following distal hypospadias repair using both 2-octyl cyanoacrylate and a standard waterproof transparent dressing. 2-octyl cyanoacrylate is a safe option for surgical dressing following distal hypospadias repair but its utilization in this setting is surgeon dependent.


Asunto(s)
Vendajes , Cianoacrilatos , Hipospadias/cirugía , Humanos , Hipospadias/patología , Lactante , Masculino , Complicaciones Posoperatorias/epidemiología , Estudios Retrospectivos , Procedimientos Quirúrgicos Urológicos Masculinos/métodos
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