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1.
Am J Hum Genet ; 111(6): 1018-1034, 2024 06 06.
Artículo en Inglés | MEDLINE | ID: mdl-38749427

RESUMEN

Evolutionary changes in the hepatitis B virus (HBV) genome could reflect its adaptation to host-induced selective pressure. Leveraging paired human exome and ultra-deep HBV genome-sequencing data from 567 affected individuals with chronic hepatitis B, we comprehensively searched for the signatures of this evolutionary process by conducting "genome-to-genome" association tests between all human genetic variants and viral mutations. We identified significant associations between an East Asian-specific missense variant in the gene encoding the HBV entry receptor NTCP (rs2296651, NTCP S267F) and mutations within the receptor-binding region of HBV preS1. Through in silico modeling and in vitro preS1-NTCP binding assays, we observed that the associated HBV mutations are in proximity to the NTCP variant when bound and together partially increase binding affinity to NTCP S267F. Furthermore, we identified significant associations between HLA-A variation and viral mutations in HLA-A-restricted T cell epitopes. We used in silico binding prediction tools to evaluate the impact of the associated HBV mutations on HLA presentation and observed that mutations that result in weaker binding affinities to their cognate HLA alleles were enriched. Overall, our results suggest the emergence of HBV escape mutations that might alter the interaction between HBV PreS1 and its cellular receptor NTCP during viral entry into hepatocytes and confirm the role of HLA class I restriction in inducing HBV epitope variations.


Asunto(s)
Virus de la Hepatitis B , Mutación , Transportadores de Anión Orgánico Sodio-Dependiente , Simportadores , Humanos , Epítopos de Linfocito T/genética , Epítopos de Linfocito T/inmunología , Genoma Viral , Genómica/métodos , Antígenos de Superficie de la Hepatitis B/genética , Virus de la Hepatitis B/genética , Hepatitis B Crónica/virología , Hepatitis B Crónica/genética , Antígenos de Histocompatibilidad Clase I/genética , Antígenos de Histocompatibilidad Clase I/metabolismo , Interacciones Huésped-Patógeno/genética , Interacciones Huésped-Patógeno/inmunología , Transportadores de Anión Orgánico Sodio-Dependiente/genética , Transportadores de Anión Orgánico Sodio-Dependiente/metabolismo , Simportadores/genética , Simportadores/metabolismo
2.
Clin Genet ; 105(1): 62-71, 2024 01.
Artículo en Inglés | MEDLINE | ID: mdl-37853563

RESUMEN

Genomic medicine has been transformed by next-generation sequencing (NGS), inclusive of exome sequencing (ES) and genome sequencing (GS). Currently, ES is offered widely in clinical settings, with a less prevalent alternative model consisting of hybrid programs that incorporate research ES along with clinical patient workflows. We were among the earliest to implement a hybrid ES clinic, have provided diagnoses to 45% of probands, and have identified several novel candidate genes. Our program is enabled by a cost-effective investment by the health system and is unique in encompassing all the processes that have been variably included in other hybrid/clinical programs. These include careful patient selection, utilization of a phenotype-agnostic bioinformatics pipeline followed by manual curation of variants and phenotype integration by clinicians, close collaborations between the clinicians and the bioinformatician, pursuit of interesting variants, communication of results to patients in categories that are predicated upon the certainty of a diagnosis, and tracking changes in results over time and the underlying mechanisms for such changes. Due to its effectiveness, scalability to GS and its resource efficiency, specific elements of our paradigm can be incorporated into existing clinical settings, or the entire hybrid model can be implemented within health systems that have genomic medicine programs, to provide NGS in a scientifically rigorous, yet pragmatic setting.


Asunto(s)
Biología Computacional , Exoma , Humanos , Exoma/genética , Fenotipo , Secuenciación del Exoma , Secuenciación de Nucleótidos de Alto Rendimiento
3.
Environ Res ; 216(Pt 3): 114659, 2023 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-36328221

RESUMEN

Photochemical transformation of pharmaceuticals plays an important role in their natural attenuation, especially in lagoon-based wastewater treatment plants and surface waters receiving substantial sunlight. In this study, the photodegradation of five important pharmaceuticals was studied in samples obtained from a wastewater treatment plant and surface water sources. Batch photodegradation studies for a mixture of pharmaceuticals (diclofenac, sulfamethoxazole, acetaminophen, carbamazepine and gemfibrozil) were carried out in a photochemical reactor. Multiple aliquots of samples removed from the reactor during the experiment were analyzed through high-performance liquid chromatography (HPLC) coupled to a photodiode array (PDA) detector. Intermediate products formed due to photodegradation were identified by ultra-high-performance liquid chromatography coupled with a time-of-flight mass spectrometry (UHPLC-MS/MS). Diclofenac and sulfamethoxazole were found to undergo direct photodegradation due to strong light absorption, whereas the indirect route of photosensitized degradation in the presence of dissolved organic matter (DOM) and model humic acid was significant for acetaminophen, carbamazepine, and gemfibrozil. The reactive radicals such as hydroxyl (OH•), singlet oxygen (1O2) and excited states of DOM (*DOM) were predominantly responsible for the indirect photodegradation of acetaminophen, gemfibrozil and carbamazepine, respectively. Computational analysis revealed that chlorine and carbon atoms belonging to the benzene ring of diclofenac were more reactive to radical attack. Sulfamethoxazole photodegradation occurred through oxidation of the NH2 group. Acetaminophen was more susceptible to electrophilic radical attack at the O-11, and N-7 positions and carbon atoms ortho to the phenolic oxygen and the amine group. The double bonds between C-7, C-8 and C-13 were the most reactive sites for carbamazepine that participated in the phototransformation pathway. Organic matter plays a critical role in the photodegradation of emerging contaminants. The coupling of DFT calculations with UHPLC-MS/MS analysis provided insights on key functional groups participating in the phototransformation pathway. Thus, both parent pharmaceuticals and the photodegradation intermediates should be considered during wastewater treatment.


Asunto(s)
Aguas Residuales , Contaminantes Químicos del Agua , Fotólisis , Aguas Residuales/química , Gemfibrozilo/análisis , Espectrometría de Masas en Tándem , Diclofenaco , Acetaminofén , Contaminantes Químicos del Agua/análisis , Sulfametoxazol , Carbono , Carbamazepina/análisis , Preparaciones Farmacéuticas
4.
Immun Ageing ; 20(1): 43, 2023 Aug 29.
Artículo en Inglés | MEDLINE | ID: mdl-37644610

RESUMEN

BACKGROUND: Women/females report more adverse events (AE) following immunization than men/males for many vaccines, including the influenza and COVID-19 vaccines. This discrepancy is often dismissed as a reporting bias, yet the relative contributions of biological sex and gender are poorly understood. We investigated the roles of sex and gender in the rate of AE following administration of the high-dose seasonal influenza vaccine to older adults (≥ 75 years) using an AE questionnaire administered 5-8 days post-vaccination. Participant sex (male or female) was determined by self-report and a gender score questionnaire was used to assign participants to one of four gender categories (feminine, masculine, androgynous, or undifferentiated). Sex steroid hormones and inflammatory cytokines were measured in plasma samples collected prior to vaccination to generate hypotheses as to the biological mechanism underpinning the AE reported. RESULTS: A total of 423 vaccines were administered to 173 participants over four influenza seasons (2019-22) and gender data were available for 339 of these vaccinations (2020-22). At least one AE was reported following 105 vaccinations (25%), by 23 males and 82 females. The majority of AE occurred at the site of injection, were mild, and transient. The odds of experiencing an AE were 3-fold greater in females than males and decreased with age to a greater extent in females than males. The effects of gender, however, were not statistically significant, supporting a central role of biological sex in the occurrence of AE. In males, estradiol was significantly associated with IL-6 and with the probability of experiencing an AE. Both associations were absent in females, suggesting a sex-specific effect of estradiol on the occurrence of AE that supports the finding of a biological sex difference. CONCLUSIONS: These data support a larger role for biological sex than for gender in the occurrence of AE following influenza vaccination in older adults and provide an initial investigation of hormonal mechanisms that may mediate this sex difference. This study highlights the complexities of measuring gender and the importance of assessing AE separately for males and females to better understand how vaccination strategies can be tailored to different subsets of the population.

5.
BMC Infect Dis ; 21(1): 570, 2021 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-34126945

RESUMEN

BACKGROUND: Cholera has been present and recurring in Zambia since 1977. However, there is a paucity of data on genetic relatedness and diversity of the Vibrio cholerae isolates responsible for these outbreaks. Understanding whether the outbreaks are seeded from existing local isolates or if the outbreaks represent separate transmission events can inform public health decisions. RESULTS: Seventy-two V. cholerae isolates from outbreaks in 2009/2010, 2016, and 2017/2018 in Zambia were characterized using multilocus variable number tandem repeat analysis (MLVA) and whole genome sequencing (WGS). The isolates had eight distinct MLVA genotypes that clustered into three MLVA clonal complexes (CCs). Each CC contained isolates from only one outbreak. The results from WGS revealed both clustered and dispersed single nucleotide variants. The genetic relatedness of isolates based on WGS was consistent with the MLVA, each CC was a distinct genetic lineage and had nearest neighbors from other East African countries. In Lusaka, isolates from the same outbreak were more closely related to themselves and isolates from other countries than to isolates from other outbreaks in other years. CONCLUSIONS: Our observations are consistent with i) the presence of random mutation and alternative mechanisms of nucleotide variation, and ii) three separate transmission events of V. cholerae into Lusaka, Zambia. We suggest that locally, case-area targeted invention strategies and regionally, well-coordinated plans be in place to effectively control future cholera outbreaks.


Asunto(s)
Cólera/transmisión , Vibrio cholerae O1/genética , Vibrio cholerae O1/aislamiento & purificación , Cólera/epidemiología , Cólera/virología , Análisis por Conglomerados , Brotes de Enfermedades , Variación Genética , Genotipo , Humanos , Repeticiones de Minisatélite/genética , Vibrio cholerae O1/clasificación , Secuenciación Completa del Genoma , Zambia/epidemiología
6.
Philos Trans A Math Phys Eng Sci ; 379(2211): 20190459, 2021 Nov 29.
Artículo en Inglés | MEDLINE | ID: mdl-34628948

RESUMEN

Lithium-rich oxychloride antiperovskites are promising solid electrolytes for enabling next-generation batteries. Here, we report a comprehensive study varying Li+ concentrations in [Formula: see text] using ab initio molecular dynamics simulations. The simulations accurately capture the complex interactions between Li+ vacancies ([Formula: see text]), the dominant mobile species in [Formula: see text]. The [Formula: see text] polarize and distort the host lattice, inducing additional non-vacancy-mediated diffusion mechanisms and correlated diffusion events that reduce the activation energy barrier at concentrations as low as 1.5% [Formula: see text]. Our analyses of discretized diffusion events in both space and time illustrate the critical interplay between correlated dynamics, polarization and local distortion in promoting ionic conductivity in [Formula: see text]. This article is part of the Theo Murphy meeting issue 'Understanding fast-ion conduction in solid electrolytes'.


Asunto(s)
Electrólitos , Litio , Suministros de Energía Eléctrica , Simulación de Dinámica Molecular
7.
Philos Trans A Math Phys Eng Sci ; 379(2211): 20190467, 2021 Nov 29.
Artículo en Inglés | MEDLINE | ID: mdl-34628943

RESUMEN

Superionic solid electrolytes have widespread use in energy devices, but the fundamental motivations for fast ion conduction are often elusive. In this Perspective, we draw upon atomistic simulations of a wide range of superionic conductors to illustrate some ways frustration can lower diffusion cation barriers in solids. Based on our studies of halides, oxides, sulfides and hydroborates and a survey of published reports, we classify three types of frustration that create competition between different local atomic preferences, thereby flattening the diffusive energy landscape. These include chemical frustration, which derives from competing factors in the anion-cation interaction; structural frustration, which arises from lattice arrangements that induce site distortion or prevent cation ordering; and dynamical frustration, which is associated with temporary fluctuations in the energy landscape due to anion reorientation or cation reconfiguration. For each class of frustration, we provide detailed simulation analyses of various materials to show how ion mobility is facilitated, resulting in stabilizing factors that are both entropic and enthalpic in origin. We propose the use of these categories as a general construct for classifying frustration in superionic conductors and discuss implications for future development of suitable descriptors and improvement strategies. This article is part of the Theo Murphy meeting issue 'Understanding fast-ion conduction in solid electrolytes'.

8.
Environ Res ; 180: 108651, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31648071

RESUMEN

A hydrothermally synthesized rhodium/antimony co-doped TiO2 nanorod and titanate nanotube (RS-TONR/TNT) composite was prepared for removal of heavy metals and organic pollutants from water under visible light irradiation. The composite provides the dual function of simultaneous adsorption of heavy metal ions and enhanced degradation of dissolved organic compounds. Acid treatment transformed titanate nanotubes to irregular tubular structures distributed homogeneously over untransformed RS/TONRs. Synergistic removal and degradation was studied with various heavy metals, Orange (II) dye, and Bisphenol A. The adsorption capacity of the composite for heavy metal ions was Pb(II) > Cd(II) > Cu(II) > Zn(II). The adsorbed metals enhanced photocatalytic degradation of the organic pollutants, but Cu was most effective, with degradation exceeding 70% for the dye and 80% for Bisphenol A after 5 h of treatment. Photocatalytic activity was enhanced more by adsorption than photodeposition of Cu ions. A decrease in XRD rutile peak intensity with adsorbed metal indicates a change in crystallinity which may enhance photocatalytic activity. Thick and bulging nanostructures in FE-SEM images signify ion adsorption within titanate pores. BET analysis indicated titanate nanotubes with adsorbed metal are mesoporous but their tubular structure persists. XPS showed more active Cu 2p3/2 states under light, supporting an active role of Cu+ in photocatalytic ROS generation. Detection of ROS and Cu species using methanol, EDTA, pCBA, and benzoic acid probes provided strong evidence for degradation via a charge transfer mechanism. Findings demonstrate the potential of the RS-TONR/TNT composite for simultaneous removal of heavy metals and degradation of organic pollutants.


Asunto(s)
Metales Pesados , Trinitrotolueno , Contaminantes Químicos del Agua , Adsorción , Luz
9.
Bioprocess Biosyst Eng ; 43(5): 821-830, 2020 May.
Artículo en Inglés | MEDLINE | ID: mdl-31919603

RESUMEN

Bacillus bacteria have major utility in large-scale production of industrial enzymes, among which proteases have particular importance. B. subtilis B22, an aerobic and chemotrophic strain, was isolated from kimchi and identified by 16S rRNA gene sequencing. Extracellular protease production was determined in basic medium, with 1% (w/v) casein as substrate, by submerged fermentation at 37 °C under blue, green, red and white light-emitting diodes (LEDs), white fluorescent light and darkness. Fermentation under blue LEDs maximized protease production (110.79 ± 1.8 U/mL at 24 h). Various agricultural waste products enhanced production and groundnut oil cake yielded the most protease (334 ± 1.8 U/mL at 72 h). Activity and stability of the purified protease were optimum at pH 7-10 and 20-60 °C. Activity increased in the presence of Ca2+, Mg2+ and Mn2+, while Fe2+, Zn2+, Co2+ and Cu2+ moderated activity, and Ni2+ and Hg2+ inhibited activity. Activity was high (98%) in the presence of ethylenediaminetetraacetic acid (EDTA) but inhibited by phenylmethanesulfonyl fluoride (PMSF). The protease was unaffected by nonionic surfactants, tolerated an anionic surfactant and oxidizing agents, and was compatible with multiple organic solvents. These properties suggest utility of protease produced by B. subtilis B22 under blue LEDs for industrial applications.


Asunto(s)
Agricultura , Bacillus subtilis/crecimiento & desarrollo , Proteínas Bacterianas/biosíntesis , Luz , Péptido Hidrolasas/biosíntesis , Administración de Residuos
10.
Environ Geochem Health ; 42(2): 443-460, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31325112

RESUMEN

Island populations are rarely studied for risk of arsenic (As) poisoning. As poisoning, multimetal contamination and people's perceptions of health risks were assessed on India's Majuli Island, the largest inhabited river island in the world. This holistic approach illustrated the association of groundwater contamination status with consequent health risk by measuring levels of inorganic arsenic (iAs) in groundwater, borehole sediment and biological samples (hair, nails and urine). Piper and Gibbs's plots discerned the underlying hydrogeochemical processes in the aquifer. Demographic data and qualitative factors were evaluated to assess the risks and uncertainties of exposure. The results exhibited significant enrichment of groundwater with As, Mn and Fe along with significant body burden. Maximum Hazard Index values indicated severe non-carcinogenic health impacts as well as a significantly elevated risk of cancer for both adults and children. Most (99%) of the locally affected population did not know about the adverse health impacts of metal contamination, and only 15% understood bodily ailments and health issues. Various aspects of the island environment were used to elucidate the status of contamination and future risk of disease. A projection showed adverse health outcomes rising significantly, especially among the young population of Majuli, due to overexposure to not only As but also Ba, Mn and Fe.


Asunto(s)
Arsénico/análisis , Exposición a Riesgos Ambientales/análisis , Agua Subterránea/química , Contaminantes Químicos del Agua/análisis , Conocimientos, Actitudes y Práctica en Salud , Humanos , India , Islas , Metales Pesados/análisis , Medición de Riesgo
11.
Genes Immun ; 20(2): 112-120, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-29535370

RESUMEN

Herpes simplex virus type 2 (HSV-2) is an incurable viral infection with severity ranging from asymptomatic to frequent recurrences. The viral shedding rate has been shown as a reproducible HSV-2 severity end point that correlates with lesion rates. We used a genome-wide association study (GWAS) to investigate the role of common human genetic variation in HSV-2 severity. We performed a GWAS on 223 HSV-2-positive participants of European ancestry. Severity was measured by viral shedding rate, as defined by the percent of days PCR+ for HSV-2 DNA over at least 30 days. Analyses were performed under linear regression models, adjusted for age, sex, and ancestry. There were no genome-wide significant (p < 5E-08) associations with HSV-2 viral shedding rate. The top nonsignificant SNP (rs75932292, p = 6.77E-08) associated with HSV-2 viral shedding was intergenic, with the nearest known biologically interesting gene (ABCA1) ~130 kbp downstream. Several other SNPs approaching significance were in or near genes with viral or neurological associations, including four SNPs in KIF1B. The current study is the first comprehensive genome-wide investigation of human genetic variation in virologic severity of established HSV-2 infection. However, no significant associations were observed with HSV-2 virologic severity, leaving the exact role of human variation in HSV-2 severity unclear.


Asunto(s)
Herpes Simple/genética , Polimorfismo de Nucleótido Simple , Transportador 1 de Casete de Unión a ATP/genética , Adulto , Anciano , Femenino , Estudio de Asociación del Genoma Completo , Herpes Simple/virología , Herpesvirus Humano 2/patogenicidad , Humanos , Cinesinas/genética , Masculino , Persona de Mediana Edad
12.
Bioprocess Biosyst Eng ; 42(4): 529-539, 2019 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-30542760

RESUMEN

Light and bacteria can be used in combination to enhance secondary metabolite production during fermentation. Red yeast rice powder (RYRP) was inoculated with Bacillus subtilis (B2) isolated from freshwater seafood and incubated under light-emitting diodes (LEDs) of different colors (blue, green, red, white), fluorescent white light, and in darkness. Blue LED-mediated fermentation with B2 significantly enhanced production of phenolic compounds (68.4 ± 1 mg GAE/g DW) and flavonoids (51.7 ± 1 mg QE/g DW) compared to white light and darkness. Total antioxidant activity of RYRP extract after fermentation with B2 was > 77%; hydroxyl radical and superoxide scavenging were > 66%. DPPH (2,2-diphenyl-1-picryl-hydrazyl-hydrate) and ABTS (2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid)) radical scavenging activities were 51% and > 67%, respectively. Reducing power was approximately twice that of extract from RYRP without B2. FTIR analysis showed a high content of hydroxyl, nitrile and carboxylic groups in the extract. Derivatives of cinnamic, benzoic and phophinodithioic acid, and quinazolinone were identified by GC-MS. Findings show that fermenting RYRP with B. subtilis B2 under blue LEDs enhances production of secondary metabolites, which should have applications in industrial fermentation processes.


Asunto(s)
Antioxidantes/metabolismo , Bacillus subtilis/crecimiento & desarrollo , Productos Biológicos/química , Luz
13.
Prep Biochem Biotechnol ; 49(2): 143-150, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-30636516

RESUMEN

A chemotrophic, aerobic bacterial strain, Bacillus subtilis B2, was used to produce amylase by submerged fermentation under different light sources. SDS-PAGE indicated that the 55 kDa enzyme belonged to the α-amylase group. B2 was incubated in basal media with 1% soluble starch (pH 7.0) under blue, green, red, and white light-emitting diodes (LEDs), and white fluorescent light. Fermentation under blue LEDs maximized amylase production (180.59 ± 1.6 U/mL at 24 h). Production at 48 h increased to 310.56 ± 1.6 U/mL with 5% glucose as a simple carbon source and to 300.51 ± 1.7 U/mL with 5% groundnut oil cake as an agricultural waste substrate. Activity and stability of the amylase were greatest at pH 7.0 and 45-55 °C. Na+, Ca2+, Mg2+, Co2+, Ba2+, and K+ increased activity, while Ni2+, Hg2+, Mn2+, Cu2+, Fe3+, and Zn2+ inhibited activity. EDTA, PMSF and DTNB reduced activity by 50% or more, while tetrafluoroethylene and 1,10-phenanthroline reduced activity by 30%. The amylase was highly tolerant of the surfactants, compatible with organic solvents, oxidizing agents and the reducing agents reduced activity. These properties suggest utility of amylase produced by B. subtilis B2 under blue LED-mediated fermentation for industrial applications.


Asunto(s)
Bacillus subtilis/metabolismo , Proteínas Bacterianas/metabolismo , Microbiología Industrial/métodos , alfa-Amilasas/metabolismo , Bacillus subtilis/química , Bacillus subtilis/efectos de la radiación , Proteínas Bacterianas/química , Cationes Bivalentes/metabolismo , Estabilidad de Enzimas , Fermentación , Concentración de Iones de Hidrógeno , Luz , Metales/metabolismo , Temperatura , alfa-Amilasas/química
14.
Clin Infect Dis ; 66(12): 1953-1956, 2018 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-29522085
15.
Proc Natl Acad Sci U S A ; 112(47): 14658-63, 2015 Nov 24.
Artículo en Inglés | MEDLINE | ID: mdl-26553974

RESUMEN

Previous genome-wide association studies (GWAS) of HIV-1-infected populations have been underpowered to detect common variants with moderate impact on disease outcome and have not assessed the phenotypic variance explained by genome-wide additive effects. By combining the majority of available genome-wide genotyping data in HIV-infected populations, we tested for association between ∼8 million variants and viral load (HIV RNA copies per milliliter of plasma) in 6,315 individuals of European ancestry. The strongest signal of association was observed in the HLA class I region that was fully explained by independent effects mapping to five variable amino acid positions in the peptide binding grooves of the HLA-B and HLA-A proteins. We observed a second genome-wide significant association signal in the chemokine (C-C motif) receptor (CCR) gene cluster on chromosome 3. Conditional analysis showed that this signal could not be fully attributed to the known protective CCR5Δ32 allele and the risk P1 haplotype, suggesting further causal variants in this region. Heritability analysis demonstrated that common human genetic variation-mostly in the HLA and CCR5 regions-explains 25% of the variability in viral load. This study suggests that analyses in non-European populations and of variant classes not assessed by GWAS should be priorities for the field going forward.


Asunto(s)
Predisposición Genética a la Enfermedad , VIH-1/genética , Interacciones Huésped-Patógeno/genética , Polimorfismo de Nucleótido Simple/genética , Carga Viral/genética , Adulto , Alelos , Aminoácidos/genética , Cromosomas Humanos Par 3/genética , Estudio de Asociación del Genoma Completo , Antígenos HLA-B/genética , Humanos , Patrón de Herencia/genética , Mapeo Físico de Cromosoma , Receptores CCR5/genética
16.
J Infect Dis ; 216(9): 1063-1069, 2017 11 27.
Artículo en Inglés | MEDLINE | ID: mdl-28968755

RESUMEN

Background: Previous genetic association studies of human immunodeficiency virus-1 (HIV-1) progression have focused on common human genetic variation ascertained through genome-wide genotyping. Methods: We sought to systematically assess the full spectrum of functional variation in protein coding gene regions on HIV-1 progression through exome sequencing of 1327 individuals. Genetic variants were tested individually and in aggregate across genes and gene sets for an influence on HIV-1 viral load. Results: Multiple single variants within the major histocompatibility complex (MHC) region were observed to be strongly associated with HIV-1 outcome, consistent with the known impact of classical HLA alleles. However, no single variant or gene located outside of the MHC region was significantly associated with HIV progression. Set-based association testing focusing on genes identified as being essential for HIV replication in genome-wide small interfering RNA (siRNA) and clustered regularly interspaced short palindromic repeats (CRISPR) studies did not reveal any novel associations. Conclusions: These results suggest that exonic variants with large effect sizes are unlikely to have a major contribution to host control of HIV infection.


Asunto(s)
Secuenciación del Exoma , Infecciones por VIH/genética , Infecciones por VIH/virología , VIH-1/genética , Interacciones Huésped-Patógeno/genética , Carga Viral/genética , Adulto , Femenino , Predisposición Genética a la Enfermedad , Variación Genética , Genotipo , Humanos , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple
17.
Ann Hum Genet ; 81(1): 27-34, 2017 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-28084001

RESUMEN

Common single-nucleotide variation in the host accounts for 25% of the variability in the plasma levels of HIV during the clinical latency stage (viral load set point). However, the role of rare variants and copy number variants remains relatively unexplored. Previous work has suggested copy number variation of a cluster of ß-defensin genes affects HIV load in treatment-naïve sub-Saharan Africans and rate of response to antiretroviral treatment. Here we analyse a total of 1827 individuals from two cohorts of HIV-infected individuals from Europe and sub-Saharan Africa to investigate the role of ß-defensin copy number variation on HIV load at set point. We find no evidence for association of copy number with viral load. We also compare distribution of ß-defensin copy number between European cases and controls and find no differences, arguing against a role of ß-defensin copy number in HIV acquisition. Taken together, our data argue against an effect of copy number variation of the ß-defensin region in the spontaneous control of HIV infection.


Asunto(s)
Síndrome de Inmunodeficiencia Adquirida/genética , VIH-1/fisiología , beta-Defensinas/genética , Síndrome de Inmunodeficiencia Adquirida/virología , Adulto , Variaciones en el Número de Copia de ADN , Progresión de la Enfermedad , Femenino , Dosificación de Gen , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Humanos , Masculino , Persona de Mediana Edad , Carga Viral
18.
Phys Chem Chem Phys ; 19(34): 22646-22658, 2017 Aug 30.
Artículo en Inglés | MEDLINE | ID: mdl-28795705

RESUMEN

Mg(BH4)2 is a promising solid-state hydrogen storage material, releasing 14.9 wt% hydrogen upon conversion to MgB2. Although several dehydrogenation pathways have been proposed, the hydrogenation process is less well understood. Here, we present a joint experimental-theoretical study that elucidates the key atomistic mechanisms associated with the initial stages of hydrogen uptake within MgB2. Fourier transform infrared, X-ray absorption, and X-ray emission spectroscopies are integrated with spectroscopic simulations to show that hydrogenation can initially proceed via direct conversion of MgB2 to Mg(BH4)2 complexes. The associated energy landscape is mapped by combining ab initio calculations with barriers extracted from the experimental uptake curves, from which a kinetic model is constructed. The results from the kinetic model suggest that initial hydrogenation takes place via a multi-step process: molecular H2 dissociation, likely at Mg-terminated MgB2 surfaces, is followed by migration of atomic hydrogen to defective boron sites, where the formation of stable B-H bonds ultimately leads to the direct creation of Mg(BH4)2 complexes without persistent BxHy intermediates. Implications for understanding the chemical, structural, and electronic changes upon hydrogenation of MgB2 are discussed.

19.
Biostatistics ; 16(2): 268-80, 2015 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-25270736

RESUMEN

Host genetics studies of HIV-1 acquisition are critically important for the identification of new targets for drug and vaccine development. Analyses of such studies typically focus on pairwise comparisons of three different groups: HIV-1 positive individuals, HIV-1 high-risk seronegative individuals, and population controls. Because there is a clear expectation of how gene frequencies of risk or protective alleles would be ordered in the three groups, we are able to construct a statistical framework that offers a consistent increase in power over a wide-range of the magnitude of risk/protective effects. In this paper, we develop tests that constrain the alternative hypothesis to appropriately reflect risk or protective trends jointly across the three groups and show that they lead to a substantial increase in power over the naive pairwise approach. We develop both likelihood-ratio and score statistics that test for genetic effects across the three groups while constraining the alternative hypothesis to reflect biologically motivated trends of risk or protection. The asymptotic distribution of both statistics (likelihood ratio and score) is derived. We investigate the performance of our approach via extensive simulation studies using a biologically motivated model of HIV-1 acquisition, and find that our proposed approach leads to an increase in power of roughly 10-28%. We illustrate our approach with an analysis of the effect of the CCR5Δ32 mutation on HIV acquisition.


Asunto(s)
Interpretación Estadística de Datos , Predisposición Genética a la Enfermedad , Infecciones por VIH/genética , Infecciones por VIH/transmisión , Modelos Teóricos , Humanos , Factores Protectores , Receptores CCR5/genética , Factores de Riesgo
20.
Pediatr Dermatol ; 33(2): e106-8, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27001331

RESUMEN

Hair follicle nevi are rare, benign, congenital hamartomas that usually occur in the distribution of the first brachial arch. Histopathologically, the distinction between hair follicle nevus, trichofolliculoma, and accessory tragus has recently come into question, and it may be that they are all on a spectrum of the same condition. We report the case of a 7-day-old boy who presented with a "tag"-like lesion on his midline chin that had been present since birth. Biopsy of the lesion proved it to be a hair follicle nevus.


Asunto(s)
Enfermedades del Cabello/patología , Folículo Piloso/patología , Nevo/patología , Neoplasias Cutáneas/patología , Mentón/patología , Diagnóstico Diferencial , Humanos , Lactante , Recién Nacido , Masculino
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