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1.
Virus Evol ; 8(2): veac072, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36533144

RESUMEN

There is a strong evolutionary tendency of the human immunodeficiency virus (HIV) to accumulate A nucleotides in its RNA genome, resulting in a mere 40 per cent A count. This A bias is especially dominant for the so-called silent codon positions where any nucleotide can be present without changing the encoded protein. However, particular silent codon positions in HIV RNA refrain from becoming A, which became apparent upon genome analysis of many virus isolates. We analyzed these 'noA' genome positions to reveal the underlying reason for their inability to facilitate the A nucleotide. We propose that local RNA structure requirements can explain the absence of A at these sites. Thus, noA sites may be prominently involved in the correct folding of the viral RNA. Turning things around, the presence of multiple clustered noA sites may reveal the presence of important sequence and/or structural elements in the HIV RNA genome.

2.
Virus Evol ; 2(1): vew005, 2016 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-27774298

RESUMEN

Several novel clades of astroviruses have recently been identified in human faecal samples. Here, we describe a novel astrovirus-like RNA virus detected in human stools, which we have tentatively named bastrovirus. The genome of this novel virus consists of 6,300 nucleotides organized in three open reading frames. Several sequence divergent strains were detected sharing 67-93 per cent nucleotide identity. Bastrovirus encodes a putative structural protein that is homologous to the capsid protein found in members of the Astroviridae family (45% amino acid identity). The virus also encodes a putative non-structural protein that is genetically distant from astroviruses but shares some homology to the non-structural protein encoded by members of the Hepeviridae family (28% amino acid identity). This novel bastrovirus is present in 8.7 per cent (35/400) of faecal samples collected from 300 HIV-1-positive and 100 HIV-1-negative individuals suggesting common occurrence of the virus. However, whether the source of the virus is infected human cells or other, for example, dietary, remains to be determined.

3.
J Clin Virol ; 73: 89-94, 2015 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-26587786

RESUMEN

BACKGROUND AND OBJECTIVE: The urgency of ebolavirus drug development is obvious in light of the current local epidemic in Western Africa with high morbidity and a risk of wider spread. We present an in silico study as a first step to identify inhibitors of ebolavirus polymerase activity based on approved antiviral nucleotide analogues. STUDY DESIGN: Since a structure model of the ebolavirus polymerase is lacking, we performed combined homology and ab initio modeling and report a similarity to known polymerases of human enterovirus, bovine diarrhea virus and foot-and-mouth disease virus. This facilitated the localization of a nucleotide binding domain in the ebolavirus polymerase. We next performed molecular docking studies with nucleotides (ATP, CTP, GTP and UTP) and nucleotide analogues, including a variety of approved antiviral drugs. RESULTS AND CONCLUSIONS: Specific combinations of nucleotide analogues significantly reduce the ligand-protein interaction energies of the ebolavirus polymerase for natural nucleotides. Any nucleotide analogue on its own did not reduce ligand-protein interaction energies. This prediction encourages specific drug testing efforts and guides future strategies to inhibit ebolavirus replication.


Asunto(s)
ARN Polimerasas Dirigidas por ADN/antagonistas & inhibidores , ARN Polimerasas Dirigidas por ADN/química , Ebolavirus/enzimología , Nucleótidos/química , Animales , Antivirales/química , Antivirales/farmacología , Sitios de Unión/efectos de los fármacos , Bovinos , Simulación por Computador , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Humanos , Simulación del Acoplamiento Molecular , Nucleótidos/farmacología , Filogenia , Homología Estructural de Proteína
4.
PLoS One ; 9(9): e106324, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25180507

RESUMEN

INTRODUCTION: Resistance of the reverse transcriptase (RT) of hepatitis B virus (HBV) to the tenofovir nucleotide drug has not been observed since its introduction for treatment of hepatitis B virus (HBV) infection in 2008. In contrast, frequent viral breakthrough and resistance has been documented for adefovir. Our computational study addresses an inventory of the structural differences between these two nucleotide analogues and their binding sites and affinities to wildtype (wt) and mutant RT enzyme structures based on in silico modeling, in comparison with the natural nucleotide substrates. RESULTS: Tenofovir and adefovir only differ by an extra CH3-moiety in tenofovir, introducing a center of chirality at the carbon atom linking the purine group with the phosphates. (R)-Tenofovir (and not (S)-tenofovir) binds significantly better to HBV-RT than adefovir. "Single hit" mutations in HBV-RT associated with adefovir resistance may affect the affinity for tenofovir, but to a level that is insufficient for tenofovir resistance. The RT-Surface protein gene overlap in the HBV genome provides an additional genetic constraint that limits the mutational freedom required to generate drug-resistance. Different pockets near the nucleotide binding motif (YMDD) in HBV-RT can bind nucleotides and nucleotide analogues with different affinities and specificities. CONCLUSION: The difference in binding affinity of tenofovir (more than two orders of magnitude in terms of local concentration), a 30x higher dosage of the (R)-tenofovir enantiomer as compared to conformational isomeric or rotameric adefovir, and the constrained mutational space due to gene overlap in HBV may explain the absence of resistance mutations after 6 years of tenofovir monotherapy. In addition, the computational methodology applied here may guide the development of antiviral drugs with better resistance profiles.


Asunto(s)
Adenina/análogos & derivados , Virus de la Hepatitis B/enzimología , Organofosfonatos/metabolismo , ADN Polimerasa Dirigida por ARN/metabolismo , Adenina/química , Adenina/metabolismo , Adenosina Trifosfato/metabolismo , Sitios de Unión , Análisis por Conglomerados , Cristalografía por Rayos X , Nucleótidos de Desoxiguanina/metabolismo , Farmacorresistencia Viral/genética , Ligandos , Modelos Moleculares , Mutación/genética , Nucleótidos/genética , Sistemas de Lectura Abierta/genética , Organofosfonatos/química , Unión Proteica , ADN Polimerasa Dirigida por ARN/química , Tenofovir , Termodinámica
5.
BMC Infect Dis ; 14: 22, 2014 Jan 13.
Artículo en Inglés | MEDLINE | ID: mdl-24410947

RESUMEN

BACKGROUND: Gastrointestinal symptoms, in particular diarrhoea, are common in non-treated HIV-1 infected individuals. Although various enteric pathogens have been implicated, the aetiology of diarrhoea remains unexplained in a large proportion of HIV-1 infected patients. Our aim is to identify the cause of diarrhoea for patients that remain negative in routine diagnostics. METHODS: In this study stool samples of 196 HIV-1 infected persons, including 29 persons with diarrhoea, were examined for enteropathogens and HIV-1. A search for unknown and unexpected viruses was performed using virus discovery cDNA-AFLP combined with Roche-454 sequencing (VIDISCA-454). RESULTS: HIV-1 RNA was detected in stool of 19 patients with diarrhoea (66%) compared to 75 patients (45%) without diarrhoea. In 19 of the 29 diarrhoea cases a known enteropathogen could be identified (66%). Next to these known causative agents, a range of recently identified viruses was identified via VIDISCA-454: cosavirus, Aichi virus, human gyrovirus, and non-A non-B hepatitis virus. Moreover, a novel virus was detected which was named immunodeficiency-associated stool virus (IASvirus). However, PCR based screening for these viruses showed that none of these novel viruses was associated with diarrhoea. Notably, among the 34% enteropathogen-negative cases, HIV-1 RNA shedding in stool was more frequently observed (80%) compared to enteropathogen-positive cases (47%), indicating that HIV-1 itself is the most likely candidate to be involved in diarrhoea. CONCLUSION: Unexplained diarrhoea in HIV-1 infected patients is probably not caused by recently described or previously unknown pathogens, but it is more likely that HIV-1 itself plays a role in intestinal mucosal abnormalities which leads to diarrhoea.


Asunto(s)
Diarrea/virología , Infecciones por VIH/complicaciones , VIH-1 , Virus/aislamiento & purificación , Adulto , Análisis del Polimorfismo de Longitud de Fragmentos Amplificados , Heces/virología , Femenino , Humanos , Masculino , Persona de Mediana Edad , Picornaviridae
6.
Virol J ; 10: 323, 2013 Oct 30.
Artículo en Inglés | MEDLINE | ID: mdl-24171716

RESUMEN

BACKGROUND: Although human torque teno viruses (TTVs) were first discovered in 1997, still many associated aspects are not clarified yet. The viruses reveal a remarkable heterogeneity and it is possible that some genotypes are more pathogenic than others. The identification of all genotypes is essential to confirm previous pathogenicity data, and an unbiased search for novel viruses is needed to identify TTVs that might be related to disease. METHOD: The virus discovery technique VIDISCA-454 was used to screen serum of 55 HIV-1 positive injecting drug users, from the Amsterdam Cohort Studies, in search for novel blood-blood transmittable viruses which are undetectable via normal diagnostics or panvirus-primer PCRs. RESULTS: A novel torque teno mini virus (TTMV) was identified in two patients and the sequence of the full genomes were determined. The virus is significantly different from the known TTMVs (< 40% amino acid identity in ORF1), yet it contains conserved characteristics that are also present in other TTMVs. The virus is chronically present in both patients, and these patients both suffered from a pneumococcal pneumonia during follow up and had extremely low B-cells counts. CONCLUSION: We describe a novel TTMV which we tentatively named TTMV-13. Further research is needed to address the epidemiology and pathogenicity of this novel virus.


Asunto(s)
ADN Viral/química , ADN Viral/genética , Genoma Viral , Infecciones por VIH/complicaciones , Suero/virología , Torque teno virus/clasificación , Torque teno virus/aislamiento & purificación , Análisis por Conglomerados , Estudios de Cohortes , Genotipo , Infecciones por VIH/virología , VIH-1/aislamiento & purificación , Humanos , Masculino , Datos de Secuencia Molecular , Países Bajos , Filogenia , Análisis de Secuencia de ADN , Homología de Secuencia , Abuso de Sustancias por Vía Intravenosa , Torque teno virus/genética
7.
RNA Biol ; 10(2): 211-5, 2013 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-23235488

RESUMEN

A bipartition of HIV-1 RNA genome sequences into single- and double-stranded nucleotides is possible based on the secondary structure model of a complete 9 kb genome. Subsequent analysis revealed that the well-known lentiviral property of A-accumulation is profoundly present in single-stranded domains, yet absent in double-stranded domains. Mutational rate analysis by means of an unrestricted model of nucleotide substitution suggests the presence of an evolutionary equilibrium to preserve this biased nucleotide distribution.


Asunto(s)
Nucleótidos de Adenina/genética , Genoma Viral , VIH-1/genética , ARN Viral/genética , Emparejamiento Base , Secuencia de Bases , Evolución Molecular , Mutación , Tasa de Mutación , Conformación de Ácido Nucleico , ARN Bicatenario/genética , Selección Genética
8.
PLoS One ; 7(11): e48940, 2012.
Artículo en Inglés | MEDLINE | ID: mdl-23145031

RESUMEN

The hepatitis B virus (HBV) genome encodes the X protein (HBx), a ubiquitous transactivator that is required for HBV replication. Expression of the HBx protein has been associated with the development of HBV infection-related hepatocellular carcinoma (HCC). Previously, we generated a 3D structure of HBx by combined homology and ab initio in silico modelling. This structure showed a striking similarity to the human thymine DNA glycosylase (TDG), a key enzyme in the base excision repair (BER) pathway. To further explore this finding, we investigated whether both proteins interfere with or complement each other's functions. Here we show that TDG does not affect HBV replication, but that HBx strongly inhibits TDG-initiated base excision repair (BER), a major DNA repair pathway. Inhibition of the BER pathway may contribute substantially to the oncogenic effect of HBV infection.


Asunto(s)
Reparación del ADN , Timina ADN Glicosilasa/antagonistas & inhibidores , Transactivadores/genética , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/metabolismo , Carcinoma Hepatocelular/virología , Replicación del ADN , Células HEK293 , Células Hep G2 , Hepatitis B/genética , Hepatitis B/metabolismo , Hepatitis B/virología , Humanos , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/metabolismo , Neoplasias Hepáticas/virología , Timina ADN Glicosilasa/genética , Timina ADN Glicosilasa/metabolismo , Proteínas Reguladoras y Accesorias Virales
9.
PLoS One ; 6(8): e23392, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-21850270

RESUMEN

Orthohepadnavirus (mammalian hosts) and avihepadnavirus (avian hosts) constitute the family of Hepadnaviridae and differ by their capability and inability for expression of protein X, respectively. Origin and functions of X are unclear. The evolutionary analysis at issue of X indicates that present strains of orthohepadnavirus started to diverge about 25,000 years ago, simultaneously with the onset of avihepadnavirus diversification. These evolutionary events were preceded by a much longer period during which orthohepadnavirus developed a functional protein X while avihepadnavirus evolved without X. An in silico generated 3D-model of orthohepadnaviral X protein displayed considerable similarity to the tertiary structure of DNA glycosylases (key enzymes of base excision DNA repair pathways). Similarity is confined to the central domain of MUG proteins with the typical DNA-binding facilities but without the capability of DNA glycosylase enzymatic activity. The hypothetical translation product of a vestigial X reading frame in the genome of duck hepadnavirus could also been folded into a DNA glycosylase-like 3D-structure. In conclusion, the most recent common ancestor of ortho- and avihepadnavirus carried an X sequence with orthology to the central domain of DNA glycosylase.


Asunto(s)
ADN Glicosilasas/química , ADN Glicosilasas/metabolismo , Transactivadores/química , Transactivadores/metabolismo , Animales , Avihepadnavirus/enzimología , ADN Glicosilasas/genética , Humanos , Orthohepadnavirus/enzimología , Estructura Secundaria de Proteína , Transactivadores/genética , Proteínas Reguladoras y Accesorias Virales
10.
BMC Evol Biol ; 9: 164, 2009 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-19604368

RESUMEN

BACKGROUND: The Picornaviridae family contains a number of important pathogenic viruses, among which the recently reclassified human parechoviruses (HPeVs). These viruses are widespread and can be grouped in several types. Understanding the evolutionary history of HPeV could answer questions such as how long the circulating lineages last shared a common ancestor and how the evolution of this viral species is shaped by its population dynamics. Using both strict and relaxed clock Bayesian phylogenetics we investigated 1) the substitutions rates of the structural P1 and capsid VP1 regions and 2) evolutionary timescale of currently circulating HPeV lineages. RESULTS: Our estimates reveal that human parechoviruses exhibit high substitution rates for both structural P1 and capsid VP1 regions, respectively 2.21 x 10(-3) (0.48 - 4.21 x 10(-3)) and 2.79 x 10(-3) (2.05 - 3.66 x 10(-3)) substitutions per site per year. These are within the range estimated for other picornaviruses. By employing a constant population size coalescent prior, the date of the most recent common ancestor was estimated to be at around 1600 (1427-1733). In addition, by looking at the frequency of synonymous and non-synonymous substitutions within the VP1 gene we show that purifying selection constitutes the dominating evolutionary force leading to strong amino acid conservation. CONCLUSION: In conclusion, our estimates provide a timescale for the evolution of HPeVs and suggest that genetic diversity of current circulating HPeV types has arisen about 400 years ago.


Asunto(s)
Evolución Molecular , Parechovirus/genética , Filogenia , Teorema de Bayes , Proteínas de la Cápside/genética , Genoma Viral , ARN Viral/genética , Alineación de Secuencia , Análisis de Secuencia de ARN
11.
Virol J ; 5: 146, 2008 Dec 11.
Artículo en Inglés | MEDLINE | ID: mdl-19077239

RESUMEN

BACKGROUND: Occult or latent hepatitis B virus (HBV) infection is defined as infection with detectable HBV DNA and undetectable surface antigen (HBsAg) in patients' blood. The cause of an overt HBV infection becoming an occult one is unknown. To gain insight into the mechanism of the development of occult infection, we compared the full-length HBV genome from a blood donor carrying an occult infection (d4) with global genotype D genomes. RESULTS: The phylogenetic analysis of polymerase, core and X protein sequences did not distinguish d4 from other genotype D strains. Yet, d4 surface protein formed the evolutionary outgroup relative to all other genotype D strains. Its evolutionary branch was the only one where accumulation of substitutions suggests positive selection (dN/dS = 1.3787). Many of these substitutions accumulated specifically in regions encoding the core/surface protein interface, as revealed in a 3D-modeled protein complex. We identified a novel RNA splicing event (deleting nucleotides 2986-202) that abolishes surface protein gene expression without affecting polymerase, core and X-protein related functions. Genotype D strains differ in their ability to perform this 2986-202 splicing. Strains prone to 2986-202 splicing constitute a separate clade in a phylogenetic tree of genotype D HBVs. A single substitution (G173T) that is associated with clade membership alters the local RNA secondary structure and is proposed to affect splicing efficiency at the 202 acceptor site. CONCLUSION: We propose an evolutionary scenario for occult HBV infection, in which 2986-202 splicing generates intracellular virus particles devoid of surface protein, which subsequently accumulates mutations due to relaxation of coding constraints. Such viruses are deficient of autonomous propagation and cannot leave the host cell until it is lysed.


Asunto(s)
Evolución Molecular , Virus de la Hepatitis B/genética , Hepatitis B/virología , Empalme del ARN , Secuencia de Bases , Genoma Viral , Genotipo , Virus de la Hepatitis B/química , Virus de la Hepatitis B/clasificación , Virus de la Hepatitis B/fisiología , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Mutación , Conformación de Ácido Nucleico , Filogenia , Unión Proteica , Proteínas Virales/química , Proteínas Virales/genética , Proteínas Virales/metabolismo , Replicación Viral
12.
J Nucl Med ; 49(8): 1380-5, 2008 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-18632808

RESUMEN

UNLABELLED: Rheumatoid arthritis (RA) involves the accumulation of monocyte-derived macrophages in the affected synovial tissue. This process of cell migration could be portrayed scintigraphically to monitor noninvasively the effects of therapy on the progress of the disease. For this purpose, labeling of purified autologous monocytes with 99mTc-hexamethylpropyleneamine oxime (99mTc-HMPAO) at very high specific radioactivity has recently been developed. The aim of this study was to assess the biodistribution and radiation dosimetry of 99mTc-HMPAO-labeled monocytes in adult patients with RA. METHODS: In 8 patients with RA, monocytes were isolated from 100 mL of blood and labeled with 99mTc-HMPAO to a yield of 10 Bq/cell. Multiple whole-body scans were performed up to 20 h after reinjection of an average of 200 MBq of 99mTc-HMPAO-labeled monocytes. Urine and blood samples were collected. The fraction of administered activity in 7 source organs was quantified from the attenuation-corrected geometric mean counts in conjugate views. Radiation-absorbed doses were estimated with OLINDA/EXM software. RESULTS: Autologous monocytes labeled with 99mTc-HMPAO at high intracellular yields showed in vivo kinetics comparable with labeled leukocytes, with initial trapping in the lungs followed by distribution into the liver, spleen, and bone marrow. The radiation-absorbed estimates for 99mTc-HMPAO-labeled monocytes were comparable with those for 99mTc-HMPAO-labeled mixed white blood cells, with an effective dose of 0.011 mSv/MBq. CONCLUSION: 99mTc-HMPAO-labeled monocytes have biodistribution and radiation dosimetry similar to those of 99mTc-HMPAO-labeled mixed white blood cells and might therefore be used for in vivo monitoring of immunomodulating therapy in patients with RA.


Asunto(s)
Artritis Reumatoide/diagnóstico por imagen , Monocitos , Exametazima de Tecnecio Tc 99m/farmacocinética , Adulto , Femenino , Humanos , Masculino , Persona de Mediana Edad , Radiometría , Cintigrafía , Radiofármacos/farmacocinética , Distribución Tisular , Imagen de Cuerpo Entero
13.
Virology ; 370(2): 362-72, 2008 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-17935747

RESUMEN

Surface protein and polymerase of hepatitis B virus provide a striking example of gene overlap. Inclusion of more coding constraints in the phylogenetic analysis forces the tree toward accepted topology. Three-dimensional protein modeling demonstrates that participation in local protein function underlies the observed mosaic patterns of amino acid conservation and variability. Conserved amino acid residues of polymerase were typically clustered at the catalytic core marked by the YMDD motif. The proposed tertiary structure of surface protein displayed the expected transmembrane helices in a 2-domain constellation. Conserved amino acids like, for instance, cysteine residues are involved in the spatial orientation of the two domains, the exposed location of the a-determinant and the dimer formation of surface protein. By means of computational alanine replacement scanning, we demonstrated that the interfaces between domains in monomeric surface protein, between the monomers in dimeric surface protein and in a capsid-surface protein complex mainly consist of relatively well-conserved amino acid residues.


Asunto(s)
Productos del Gen pol/química , Antígenos de Superficie de la Hepatitis B/química , Virus de la Hepatitis B/química , Secuencia de Aminoácidos , Sustitución de Aminoácidos , Secuencia de Bases , Secuencia Conservada , ADN Viral/genética , Dimerización , Productos del Gen pol/genética , Genes Virales , Antígenos de Superficie de la Hepatitis B/genética , Virus de la Hepatitis B/enzimología , Virus de la Hepatitis B/genética , Humanos , Imagenología Tridimensional , Modelos Moleculares , Mosaicismo , Filogenia , Conformación Proteica , Estructura Cuaternaria de Proteína , Estructura Terciaria de Proteína , Sistemas de Lectura , Termodinámica
14.
Nucl Med Biol ; 34(8): 933-8, 2007 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-17998095

RESUMEN

Rheumatoid arthritis of joints involves the accumulation of monocyte-derived macrophages in the affected synovial tissue. This process of cell migration can be portrayed scintigraphically in order to monitor noninvasive effects of therapy on the progress of the disease. Scintigraphic detection of inflammation by means of technetium 99m-hexamethylpropylene amine oxime (99mTc-HMPAO)-labeled leukocytes provides a classic example. Present state-of-the-art methods in cell biology allow the isolation of cells like lymphocytes or monocytes, which are less abundant than main blood constituents but, instead, harbor particular functions like specific homing properties. To facilitate scintigraphic imaging of the cell functions involved, the relatively small population of cells must be labeled to radioactive yields as high as possible. We demonstrate that autologous monocytes isolated from 100 ml of peripheral blood can be radiolabeled to a yield of 10 (instead of 1) Bq per cell, allowing scintigraphic analysis of rheumatoid arthritis up to 20 h post injection of patients. The method is based on the instantaneous distribution of lipophilic 99mTc-HMPAO between the hydrophobic inside of cells and the hydrophilic (aqueous) surrounding of cells, followed by decomposition of the radiopharmaceutical into compounds that are unable to cross the cellular membrane. The procedure provides a method of choice for cell-mediated scintigraphy at low availability of cells with the correct homing properties.


Asunto(s)
Artritis Reumatoide/diagnóstico por imagen , Artritis Reumatoide/patología , Monocitos/diagnóstico por imagen , Exametazima de Tecnecio Tc 99m , Artritis Reumatoide/sangre , Células Cultivadas , Humanos , Marcaje Isotópico/métodos , Cintigrafía , Radiofármacos
15.
J Gen Virol ; 88(Pt 8): 2137-2143, 2007 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-17622615

RESUMEN

The genome of hepatitis B virus (HBV) provides a striking example of gene overlapping. In particular, the surface protein gene S is overlapped completely by the polymerase gene P. Evolutionary constraints in overlapping genes have been demonstrated for many viruses, with one of the two overlapping genes being subjected to positive selection (adaptive evolution), while the other one is subjected to purifying selection. Yet, for HBV to persist successfully, adaptive evolution of both the P and S genes is essential. We propose that HBV employs a mechanism that allows the independent adaptive evolution of both genes. We hypothesize that (i) the adaptive evolution of P occurs via p1/s3 non-synonymous substitutions, which are synonymous in S, (ii) the adaptive evolution of S occurs via p3/s2 non-synonymous substitutions, which are synonymous in P, and (iii) p2/s1 substitutions are rare. Analysis of 450 HBV sequences demonstrated that this mechanism is operational in HBV evolution both within and among genotypes. Positions were identified in both genes where adaptive evolution is operational. Whilst significant parts of the P and S genes were subjected to positive selection, with the K(a)/K(s) ratio for either the P or the S gene being >1, there were only a few regions where the K(a)/K(s) ratios in both genes were >1. This mechanism of independent evolution of the overlapping regions could also apply to other viruses, taking into account the increased frequency of amino acids with a high level of degeneracy in the proteins encoded by overlapping genes of viruses.


Asunto(s)
Productos del Gen pol/genética , Genes Virales/genética , Virus de la Hepatitis B/genética , ADN Polimerasa Dirigida por ARN/genética , Proteínas del Envoltorio Viral/genética , Evolución Molecular , Genes Sobrepuestos
16.
Virol J ; 4: 25, 2007 Mar 07.
Artículo en Inglés | MEDLINE | ID: mdl-17343744

RESUMEN

BACKGROUND: Complete genome sequences of the Astroviridae include human, non-human mammalian and avian species. A consensus topology of astroviruses has been derived from nucleotide substitutions in the full-length genomes and from non-synonymous nucleotide substitutions in each of the three ORFs. Analyses of synonymous substitutions displayed a loss of tree structure, suggesting either saturation of the substitution model or a deviant pattern of synonymous substitutions in certain virus species. RESULTS: We analyzed the complete Astroviridae family for the inference of adaptive molecular evolution at sites and in branches. High rates of synonymous mutations are observed among the non-human virus species. Deviant patterns of synonymous substitutions are found in the capsid structural genes. Purifying selection is a dominant force among all astrovirus genes and only few codon sites showed values for the dN/dS ratio that may indicate site-specific molecular adaptation during virus evolution. One of these sites is the glycine residue of a RGD motif in ORF2 of human astrovirus serotype 1. RGD or similar integrin recognition motifs are present in nearly all astrovirus species. CONCLUSION: Phylogenetic analysis directed by maximum likelihood approximation allows the inclusion of significantly more evolutionary history and thereby, improves the estimation of dN and dS. Sites with enhanced values for dN/dS are prominent at domains in charge of environmental communication (f.i. VP27 and domain 4 in ORF1a) more than at domains dedicated to intrinsic virus functions (f.i. VP34 and ORF1b (the virus polymerase)). Integrin recognition may play a key role in astrovirus to target cell attachment.


Asunto(s)
Astroviridae/genética , Proteínas de la Cápside/metabolismo , Genes Virales , Mutación , Proteínas Virales/metabolismo , Animales , Astroviridae/clasificación , Astroviridae/metabolismo , Aves , Proteínas de la Cápside/genética , Gatos , Evolución Molecular , Humanos , Sistemas de Lectura Abierta/genética , Selección Genética , Ovinos , Especificidad de la Especie , Porcinos , Proteínas Virales/genética
17.
Virology ; 361(2): 447-54, 2007 May 10.
Artículo en Inglés | MEDLINE | ID: mdl-17188318

RESUMEN

The evolutionary history of the Astroviridae comprises the ancient separation between avian and mammalian astrovirus lineages followed by diversification among mammalian astroviruses. The latter process included several cross-species transmissions. We found that the recent, but not the ancient, evolution of astroviruses was associated with a switch in nucleotide composition and codon usage among non-human mammalian versus human/avian astroviruses. Virus and hosts phylogenies based on codon usage agreed with each other and matched the hosts' evolutionary emergence order. This recent switch in driving forces acting at the synonymous level points to the adaptation of codon usage by viruses to that of their hosts after cross-species transmissions. This is the first demonstration of nucleotide composition and codon usage being active driving forces during the recent evolutionary history of a virus group in the host-parasite system.


Asunto(s)
Astroviridae/genética , Animales , Astroviridae/clasificación , Composición de Base , Aves/genética , Aves/virología , Codón , Evolución Molecular , Humanos , Mamíferos/genética , Mamíferos/virología , Nucleótidos , Sistemas de Lectura Abierta/genética , Filogenia , Análisis de Secuencia , Especificidad de la Especie
18.
Ann Nucl Med ; 20(8): 575-81, 2006 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-17134028

RESUMEN

BACKGROUND: The combined application of potent beta-emitting isotopes for therapy with remitting isotopes for scintigraphy requires a profound regimen concerning team member safety and radionuclide quantification. METHODS: We have developed materials and methods for a proper and easy manipulation of 90Y during preparation and administration of 90Y/111In pharmaceuticals used for radioimmunotherapy. RESULTS: The efficacy of the shielding measures is documented. Protocols for the calibration of gamma-dose calibrators with respect to 90Y are extended to the assessment of quench-corrected liquid scintillation counting of 90Y. The contribution of 90Y backscatter to 111 In counting is quantified. Newly developed shielding equipment allows an adequate administration of relatively large volumes (100 ml) of 90Y/111In labeled pharmaceuticals to patients. CONCLUSIONS: The procedures described combine pharmaceutical (Good Manufacturing Practice) and radiation safety requirements with an accurate logging of relevant data.


Asunto(s)
Anticuerpos/administración & dosificación , Anticuerpos/química , Radioisótopos de Indio , Radioinmunodetección/métodos , Radiofármacos/uso terapéutico , Radioisótopos de Itrio , Calibración , Diseño de Equipo , Humanos , Radioinmunodetección/instrumentación , Radioinmunoterapia/métodos , Cintigrafía/métodos , Radiofármacos/metabolismo , Factores de Tiempo
19.
Ann Nucl Med ; 19(4): 345-9, 2005 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-16097648

RESUMEN

BACKGROUND: Scintigraphic image analysis of 99mTc-mertiatide (Mag-3, mercaptoacetyltriglycine) clearance provides the determination of the blood flow, the tubular transit time and the excretion as well from both kidneys. Radiopharmaceutical routine recommends a radiochemical purity control before administration of the product to a patient. The main objective of this study is to develop a Mag-3 labeling procedure that fits better than the previous one in our daily routine production of radiopharmaceuticals. METHODS: Increasing proportions of 99mTc-Mag-3 were measured during the heating and cooling steps of the Mag-3 labeling procedure. HPLC analysis was used to confirm the results of a rapid radiochemical quality control assay on standard ITLC-SG paper. RESULTS: The reconstitution time takes 20-25 minutes from the harvest of pertechnetate to a ready-for-use calibrated patient syringe. The HPLC profile of 99mTc-Mag-3 including its minor impurities remains unchanged for 24-48 hours after reconstitution. CONCLUSIONS: The application of a programmable Peltier-directed device for heating/cooling provides a better control of the temperature course. The procedure proposed fully meets the labeling criteria recommended by the supplier and can be performed with a minimum of attention within a time-span that we formerly needed for solely the radiochemical purity control assay. Moreover, 99mTc-Mag-3 prepared in this way seems to be considerably more stable than mentioned in the manufacturer's instructions.


Asunto(s)
Tecnecio Tc 99m Mertiatida/análisis , Tecnecio Tc 99m Mertiatida/química , Cromatografía/métodos , Marcaje Isotópico/métodos , Radiofármacos/análisis , Radiofármacos/síntesis química
20.
J Nucl Med ; 45(5): 842-8, 2004 May.
Artículo en Inglés | MEDLINE | ID: mdl-15136635

RESUMEN

UNLABELLED: Anthracyclines are widely used in chemotherapy regimens for several malignancies, with cardiotoxicity being the major limiting factor in high-dose schedules. Recently, it was reported that doxorubicin induces apoptosis in cardiac muscle cells in vivo and, as such, is expected to be involved in the genesis of doxorubicin-induced cardiomyopathy. The aim of this study was to validate an animal model for in vivo monitoring of doxorubicin cardiotoxicity by means of scintigraphic detection of apoptosis. METHODS: Three groups of 5 male Wistar rats each were treated for 3, 4, and 5 times with a weekly intraperitoneal injection of doxorubicin at 2.5 mg/kg. At 24 h before and 24 h after the final treatment, (99m)Tc-annexin pinhole scintigraphy was performed. A control group of 5 rats was scanned without doxorubicin treatment. A cardiac uptake ratio was calculated from planar scintigraphy results with the following formula: (mediastinum - fat)/fat. After scintigraphy, the rats were sacrificed, and the heart was processed for histologic analysis. RESULTS: Incremental general signs of illness were observed with increasing total cumulative doxorubicin dose. Rats treated for 3, 4, and 5 wk with doxorubicin showed significantly higher uptake ratios of, respectively, 4.0 +/- 0.52 (mean +/- SEM), 4.8 +/- 0.46, and 5.2 +/- 0.17 after the final treatment; the ratio for controls was 1.84 +/- 0.05 (P < 0.05). Histologic analysis confirmed cardiac stress in treated groups, with an increasing left ventricular atrial natriuretic factor messenger RNA expression level with increasing cumulative doxorubicin dose. Late apoptosis was confirmed by terminal deoxynucleotidyltransferase-mediated dUTP nick-end labeling in the rats treated for 5 wk. CONCLUSION: Acute doxorubicin-induced cardiomyopathy based on early apoptosis can be assessed and imaged with annexin V scintigraphy in rats. This finding makes it possible to use this animal model for repetitive noninvasive evaluation of cardioprotective regimens for anthracycline cardiotoxicity.


Asunto(s)
Anexina A5 , Antibióticos Antineoplásicos/toxicidad , Doxorrubicina/toxicidad , Corazón/efectos de los fármacos , Miocitos Cardíacos/efectos de los fármacos , Compuestos de Organotecnecio , Animales , Apoptosis , Factor Natriurético Atrial/metabolismo , Masculino , ARN Mensajero/genética , Radiofármacos , Ratas , Ratas Wistar , Factores de Tiempo
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