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1.
Proc Natl Acad Sci U S A ; 119(34): e2204435119, 2022 08 23.
Artículo en Inglés | MEDLINE | ID: mdl-35972964

RESUMEN

To assess the conventional treatment in evolutionary inference of alignment gaps as missing data, we propose a simple nonparametric test of the null hypothesis that the locations of alignment gaps are independent of the nucleotide substitution or amino acid replacement process. When we apply the test to 1,390 protein alignments that are informed by protein tertiary structure and use a 5% significance level, the null hypothesis of independence between amino acid replacement and gap location is rejected for ∼65% of datasets. Via simulations that include substitution and insertion-deletion, we show that the test performs well with true alignments. When we simulate according to the null hypothesis and then apply the test to optimal alignments that are inferred by each of four widely used software packages, the null hypothesis is rejected too frequently. Via further simulations and analyses, we show that the overly frequent rejections of the null hypothesis are not solely due to weaknesses of widely used software for finding optimal alignments. Instead, our evidence suggests that optimal alignments are unrepresentative of true alignments and that biased evolutionary inferences may result from relying upon individual optimal alignments.


Asunto(s)
Aminoácidos , Nucleótidos , Proteínas , Algoritmos , Sustitución de Aminoácidos , Aminoácidos/genética , Nucleótidos/genética , Proteínas/genética , Alineación de Secuencia , Programas Informáticos
2.
Syst Biol ; 71(3): 630-648, 2022 04 19.
Artículo en Inglés | MEDLINE | ID: mdl-34469581

RESUMEN

Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the effective sequence length (ESL) of an aligned data set. The ESL can differ from the actual number of columns in a sequence alignment because of the presence of alignment gaps. Furthermore, the estimation of phylogenetic information is affected by model misspecification. Inevitably, the actual process of molecular evolution differs from the probabilistic models employed to describe this process. This disparity means the amount of phylogenetic information in an actual sequence alignment will differ from the amount in a simulated data set of equal size, which motivated us to develop a new test for model adequacy. Via theory and empirical data analysis, we show how to disentangle the effects of gaps and model misspecification. By comparing the Fisher information of actual and simulated sequences, we identify which alignment sites and tree branches are most affected by gaps and model misspecification. [Fisher information; gaps; insertion; deletion; indel; model adequacy; goodness-of-fit test; sequence alignment.].


Asunto(s)
Evolución Molecular , Mutación INDEL , Modelos Genéticos , Modelos Estadísticos , Filogenia , Alineación de Secuencia
3.
Syst Biol ; 67(4): 616-632, 2018 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-29309694

RESUMEN

When inferring phylogenies, one important decision is whether and how nucleotide substitution parameters should be shared across different subsets or partitions of the data. One sort of partitioning error occurs when heterogeneous subsets are mistakenly lumped together and treated as if they share parameter values. The opposite kind of error is mistakenly treating homogeneous subsets as if they result from distinct sets of parameters. Lumping and splitting errors are not equally bad. Lumping errors can yield parameter estimates that do not accurately reflect any of the subsets that were combined whereas splitting errors yield estimates that did not benefit from sharing information across partitions. Phylogenetic partitioning decisions are often made by applying information criteria such as the Akaike information criterion (AIC). As with other information criteria, the AIC evaluates a model or partition scheme by combining the maximum log-likelihood value with a penalty that depends on the number of parameters being estimated. For the purpose of selecting an optimal partitioning scheme, we derive an adjustment to the AIC that we refer to as the AIC$^{(p)}$ and that is motivated by the idea that splitting errors are less serious than lumping errors. We also introduce a similar adjustment to the Bayesian information criterion (BIC) that we refer to as the BIC$^{(p)}$. Via simulation and empirical data analysis, we contrast AIC and BIC behavior to our suggested adjustments. We discuss these results and also emphasize why we expect the probability of lumping errors with the AIC$^{(p)}$ and the BIC$^{(p)}$ to be relatively robust to model parameterization.


Asunto(s)
Biología Computacional/métodos , Filogenia , Teorema de Bayes , Modelos Biológicos , Modelos Genéticos
4.
Cells ; 12(20)2023 10 23.
Artículo en Inglés | MEDLINE | ID: mdl-37887348

RESUMEN

The mTOR signaling pathway integrates signaling inputs from nutrients, including glucose and amino acids, which are precisely regulated by transporters depending on nutrient levels. The L-type amino acid transporter 1 (LAT1) affects the activity of mTORC1 through upstream regulators that sense intracellular amino acid levels. While mTORC1 activation by LAT1 has been thoroughly investigated in cultured cells, the effects of LAT1 expression on the activity of mTORC2 has scarcely been studied. Here, we provide evidence that LAT1 recruits and activates mTORC2 on the lysosome for PMA-induced cell migration. LAT1 is translocated to the lysosomes in cells treated with PMA in a dose- and time-dependent manner. Lysosomal LAT1 interacted with mTORC2 through a direct interaction with Rictor, leading to the lysosomal localization of mTORC2. Furthermore, the depletion of LAT1 reduced PMA-induced cell migration in a wound-healing assay. Consistent with these results, the LAT1 N3KR mutant, which is defective in PMA-induced endocytosis and lysosomal localization, did not induce mTORC2 recruitment to the lysosome, with the activation of mTORC2 determined via Akt phosphorylation or the LAT1-mediated promotion of cell migration. Taken together, lysosomal LAT1 recruits and activates the mTORC2 complex and downstream Akt for PMA-mediated cell migration. These results provide insights into the development of therapeutic drugs targeting the LAT1 amino acid transporter to block metastasis, as well as disease progression in various types of cancer.


Asunto(s)
Transportador de Aminoácidos Neutros Grandes 1 , Lisosomas , Proteínas Proto-Oncogénicas c-akt , Movimiento Celular/fisiología , Lisosomas/metabolismo , Diana Mecanicista del Complejo 1 de la Rapamicina , Diana Mecanicista del Complejo 2 de la Rapamicina/metabolismo , Proteínas Proto-Oncogénicas c-akt/metabolismo , Transportador de Aminoácidos Neutros Grandes 1/metabolismo
5.
Mol Phylogenet Evol ; 62(1): 329-45, 2012 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-22040765

RESUMEN

The phylum Cnidaria is comprised of remarkably diverse and ecologically significant taxa, such as the reef-forming corals, and occupies a basal position in metazoan evolution. The origin of this phylum and the most recent common ancestors (MRCAs) of its modern classes remain mostly unknown, although scattered fossil evidence provides some insights on this topic. Here, we investigate the molecular divergence times of the major taxonomic groups of Cnidaria (27 Hexacorallia, 16 Octocorallia, and 5 Medusozoa) on the basis of mitochondrial DNA sequences of 13 protein-coding genes. For this analysis, the complete mitochondrial genomes of seven octocoral and two scyphozoan species were newly sequenced and combined with all available mitogenomic data from GenBank. Five reliable fossil dates were used to calibrate the Bayesian estimates of divergence times. The molecular evidence suggests that cnidarians originated 741 million years ago (Ma) (95% credible region of 686-819), and the major taxa diversified prior to the Cambrian (543 Ma). The Octocorallia and Scleractinia may have originated from radiations of survivors of the Permian-Triassic mass extinction, which matches their fossil record well.


Asunto(s)
Antozoos/genética , Evolución Molecular , Genes Mitocondriales , Especiación Genética , Escifozoos/genética , Animales , Antozoos/clasificación , Teorema de Bayes , Calibración , Extinción Biológica , Fósiles , Variación Genética , Genoma Mitocondrial , Funciones de Verosimilitud , Modelos Genéticos , Filogenia , ARN de Transferencia/genética , Escifozoos/clasificación
6.
Int J Biol Macromol ; 194: 347-357, 2022 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-34801583

RESUMEN

Site-specific ubiquitination can regulate the functions of Rab proteins in membrane trafficking. Previously we showed that site-specific monoubiquitination on Rab5 downregulates its function. Rab7 acts in the downstream of Rab5. Although site-specific ubiquitination of Rab7 can affect its function, it remains elusive how the ubiquitination is involved in modulation of the function of Rab7 at molecular level. Here, we report molecular basis for the regulation of Rab7 by site-specific monoubiquitination. Rab7 was predominantly monoubiquitinated at multiple sites in the membrane fraction of cultured cells. Two major ubiquitination sites (K191 and K194), identified by mutational analysis with single K mutants, were responsible for membrane localization of monoubiquitinated Rab7. Using small-angle X-ray scattering, we derived structural models of site-specifically monoubiquitinated Rab7 in solution. Structural analysis combined with molecular dynamics simulation corroborated that the ubiquitin moieties on K191 and K194 are key determinants for exclusion of Rab7 from the endosomal membrane. Ubiquitination on the two major sites apparently mitigated colocalization of Rab7 with ORF3a of SARS-CoV-2, potentially deterring the egression of SARS-CoV-2. Our results establish that the regulatory effects of a Rab protein through site-specific monoubiquitination are commonly observed among Rab GTPases while the ubiquitination sites differ in each Rab protein.


Asunto(s)
SARS-CoV-2/metabolismo , Proteínas Virales/metabolismo , Proteínas de Unión a GTP rab7/metabolismo , Células HEK293 , Células HeLa , Humanos , Unión Proteica , Ubiquitinación
7.
Taehan Yongsang Uihakhoe Chi ; 82(1): 99-115, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-36237474

RESUMEN

Various sequences have been developed for MRI to aid in the radiologic diagnosis. Among the various MR sequences, susceptibility-weighted imaging (SWI) is a high-spatial-resolution, three-dimensional gradient-echo MR sequence, which is very sensitive in detecting deoxyhemoglobin, ferritin, hemosiderin, and bone minerals through local magnetic field distortion. In this regard, SWI has been used for the diagnosis and treatment of various neurologic disorders, and the improved image quality has enabled to acquire more useful information for radiologists. Here, we explain the principle of various signals on SWI arising in neurological disorders and provide a retrospective review of many cases of clinically or pathologically proven disease or components with distinctive imaging features of various neurological diseases. Additionally, we outline a short and condensed overview of principles of SWI in relation to neurological disorders and describe various cases with characteristic imaging features on SWI. There are many different types diseases involving the brain parenchyma, and they have distinct SWI features. SWI is an effective imaging tool that provides complementary information for the diagnosis of various diseases.

8.
J Mol Evol ; 71(4): 250-67, 2010 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-20740280

RESUMEN

Species identification is one of the most important issues in biological studies. Due to recent increases in the amount of genomic information available and the development of DNA sequencing technologies, the applicability of using DNA sequences to identify species (commonly referred to as "DNA barcoding") is being tested in many areas. Several methods have been suggested to identify species using DNA sequences, including similarity scores, analysis of phylogenetic and population genetic information, and detection of species-specific sequence patterns. Although these methods have demonstrated good performance under a range of circumstances, they also have limitations, as they are subject to loss of information, require intensive computation and are sensitive to model mis-specification, and can be difficult to evaluate in terms of the significance of identification. Here, we suggest a new DNA barcoding method in which support vector machine (SVM) procedures are adopted. Our new method is nonparametric and thus is expected to be robust for a wide range of evolutionary scenarios as well as multilocus analyses. Furthermore, we describe bootstrap procedures that can be used to test the significances of species identifications. We implemented a novel conversion technique for transforming sequence data to real-valued vectors, and therefore, bootstrap procedures can be easily combined with our SVM approach. In this study, we present the results of simulation studies and empirical data analyses to demonstrate the performance of our method and discuss its properties.


Asunto(s)
Algoritmos , Código de Barras del ADN Taxonómico/métodos , ADN/clasificación , Inteligencia Artificial , Secuencia de Bases , Simulación por Computador , ADN/genética , ADN Concatenado , Sitios Genéticos/genética , Datos de Secuencia Molecular , Nucleótidos/genética , Filogenia
9.
Syst Biol ; 58(2): 199-210, 2009 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-20525578

RESUMEN

Statistical models for the evolution of molecular sequences play an important role in the study of evolutionary processes. For the evolutionary analysis of protein-coding sequences, 3 types of evolutionary models are available: 1) nucleotide, 2) amino acid, and 3) codon substitution models. Selecting appropriate models can greatly improve the estimation of phylogenies and divergence times and the detection of positive selection. Although much attention has been paid to the comparisons among the same types of models, relatively little attention has been paid to the comparisons among the different types of models. Additionally, because such models have different data structures, comparison of those models using conventional model selection criteria such as Akaike information criterion (AIC) or Bayesian information criterion (BIC) is not straightforward. Here, we suggest new procedures to convert models of the above-mentioned 3 types to 64-dimensional models with nucleotide triplet substitution. These conversion procedures render it possible to statistically compare the models of these 3 types by using AIC or BIC. By analyzing divergent and conserved interspecific mammalian sequences and intraspecific human population data, we show the superiority of the codon substitution models and discuss the advantages and disadvantages of the models of the 3 types.


Asunto(s)
Evolución Molecular , Modelos Genéticos , Modelos Estadísticos
10.
Endocrinol Metab (Seoul) ; 35(1): 142-148, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32207274

RESUMEN

BACKGROUND: This study was conducted to compare glycaemic control with insulin detemir administered according to two titration algorithms (3-0-3 and 2-4-6-8) after 20 weeks of treatment in subjects with type 2 diabetes mellitus inadequately controlled on metformin. METHODS: This was a 20-week, randomised, multicentre, open-labelled, treat-to-target trial. Forty-six patients were randomised in a 1:1 manner to either the 3-0-3 (G3, n=23) or 2-4-6-8 (G2, n=23) algorithm. The primary endpoint was change of haemoglobin A1c (HbA1c), and the secondary safety endpoint included hypoglycaemic events. RESULTS: After 20 weeks, HbA1c decreased similarly in the G3 and G2 groups, with a mean change of -0.9% from baseline. The mean change in fasting plasma glucose was numerically similar in both groups. The hypoglycaemia event rate per 100-patient-years of exposure (r) in the G2 group (r=1,427) was higher than that in the G3 group (r=807). CONCLUSION: Both treatment groups had numerically similar HbA1c reductions. A trend towards fewer hypoglycaemia episodes after dose stabilisation was seen with the simpler G3. Clinically, this may be an important observation, as a simpler titration algorithm may support self-management and maintenance of insulin therapy.


Asunto(s)
Algoritmos , Biomarcadores/análisis , Glucemia/análisis , Diabetes Mellitus Tipo 2/tratamiento farmacológico , Hipoglucemiantes/administración & dosificación , Insulina Detemir/administración & dosificación , Adulto , Anciano , Diabetes Mellitus Tipo 2/sangre , Diabetes Mellitus Tipo 2/patología , Relación Dosis-Respuesta a Droga , Esquema de Medicación , Femenino , Estudios de Seguimiento , Hemoglobina Glucada/análisis , Humanos , Masculino , Persona de Mediana Edad , Pronóstico
11.
Mol Biol Evol ; 25(5): 960-71, 2008 May.
Artículo en Inglés | MEDLINE | ID: mdl-18281270

RESUMEN

Phylogeny estimation is extremely crucial in the study of molecular evolution. The increase in the amount of available genomic data facilitates phylogeny estimation from multilocus sequence data. Although maximum likelihood and Bayesian methods are available for phylogeny reconstruction using multilocus sequence data, these methods require heavy computation, and their application is limited to the analysis of a moderate number of genes and taxa. Distance matrix methods present suitable alternatives for analyzing huge amounts of sequence data. However, the manner in which distance methods can be applied to multilocus sequence data remains unknown. Here, we suggest new procedures to estimate molecular phylogeny using multilocus sequence data and evaluate its significance in the framework of the distance method. We found that concatenation of the multilocus sequence data may result in incorrect phylogeny estimation with an extremely high bootstrap probability (BP), which is due to incorrect estimation of the distances and intentional ignorance of the intergene variations. Therefore, we suggest that the distance matrices for multilocus sequence data be estimated separately and these matrices be subsequently combined to reconstruct phylogeny instead of phylogeny reconstruction using concatenated sequence data. To calculate the BPs of the reconstructed phylogeny, we suggest that 2-stage bootstrap procedures be adopted; in this, genes are resampled followed by resampling of the sequence columns within the resampled genes. By resampling the genes during calculation of BPs, intergene variations are properly considered. Via simulation studies and empirical data analysis, we demonstrate that our 2-stage bootstrap procedures are more suitable than the conventional bootstrap procedure that is adopted after sequence concatenation.


Asunto(s)
Filogenia , Probabilidad , Animales , Simulación por Computador , Evolución Molecular , Heterogeneidad Genética , Variación Genética , Mamíferos/genética , Modelos Genéticos
12.
Am J Cancer Res ; 9(1): 94-107, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-30755814

RESUMEN

Covalent conjugations of the SUMO-1 moiety on a target protein play important roles in the regulation of cellular protein function. SUMO-conjugation of PML is a regulatory step for PML nuclear body (PML-NB) formation, and HIPK2 is SUMO-conjugated and recruited into the PML-NBs. Although HIPK2 mutations (R861W and N951I) were found in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) patients, little is known about the underlying mechanisms by which HIPK2 mutations are associated with the pathogenesis of leukemia. Here we show that HIPK2 mutants found in AML and MDS patients are defective in SUMO-interacting motif (SIM) function. Due to defective SIM function, the HIPK2 mutants were not modified with SUMO-1, and not recruited to the PML-NBs. However, the HIPK2 mutants can normally bind to and phosphorylate AML1b. Therefore, the HIPK2 mutants can sequestrate the AML1 complex out of the PML-NBs, resulting in the disruption of AML1-mediated activation of target genes for myeloid differentiation. In addition, the differentiation of K562 blast cells was impaired by the expression of the HIPK2 SIM-defective mutants. These results suggest that HIPK2 targeting into the PML-NBs via the SIMs is crucial for HIPK2-mediated induction of myeloid differentiation, and is associated with AML pathogenesis.

13.
Mol Phylogenet Evol ; 49(1): 327-42, 2008 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-18682295

RESUMEN

Identifying causes of genetic divergence is a central goal in evolutionary biology. Although rates of nucleotide substitution vary among taxa and among genes, the causes of this variation tend to be poorly understood. In the present study, we examined the rate and pattern of molecular evolution for five DNA regions over a phylogeny of Cornus, the single genus of Cornaceae. To identify evolutionary mechanisms underlying the molecular variation, we employed Bayesian methods to estimate divergence times and to infer how absolute rates of synonymous and nonsynonymous substitutions and their ratios change over time. We found that the rates vary among genes, lineages, and through time, and differences in mutation rates, selection type and intensity, and possibly genetic drift all contributed to the variation of substitution rates observed among the major lineages of Cornus. We applied independent contrast analysis to explore whether speciation rates are linked to rates of molecular evolution. The results showed no relationships for individual genes, but suggested a possible localized link between species richness and rate of nonsynonymous nucleotide substitution for the combined cpDNA regions. Furthermore, we detected a positive correlation between rates of molecular evolution and morphological change in Cornus. This was particularly pronounced in the dwarf dogwood lineage, in which genome-wide acceleration in both molecular and morphological evolution has likely occurred.


Asunto(s)
Cornus/clasificación , Cornus/genética , Evolución Molecular , Especiación Genética , Teorema de Bayes , Cloroplastos/genética , Cornus/anatomía & histología , ADN de Cloroplastos/genética , ADN de Plantas/genética , Fósiles , Genes de Plantas , Genoma del Cloroplasto , Modelos Genéticos , Nucleótidos/genética , Filogenia , Análisis de Secuencia de ADN
14.
Artículo en Inglés | WPRIM | ID: wpr-875134

RESUMEN

Various sequences have been developed for MRI to aid in the radiologic diagnosis. Among the various MR sequences, susceptibility-weighted imaging (SWI) is a high-spatial-resolution, threedimensional gradient-echo MR sequence, which is very sensitive in detecting deoxyhemoglobin, ferritin, hemosiderin, and bone minerals through local magnetic field distortion. In this regard, SWI has been used for the diagnosis and treatment of various neurologic disorders, and the improved image quality has enabled to acquire more useful information for radiologists.Here, we explain the principle of various signals on SWI arising in neurological disorders and provide a retrospective review of many cases of clinically or pathologically proven disease or components with distinctive imaging features of various neurological diseases. Additionally, we outline a short and condensed overview of principles of SWI in relation to neurological disorders and describe various cases with characteristic imaging features on SWI. There are many different types diseases involving the brain parenchyma, and they have distinct SWI features.SWI is an effective imaging tool that provides complementary information for the diagnosis of various diseases.

15.
Sci Rep ; 6: 23058, 2016 Mar 11.
Artículo en Inglés | MEDLINE | ID: mdl-26965201

RESUMEN

We have developed a method for the three-dimensional (3D) printing of continuous fiber-reinforced thermoplastics based on fused-deposition modeling. The technique enables direct 3D fabrication without the use of molds and may become the standard next-generation composite fabrication methodology. A thermoplastic filament and continuous fibers were separately supplied to the 3D printer and the fibers were impregnated with the filament within the heated nozzle of the printer immediately before printing. Polylactic acid was used as the matrix while carbon fibers, or twisted yarns of natural jute fibers, were used as the reinforcements. The thermoplastics reinforced with unidirectional jute fibers were examples of plant-sourced composites; those reinforced with unidirectional carbon fiber showed mechanical properties superior to those of both the jute-reinforced and unreinforced thermoplastics. Continuous fiber reinforcement improved the tensile strength of the printed composites relative to the values shown by conventional 3D-printed polymer-based composites.

16.
PLoS One ; 11(6): e0157032, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27309961

RESUMEN

Antarctica is considered a relatively uncontaminated region with regard to the infectious diseases because of its extreme environment, and isolated geography. For the genetic characterization and molecular epidemiology of the newly found penguin adenovirus in Antarctica, entire genome sequencing and annual survey of penguin adenovirus were conducted. The entire genome sequences of penguin adenoviruses were completed for two Chinstrap penguins (Pygoscelis antarctica) and two Gentoo penguins (Pygoscelis papua). The whole genome lengths and G+C content of penguin adenoviruses were found to be 24,630-24,662 bp and 35.5-35.6%, respectively. Notably, the presence of putative sialidase gene was not identified in penguin adenoviruses by Rapid Amplification of cDNA Ends (RACE-PCR) as well as consensus specific PCR. The penguin adenoviruses were demonstrated to be a new species within the genus Siadenovirus, with a distance of 29.9-39.3% (amino acid, 32.1-47.9%) in DNA polymerase gene, and showed the closest relationship with turkey adenovirus 3 (TAdV-3) in phylogenetic analysis. During the 2008-2013 study period, the penguin adenoviruses were annually detected in 22 of 78 penguins (28.2%), and the molecular epidemiological study of the penguin adenovirus indicates a predominant infection in Chinstrap penguin population (12/30, 40%). Interestingly, the genome of penguin adenovirus could be detected in several internal samples, except the lymph node and brain. In conclusion, an analysis of the entire adenoviral genomes from Antarctic penguins was conducted, and the penguin adenoviruses, containing unique genetic character, were identified as a new species within the genus Siadenovirus. Moreover, it was annually detected in Antarctic penguins, suggesting its circulation within the penguin population.


Asunto(s)
Infecciones por Adenoviridae/virología , Adenoviridae/patogenicidad , Epidemiología Molecular , Spheniscidae/virología , Infecciones por Adenoviridae/genética , Animales , Regiones Antárticas , Filogenia , Spheniscidae/genética
17.
Genetics ; 160(4): 1283-93, 2002 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-11973287

RESUMEN

Using pseudomaximum-likelihood approaches to phylogenetic inference and coalescent theory, we develop a computationally tractable method of estimating effective population size from serially sampled viral data. We show that the variance of the maximum-likelihood estimator of effective population size depends on the serial sampling design only because internal node times on a coalescent genealogy can be better estimated with some designs than with others. Given the internal node times and the number of sequences sampled, the variance of the maximum-likelihood estimator is independent of the serial sampling design. We then estimate the effective size of the HIV-1 population within nine hosts. If we assume that the mutation rate is 2.5 x 10(-5) substitutions/generation and is the same in all patients, estimated generation lengths vary from 0.73 to 2.43 days/generation and the mean (1.47) is similar to the generation lengths estimated by other researchers. If we assume that generation length is 1.47 days and is the same in all patients, mutation rate estimates vary from 1.52 x 10(-5) to 5.02 x 10(-5). Our results indicate that effective viral population size and evolutionary rate per year are negatively correlated among HIV-1 patients.


Asunto(s)
VIH-1/crecimiento & desarrollo , Funciones de Verosimilitud , Carga Viral/métodos , Teorema de Bayes , Humanos , Modelos Biológicos , Mutación
18.
Eur J Pharm Biopharm ; 59(1): 169-75, 2005 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-15567315

RESUMEN

The purpose of the present study was to develop implantable BCNU-loaded poly(D,L-lactide-co-glycolide) (PLGA) wafer for the controlled release of 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) and to evaluate its in vitro and in vivo antitumor activity. The release rate of BCNU from PLGA wafer increased with the increase of BCNU amount loaded and the release was continued until 7 days. In vitro and in vivo antitumor activity of BCNU-loaded PLGA wafer was investigated using in vitro cytotoxicity against 9L gliosarcoma cells and a subcutaneous (s.c.) solid tumor model of 9L gliosarcoma, respectively. The wafers containing BCNU showed more effective cytotoxicity than BCNU powder due to its short half-life and inhibited the proliferation of 9L gliosarcoma cells. BCNU-loaded PLGA wafer delayed the growth of the tumors significantly and increasing the dose of BCNU in the wafer resulted in a substantial regression of the tumor. These results of antitumor activity of BCNU-loaded PLGA wafer demonstrate the feasibility of the wafers for clinical application.


Asunto(s)
Antineoplásicos/administración & dosificación , Antineoplásicos/farmacocinética , Carmustina/administración & dosificación , Carmustina/farmacocinética , Gliosarcoma/metabolismo , Ácido Láctico/administración & dosificación , Ácido Láctico/farmacocinética , Ácido Poliglicólico/administración & dosificación , Ácido Poliglicólico/farmacocinética , Polímeros/administración & dosificación , Polímeros/farmacocinética , Animales , Línea Celular Tumoral , Supervivencia Celular/efectos de los fármacos , Supervivencia Celular/fisiología , Evaluación Preclínica de Medicamentos/métodos , Gliosarcoma/tratamiento farmacológico , Masculino , Copolímero de Ácido Poliláctico-Ácido Poliglicólico , Ratas , Ratas Endogámicas F344
19.
Artículo en Inglés | WPRIM | ID: wpr-816619

RESUMEN

BACKGROUND: This study was conducted to compare glycaemic control with insulin detemir administered according to two titration algorithms (3-0-3 and 2-4-6-8) after 20 weeks of treatment in subjects with type 2 diabetes mellitus inadequately controlled on metformin.METHODS: This was a 20-week, randomised, multicentre, open-labelled, treat-to-target trial. Forty-six patients were randomised in a 1:1 manner to either the 3-0-3 (G3, n=23) or 2-4-6-8 (G2, n=23) algorithm. The primary endpoint was change of haemoglobin A1c (HbA1c), and the secondary safety endpoint included hypoglycaemic events.RESULTS: After 20 weeks, HbA1c decreased similarly in the G3 and G2 groups, with a mean change of −0.9% from baseline. The mean change in fasting plasma glucose was numerically similar in both groups. The hypoglycaemia event rate per 100-patient-years of exposure (r) in the G2 group (r=1,427) was higher than that in the G3 group (r=807).CONCLUSION: Both treatment groups had numerically similar HbA1c reductions. A trend towards fewer hypoglycaemia episodes after dose stabilisation was seen with the simpler G3. Clinically, this may be an important observation, as a simpler titration algorithm may support self-management and maintenance of insulin therapy.


Asunto(s)
Humanos , Glucemia , Diabetes Mellitus Tipo 2 , Ayuno , Hiperglucemia , Insulina Detemir , Insulina , Metformina , Autocuidado
20.
Int J Pharm ; 251(1-2): 1-12, 2003 Jan 30.
Artículo en Inglés | MEDLINE | ID: mdl-12527170

RESUMEN

Implantable polymeric device that can release chemotherapeutic agent directly into central nervous system (CNS) has had an impact on malignant glioma therapy. The purpose of our study was to develop an implantable polymeric device, which can release intact 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) for long-term period over 1 month, and to evaluate its cytotoxicity against XF 498 human CNS tumor cells in vitro. BCNU was incorporated into biodegradable poly(D,L-lactide-co-glycolide) (PLGA), by using spray-drying method. BCNU-loaded PLGA microparticles were characterized by scanning electron microscopy (SEM), powder X-ray diffraction, and differential scanning calorimetry. SEM observation of the microparticles showed that the microparticles were spherical, i.e. microspheres. Homogeneous distribution of BCNU in PLGA microsphere was confirmed by significant reduction of crystallinity of BCNU. Microspheres were fabricated into wafers with flat and smooth surface by direct compression method. In vitro release of BCNU in pH 7.4 phosphate buffered saline was prolonged up to 8 weeks after short initial burst period. Antitumor activity of BCNU-loaded PLGA wafer against XF 498 human CNS tumor cells continued over 1 month and, PLGA only did not affect the growth of the cells. Meanwhile, the cytotoxic activity of BCNU powder disappeared within 12 h. These results strongly suggest that the BCNU/PLGA formulations increase release period of carmustine in vivo and also be useful in the development of implantable polymeric device for malignant glioma.


Asunto(s)
Antineoplásicos Alquilantes/farmacología , Carmustina/farmacología , Neoplasias del Sistema Nervioso Central/tratamiento farmacológico , Portadores de Fármacos/farmacocinética , Ácido Láctico/farmacología , Ácido Poliglicólico/farmacología , Polímeros/farmacología , Antineoplásicos Alquilantes/química , Antineoplásicos Alquilantes/farmacocinética , Carmustina/química , Carmustina/farmacocinética , Neoplasias del Sistema Nervioso Central/metabolismo , Neoplasias del Sistema Nervioso Central/patología , Portadores de Fármacos/química , Portadores de Fármacos/farmacología , Ensayos de Selección de Medicamentos Antitumorales , Humanos , Ácido Láctico/química , Ácido Láctico/farmacocinética , Ácido Poliglicólico/química , Ácido Poliglicólico/farmacocinética , Copolímero de Ácido Poliláctico-Ácido Poliglicólico , Polímeros/química , Polímeros/farmacocinética , Células Tumorales Cultivadas
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