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1.
Int J Mol Sci ; 24(6)2023 Mar 22.
Artículo en Inglés | MEDLINE | ID: mdl-36983040

RESUMEN

Persistent inflammation can trigger altered epigenetic, inflammatory, and bioenergetic states. Inflammatory bowel disease (IBD) is an idiopathic disease characterized by chronic inflammation of the gastrointestinal tract, with evidence of subsequent metabolic syndrome disorder. Studies have demonstrated that as many as 42% of patients with ulcerative colitis (UC) who are found to have high-grade dysplasia, either already had colorectal cancer (CRC) or develop it within a short time. The presence of low-grade dysplasia is also predictive of CRC. Many signaling pathways are shared among IBD and CRC, including cell survival, cell proliferation, angiogenesis, and inflammatory signaling pathways. Current IBD therapeutics target a small subset of molecular drivers of IBD, with many focused on the inflammatory aspect of the pathways. Thus, there is a great need to identify biomarkers of both IBD and CRC, that can be predictive of therapeutic efficacy, disease severity, and predisposition to CRC. In this study, we explored the changes in biomarkers specific for inflammatory, metabolic, and proliferative pathways, to help determine the relevance to both IBD and CRC. Our analysis demonstrated, for the first time in IBD, the loss of the tumor suppressor protein Ras associated family protein 1A (RASSF1A), via epigenetic changes, the hyperactivation of the obligate kinase of the NOD2 pathogen recognition receptor (receptor interacting protein kinase 2 [RIPK2]), the loss of activation of the metabolic kinase, AMP activated protein kinase (AMPKα1), and, lastly, the activation of the transcription factor and kinase Yes associated protein (YAP) kinase, that is involved in proliferation of cells. The expression and activation status of these four elements are mirrored in IBD, CRC, and IBD-CRC patients and, importantly, in matched blood and biopsy samples. The latter would suggest that biomarker analysis can be performed non-invasively, to understand IBD and CRC, without the need for invasive and costly endoscopic analysis. This study, for the first time, illustrates the need to understand IBD or CRC beyond an inflammatory perspective and the value of therapeutics directed to reset altered proliferative and metabolic states within the colon. The use of such therapeutics may truly drive patients into remission.


Asunto(s)
Colitis Ulcerosa , Neoplasias Colorrectales , Enfermedades Inflamatorias del Intestino , Humanos , Neoplasias Colorrectales/patología , Enfermedades Inflamatorias del Intestino/patología , Inflamación , Biomarcadores , Hiperplasia , Factores de Riesgo
2.
Dig Dis Sci ; 66(11): 3985-3992, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-33184796

RESUMEN

BACKGROUND AND AIMS: While there is recent literature to support the discontinuation of 5-aminosalicylate (5-ASA) upon the initiation of biologics, continuing 5-ASA after treatment failure is relatively common. We aimed to assess the impact of concomitant 5-ASA therapy on clinical outcomes in ulcerative colitis (UC) patients escalated to infliximab. METHODS: This is a retrospective chart review of patients with moderate-to-severe UC started on infliximab between January 2012 and December 2017 at the University of Alberta. The primary outcome was clinical remission (partial Mayo score < 2) at 6 and 12 months. Secondary outcomes included endoscopic (endoscopic Mayo < 2) and deep remission (combined clinical and endoscopic remission) as well as the need for rescue therapy, hospitalization or colectomy. Univariate and multivariate logistic regression models were used to estimate the odds ratios and 95% CI for the outcomes. RESULTS: One hundred and twenty-one patients were followed over a period of 47 (SD = 34) months. Patients on 5-ASA had increased concomitant immunomodulator use (73.3% vs. 54.1%, p = 0.03). There was no difference in clinical remission at 6 (aOR 2.59, p = 0.07) or 12 months (aOR 0.43, p = 0.06). At 12 months, patients on concomitant 5-ASA were less likely to achieve endoscopic (aOR 0.08, p = 0.01) and deep remission (aOR 0.07, p = 0.02). Adverse outcomes such as need for rescue therapy, hospitalization, and colectomy did not differ between the groups. CONCLUSIONS: Our data suggest that 5-ASA may be stopped in patients with moderate-to-severe UC who have been escalated to infliximab therapy as it has no additional benefit to control inflammation.


Asunto(s)
Colitis Ulcerosa/tratamiento farmacológico , Infliximab/administración & dosificación , Infliximab/uso terapéutico , Mesalamina/administración & dosificación , Mesalamina/uso terapéutico , Adulto , Antiinflamatorios no Esteroideos/administración & dosificación , Antiinflamatorios no Esteroideos/uso terapéutico , Estudios de Cohortes , Quimioterapia Combinada , Femenino , Fármacos Gastrointestinales/administración & dosificación , Fármacos Gastrointestinales/uso terapéutico , Humanos , Masculino , Mesalamina/efectos adversos , Persona de Mediana Edad , Inducción de Remisión , Estudios Retrospectivos , Adulto Joven
3.
J Am Chem Soc ; 135(49): 18458-68, 2013 Dec 11.
Artículo en Inglés | MEDLINE | ID: mdl-24199651

RESUMEN

The dynamic properties of the capsid of the human papillomavirus (HPV) type 16 were examined using classical molecular dynamics simulations. By systematically comparing the structural fluctuations of the capsid protein, a strong dynamic allosteric connection between the epitope containing loops and the h4 helix located more than 50 Å away is identified, which was not recognized thus far. Computer simulations show that restricting the structural fluctuations of the h4 helix is key to rigidifying the epitopes, which is thought to be required for eliciting a proper immune response. The allostery identified in the components of the HPV is nonclassical because the mean structure of the epitope carrying loops remains unchanged, but as a result of allosteric effect the structural fluctuations are altered significantly, which in turn changes the biochemical reactivity profile of the epitopes. Exploiting this novel insight, a new vaccine design strategy is proposed wherein a relatively small virus capsid fragment is deposited on a silica nanoparticle in such a way that the fluctuations of the h4 helix are suppressed. The structural and dynamic properties of the epitope carrying loops on this hybrid nanoparticle match the characteristics of epitopes found on the full virus-like particle precisely, suggesting that these nanoparticles may serve as potent, cost-effective, and safe alternatives to traditionally developed vaccines. The structural and dynamic properties of the hybrid nanoparticle are examined in detail to establish the general concepts of the proposed new design.


Asunto(s)
Epítopos/inmunología , Papillomaviridae/inmunología , Vacunas contra Papillomavirus/administración & dosificación , Vacunas Virales/inmunología , Regulación Alostérica , Vacuna Tetravalente Recombinante contra el Virus del Papiloma Humano Tipos 6, 11 , 16, 18 , Humanos , Vacunas Virales/administración & dosificación
4.
Ren Fail ; 35(1): 49-55, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23078600

RESUMEN

BACKGROUND: Gastrointestinal complications are frequent in patients with renal disease and are responsible for substantial morbidity and mortality among these patients in developing countries. Many times, these patients are subjected to endoscopic evaluation and mucosal biopsies are taken for definitive diagnosis. This study explores the various upper and lower nonneoplastic gastrointestinal complications in patients with chronic kidney disease (CKD) and the role of endoscopic mucosal biopsies in the management of these patients. METHODS: Sixty-three patients with CKD, who were referred to endoscopic evaluation and biopsy due to significant gastrointestinal symptoms between January 2007 and December 2011 form the study group. Patients were divided into two groups: group 1 and group 2. Group 1 consisted of patients with CKD stages 1-5 and group 2 consisted of renal allograft recipients. All biopsies were reviewed by an experienced pathologist. Clinical data were collected from patient's medical records. RESULTS: There were 38 patients in group 1 and 25 patients in group 2. Twenty-nine out of 38 patients in group 1 presented with upper gastrointestinal (GI) symptoms and underwent esophagogastroduodenoscopy (OGD) evaluation, which showed erosive gastritis as the most common biopsy finding followed by ulcerative esophagitis and duodenitis. These patients were also found to be susceptible to develop ischemic colitis due to hypotensive episodes during dialysis, which are likely to occur during the initial stages of dialysis. The most frequent symptom in group 2 was chronic diarrhea (13 out of 25 patients) for which a colonoscopic examination was done which revealed various infection and drug-related colitis, mycophenolate mofetil (MMF) being a major culprit. CONCLUSION: CKD patients with high urea level are prone to develop upper GI symptoms and mostly show erosive gastritis, ulcerative esophagitis, and duodenitis on biopsy. On the contrary, renal allograft recipients mostly develop opportunistic infections and drug-related toxicity in the colon. MMF-related GI toxicity is an underrecognized entity and further prospective studies are required for its better understanding.


Asunto(s)
Enfermedades Gastrointestinales/etiología , Insuficiencia Renal Crónica/complicaciones , Centros de Atención Terciaria , Adulto , Anciano , Biopsia , Endoscopía Gastrointestinal , Femenino , Estudios de Seguimiento , Enfermedades Gastrointestinales/diagnóstico , Enfermedades Gastrointestinales/epidemiología , Humanos , India/epidemiología , Mucosa Intestinal/patología , Masculino , Persona de Mediana Edad , Morbilidad/tendencias , Pronóstico , Insuficiencia Renal Crónica/terapia , Estudios Retrospectivos , Factores de Riesgo , Tasa de Supervivencia/tendencias , Factores de Tiempo , Adulto Joven
5.
Inflamm Bowel Dis ; 28(7): 1045-1052, 2022 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-34525186

RESUMEN

INTRODUCTION: Active disease in inflammatory bowel disease patients during pregnancy is associated with poor maternal and fetal outcomes. Objective evaluation of disease activity is a core strategy in IBD, and during pregnancy noninvasive modalities are preferred. We aimed to evaluate feasibility and accuracy of intestinal ultrasound (IUS) to objectify disease activity throughout pregnancy. METHODS: Pregnant patients with known IBD were included and followed throughout pregnancy for clinical disease activity, with fecal calprotectin (FCP) and with IUS every trimester. Feasibility of IUS was assessed for all colonic segments and terminal ileum (TI). Intestinal ultrasound outcomes to detect active disease and treatment response were compared with clinical scores combined with FCP. RESULTS: In total, 38 patients (22 CD, 16 UC) were included, with 27 patients having serial IUS. Feasibility of IUS decreases significantly in third trimester for TI (first vs third trimester: 91.3% vs 21.7%, P < .0001) and sigmoid (first vs third trimester: 95.6% vs 69.5%, P = .023). Intestinal ultrasound activity showed moderate to strong correlation with clinical activity (r = 0.60, P < .0001) and FCP (r = 0.73, P < .0001). Throughout pregnancy, IUS distinguished active from quiescent disease with 84% sensitivity and 98% specificity according to FCP combined with clinical activity. IUS showed disease activity in >1 segment in 52% of patients and detected treatment response with 80% sensitivity and 92% specificity. CONCLUSIONS: IUS is feasible and accurate throughout pregnancy, although visualization of the sigmoid and TI decreases in the third trimester. IUS provides objective information on disease activity, extent, and treatment response, even during second and third trimester, and offers a noninvasive strategy to closely monitor patients during pregnancy.


Asunto(s)
Enfermedades Inflamatorias del Intestino , Heces , Femenino , Humanos , Enfermedades Inflamatorias del Intestino/diagnóstico por imagen , Intestinos/diagnóstico por imagen , Complejo de Antígeno L1 de Leucocito , Embarazo , Ultrasonografía
6.
Proc Natl Acad Sci U S A ; 105(41): 15743-8, 2008 Oct 14.
Artículo en Inglés | MEDLINE | ID: mdl-18840679

RESUMEN

Tubulin heterodimers are the building blocks of microtubules, a major component of the cytoskeleton, whose mechanical properties are fundamental for the life of the cell. We uncover the microscopic origins of the mechanical response in microtubules by probing features of the energy landscape of the tubulin monomers and tubulin heterodimer. To elucidate the structures of the unfolding pathways and reveal the multiple unfolding routes, we performed simulations of a self-organized polymer (SOP) model of tubulin. The SOP representation, which is a coarse-grained description of chains, allows us to perform force-induced simulations at loading rates and time scales that closely match those used in single-molecule experiments. We show that the forced unfolding of each monomer involves a bifurcation in the pathways to the stretched state. After the unfolding of the C-term domain, the unraveling continues either from the N-term domain or from the middle domain, depending on the monomer and the pathway. In contrast to the unfolding complexity of the monomers, the dimer unfolds according to only one route corresponding to the unraveling of the C-term domain and part of the middle domain of beta-tubulin. We find that this surprising behavior is due to the viscoelastic properties of the interface between the monomers. We map precise features of the complex energy landscape of tubulin by surveying the structures of the various metastable intermediates, which, in the dimer case, are characterized only by changes in the beta-tubulin monomer.


Asunto(s)
Simulación por Computador , Tubulina (Proteína)/ultraestructura , Dimerización , Modelos Moleculares , Desnaturalización Proteica , Pliegue de Proteína , Tubulina (Proteína)/química
7.
Hepatol Forum ; 2(1): 34-35, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-35782887

RESUMEN

A 63-year-old teetotaller male, previously treated for hepatitis C-related compensated cirrhosis, presented with acute-onset encephalopathy with no focal neurological deficit and stable vitals. Investigations revealed elevated serum creatinine (2.94 mg/dL), hypercalcemia, hypophosphatemia, and high serum PTH levels. He was diagnosed with right parathyroid adenoma (1.3×1.2×0.7 cm) with the help of a neck ultrasound. His encephalopathy and renal failure persisted despite adequate IV fluids, calcitonin, and bisphosphonates. Urgent hemi-parathyroidectomy was performed on day four, following which he recovered completely.

8.
J Clin Transl Hepatol ; 9(6): 878-888, 2021 Dec 28.
Artículo en Inglés | MEDLINE | ID: mdl-34966651

RESUMEN

BACKGROUND AND AIMS: The impact of coronavirus disease-2019 (COVID-19) on liver function remains to be fully elucidated. This study was designed to investigate such and determine the clinical significance in determining mortality risk. METHODS: A retrospective study was conducted in patients with COVID-19 from March 2020 to July 2020. Clinical details were retrieved from electronic medical records to obtain clinical characteristics, medical history, laboratory tests, therapeutic intervention, and outcome data. RESULTS: A total of 184 patients with COVID-19 were included (median age: 45.5 years), comprised of 62.5% men. In total, 22 (12.0%) patients had severe infection and 162 (88.0%) had mild to moderate infection. Overall, 95 (51.6%) showed abnormal liver function test (LFT) and 17 (9.2%) showed normal LFT at admission. The median age, hospital stay, and LFT were significantly higher in severe vs. non-severe infection (p<0.001). Out of 12 deaths, the majority were due to severe infection (n=11). Deaths were also due to acute respiratory distress syndrome (n=5), cardiac reasons (n=3), and sepsis with multiorgan failure (n=3). The median age, hospital stay and number of intensive care unit admissions were higher in patients having abnormal LFT compared to normal LFT. Incidence of elevated aspartate aminotransferase (42.8% and 40.4%), alanine transaminase (43.7% and 41.6%), and hypoalbuminemia (71.4% and72.7%) at admission and discharge were more common in severe infection. The mean survival was significantly lower in severe infection compared to those with non-severe disease (17.2 vs. 52.3 days; p<0.001). CONCLUSIONS: Incidence of abnormal liver function was higher in patients with severe COVID-19 and was associated with prolonged hospital stay; mortality was associated with severity of COVID-19. For ruling out the risk of liver injury, it is crucial to vigilantly monitor the liver function parameters in patients with COVID-19 admitted to hospital.

9.
Biophys J ; 98(4): 657-66, 2010 Feb 17.
Artículo en Inglés | MEDLINE | ID: mdl-20159162

RESUMEN

Decomposition of the intrinsic dynamics of proteins into collective motions among distant regions of the protein structure provides a physically appealing approach that couples the dynamics of the system with its functional role. The cellular functions of microtubules (an essential component of the cytoskeleton in all eukaryotic cells) depend on their dynamic instability, which is altered by various factors among which applied forces are central. To shed light on the coupling between forces and the dynamic instability of microtubules, we focus on the investigation of the response of the microtubule subunits (tubulin) to applied forces. We address this point by adapting an approach designed to survey correlations for the equilibrium dynamics of proteins to the case of correlations for proteins forced-dynamics. The resulting collective motions in tubulin have a number of functional implications, such as the identification of long-range couplings with a role in blocking the dynamic instability of microtubules. A fundamental implication of our study for the life of a cell is that, to increase the likelihood of unraveling of large cytoskeletal filaments under physiological forces, molecular motors must use a combination of pulling and torsion rather than just pulling.


Asunto(s)
Movimiento , Tubulina (Proteína)/química , Tubulina (Proteína)/metabolismo , Fenómenos Biomecánicos , Análisis por Conglomerados , Modelos Moleculares , Desnaturalización Proteica , Multimerización de Proteína , Estructura Cuaternaria de Proteína , Estructura Terciaria de Proteína , Rotación
10.
Hepatol Forum ; 1(3): 109-111, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-35949722

RESUMEN

A common practice among young athletes and body-builders is the adoption, use, and self-administration of androgenic anabolic steroid commonly referred to as AASs. Prime classification of these anabolic steroids is either testosterone or synthetic testosterone derivatives. They are primarily used for performance and endurance enhancement. However, the use of steroids is not without adverse effects. Steroid-induced liver diseases may range from chronic hepatitis to vascular or bile ductular injury and death. Presented herein is a case of Vanishing Bile Duct Syndrome due to the anabolic steroid consumption by a young, healthy male.

11.
Proteins ; 76(1): 30-46, 2009 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-19089975

RESUMEN

Hyaluronan lyase (Hyal) is a surface enzyme occurring in many bacterial organisms including members of Streptococcus species. Streptococcal Hyal primarily degrades hyaluronan-substrate (HA) of the extracellular matrix. This degradation appears to facilitate the spread of this bacterium throughout host tissues. Unlike purely endolytic degradation of its other substrates, unsulfated chondroitin or some chondroitin sulfates, the degradation of HA by Hyal proceeds by processive exolytic cleavage of one disaccharide at a time following an initial endolytic cut. Molecular dynamics (MD) studies of Hyal from Streptococcus pneumoniae are presented that address the enzyme's molecular mechanism of action and the role of domain motions for processive functionality. The analysis of extensive sub-microsecond MD simulations of this enzyme action on HA-substrates of different lengths and the connection between the domain dynamics of Hyal and the translocation of the HA-substrate reveals that opening/closing and twisting domain motions of the Hyal are intimately linked to processive HA degradation. Enforced simulations confirmed this finding as the domain motions in SpnHyal were found to be induced by enforced substrate translocation. These results establish the dynamic interplay between Hyal flexibility and substrate translocation and provide insight into the processive mechanism of Hyal.


Asunto(s)
Ácido Hialurónico/metabolismo , Polisacárido Liasas/metabolismo , Streptococcus pneumoniae/enzimología , Simulación por Computador , Ácido Hialurónico/química , Modelos Moleculares , Polisacárido Liasas/química , Estructura Terciaria de Proteína , Termodinámica
13.
J Mol Biol ; 358(4): 1165-78, 2006 May 12.
Artículo en Inglés | MEDLINE | ID: mdl-16569416

RESUMEN

Streptococcus pneumoniae hyaluronan lyase is a surface enzyme of this Gram-positive bacterium. The enzyme degrades several biologically important, information-rich linear polymeric glycans: hyaluronan, unsulfated chondroitin, and some chondroitin sulfates. This degradation facilitates spreading of bacteria throughout the host tissues and presumably provides energy and a carbon source for pneumococcal cells. Its beta-elimination catalytic mechanism is an acid/base process termed proton acceptance and donation leading to cleavage of beta-1,4 linkages of the substrates. The degradation of hyaluronan occurs in two stages, initial endolytic cuts are followed by processive exolytic cleavage of one disaccharide at a time. In contrast, the degradation of chondroitins is purely endolytic. Structural studies together with flexibility analyses of two streptococcal enzymes, from S.pneumoniae and Streptococcus agalactiae, allowed for insights into this enzyme's molecular mechanism. Here, two new X-ray crystal structures of the pneumococcal enzyme in novel conformations are reported. These new conformations, complemented by molecular dynamics simulation results, directly confirm the predicted domain motions presumed to facilitate the processive degradative process. One of these new structures resembles the S.agalactiae enzyme conformation, and provides evidence of a uniform mechanistic/dynamic behavior of this protein across different bacteria.


Asunto(s)
Polisacárido Liasas/química , Streptococcus pneumoniae/enzimología , Dominio Catalítico , Cristalografía por Rayos X , Modelos Moleculares , Polisacárido Liasas/metabolismo , Conformación Proteica , Especificidad de la Especie , Streptococcus agalactiae/enzimología , Termodinámica
14.
J Grad Med Educ ; 6(2): 338-40, 2014 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-24949144

RESUMEN

BACKGROUND: The recruitment of skilled candidates into internal medicine residency programs has relied on traditional interviewing techniques with varying degrees of success. The development of simulated medical technology has provided a new arena in which to assess candidates' clinical skills, knowledge base, situational awareness, and problem-solving dexterities within a standardized environment for educational and assessment purposes. OBJECTIVE: The purpose of this study was to investigate the interest of program candidates in incorporating simulation medicine into the internal medicine residency interview process. METHODS: As a prospective, survey-based analysis, potential candidates who completed an interview between October 2012 and January 2013 with an accredited internal medicine residency program were sent a postmatch survey that incorporated 3 additional questions relating to their prior experience with medical simulation and their views on incorporating the technology into the interview format. RESULTS: Of the 88 candidates who completed an interview, 92% (n  =  81) were scheduled to graduate medical school in 2013 and were graduates of a US medical school. All survey responders described previous experience with medical simulation. Fifty-eight percent (n  =  51) of responders described being "less likely" to interview with or join a residency program if they were required to participate in a 10-minute medical simulation during the interview process. CONCLUSIONS: The results of this study suggest that despite the increasing role of technology in medical education, its role in high-stakes evaluations (such as residency interviews) requires further maturation before general acceptance by residency candidates can be expected.

15.
Indian J Gastroenterol ; 33(5): 458-65, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25138788

RESUMEN

INTRODUCTION: Prophylactic antibiotics are used frequently for acute pancreatitis (AP). Consensus guidelines do not recommend this currently, based on moderate quality evidence. In this study, we aimed to evaluate the antibiotic use pattern in AP in India and propose a risk-directed approach to antibiotic use in AP. MATERIAL AND METHODS: This multicenter study was conducted from 1 May 2013 to 31 July 2013. Eleven participants from eight tertiary centers completed a questionnaire that captured patient demographics, etiology, admission status, presence of (peri)pancreatic necrosis, severity of pancreatitis, details of antibiotic use, and clinical outcomes (total hospital stay, persistent organ failure, need for ICU, total days in ICU, development of infections, in-hospital mortality). RESULTS: A total of 200 proformas were analyzed. Seventy-three (36.5 %) had acute necrotizing pancreatitis (ANP). Eighty-nine (44.5 %), 52 (26 %), and 55 (27.5 %) patients had mild AP (MAP), moderately severe AP (MSAP), and severe AP (SAP), respectively. Forty-five (22.5 %) patients developed infections (unifocal 29; multifocal 16). One hundred thirty-four (67 %) patients received antibiotics, of which 89 (66.4 %) received prophylactic, while 45 (33.6 %) received therapeutic antibiotics. The distribution of antibiotic use according to the severity of AP was 43 (48.3 %) in patients with MAP (prophylactic in 41; therapeutic in 2), 36 (69.2 %) in patients with MSAP (prophylactic in 29; therapeutic in 7), and 55 (100 %) in patients with SAP (prophylactic in 19; therapeutic in 36). Therapeutic antibiotics were prescribed based on culture and sensitivity in 21 (46.7 %) patients. CONCLUSIONS: Despite nonrecommendation, prophylactic antibiotics are used frequently in AP. We emphasize on the need for multicenter randomized controlled trials on prophylactic antibiotics for AP based on a risk-directed approach, rather than a "blanket approach."


Asunto(s)
Antibacterianos/administración & dosificación , Profilaxis Antibiótica/estadística & datos numéricos , Estudios Multicéntricos como Asunto , Pancreatitis Aguda Necrotizante/tratamiento farmacológico , Ensayos Clínicos Controlados Aleatorios como Asunto , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Niño , Contraindicaciones , Femenino , Humanos , India/epidemiología , Masculino , Persona de Mediana Edad , Pancreatitis Aguda Necrotizante/epidemiología , Pancreatitis Aguda Necrotizante/prevención & control , Riesgo , Índice de Severidad de la Enfermedad , Encuestas y Cuestionarios , Adulto Joven
16.
Vaccine ; 31(42): 4841-7, 2013 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-23933338

RESUMEN

Developing antiviral vaccines is increasingly challenging due to associated time and cost of production as well as emerging drug-resistant strains. A computer-aided vaccine design strategy is presented that could greatly accelerate the discovery process and yield vaccines with high immunogenicity and thermal stability. Our strategy is based on foreign viral epitopes engineered onto well-established virus-like particles (VLPs) and demonstrates that such constructs present similar affinity for antibodies as does a native virus. This binding affinity serves as one molecular metric of immunogenicity. As a demonstration, we engineered a preS1 epitope of hepatitis B virus (HBV) onto the EF loop of human papillomavirus VLP (HPV-VLP). HBV-associated HzKR127 antibody displayed binding affinity for this structure at distances and strengths similar to those for the complex of the antibody with the full HBV (PDBID: 2EH8). This antibody binding affinity assessment, along with other molecular immunogenicity metrics, could be a key component of a computer-aided vaccine design strategy.


Asunto(s)
Anticuerpos Antivirales/inmunología , Epítopos/inmunología , Vacunas de Partículas Similares a Virus/genética , Vacunas de Partículas Similares a Virus/inmunología , Vacunas Virales/genética , Vacunas Virales/inmunología , Biología Computacional/métodos , Descubrimiento de Drogas/métodos , Epítopos/genética , Virus de la Hepatitis B/genética , Virus de la Hepatitis B/inmunología , Humanos , Papillomaviridae/genética , Papillomaviridae/inmunología , Vacunas Sintéticas/genética , Vacunas Sintéticas/inmunología
17.
J Phys Chem B ; 116(29): 8423-34, 2012 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-22356532

RESUMEN

Coarse-grained features of macromolecular assemblies are understood via a set of order parameters (OPs) constructed in terms of their all-atom configuration. OPs are shown to be slowly changing in time and capture the large-scale spatial features of macromolecular assemblies. The relationship of these variables to the classic notion of OPs based on symmetry breaking phase transitions is discussed. OPs based on space warping transformations are analyzed in detail as they naturally provide a connection between overall structure of an assembly and all-atom configuration. These OPs serve as the basis of a multiscale analysis that yields Langevin equations for OP dynamics. In this context, the characteristics of OPs and PCA modes are compared. The OPs enable efficient all-atom multiscale simulations of the dynamics of macromolecular assemblies in response to changes in microenvironmental conditions, as demonstrated on the structural transitions of cowpea chlorotic mottle virus capsid (CCMV) and RNA of the satellite tobacco mosaic virus (STMV).


Asunto(s)
Bromovirus/química , Cápside/química , Sustancias Macromoleculares/química , Simulación de Dinámica Molecular , ARN Viral/química , Virus Satélite del Mosaico del Tabaco/química , Ambiente
18.
Prog Biophys Mol Biol ; 107(1): 200-17, 2011 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-21802438

RESUMEN

A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin.


Asunto(s)
Simulación de Dinámica Molecular , Virus/química , Virus/metabolismo , Proteínas de la Cápside/química , Proteínas de la Cápside/metabolismo , Epítopos/inmunología , Conformación Proteica , ARN Viral/química , ARN Viral/metabolismo , Programas Informáticos , Termodinámica , Virus/genética , Virus/inmunología
19.
Vaccine ; 29(51): 9423-30, 2011 Nov 28.
Artículo en Inglés | MEDLINE | ID: mdl-22027487

RESUMEN

Immunogenicity varies between the human papillomavirus (HPV) L1 monomer assemblies of various sizes (e.g., monomers, pentamers or whole capsids). The hypothesis that this can be attributed to the intensity of fluctuations of important loops containing neutralizing epitopes for the various assemblies is proposed for HPV L1 assemblies. Molecular dynamics simulations were utilized to begin testing this hypothesis. Fluctuations of loops that contain critical neutralizing epitopes (especially FG loop) were quantified via root-mean-square fluctuation and features in the frequency spectrum of dynamic changes in loop conformation. If this fluctuation-immunogenicity hypothesis is a universal aspect of immunogenicity (i.e., immune system recognition of an epitope within a loop is more reliable when it is presented via a more stable delivery structure), then fluctuation measures can serve as one predictor of immunogenicity as part of a computer-aided vaccine design strategy.


Asunto(s)
Proteínas de la Cápside/química , Proteínas de la Cápside/inmunología , Papillomavirus Humano 16/inmunología , Simulación de Dinámica Molecular , Proteínas Oncogénicas Virales/química , Proteínas Oncogénicas Virales/inmunología , Anticuerpos Antivirales/inmunología , Cápside/inmunología , Epítopos , Femenino , Humanos , Modelos Moleculares , Pruebas de Neutralización , Vacunas contra Papillomavirus , Conformación Proteica , Estructura Terciaria de Proteína , Neoplasias del Cuello Uterino/prevención & control
20.
J Phys Chem A ; 111(37): 9111-21, 2007 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-17722897

RESUMEN

The influence of a uniform static external electric field on some aliphatic and aromatic molecular species is studied within the density functional theory (DFT) employing the 6-311++G(2d,2p) basis set with B3LYP exchange-correlation prescription. The electric field perturbs the molecular geometry but drastically alters the dipole moments and engenders, to a varying degree, the molecular vibrational Stark effect, i.e., shifts in the infrared (IR) vibrational frequencies accompanied by spectral intensity redistribution. For polar molecules, significant negative ("red") and positive ("blue") frequency shifts are observed for field orientations both parallel and antiparallel to their permanent dipole moments. Further, a selective reordering of frontier orbitals is observed to be brought about by moderately intense fields. In particular, molecules having a lowest unoccupied molecular orbital (LUMO) with predominant pi character possess a threshold field beyond which energy gap between the highest occupied molecular orbital (HOMO) and LUMO diminishes rapidly. A time-dependent (TD) DFT analysis reveals that an increase in the applied field strength by and large increases the excitation energies corresponding to significant electronic transitions among frontier MOs with a concomitant decrease in their oscillator strengths.

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