Publications by authors named "Pilar Moreno"

48 Publications

Generating New FANCA-Deficient HNSCC Cell Lines by Genomic Editing Recapitulates the Cellular Phenotypes of Fanconi Anemia.

Genes (Basel) 2021 Apr 9;12(4). Epub 2021 Apr 9.

Biomedical Research Institute I+12, University Hospital 12 de Octubre, 28041 Madrid, Spain.

Fanconi anemia (FA) patients have an exacerbated risk of head and neck squamous cell carcinoma (HNSCC). Treatment is challenging as FA patients display enhanced toxicity to standard treatments, including radio/chemotherapy. Therefore, better therapies as well as new disease models are urgently needed. We have used CRISPR/Cas9 editing tools in order to interrupt the human gene by the generation of insertions/deletions (indels) in exon 4 in two cancer cell lines from sporadic HNSCC having no mutation in FA-genes: CAL27 and CAL33 cells. Our approach allowed efficient editing, subsequent purification of single-cell clones, and Sanger sequencing validation at the edited locus. Clones having frameshift indels in homozygosis did not express FANCA protein and were selected for further analysis. When compared with parental CAL27 and CAL33, -mutant cell clones displayed a FA-phenotype as they (i) are highly sensitive to DNA interstrand crosslink (ICL) agents such as mitomycin C (MMC) or cisplatin, (ii) do not monoubiquitinate FANCD2 upon MMC treatment and therefore (iii) do not form FANCD2 nuclear foci, and (iv) they display increased chromosome fragility and G2 arrest after diepoxybutane (DEB) treatment. These -mutant clones display similar growth rates as their parental cells. Interestingly, mutant cells acquire phenotypes associated with more aggressive disease, such as increased migration in wound healing assays. Therefore, CAL27 and CAL33 cells with mutations are phenocopies of FA-HNSCC cells.
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http://dx.doi.org/10.3390/genes12040548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8069753PMC
April 2021

Resistance-associated substitutions and response to treatment in a chronic hepatitis C virus infected-patient: an unusual virological response case report.

BMC Infect Dis 2021 Apr 26;21(1):387. Epub 2021 Apr 26.

Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Mataojo 2055, ZIP: 11400, Montevideo, Uruguay.

Background: Direct-Acting agents (DAAs) target and inhibit essential viral replication proteins. They have revolutionized the treatment of Hepatitis C virus (HCV) infection reaching high levels of sustained virologic response. However, the detection of basal resistance-associated substitutions (RASs) to DAAs in naïve patients could be important in predicting the treatment outcome in some patients exhibiting failures to DAA-based therapies. Therefore, the aim of this work was to evaluate the presence of RASs as minority variants within intra-host viral populations, and assess their relationship to response to therapy on a multiple times relapser patient infected chronically with HCV.

Case Presentation: A male HCV infected-patient with a genotype 1a strain was evaluated. He had previously not responded to dual therapy (pegylated interferon-α plus ribavirin) and was going to start a direct-acting agent-based therapy (DAAs). He showed no significant liver fibrosis (F0). Viral RNA was extracted from serum samples taken prior and after therapy with DAAs (sofosbubir/ledipasvir/ribavirin). NS5A and NS5B genomic regions were PCR-amplified and the amplicons were sequenced using Sanger and next-generation sequencing (NGS) approaches. RASs were searched in in-silico translated sequences for all DAAs available and their frequencies were determined for those detected by NGS technology. Sanger sequencing did not reveal the presence of RASs in the consensus sequence neither before nor after the DAA treatment. However, several RASs were found at low frequencies, both before as well as after DAA treatment. RASs found as minority variants (particularly substitutions in position 93 within NS5A region) seem to have increased their frequency after DAA pressure. Nevertheless, these RASs did not become dominant and the patient still relapsed, despite perfect adherence to treatment and having no other complications beyond the infection (no significant fibrosis, no drug abuse).

Conclusions: This report shows that some patients might relapse after a DAA-based therapy even when RASs (pre- and post-treatment) are detected in very low frequencies (< 1%) within intra-host viral populations. Increased awareness of this association may improve detection and guide towards a personalized HCV treatment, directly improving the outcome in hard-to-treat patients.
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http://dx.doi.org/10.1186/s12879-021-06080-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8077789PMC
April 2021

Evaluation of SYBR Green real time PCR for detecting SARS-CoV-2 from clinical samples.

J Virol Methods 2021 03 4;289:114035. Epub 2020 Dec 4.

Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay. Electronic address:

The pandemic caused by SARS-CoV-2 has triggered an extraordinary collapse of healthcare systems and hundred thousand of deaths worldwide. Following the declaration of the outbreak as a Public Health Emergency of International Concern by the World Health Organization (WHO) on January 30th, 2020, it has become imperative to develop diagnostic tools to reliably detect the virus in infected patients. Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. In addition, these methods have been recommended by the WHO for laboratory diagnosis. Since most of these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques can be difficult to perform given the limited supply of reagents in low- and middle-income countries. In order to develop an inexpensive SARS-CoV-2 detection protocol using available resources we evaluated the SYBR Green based detection of SARS-CoV-2 to establish a suitable assay. To do so, we adapted one of the WHO recommended TaqMan-based one-step real time PCR protocols (from the University of Hong Kong) to SYBR Green. Our results indicate that SYBR-Green detection of ORF1b-nsp14 target represents a reliable cost-effective alternative to increase the testing capacity.
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http://dx.doi.org/10.1016/j.jviromet.2020.114035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7831559PMC
March 2021

Experimentally induced intrasexual mating competition and sex-specific evolution in female and male nematodes.

J Evol Biol 2020 12 1;33(12):1677-1688. Epub 2020 Oct 1.

Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden.

Sexual dimorphism in life history traits and their trade-offs is widespread among sexually reproducing animals and is strongly influenced by the differences in reproductive strategies between the sexes. We investigated how intrasexual competition influenced specific life history traits, important to fitness and their trade-offs in the outcrossing nematode Caenorhabditis remanei. Here, we altered the strength of sex-specific selection through experimental evolution with increased potential for intrasexual competition by skewing the adult sex ratio towards either females or males (1:10 or 10:1) over 30 generations and subsequently measured the phenotypic response to selection in three traits related to fitness: body size, fecundity and tolerance to heat stress. We observed a greater evolutionary change in females than males for body size and peak fitness, suggesting that females may experience stronger net selection and potentially harbour higher amounts of standing genetic variance compared to males. Our study highlights the importance of investigating direct and indirect effects of intrasexual competition in both sexes in order to capture sex-specific responses and understand the evolution of sexual dimorphism in traits expressed by both sexes.
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http://dx.doi.org/10.1111/jeb.13706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756511PMC
December 2020

Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: Detection of viral proteins and host's biological processes altered by the infection.

Data Brief 2020 Oct 5;32:106121. Epub 2020 Aug 5.

Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo & Instituto de Investigaciones Biológicas Clemente Estable, Mataojo 2020, CP 11400 Montevideo, Uruguay.

Since January 2020, the world is facing the COVID-19 pandemic caused by SARS-CoV-2. In a big effort to cope with this outbreak, two Uruguayan institutions, Institut Pasteur de Montevideo and Universidad de la República, have developed and implemented a diagnosis pipeline based on qRT-PCR using entirely local resources. In this context, we performed comparative quantitative proteomic analysis from oro- and naso-pharyngeal swabs used for diagnosis. Tryptic peptides obtained from five positive and five negative samples were analysed by nano-LC-MS/MS using a Q-Exactive Plus mass spectrometer. Data analysis was performed using PatternLab for Proteomics software. From all SARS-CoV-2 positive swabs we were able to detect peptides of the SARS-CoV-2 nucleoprotein that encapsulates and protect the RNA genome. Additionally, we detected an average of 1100 human proteins from each sample. The most abundant proteins exclusively detected in positive swabs were "Guanylate-binding protein 1", "Tapasin" and "HLA class II histocompatibility antigen DR beta chain". The biological processes overrepresented in infected host cells were "SRP-dependent cotranslational protein targeting to membrane", "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay", "viral transcription" and "translational initiation". Data is available via ProteomeXchange with identifier PXD020394. We expect that this data can contribute to the future development of mass spectrometry based approaches for COVID-19 diagnosis. Also, we share this preliminary proteomic characterization concerning the host response to infection for its reuse in basic investigation.
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http://dx.doi.org/10.1016/j.dib.2020.106121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7405904PMC
October 2020

Prevalence and molecular epidemiology of bovine leukemia virus in Colombian cattle.

Infect Genet Evol 2020 06 3;80:104171. Epub 2020 Jan 3.

Grupo de Enfermedades Infecciosas, Laboratorio de Virología, Departamento de Microbiología, Pontificia Universidad Javeriana, Carrera 7 No. 40 - 62, Bogotá́ 11001000, Colombia. Electronic address:

Bovine leukemia virus (BLV) is one of the five agents considered most significant for cattle. It is important to determine the prevalence and molecular epidemiology of BLV throughout the country in order to gain a more thorough understanding of the current situation of BLV and to reveal the possibility of masked genotypes that the primers used by OIE are unable to identify. Blood samples were collected at random from 289 cows distributed in 75 farms across the country. PCR amplification of env, gag and tax gene segments was performed. The obtained amplicons were sequenced and then subjected to phylogenetic analyses. A total of 62% of the cows present at 92% of the farms were BLV-positive for gag fragment. Genotype 1 was exclusively detected by env gene segment when analyzed using previously reported primers. However, tax gene analysis revealed circulation of genotype 6 variants, which were also detected based on env gene analysis with newly designed primers. These results indicate that current genotyping approaches based on partial env sequencing may bias BLV genetic variability approaches and underestimate the diversity of the detected BLV genotypes. This report is one of the first molecular and epidemiological studies of BLV conducted in Colombia, which contributes to the global epidemiology of the virus; it also highlights the substantial impact of BLV on the country's livestock and thus is a useful resource for farmers and government entities.
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http://dx.doi.org/10.1016/j.meegid.2020.104171DOI Listing
June 2020

Comparison of Fundus Biomicroscopy Examination of the Optic Nerve Head with and without Mydriasis.

Ophthalmic Res 2020 27;63(1):8-12. Epub 2019 Aug 27.

Glaucoma Service, Department of Ophthalmology and Visual Science, Federal University of São Paulo, São Paulo, Brazil,

Background: Notwithstanding the significant advances in automated imaging techniques in the past 2 decades, subjective evaluation of the optic disc still remains an important part of glaucoma propaedeutic. In places with limited resources and a high demand for ophthalmic care, anatomical evaluation of glaucoma cases often relies solely on slit-lamp-based fundus biomicroscopic examination, which is frequently performed without mydriasis.

Objective: The aim of this study was to compare metrics related to fundus biomicroscopy examination of the optic nerve head and peripapillary retinal nerve fiber layer (pRNFL) with and without mydriasis.

Material And Methods: Healthy individuals, patients with early glaucoma, and glaucoma suspects were prospectively enrolled. Patients were examined before and after mydriasis by three glaucoma specialists, who estimated patients' vertical cup-to-disc ratio (CDR) and evaluated the presence of glaucomatous signs: laminar dot sign, disc hemorrhage, disc saucering, disc notching, peripapillary atrophy, localized pRNFL defect, and loss of the ISNT pattern. Main outcome measures were the intra-observer comparison, the inter-observer agreement, and the abilities to identify glaucomatous signs before and after mydriasis.

Results: Thirty patients (60 eyes) were enrolled (mean age, 62.3 ± 11.6 years). Considering the evaluation of the three examiners, the mean vertical CDR increased from 0.41 to 0.44 (p = 0.02), and the median of the coefficient of variation of the measures was reduced from 0.24 to 0.11 (p = 0.01) after mydriasis. Regarding the inter-observer agreement evaluation, the kappa coefficient values ranged from 0.64 to 0.72 before mydriasis and from 0.71 to 0.77 after mydriasis. Dot sign and disc notching were better identified through fundoscopic examination with mydriasis compared to the nonmydriatic examination (p < 0.01).

Conclusion: Our results suggest that fundus biomicroscopy should be performed with mydriasis whenever possible, as it yells a better intra- and inter-observer agreement and improves the detection of glaucomatous signs. Moreover, examiners seem to underestimate CDR values without mydriasis. Further investigation is warranted to validate these findings by general ophthalmologists and in different populations.
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http://dx.doi.org/10.1159/000500980DOI Listing
February 2020

An Evolutionary Insight into Zika Virus Strains Isolated in the Latin American Region.

Viruses 2018 12 8;10(12). Epub 2018 Dec 8.

Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay.

Zika virus (ZIKV) is an emerging pathogen member of the family. ZIKV has spread rapidly in the Latin American region, causing hundreds of thousands of cases of ZIKV disease, as well as microcephaly in congenital infections. Detailed studies on the pattern of evolution of ZIKV strains have been extremely important to our understanding of viral survival, fitness, and evasion of the host's immune system. For these reasons, we performed a comprehensive phylogenetic analysis of ZIKV strains recently isolated in the Americas. The results of these studies revealed evidence of diversification of ZIKV strains circulating in the Latin American region into at least five different genetic clusters. This diversification was also reflected in the different trends in dinucleotide bias and codon usage variation. Amino acid substitutions were found in E and prM proteins of the ZIKV strains isolated in this region, revealing the presence of novel genetic variants circulating in Latin America.
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http://dx.doi.org/10.3390/v10120698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316622PMC
December 2018

Pretreatment Hepatitis C Virus NS5A/NS5B Resistance-Associated Substitutions in Genotype 1 Uruguayan Infected Patients.

Dis Markers 2018 14;2018:2514901. Epub 2018 Aug 14.

Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay.

Hepatitis C Virus (HCV) infection treatment has dramatically changed with the advent of direct-acting antiviral agents (DAAs). However, the efficacy of DAAs can be attenuated by the presence of resistance-associated substitutions (RASs) before and after treatment. Indeed, RASs detected in DAA treatment-naïve HCV-infected patients could be useful for clinical management and outcome prediction. Although the frequency of naturally occurring HCV NS5A and NS5B RASs has been addressed in many countries, there are only a few reports on their prevalence in the South American region. The aim of this study was to investigate the presence of RASs to NS5A and NS5B inhibitors in a DAA treatment naïve cohort of Uruguayan patients infected with chronic hepatitis C and compare them with reports from other South American countries. Here, we found that naturally occurring substitutions conferring resistance to NS5A and NS5B inhibitors were present in 8% and 19.2%, respectively, of treatment-naïve HCV genotype 1 infected patients. Importantly, the baseline substitutions in NS5A and NS5B herein identified differ from the studies previously reported in Brazil. Furthermore, Uruguayan strains subtype 1a clustered within all major world clades, showing that HCV variants currently circulating in this country are characterized by a remarkable genetic diversity.
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http://dx.doi.org/10.1155/2018/2514901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6112080PMC
January 2019

[The City of Girls and Boys of Huesca (Spain), an opportunity for designing healthy environment and public policies].

Gac Sanit 2019 May - Jun;33(3):296-298. Epub 2018 Jul 18.

Grupo Promotor del Proyecto La Ciudad de las Niñas y los Niños, Facultad de Ciencias Humanas y de la Educación, Huesca, España.

The City of Girls and Boys of Huesca (Spain) is an international project that seeks to foster children's autonomy and full participation in the construction of the city. Following its formal approval at the City Council of Huesca, the Girls and Boys Board and the City Laboratory were created, both of which include children from all the schools of Huesca. To highlightthe work on health, activities such as "Healthy School Paths", in which the asset mapping technique is used, were incorporated. Besides the interdisciplinary work among different areas of the city council, professionals from education (schools and university), health and social services, effects on the urban physical environment, with one street, park and square remodelled; and on the children's lifestyles, with more children walking to school alone, have been observed.
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http://dx.doi.org/10.1016/j.gaceta.2018.04.011DOI Listing
December 2019

Myofascial Pain: Ultrasound Width of the Masseter Muscle.

J Oral Facial Pain Headache Summer 2018;32(3):298–303. Epub 2018 Mar 21.

Aims: To determine whether subjects with temporomandibular disorders (TMD) manifesting as chronic myofascial pain (MFP) involving the masseter muscle present with significantly greater masseter muscle width, as evidenced by ultrasound, compared to individuals without MFP.

Methods: A case-control study was carried out. A total of 31 subjects presenting with MFP of the masticatory muscles involving the masseter muscle and 35 controls with TMD but no diagnosis of MFP, matched by age and sex, were included. Ultrasound was used to measure the maximum width of both masseter muscles at the intermediate point between the origin and insertion of the muscle in the light occlusal contact (LOC) position and under maximum contraction. Each side was analyzed separately. Means were compared by using single-factor analysis of variance and Mann-Whitney U test; P < .05 was considered to reflect statistical significance.

Results: In the study group, the right masseter muscle had a mean ± standard deviation width of 8.6 ± 1.8 mm under LOC (controls: 8.6 ± 1.6 mm; P = .85) and 11.5 ± 2.1 mm under maximum contraction (controls: 11.7 ± 1.9 mm; P = .86). The analagous measures in the left masseter muscle were 8.6 ± 1.6 mm under LOC (controls: 8.2 ± 1.5 mm; P = .42) and 11.3 ± 1.8 mm under maximum contraction (controls: 11.5 ± 1.8 mm) (P = .79), respectively. The increase in width of the right masseter muscle was 2.9 ± 2.1 mm (controls: 3.1 ± 1.2 mm; P = .67) in absolute terms and 1.4 ± 0.3 mm (controls: 1.4 ± 0.2 mm; P = .91) in relative values (width at maximum contraction/LOC width). In the case of the left masseter muscle, the respective values were 2.8 ± 1.7 mm (controls: 3.2 ± 0.9 mm; P = .25) and 1.3 ± 0.2 mm (controls: 1.4 ± 0.1 mm; P = .32).

Conclusion: There were no statistically significant differences in masseter muscle width between MFP subjects and control subjects under LOC conditions or maximum contraction. The increase in width under maximum contraction was likewise not significantly different between the groups.
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http://dx.doi.org/10.11607/ofph.1944DOI Listing
November 2018

IL28B gene polymorphism rs12979860, but not rs8099917, contributes to the occurrence of chronic HCV infection in Uruguayan patients.

Virol J 2018 03 2;15(1):40. Epub 2018 Mar 2.

Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 2055, Montevideo, Mataojo, Uruguay.

Background: Host single-nucleotide polymorphisms (SNPs) near the interleukin 28B (IL28B) locus are associated with sustained virological response to antiviral therapy and with spontaneous Hepatitis C Virus (HCV) clearance. Prevalence of these SNPs varies depending on ethnicity. The impact of IL28B SNPs in HCV-infected patients is currently unknown in Uruguay. Therefore, the aim of this study was to evaluate and compare the distribution of polymorphisms in the IL28B gene (rs12979860 and rs8099917) among HCV-infected patients and healthy individuals in Uruguay and thus assess their possible association with the establishment of HCV infection.

Methods: DNA was recovered from 92 non-infected individuals and 78 HCV-infected patients and SNPs were determined by RFLP and allelic discrimination by real-time PCR.

Results: The distribution of rs12979860 genotypes for the infected population was 29.5%-CC, 47.4%-CT and 23.1%-TT and for the control group 45.7%, 42.4% and 11.9%, respectively. Prevalence in both infected and uninfected individuals is similar to that reported in other countries with admixed populations. The distribution of rs8099917 genotypes for the infected population was 57.7%-TT, 27.2%-TG and 14.1%-GG and for the control group 60.9%, 33.7% and 5.4%, respectively. The comparison of rs12979860 genotype distribution between the two populations evidenced a higher prevalence of the favourable genotype (CC) in the uninfected control group (p < 0.05). Additionally, results generated using logistic regression analysis show that individuals carrying rs12979860-TT or CT genotypes have a higher likelihood of developing chronic hepatitis upon infection with HCV, when compared to CC carriers, considering rs8099917 genotype as constant.

Conclusion: Patients with HCV infection have a statistically significant lower prevalence of the favourable rs12979860 genotype when compared to uninfected individuals; therefore we can establish that only IL28B rs12979860-CT and TT genotypes seem to contribute to the occurrence of chronic HCV infection in the cohort of Uruguayan population studied. Considering that a trend towards a higher frequency of "good" response genotypes was observed in responder patients, we believe that IL28B rs12979860 genotyping could be a useful tool for predicting different therapies outcome, including in the DAA era.
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http://dx.doi.org/10.1186/s12985-018-0946-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5833045PMC
March 2018

Ultrasonic Echo Intensity as a New Noninvasive In Vivo Biomarker of Frailty.

J Am Geriatr Soc 2017 Dec 7;65(12):2685-2690. Epub 2017 Sep 7.

Department of Physiology, Universidad de Valencia/INCLIVA, Valencia, Spain.

Objectives: To investigate whether muscle quality based on echo intensity (EI) is associated with muscle strength (MS) and correlates with risk of frailty in elderly outpatients.

Design: Cross-sectional, experimental study.

Setting: Outpatient clinic.

Participants: Individuals aged 20 to 90 (N = 112). Individuals aged 20 to 59 participated as controls. Those aged 60 and older participated in the experimental group and were subdivided into robust, prefrail, and frail according to the Fried frailty criteria.

Measurements: EI, muscle thickness (MT), and subcutaneous fat thickness (SFT) of the anterior compartment of the thigh were measured using ultrasound images. MS was quantified using a hand dynamometer. Participants responded to a questionnaire asking about demographic and physical characteristics, frailty criteria, and quality of life.

Results: There was a significant negative correlation between EI and MS (Women: correlation coefficient (r) = -.522, P < .001; Men: r = -.355, P < .001). A similar trend was found for MT but not SFT. Statistically significant differences were also found between EI values, MT, MS, and quality of life and the different stages of frailty (P < .01).

Conclusions: Higher levels of EI were associated with lower levels of strength and greater frailty. These results, although needing to be replicated in larger and more-diverse populations, suggest that EI obtained using ultrasound images might be used as noninvasive imaging biomarker of frailty in elderly adults and opens the possibility of accurately testing interventions performed to prevent it.
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http://dx.doi.org/10.1111/jgs.15002DOI Listing
December 2017

Emergence and Spreading Potential of Zika Virus.

Front Microbiol 2016 20;7:1667. Epub 2016 Oct 20.

Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay.

Zika virus (ZIKV) is an arthropod-borne (family ) closely related to dengue, yellow fever and West Nile viruses. ZIKV remained neglected, confined to enzootic transmission cycles in Africa and Asia, until the first significant outbreak was reported in Micronesia in 2007. Subsequent epidemics of growing incidence occurred in French Polynesia and other South Pacific Islands, and recently, in the Americas. The latter and currently ongoing outbreak of unprecedented incidence revealed the association of ZIKV infection with the occurrence of severe congenital malformations and neurological diseases, leading to a widespread concern about its potential to pose a global public health threat. Serological and molecular data suggest that the genetic and geographic diversification of ZIKV may be greatly underestimated. Here we discuss several ecological and epidemiological aspects, together with the evolutionary processes that may have driven the emergence and abrupt spread of ZIKV in the Americas.
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http://dx.doi.org/10.3389/fmicb.2016.01667DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5071320PMC
October 2016

Identification of the Most Accurate Spectral-domain Optical Coherence Tomography Parameters in Eyes With Early High-Tension and Low-Tension Glaucoma.

J Glaucoma 2016 10;25(10):854-859

*Department of Ophthalmology, Federal University of São Paulo, São Paulo ‡Hospital Oftalmológico Medicina dos Olhos, Osasco, Brazil †Department of Ophthalmology, Hamilton Glaucoma Center, University of California, San Diego, La Jolla, CA.

Purpose: The aim of the study was to compare the diagnostic ability of macular ganglion cell complex (GCC) and peripapillary retinal nerve fiber layer (pRNFL) thickness in high-tension glaucoma (HTG) and low-tension glaucoma (LTG).

Patients And Methods: Glaucoma was defined as glaucomatous optic neuropathy and reproducible visual field defects. Patients were classified as having LTG if untreated intraocular pressure was ≤21 mm Hg on 2 different occasions. Only eyes with early glaucoma (mean deviation <-6 dB) were included. All patients underwent spectral-domain optical coherence tomography (SDOCT) imaging.

Results: A total of 56 normal subjects, 64 HTG patients, and 35 LTG patients were enrolled. Overall, after adjusting for mean deviation and age, the average pRNFL thickness in eyes with LTG was 18.7 µm thinner than in eyes with HTG (17% difference, P<0.01). In the HTG group, no significant difference was found between areas under the receiver operating characteristic curve (AUCs) for average GCC and average pRNFL thicknesses (0.77 vs. 0.68, P=0.06). In the LTG group, average pRNFL thickness had a significantly larger AUC compared with average GCC thickness (0.95 vs. 0.81, P<0.001). Comparing AUCs between HTG and LTG groups, although the average GCC had similar AUCs in both groups (P=0.47), the average pRNFL thickness had a significantly larger AUC in the LTG group (P<0.001).

Conclusions: In eyes with early glaucoma, the pRNFL thickness scan seems to be a more accurate SDOCT protocol to identify those with LTG compared with the GCC thickness scan.
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http://dx.doi.org/10.1097/IJG.0000000000000406DOI Listing
October 2016

Naturally occurring NS3 resistance-associated variants in hepatitis C virus genotype 1: Their relevance for developing countries.

Virus Res 2016 09 19;223:140-6. Epub 2016 Jul 19.

Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay. Electronic address:

Hepatitis C virus (HCV) is a major cause of global morbidity and mortality, with an estimated 130-150 million infected individuals worldwide. HCV is a leading cause of chronic liver diseases including cirrhosis and hepatocellular carcinoma. Current treatment options in developing countries involve pegylated interferon-α and ribavirin as dual therapy or in combination with one or more direct-acting antiviral agents (DAA). The emergence of resistance-associated variants (RAVs) after treatment reveals the great variability of this virus leading to a great difficulty in developing effective antiviral strategies. Baseline RAVs detected in DAA treatment-naïve HCV-infected patients could be of great importance for clinical management and outcome prediction. Although the frequency of naturally occurring HCV NS3 protease inhibitor mutations has been addressed in many countries, there are only a few reports on their prevalence in South America. In this study, we investigated the presence of RAVs in the HCV NS3 serine protease region by analysing a cohort of Uruguayan patients with chronic hepatitis C who had not been treated with any DAAs and compare them with the results found for other South American countries. The results of these studies revealed that naturally occurring mutations conferring resistance to NS3 inhibitors exist in a substantial proportion of Uruguayan treatment-naïve patients infected with HCV genotype 1 enrolled in these studies. The identification of these baseline RAVs could be of great importance for patients' management and outcome prediction in developing countries.
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http://dx.doi.org/10.1016/j.virusres.2016.07.008DOI Listing
September 2016

Bayesian coalescent inference reveals high evolutionary rates and diversification of Zika virus populations.

J Med Virol 2016 10 20;88(10):1672-6. Epub 2016 Jun 20.

Molecular Virology Laboratory, CIN, Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay.

Zika virus (ZIKV) is a member of the family Flaviviridae. In 2015, ZIKV triggered an epidemic in Brazil and spread across Latin America. By May of 2016, the World Health Organization warns over spread of ZIKV beyond this region. Detailed studies on the mode of evolution of ZIKV strains are extremely important for our understanding of the emergence and spread of ZIKV populations. In order to gain insight into these matters, a Bayesian coalescent Markov Chain Monte Carlo analysis of complete genome sequences of recently isolated ZIKV strains was performed. The results of these studies revealed a mean rate of evolution of 1.20 × 10(-3) nucleotide substitutions per site per year (s/s/y) for ZIKV strains enrolled in this study. Several variants isolated in China are grouped together with all strains isolated in Latin America. Another genetic group composed exclusively by Chinese strains were also observed, suggesting the co-circulation of different genetic lineages in China. These findings indicate a high level of diversification of ZIKV populations. Strains isolated from microcephaly cases do not share amino acid substitutions, suggesting that other factors besides viral genetic differences may play a role for the proposed pathogenesis caused by ZIKV infection. J. Med. Virol. 88:1672-1676, 2016. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/jmv.24596DOI Listing
October 2016

Geographical and Temporal Structures of Legionella pneumophila Sequence Types in Comunitat Valenciana (Spain), 1998 to 2013.

Appl Environ Microbiol 2015 Oct 31;81(20):7106-13. Epub 2015 Jul 31.

Joint Research Unit Infección y Salud, FISABIO-Universidad de Valencia, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain CIBER en Epidemiología y Salud Pública, Valencia, Spain

Legionella pneumophila is an accidental human pathogen associated with aerosol formation in water-related sources. High recombination rates make Legionella populations genetically diverse, and nearly 2,000 different sequence types (STs) have been described to date for this environmental pathogen. The spatial distribution of STs is extremely heterogeneous, with some variants being present worldwide and others being detected at only a local scale. Similarly, some STs have been associated with disease outbreaks, such as ST578 or ST23. Spain is among the European countries with the highest incidences of reported legionellosis cases, and specifically, Comunitat Valenciana (CV) is the second most affected area in the country. In this work, we aimed at studying the overall diversity of Legionella pneumophila populations found in the period from 1998 to 2013 in 79 localities encompassing 23 regions within CV. To do so, we performed sequence-based typing (SBT) on 1,088 L. pneumophila strains detected in the area from both environmental and clinical sources. A comparison with the genetic structuring detected in a global data set that included 20 European and 7 non-European countries was performed. Our results reveal a level of diversity in CV that can be considered representative of the diversity found in other countries worldwide.
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http://dx.doi.org/10.1128/AEM.02196-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579446PMC
October 2015

An evolutionary insight into Newcastle disease viruses isolated in Antarctica.

Arch Virol 2015 Aug 27;160(8):1893-900. Epub 2015 May 27.

Laboratorio de Virologia Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la Republica, Igua 4225, 11400, Montevideo, Uruguay.

The disease caused by Newcastle disease virus (NDV) is a severe threat to the poultry industry worldwide. Recently, NDV has been isolated in the Antarctic region. Detailed studies on the mode of evolution of NDV strains isolated worldwide are relevant for our understanding of the evolutionary history of NDV. For this reason, we have performed Bayesian coalescent analysis of NDV strains isolated in Antarctica to study evolutionary rates, population dynamics, and patterns of evolution. Analysis of F protein cleavage-site sequences of NDV isolates from Antarctica suggested that these strains are lentogenic. Strains isolated in Antarctica and genotype I reference strain Ulster/67 diverged from ancestors that existed around 1958. The time of the most recent common ancestor (MRCA) was established to be around 1883 for all class II viruses. A mean rate of evolution of 1.78 × 10(-3) substitutions per site per year (s/s/y) was obtained for the F gene sequences of NDV strains examined in this study. A Bayesian skyline plot indicated a decline in NDV population size in the last 25 years. The results are discussed in terms of the possible role of Antarctica in emerging or re-emerging viruses and the evolution of NDV populations worldwide.
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http://dx.doi.org/10.1007/s00705-015-2434-yDOI Listing
August 2015

Hepatitis C virus genetic variability and evolution.

World J Hepatol 2015 Apr;7(6):831-45

Natalia Echeverría, Gonzalo Moratorio, Juan Cristina, Pilar Moreno, Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay.

Hepatitis C virus (HCV) has infected over 170 million people worldwide and creates a huge disease burden due to chronic, progressive liver disease. HCV is a single-stranded, positive sense, RNA virus, member of the Flaviviridae family. The high error rate of RNA-dependent RNA polymerase and the pressure exerted by the host immune system, has driven the evolution of HCV into 7 different genotypes and more than 67 subtypes. HCV evolves by means of different mechanisms of genetic variation. On the one hand, its high mutation rates generate the production of a large number of different but closely related viral variants during infection, usually referred to as a quasispecies. The great quasispecies variability of HCV has also therapeutic implications since the continuous generation and selection of resistant or fitter variants within the quasispecies spectrum might allow viruses to escape control by antiviral drugs. On the other hand HCV exploits recombination to ensure its survival. This enormous viral diversity together with some host factors has made it difficult to control viral dispersal. Current treatment options involve pegylated interferon-α and ribavirin as dual therapy or in combination with a direct-acting antiviral drug, depending on the country. Despite all the efforts put into antiviral therapy studies, eradication of the virus or the development of a preventive vaccine has been unsuccessful so far. This review focuses on current available data reported to date on the genetic mechanisms driving the molecular evolution of HCV populations and its relation with the antiviral therapies designed to control HCV infection.
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http://dx.doi.org/10.4254/wjh.v7.i6.831DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411526PMC
April 2015

Phylogenetic analysis of the neuraminidase gene of pandemic H1N1 influenza A virus circulating in the South American region.

Virus Res 2015 Feb 3;197:1-7. Epub 2014 Dec 3.

Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay. Electronic address:

Molecular characterization of circulating influenza A viruses (IAV) in all regions of the world is essential to detect mutations potentially involved in increased virulence, anti-viral resistance and immune escape. In order to gain insight into these matters, a phylogenetic analysis of the neuraminidase (NA) gene of 146 pandemic H1N1 (H1N1pdm) influenza A virus strains isolated in Argentina, Brazil, Chile, Paraguay, Peru and Uruguay from 2009 to 2013 was performed. Comparison of vaccine strain A/California/7/2009 included in the influenza vaccine recommended for the Southern hemisphere from 2010 through 2013 influenza seasons and strains isolated in South America revealed several amino acid substitutions. Mapping of these substitutions revealed that most of them are located at the surface of the protein and do not interfere with the active site. 3.4% of the strains enrolled in these studies carried the H275Y substitution that confers resistance to oseltamivir. Strains isolated in South America differ from vaccine in two predicted B-cell epitope regions present at positions 102-103 and 351-352 of the NA protein. Moreover, vaccine and strains isolated in Paraguay differ also in an epitope present at position 229. These differences among strains isolated in South America and vaccine strain suggests that these epitopes may not be present in strains isolated in this region. A potential new N-linked glycosylation site was observed in the NA protein of an H1N1pdm IAV strain isolated in Brazil. The results of these studies revealed several genetic and antigenic differences in the NA of H1N1pdm IAV among vaccine and strains circulating in South America. All these findings contribute to our understanding of the course of genetic and antigenic evolution of H1N1pdm IAV populations circulating in the South American region and, consequently, contribute to the study and selection of future and more appropriate vaccines and anti-viral drugs.
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http://dx.doi.org/10.1016/j.virusres.2014.11.008DOI Listing
February 2015

Genome-wide analysis of codon usage bias in Ebolavirus.

Virus Res 2015 Jan 14;196:87-93. Epub 2014 Nov 14.

Laboratorio de Organización y Evolución del Genoma, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.

Ebola virus (EBOV) is a member of the family Filoviridae and its genome consists of a 19-kb, single-stranded, negative sense RNA. EBOV is subdivided into five distinct species with different pathogenicities, being Zaire ebolavirus (ZEBOV) the most lethal species. The interplay of codon usage among viruses and their hosts is expected to affect overall viral survival, fitness, evasion from host's immune system and evolution. In the present study, we performed comprehensive analyses of codon usage and composition of ZEBOV. Effective number of codons (ENC) indicates that the overall codon usage among ZEBOV strains is slightly biased. Different codon preferences in ZEBOV genes in relation to codon usage of human genes were found. Highly preferred codons are all A-ending triplets, which strongly suggests that mutational bias is a main force shaping codon usage in ZEBOV. Dinucleotide composition also plays a role in the overall pattern of ZEBOV codon usage. ZEBOV does not seem to use the most abundant tRNAs present in the human cells for most of their preferred codons.
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http://dx.doi.org/10.1016/j.virusres.2014.11.005DOI Listing
January 2015

Human endogenous retrovirus np9 gene is over expressed in chronic lymphocytic leukemia patients.

Leuk Res Rep 2014 25;3(2):70-2. Epub 2014 Jul 25.

Laboratory of Molecular Virology, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay ; Protein Recombinant Unit, Institut Pasteur, Montevideo, Uruguay.

The human genome contains a large number of endogenous retroviruses (HERVs). Their reactivation has frequently been observed in patients with cancer. Considering their role in the carcinogenesis process, we aimed to study the possible relationship between HERVs gene expression and Chronic Lymphocytic Leukemia (CLL). We focused on two viral genes gag and np9, the latter presumably an oncogene. We found that the transcriptional activity of HERV-K np9 gene was greater in CLL patients than in healthy donors. However, gag expression was not significantly increased. These findings suggest a noteworthy relationship between CLL disease and HERV-K np9 expression.
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http://dx.doi.org/10.1016/j.lrr.2014.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145164PMC
September 2014

[Design, implementation and evaluation of a management model of patient safety in hospitals in Catalonia, Spain].

Med Clin (Barc) 2014 Jul;143 Suppl 1:48-54

Institut Universitari Avedis Donabedian, Barcelona, España.

Since its inception in 2006, the Alliance for Patient Safety in Catalonia has played a major role in promoting and shaping a series of projects related to the strategy of the Ministry of Health, Social Services and Equality, for improving patient safety. One such project was the creation of functional units or committees of safety in hospitals in order to facilitate the management of patient safety. The strategy has been implemented in hospitals in Catalonia which were selected based on criteria of representativeness. The intervention was based on two lines of action, one to develop the model framework and the other for its development. Firstly the strategy for safety management based on EFQM (European Foundation for Quality Management) was defined with the development of standards, targets and indicators to implement security while the second part involved the introduction of tools, methodologies and knowledge to the management support of patient safety and risk prevention. The project was developed in four hospital areas considered higher risk, each assuming six goals for safety management. Some of these targets such as the security control panel or system of adverse event reporting were shared. 23 hospitals joined the project in Catalonia. Despite the different situations in each centre, high compliance was achieved in the development of the objectives. In each of the participating areas the security control panel was developed. Stable structures for safety management were established or strengthened. Training in patient safety played and important role, 1415 professionals participated. Through these kind of projects not only have been introduced programs of proven effectiveness in reducing risks, but they also provide to the facilities a work system that allows autonomy in diagnosis and analysis of the different risk situations or centre specific safety issues.
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http://dx.doi.org/10.1016/j.medcli.2014.07.011DOI Listing
July 2014

Role of Laser Iridoplasty in the Management of Angle Closure Mechanisms other than Pupillary Block.

J Curr Glaucoma Pract 2014 May-Aug;8(2):82-4. Epub 2014 Jun 12.

Associate Professor, Department of Ophthalmology, Glaucoma Services, Fiederal University of São Paulo, Hospital Medicina dos Olhos, São Paulo, Brazil.

Purpose: To investigate the treatment outcomes of argon laser peripheral iridoplasty (ALPI) in angle closure mechanisms other than pupillary block.

Methods: We conducted a comprehensive chart review to evaluate consecutive patients who underwent ALPI due to unsuccessful laser iridotomy (whenever the angles remained occludable) between July 2009 and April-2012. An occludable angle was defined as the posterior trabecular meshwork not visible for ≤180° without indentation on dark room gonioscopy. Eyes with previous incisional surgery or more than 90° of peripheral anterior synechiae were excluded. Main data collected were age, presence of glaucoma, pre- and postlaser intraocular pressure (IOP), angle-status, and underlying angle closure mechanism. Main outcomes were post ALPI angle widening on gonioscopy and magnitude of IOP reduction.

Results: A total of 41 eyes (27 patients) with persistent occlu-dable angles were initially included in the analysis, comprising approximately 14% of the 196 patients (321 eyes) that had under gone laser iridotomy during the predefined period. Among these cases, most common angle closure mechanisms were plateauiris (56%) and lens-induced component (34%). Patients with plateau iris were mostly women and younger than those with lens-induced component (p ≤ 0.03). A total of 35 eyes (23 patients) underwent ALPI (63% had glaucoma). Mean IOP was significantly reduced from 18. 2 ± 4.7 to 14.6 ± 3.8 (p < 0.01), with no significant difference between patients with plateau iris and lens-induced components (p = 0.22). Over 91% of these eyes showed nonoccludable angles following ALPI (follow-up of 11.8 ± 3.3 months).

Conclusion: In this series of middle-aged patients with occlu-dable angles, despite a patent iridotomy, ALPI was a useful procedure independent of the underlying mechanism, leading to angle widening and moderate IOP reduction in most cases. How to cite this article: Prado VG, Dorairaj S, Biteli LG, Sousa AKS, Moreno PAM, Lopes FS, Prata TS. Role of Laser Iridoplasty in the Management of Angle Closure Mechanisms other than Pupillary Block. J Curr Glaucoma Pract 2014;8(2):82-84.
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http://dx.doi.org/10.5005/jp-journals-10008-1166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4741172PMC
March 2016

Low field nuclear magnetic resonance (LF-NMR) relaxometry in hake (Merluccius merluccius, L.) muscle after different freezing and storage conditions.

Food Chem 2014 Jun 21;153:250-7. Epub 2013 Dec 21.

Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), C/José Antonio Novais n-10, E-28040 Madrid, Spain.

Low field NMR T2 transverse relaxation measurements were performed on muscle samples from sixty hake (Merluccius merluccius, L.). Fish fillets from hake stored in ice for 3 and 14 days were subjected to different freezing methods (air blast, liquid nitrogen or walk-in freezer) and storage conditions (-20 and -10°C for 5 days, 8 and 18 weeks). Distribution analysis of T2 data of unfrozen muscle displayed a major band (T21), accounting for 90-92% of the total signal, with a relaxation time centred at 47-60 ms and a broad band with protons of higher mobility between 300 and 800 ms, accounting for 3-5% of the signal. Upon freezing, T21 became wider and an extra band appeared within the range 120-360 ms. Whereas no changes were detected at -20°C, the T21 time constant decreased during frozen storage at -10°C in a similar way for all three freezing methods. The relative abundance of T21 declined with storage time but differences were found as a function of freezing. Results are discussed in the light of morphological alterations and protein denaturation, and it is concluded that LF NMR relaxometry is sensitive to different freezing and frozen storage conditions which can have important implications for the quality of fish muscle.
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http://dx.doi.org/10.1016/j.foodchem.2013.12.060DOI Listing
June 2014

Biphasic regulation of type II phosphatidylinositol-4 kinase by sphingosine: cross talk between glycero- and sphingolipids in the kidney.

Biochim Biophys Acta 2014 Mar 19;1838(3):1003-9. Epub 2013 Dec 19.

Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21949-902, Ilha do Fundão, Rio de Janeiro, Brazil; Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil. Electronic address:

Phosphatidylinositol-4 kinase (PI-4K) is responsible for the generation of phosphatidylinositol-4 phosphate (PtdIns(4)P), a bioactive signaling molecule involved in several biological functions. In this study, we show that sphingosine modulates the activity of the PI-4K isoform associated with the basolateral membranes (BLM) from kidney proximal tubules. Immunoblotting with an anti-α subunit PI-4K polyclonal antibody revealed the presence of two bands of 57 and 62kDa in the BLM. BLM-PI-4K activity retains noteworthy biochemical properties; it is adenosine-sensitive, not altered by wortmanin, and significantly inhibited by Ca(2+) at the μM range. Together, these observations indicate the presence of a type II PI-4K. Endogenous phosphatidylinositol (PI) alone reaches PI-4K half-maximal activity, revealing that even slight modifications in PI levels at the membrane environment promote significant variations in BLM-associated-PI-4K activity. ATP-dependence assays suggested that the Mg.ATP(2-) complex is the true substrate of the enzyme and that free Mg(2+) is an essential cofactor. Another observation indicated that higher concentrations of free ATP are inhibitory. BLM-associated-PI-4K activity was ~3-fold stimulated in the presence of increasing concentration of sphingosine, while in concentrations higher than 0.4mM, in which S1P is pronouncedly formed, there was an inhibitory effect on PtdIns(4)P formation. We propose that a tightly coupled regulatory network involving phosphoinositides and sphingolipids participate in the regulation of key physiological processes in renal BLM carried out by PI-4K.
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http://dx.doi.org/10.1016/j.bbamem.2013.12.007DOI Listing
March 2014

Methylation status regulates lipoprotein lipase expression in chronic lymphocytic leukemia.

Leuk Lymphoma 2013 Aug 21;54(8):1844-8. Epub 2013 Jun 21.

Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.

Among different prognostic factors in chronic lymphocytic leukemia (CLL), we previously demonstrated that lipoprotein lipase (LPL) is associated with an unmutated immunoglobulin profile and clinical poor outcome. Despite the usefulness of LPL for CLL prognosis, its functional role and the molecular mechanism regulating its expression are still open questions. Interaction of CLL B-cells with the tissue microenvironment favors disease progression by promoting malignant B-cell growth. Since tissue methylation can be altered by environmental factors, we investigated the methylation status of the LPL gene and the possibility that overexpression could be associated with microenvironment signals. Our results show that a demethylated state of the LPL gene is responsible for its anomalous expression in unmutated CLL cases and that this expression is dependent on microenvironment signals. Overall, this work proposes that an epigenetic mechanism, triggered by the microenvironment, regulates LPL expression in CLL disease.
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http://dx.doi.org/10.3109/10428194.2013.796057DOI Listing
August 2013

A detailed comparative analysis on the overall codon usage patterns in West Nile virus.

Infect Genet Evol 2013 Mar 16;14:396-400. Epub 2013 Jan 16.

Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.

West Nile virus (WNV) is a member of the family Flaviviridae and its genome consists of an 11-kb single-stranded, positive-sense RNA. WNV is maintained in an enzootic cycle between mosquitoes and birds, but can also infect and cause disease in horses and humans, which serve as incidental dead-end hosts. Understanding the extent and causes of biases in codon usage is essential to the comprehension of viral evolution. In this study, we performed a comprehensive analysis of 449 WNV strains, for which complete genome sequences are available. Effective number of codons (ENC) indicates that the overall codon usage among WNV strains is only slightly biased. Codon adaptation index (CAI) values found for WNV genes are different from the CAI values found for human genes. The relative synonymous codon usage among WNV strains isolated from birds, equines, humans and mosquitoes are roughly similar and are influenced by the relative dinucleotide frequencies. Taking together, the results of this work suggest that WNV genomic biases are the result of the evolution of genome composition, the need to escape the antiviral cell responses and a dynamic process of mutation and selection to re-adapt its codon usage to different environments.
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http://dx.doi.org/10.1016/j.meegid.2013.01.001DOI Listing
March 2013