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1.
Mol Neurobiol ; 59(11): 6754-6770, 2022 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-36002781

RESUMEN

Impairments in mitochondrial physiology play a role in the progression of multiple neurodegenerative conditions, including peripheral neuropathy in diabetes. Blockade of muscarinic acetylcholine type 1 receptor (M1R) with specific/selective antagonists prevented mitochondrial dysfunction and reversed nerve degeneration in in vitro and in vivo models of peripheral neuropathy. Specifically, in type 1 and type 2 models of diabetes, inhibition of M1R using pirenzepine or muscarinic toxin 7 (MT7) induced AMP-activated protein kinase (AMPK) activity in dorsal root ganglia (DRG) and prevented sensory abnormalities and distal nerve fiber loss. The human neuroblastoma SH-SY5Y cell line has been extensively used as an in vitro model system to study mechanisms of neurodegeneration in DRG neurons and other neuronal sub-types. Here, we tested the hypothesis that pirenzepine or MT7 enhance AMPK activity and via this pathway augment mitochondrial function in SH-SY5Y cells. M1R expression was confirmed by utilizing a fluorescent dye, ATTO590-labeled MT7, that exhibits great specificity for this receptor. M1R antagonist treatment in SH-SY5Y culture increased AMPK phosphorylation and mitochondrial protein expression (OXPHOS). Mitochondrial membrane potential (MMP) was augmented in pirenzepine and MT7 treated cultured SH-SY5Y cells and DRG neurons. Compound C or AMPK-specific siRNA suppressed pirenzepine or MT7-induced elevation of OXPHOS expression and MMP. Moreover, muscarinic antagonists induced hyperpolarization by activating the M-current and, thus, suppressed neuronal excitability. These results reveal that negative regulation of this M1R-dependent pathway could represent a potential therapeutic target to elevate AMPK activity, enhance mitochondrial function, suppress neuropathic pain, and enhance nerve repair in peripheral neuropathy.


Asunto(s)
Neuroblastoma , Enfermedades del Sistema Nervioso Periférico , Proteínas Quinasas Activadas por AMP/metabolismo , Acetilcolina , Transporte de Electrón , Colorantes Fluorescentes , Humanos , Potencial de la Membrana Mitocondrial , Proteínas Mitocondriales/metabolismo , Antagonistas Muscarínicos/farmacología , Neuronas/metabolismo , Pirenzepina/farmacología , ARN Interferente Pequeño/metabolismo , Receptores Muscarínicos/metabolismo
2.
Sci Rep ; 10(1): 18415, 2020 10 28.
Artículo en Inglés | MEDLINE | ID: mdl-33116243

RESUMEN

The gastrointestinal tract transmits feeding-regulatory signals to the brain via neuronal and hormonal pathways. Here we studied the interaction between the orexigenic gastric peptide, ghrelin, and the anorectic intestinal peptide, glucagon-like peptide 1 (GLP-1), in terms of feeding regulation via the vagal afferents. GLP-1 preadministration 30 min before ghrelin administration to rats and mice abolished ghrelin-induced food intake, while ghrelin preadministration abolished the anorectic effect of GLP-1. Ghrelin preadministration suppressed GLP-1-induced Fos expression in the nodose ganglia (NG). Electrophysiological assessment confirmed that the initially administered peptide abolished the vagal afferent electrical alteration induced by the subsequently administered peptide. Both the growth hormone secretagogue receptor (GHSR) and the GLP-1 receptor (GLP-1R) are co-localised in a major proportion of NG neurons that innervate the stomach. In these Ghsr+Glp1r+ neurons, ghrelin preadministration abolished the GLP-1-induced calcium response. Ghrelin generated a hyperpolarising current and GLP-1 generated a depolarising current in isolated NG neurons in a patch-clamp experiment. Ghrelin and GLP-1 potently influenced each other in terms of vagally mediated feeding regulation. This peptidergic interaction allows for fine control of the electrophysiological properties of NG neurons.


Asunto(s)
Vías Aferentes/fisiología , Regulación del Apetito , Ghrelina/fisiología , Péptido 1 Similar al Glucagón/fisiología , Ganglio Nudoso/fisiología , Animales , Calcio/metabolismo , Receptor del Péptido 1 Similar al Glucagón/fisiología , Masculino , Ratones Endogámicos C57BL , Ratas Wistar , Receptores de Ghrelina/metabolismo
3.
Anim Reprod Sci ; 212: 106237, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31864500

RESUMEN

The study aim was to estimate gestational age (GA), expected parturition date (EPD) and growth rate by determining fetal trunk diameter (TD). Effects of fetal-dam pelvis alignment and in utero fetal position at time of ultrasonography (UG) on fetal numbers and sex determination were also studied. Trans-abdominal UG (3-6.5 MHz) was conducted on 37 ewes with known breeding dates from Days 25-120 of pregnancy. Errors in GA and EPD were studied using an equation in the same ewes at their successive breeding when date of breeding was unknown. There were four equations, Y = 1.28861X+32.656 (R2 = 0.92), for Indigenous; Y = 1.2603X+38.075 (R2 = 0.85), for Indigenous × Garole; and Y = 0.8932X+45.916 (R²â€¯= 0.99), for Garole fetuses; and the equation, Y = 1.3565X + 32.604 (R2 = 0.94), independent of breed were computed to estimate GA and the relationship between GA and TD of different breeds. The error in estimated GA and EPD using these four equations was determined and there was comparison with the data collected using US and the previously described equations. Results indicate there was the greatest (P <  0.01) error for GA and EPD values using the US TD equation for all breeds. There was the least error in estimated EPD using the breed specific equations. Error in the sex determination was 4.8 % and fetal number determination was 16.7 % with singleton and 7.7 % twin fetuses. The results indicate there is a breed specific fetal TD that is useful for predicting GA in sheep.


Asunto(s)
Desarrollo Fetal/genética , Edad Gestacional , Ovinos/embriología , Ovinos/genética , Ultrasonografía Prenatal/veterinaria , Animales , Femenino , Embarazo
4.
J Mol Endocrinol ; 60(2): 109-118, 2018 02.
Artículo en Inglés | MEDLINE | ID: mdl-29233861

RESUMEN

High-fat diet (HFD)-induced metabolic inflammation in the central and peripheral organs contributes to the pathogenesis of obesity. Long-term HFD blunts signaling by ghrelin, a gastric-derived orexigenic peptide, in the vagal afferent nerve via a mechanism involving in situ activation of inflammation. This study was undertaken to investigate whether ghrelin resistance is associated with progressive development of metabolic inflammation. In mice, ghrelin's orexigenic activity was abolished 2-4 weeks after the commencement of HFD (60% of energy from fat), consistent with the timing of accumulation and activation of macrophages and microglia in the nodose ganglion and hypothalamus. Calorie-restricted weight loss after 12-week HFD feeding restored ghrelin responsiveness and alleviated the upregulation of macrophage/microglia activation markers and inflammatory cytokines. HSP72, a chaperone protein, was upregulated in the hypothalamus of HFD-fed mice, potentially contributing to prevention of irreversible neuron damage. These results demonstrate that ghrelin resistance is reversible following reversal of the HFD-induced inflammation and obesity phenotypes.


Asunto(s)
Ghrelina/farmacología , Inflamación/metabolismo , Pérdida de Peso , Animales , Biomarcadores/metabolismo , Restricción Calórica , Dieta Alta en Grasa , Ingestión de Alimentos/efectos de los fármacos , Metabolismo Energético/efectos de los fármacos , Regulación de la Expresión Génica/efectos de los fármacos , Inflamación/genética , Inflamación/patología , Macrófagos/efectos de los fármacos , Macrófagos/metabolismo , Masculino , Ratones Endogámicos C57BL , ARN Mensajero/genética , ARN Mensajero/metabolismo , Receptores de Ghrelina/genética , Receptores de Ghrelina/metabolismo , Pérdida de Peso/efectos de los fármacos
5.
Accid Anal Prev ; 110: 52-61, 2018 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-29101789

RESUMEN

Melbourne, Australia has the largest tram/streetcar network in the world including the largest mixed traffic tram operating environment. Therefore, Melbourne tram drivers are responsible for controlling one of the heaviest vehicles on road ranging from shared tram lanes to exclusive tram lanes. In addition to different tram lane configurations, tram drivers need to follow different traffic signal phases at intersections including tram priority signals as well as need to serve passengers at various types of closely spaced tram stops. Despite all these challenges, no research has explored tram driver perceptions of the risk factors on different tram route road design configurations. Therefore, the aim of this study is to investigate how tram drivers' safety perceptions alter along various tram route sections, signal settings and stop configurations. A tram driver focus group approach was adopted for this research involving thirty tram drivers (4 female and 26 male drivers). The tram drivers' age ranged from 29 to 63 years, with an average age of 47.6 years (standard deviation of 10.1 years), and their experience of tram driving ranged from 1.17 to 31 years, with an average experience of 12.5 years (standard deviation of 10.2 years). The participating tram drivers perceived that the raised tram tracks and tramways with raised yellow curbing beside tracks are safer lane priority features on the Melbourne tram network compared to full-time, part-time and mixed traffic tram lanes. They regarded 'hook turns' as a safe form of tram signal priority treatment at intersections and platform tram stops as the safest tram stop design for all passengers among all other tram stop designs in Melbourne. Findings of this research could enhance the understanding of crash risk factors for different tram route features and thus can offer effective planning strategies for transit agencies to improve tram road safety.


Asunto(s)
Accidentes de Tránsito/prevención & control , Conducción de Automóvil , Planificación Ambiental , Vehículos a Motor , Seguridad , Adulto , Australia , Femenino , Grupos Focales , Humanos , Masculino , Persona de Mediana Edad , Factores de Riesgo
6.
Eur J Pharmacol ; 794: 37-44, 2017 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-27876617

RESUMEN

Chronic inflammation in systemic organs, such as adipose tissue, nodose ganglion, hypothalamus, and skeletal muscles, is closely associated with obesity and diabetes mellitus. Because sodium glucose cotransporter 2 (SGLT2) inhibitors exert both anti-diabetic and anti-obesity effects by promoting urinary excretion of glucose and subsequent caloric loss, we investigated the effect of canagliflozin, an SGLT2 inhibitor, on obesity-induced inflammation in neural tissues and skeletal muscles of mice. High-fat diet (HFD)-fed male C57BL/6J mice were treated with canagliflozin for 8 weeks. Canagliflozin attenuated the HFD-mediated increases in body weight, liver weight, and visceral and subcutaneous fat weight. Additionally, canagliflozin decreased blood glucose as well as the fat, triglyceride, and glycogen contents of the liver. Along with these metabolic corrections, canagliflozin attenuated the increases in the mRNA levels of the proinflammatory biomarkers Iba1 and Il6 and the number of macrophages/microglia in the nodose ganglion and hypothalamus. In the skeletal muscle of HFD-fed obese mice, canagliflozin decreased inflammatory cytokine levels, macrophage accumulation, and the mRNA level of the specific atrophic factor atrogin-1. Canagliflozin also increased the mRNA level of insulin-like growth factor 1, protected against muscle mass loss, and restored the contractile force of muscle. These findings suggested that SGLT2 inhibition disrupts the vicious cycle of obesity and inflammation, not only by promoting caloric loss, but also by suppression of obesity-related inflammation in both the nervous system and skeletal muscle.


Asunto(s)
Canagliflozina/farmacología , Hipotálamo/efectos de los fármacos , Músculo Esquelético/efectos de los fármacos , Ganglio Nudoso/efectos de los fármacos , Obesidad/tratamiento farmacológico , Inhibidores del Cotransportador de Sodio-Glucosa 2 , Tejido Adiposo Blanco/efectos de los fármacos , Tejido Adiposo Blanco/patología , Animales , Metabolismo Basal/efectos de los fármacos , Canagliflozina/uso terapéutico , Dieta Alta en Grasa/efectos adversos , Hipotálamo/metabolismo , Hipotálamo/fisiopatología , Inflamación/complicaciones , Hígado/efectos de los fármacos , Hígado/patología , Masculino , Ratones , Ratones Endogámicos C57BL , Contracción Muscular/efectos de los fármacos , Músculo Esquelético/fisiopatología , Ganglio Nudoso/metabolismo , Ganglio Nudoso/fisiopatología , Obesidad/inducido químicamente , Obesidad/metabolismo , Obesidad/patología , Transducción de Señal/efectos de los fármacos
7.
Accid Anal Prev ; 94: 238-44, 2016 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-27352035

RESUMEN

Previous research is limited regarding factors influencing tram-involved serious injury crashes. The aim of this study is to identify key vehicle, road, environment and driver related factors associated with tram-involved serious injury crashes. Using a binary logistic regression modelling approach, the following factors were identified to be significant in influencing tram-involved fatal crashes in Melbourne: tram floor height, tram age, season, traffic volume, tram lane priority and tram travel speed. Low floor trams, older trams, tram priority lanes and higher tram travelling speeds are more likely to increase tram-involved fatal crashes. Higher traffic volume decreases the likelihood of serious crashes. Fatal crashes are more likely to occur during spring and summer. Findings from this study may offer ideas for future research in the area of tram safety and help to develop countermeasures to prevent specific fatality types from occurring.


Asunto(s)
Accidentes/estadística & datos numéricos , Vías Férreas/estadística & datos numéricos , Heridas y Lesiones/etiología , Accidentes/mortalidad , Adulto , Anciano , Anciano de 80 o más Años , Humanos , Modelos Logísticos , Persona de Mediana Edad , Factores de Riesgo , Seguridad , Índices de Gravedad del Trauma , Victoria/epidemiología , Heridas y Lesiones/mortalidad
8.
Accid Anal Prev ; 92: 15-21, 2016 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-27035395

RESUMEN

Safety is a key concern in the design, operation and development of light rail systems including trams or streetcars as they impose crash risks on road users in terms of crash frequency and severity. The aim of this study is to identify key traffic, transit and route factors that influence tram-involved crash frequencies along tram route sections in Melbourne. A random effects negative binomial (RENB) regression model was developed to analyze crash frequency data obtained from Yarra Trams, the tram operator in Melbourne. The RENB modelling approach can account for spatial and temporal variations within observation groups in panel count data structures by assuming that group specific effects are randomly distributed across locations. The results identify many significant factors effecting tram-involved crash frequency including tram service frequency (2.71), tram stop spacing (-0.42), tram route section length (0.31), tram signal priority (-0.25), general traffic volume (0.18), tram lane priority (-0.15) and ratio of platform tram stops (-0.09). Findings provide useful insights on route section level tram-involved crashes in an urban tram or streetcar operating environment. The method described represents a useful planning tool for transit agencies hoping to improve safety performance.


Asunto(s)
Accidentes de Tránsito/estadística & datos numéricos , Planificación Ambiental/estadística & datos numéricos , Australia , Humanos , Modelos Estadísticos , Vehículos a Motor , Vías Férreas , Seguridad
9.
Accid Anal Prev ; 86: 1-8, 2016 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-26476596

RESUMEN

Tram stops in mixed traffic environments present a variety of safety, accessibility and transport efficiency challenges. In Melbourne, Australia the hundred year-old electric tram system is progressively being modernized to improve passenger accessibility. Platform stops, incorporating raised platforms for level entry into low floor trams, are being retro-fitted system-wide to replace older design stops. The aim of this study was to investigate the safety impacts of platform stops over older design stops (i.e. Melbourne safety zone tram stops) on pedestrians in the context of mixed traffic tram operation in Melbourne, using an advanced before-after crash analysis approach, the comparison group (CG) method. The CG method evaluates safety impacts by taking into account the general trends in safety and the unobserved factors at treatment and comparison sites that can alter the outcomes of a simple before-after analysis. The results showed that pedestrian-involved all injury crashes reduced by 43% after platform stop installation. This paper also explores a concern that the conventional CG method might underestimate safety impacts as a result of large differences in passenger stop use between treatment and comparison sites, suggesting differences in crash risk exposure. To adjust for this, a modified analysis explored crash rates (crash counts per 10,000 stop passengers) for each site. The adjusted results suggested greater reductions in pedestrian-involved crashes after platform stop installation: an 81% reduction in pedestrian-involved all injury crashes and 86% reduction in pedestrian-involved FSI crashes, both are significant at the 95% level. Overall, the results suggest that platform stops have considerable safety benefits for pedestrians. Implications for policy and areas for future research are explored.


Asunto(s)
Accidentes de Tránsito/prevención & control , Peatones , Vías Férreas/normas , Seguridad , Accidentes de Tránsito/estadística & datos numéricos , Australia , Humanos , Peatones/estadística & datos numéricos , Vías Férreas/métodos
10.
Traffic Inj Prev ; 17(1): 91-7, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-25837409

RESUMEN

OBJECTIVE: Streetcars/tram systems are growing worldwide, and many are given priority to increase speed and reliability performance in mixed traffic conditions. Research related to the road safety impact of tram priority is limited. This study explores the road safety impacts of tram priority measures including lane and intersection/signal priority measures. METHOD: A before-after crash study was conducted using the empirical Bayes (EB) method to provide more accurate crash impact estimates by accounting for wider crash trends and regression to the mean effects. Before-after crash data for 29 intersections with tram signal priority and 23 arterials with tram lane priority in Melbourne, Australia, were analyzed to evaluate the road safety impact of tram priority. RESULTS: The EB before-after analysis results indicated a statistically significant adjusted crash reduction rate of 16.4% after implementation of tram priority measures. Signal priority measures were found to reduce crashes by 13.9% and lane priority by 19.4%. A disaggregate level simple before-after analysis indicated reductions in total and serious crashes as well as vehicle-, pedestrian-, and motorcycle-involved crashes. In addition, reductions in on-path crashes, pedestrian-involved crashes, and collisions among vehicles moving in the same and opposite directions and all other specific crash types were found after tram priority implementation. CONCLUSIONS: Results suggest that streetcar/tram priority measures result in safety benefits for all road users, including vehicles, pedestrians, and cyclists. Policy implications and areas for future research are discussed.


Asunto(s)
Accidentes de Tránsito/prevención & control , Teorema de Bayes , Vehículos a Motor , Seguridad , Accidentes de Tránsito/estadística & datos numéricos , Australia , Humanos , Motocicletas , Peatones , Reproducibilidad de los Resultados
11.
Biochem Biophys Res Commun ; 464(4): 1157-1162, 2015 Sep 04.
Artículo en Inglés | MEDLINE | ID: mdl-26208455

RESUMEN

A high-fat diet (HFD) induces inflammation in systemic organs including the hypothalamus, resulting in obesity and diabetes. The vagus nerve connects the visceral organs and central nervous system, and the gastric-derived orexigenic peptide ghrelin transmits its starvation signals to the hypothalamus via the vagal afferent nerve. Here we investigated the inflammatory response in vagal afferent neurons and the hypothalamus in mice following one day of HFD feeding. This treatment increased the number of macrophages/microglia in the nodose ganglion and hypothalamus. Furthermore, one-day HFD induced expression of Toll-like receptor 4 in the goblet cells of the colon and upregulated mRNA expressions of the proinflammatory biomarkers Emr1, Iba1, Il6, and Tnfα in the nodose ganglion and hypothalamus. Both subcutaneous administration of ghrelin and celiac vagotomy reduced HFD-induced inflammation in these tissues. HFD intake triggered inflammatory responses in the gut, nodose ganglion, and subsequently in the hypothalamus within 24 h. These findings suggest that the vagal afferent nerve may transfer gut-derived inflammatory signals to the hypothalamus via the nodose ganglion, and that ghrelin may protect against HFD-induced inflammation.


Asunto(s)
Dieta Alta en Grasa/efectos adversos , Encefalitis/inmunología , Ghrelina/inmunología , Hipotálamo/inmunología , Ganglio Nudoso/inmunología , Enfermedades del Nervio Vago/inmunología , Animales , Encefalitis/etiología , Encefalitis/patología , Hipotálamo/patología , Masculino , Ratones , Ratones Endogámicos C57BL , Ganglio Nudoso/patología , Enfermedades del Nervio Vago/etiología , Enfermedades del Nervio Vago/patología
12.
J Endocrinol ; 226(1): 81-92, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-26016745

RESUMEN

Ghrelin, a stomach-derived orexigenic peptide, transmits starvation signals to the hypothalamus via the vagus afferent nerve. Peripheral administration of ghrelin does not induce food intake in high fat diet (HFD)-induced obese mice. We investigated whether this ghrelin resistance was caused by dysfunction of the vagus afferent pathway. Administration (s.c.) of ghrelin did not induce food intake, suppression of oxygen consumption, electrical activity of the vagal afferent nerve, phosphorylation of ERK2 and AMP-activated protein kinase alpha in the nodose ganglion, or Fos expression in hypothalamic arcuate nucleus of mice fed a HFD for 12 weeks. Administration of anti-ghrelin IgG did not induce suppression of food intake in HFD-fed mice. Expression levels of ghrelin receptor mRNA in the nodose ganglion and hypothalamus of HFD-fed mice were reduced. Inflammatory responses, including upregulation of macrophage/microglia markers and inflammatory cytokines, occurred in the nodose ganglion and hypothalamus of HFD-fed mice. A HFD blunted ghrelin signaling in the nodose ganglion via a mechanism involving in situ activation of inflammation. These results indicate that ghrelin resistance in the obese state may be caused by dysregulation of ghrelin signaling via the vagal afferent.


Asunto(s)
Dieta Alta en Grasa/efectos adversos , Ghrelina/fisiología , Obesidad/etiología , Obesidad/fisiopatología , Proteínas Quinasas Activadas por AMP/metabolismo , Animales , Ingestión de Alimentos/efectos de los fármacos , Ingestión de Alimentos/fisiología , Ghrelina/administración & dosificación , Ghrelina/sangre , Hipotálamo/fisiopatología , Inflamación/etiología , Inflamación/genética , Inflamación/fisiopatología , Leptina/administración & dosificación , Leptina/fisiología , Sistema de Señalización de MAP Quinasas/efectos de los fármacos , Masculino , Ratones , Ratones Endogámicos C57BL , Ganglio Nudoso/fisiopatología , Obesidad/genética , Fosforilación , Proteínas Proto-Oncogénicas c-fos/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Receptores de Ghrelina/genética , Transducción de Señal
13.
Biochem Biophys Res Commun ; 428(4): 512-7, 2012 Nov 30.
Artículo en Inglés | MEDLINE | ID: mdl-23111332

RESUMEN

Neuroendocrine regulatory peptide (NERP)-2, recently identified as a bioactive peptide involved in vasopressin secretion and feeding regulation in the central nervous system, is abundantly expressed in endocrine cells in peripheral tissues. To explore the physiological roles of NERP-2 in the pancreas, we examined its effects on insulin secretion. NERP-2 increased glucose-stimulated insulin secretion (GSIS) in a dose-dependent manner, with a lowest effective dose of 10(-7) M, from the pancreatic ß-cell line MIN6 and isolated mouse pancreatic islets. NERP-2 did not affect insulin secretion under the low-glucose conditions. Neither NERP-1 nor NERP-2-Gly (nonamidated NERP-2) stimulated insulin secretion. NERP-2 significantly augmented GSIS after intravenous administration to anesthetized rats or intraperitoneal injection to conscious mice. We detected NERP-2 in pancreatic islets, where it co-localized extensively with insulin. Calcium-imaging analysis demonstrated that NERP-2 increased the calcium influx in MIN6 cells. These findings reveal that NERP-2 regulates GSIS by elevating intracellular calcium concentrations.


Asunto(s)
Glucosa/metabolismo , Células Secretoras de Insulina/metabolismo , Insulina/metabolismo , Proteínas del Tejido Nervioso/fisiología , Neuropéptidos/fisiología , Animales , Línea Celular Tumoral , Glucosa/farmacología , Secreción de Insulina , Células Secretoras de Insulina/efectos de los fármacos , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Factores de Crecimiento Nervioso , Proteínas del Tejido Nervioso/genética , Proteínas del Tejido Nervioso/farmacología , Neuropéptidos/genética , Neuropéptidos/farmacología , Ratas , Ratas Wistar
14.
BMC Bioinformatics ; 12: 353, 2011 Aug 25.
Artículo en Inglés | MEDLINE | ID: mdl-21867510

RESUMEN

BACKGROUND: Many Bioinformatics studies begin with a multiple sequence alignment as the foundation for their research. This is because multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence structure relationships. RESULTS: In this paper, we have proposed a Vertical Decomposition with Genetic Algorithm (VDGA) for Multiple Sequence Alignment (MSA). In VDGA, we divide the sequences vertically into two or more subsequences, and then solve them individually using a guide tree approach. Finally, we combine all the subsequences to generate a new multiple sequence alignment. This technique is applied on the solutions of the initial generation and of each child generation within VDGA. We have used two mechanisms to generate an initial population in this research: the first mechanism is to generate guide trees with randomly selected sequences and the second is shuffling the sequences inside such trees. Two different genetic operators have been implemented with VDGA. To test the performance of our algorithm, we have compared it with existing well-known methods, namely PRRP, CLUSTALX, DIALIGN, HMMT, SB_PIMA, ML_PIMA, MULTALIGN, and PILEUP8, and also other methods, based on Genetic Algorithms (GA), such as SAGA, MSA-GA and RBT-GA, by solving a number of benchmark datasets from BAliBase 2.0. CONCLUSIONS: The experimental results showed that the VDGA with three vertical divisions was the most successful variant for most of the test cases in comparison to other divisions considered with VDGA. The experimental results also confirmed that VDGA outperformed the other methods considered in this research.


Asunto(s)
Alineación de Secuencia/métodos , Análisis de Secuencia de ADN/métodos , Algoritmos , Secuencia de Bases , Niño , Biología Computacional/métodos , Evolución Molecular , Humanos
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