Ten millennia of hepatitis B virus evolution

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic

Determinación de HLA en pacientes con Síndrome de Parry Romberg atendidos en el Servicio de Cirugía Plástica y Reconstructiva del Hospital General "Dr. Manuel Gea González"

Introducción y Objetivo. El síndrome de Parry Romberg se caracteriza por atrofia hemifacial progresiva; afecta piel y tejidos blandos y en ocasiones provoca también atrofia de músculos, cartílago y estructuras óseas subyacentes. Su diagnóstico diferencial incluye: esclerodermia generalizada, morfea y síndrome de CREST. Las alteraciones en piel se asocian con variantes alélicas (polimórficas) del sistema HLA (antígeno leucocitario humano). La esclerodermia se ha asociado con HLA DR11, el CREST con DR1 y DR3, en tanto que la morfea no parece asociarse a genes del HLA en población mexicana. El propósito de este trabajo es explorar la posibilidad de asociación del síndrome de Parry Romberg con algún alelo del sistema HLA con el fin de entender el mecanismo fisiopatogénico y el probable papel de la etnicidad en la prevalencia e incidencia de esta enfermedad en individuos mestizos mexicanos. Material y método. Estudiamos 24 pacientes con Parry Romberg, de la consulta externa de Cirugía Plástica y Reconstructiva del Hospital General "Dr. Manuel Gea González" de la Ciudad de México. El diagnóstico se basó en hallazgos clínicos, imagenología e histopatología de las lesiones dérmicas. Establecimos las frecuencias génicas y haplotípicas de los antígenos del sistema HLA en los 24 pacientes (48 haplotipos). El estudio incluyó los loci HLA A, B, DR, DQ. Comparamos los resultados con las frecuencias presentes en un grupo de 99 controles mestizos mexicanos sin antecedentes de enfermedades autoinmunes y/o metabólicas. Analizamos las diferencias en las frecuencias génicas mediante estadística no paramétrica que incluyó prueba de Chi cuadrado y exacta de Fisher, además de determinación de RM (razón de momios) e intervalos de confianza de 95%. Resultados. Encontramos en los pacientes con Parry Romberg aumento significativo del HLA DRB1*16 (frecuencia génica: 14% en SPR vs 1% en normales. p=0.002, OR: 6.5, IC 95%: 1.9-21.7) y disminución del HLA DR7 (2% en SPR vs 11% en sujetos sanos. p=0.03, OR: 0.17, IC 95% 0.02-1.2) Además, que el HLA DR16 es parte de los haplotipos HLA- DRB1*16, DQB1*0301, en combinación con los alelos HLA-B*39, B*15, y B*35. En población sana el alelo de DQ es DQB0502. Conclusiones. A nuestro conocimiento, nunca antes se había realizado un estudio a esta escala y de ésta naturaleza en Parry Romberg a nivel mundial. Los datos sugieren que el haplotipo de riesgo para Parry Romberg es HLA-DRB1*16- DQB1*0301. Dado que este haplotipo es de origen indígena, sugiere que el mestizo mexicano que padece el síndrome está influido por el fondo genético amerindio, y puesto que los alelos de riesgo (DR11, DR1 y DR3) para las enfermedades típicamente relacionadas al síndrome estuvieron disminuidos, sugiere que el Síndrome de Parry Romberg es una entidad clínica independiente, única y extraordinaria

Origin and Health Status of First-Generation Africans from Early Colonial Mexico

The forced relocation of several thousand Africans during Mexico’s historic period has so far been documented mostly through archival sources, which provide only sparse detail on their origins and lived experience. Here, we employ a bioarchaeological approach to explore the life history of three 16th century Africans from a mass burial at the San José de los Naturales Royal Hospital in Mexico City. Our approach draws together ancient genomic data, osteological analysis, strontium isotope data from tooth enamel, δ13C and δ15N isotope data from dentine, and ethnohistorical information to reveal unprecedented detail on their origins and health. Analyses of skeletal features, radiogenic isotopes, and genetic data from uniparental, genome-wide, and human leukocyte antigen (HLA) markers are consistent with a Sub-Saharan African origin for all three individuals. Complete genomes of Treponema pallidum sub. pertenue (causative agent of yaws) and hepatitis B virus (HBV) recovered from these individuals provide insight into their health as related to infectious disease. Phylogenetic analysis of both pathogens reveals their close relationship to strains circulating in current West African populations, lending support to their origins in this region. The further relationship between the treponemal genome retrieved and a treponemal genome previously typed in an individual from Colonial Mexico highlights the role of the transatlantic slave trade in the introduction and dissemination of pathogens into the New World. Putting together all lines of evidence, we were able to create a biological portrait of three individuals whose life stories have long been silenced by disreputable historical events

Bacteria from Jatropha curcas rhizosphere, degrades aromatic hydrocarbons and promotes growth in Zea mays

The rhizosphere is one of the most important reservoirs of microorganisms. Because of the microbial metabolic activities, these can be used for various biotechnological, agricultural and environmental purposes. In this study we evaluated five genetically related bacterial strains; Pseudomonas aeruginosa N7B1 (MG457074), Pseudomonas sp. (MG457075), Pseudomonas sp., Bf1 (MG457076) and Pseudomonas aeruginosa F23 (MG457077), isolated from Jatropha curcas rhizosphere, capable of growing and degradating benzene and phenanthrene. The hydrocarbon degradation by these strains was quantified by gas chromatography coupled to mass spectrophotometry. The Pseudomonas aeruginosa N7B1 strain removed 84% of phenanthrene and 45% of benzene in a seven-day period, while the other strains showed a lower hydrocarbon degradation capacity. Another biotechno-logical feature of these strains is maize growth promotion, in a substrate enriched with 0.5% of phenanthrene and 1.0% of benzene. Pseudomonas aeruginosa N7B1 and Pseudomonas aeruginosa F23 showed an increase in root and shoot fresh and dry weight, plant height and root length variables. These results open the possible use of these strains as bioinoculants to promote the growth of maize plants in phenanthrene and benzene polluted soils

Nematicidal Activity of the Endophyte <i>Serratia ureilytica</i> against <i>Nacobbus aberrans</i> in Chili Plants (<i>Capsicum annuum</i> L.) and Identification of Genes Related to Biological Control

The genus Serratia is widely distributed in soil, water, plants, animals, invertebrates, and humans. Some species of this genus have antifungal, antibacterial, and nematicidal activity. In this work, the nematicidal activity of the endophytic strain of Serratia sp. in chili, Capsicum annuum L., is reported, where at a bacterial concentration of 4 × 109 cel/mL, the penetration of nematodes into the roots significantly decreased by 91 and 55% at 7 and 21 days after inoculation. This bacterial concentration also significantly decreased the number of galls, eggs, egg masses and reproduction factor produced by Nacobbus aberrans in Chili plants, with respect to the control where this bacterial strain was not applied. In the analysis of the genome of the strain, based on average nucleotide identity (ANI), the isolate could be affiliated to the species Serratia ureilytica. The size of the genome is 5.4 Mb, with a 59.3% content of GC. Genes related to the synthesis of chitinases, siderophores, proteases C, serralisins, hemolysin, and serrawettin W2 that have been reported for biocontrol of nematodes were identified in the genome. It is the first report of Serratia ureilytica with nematicidal activity. Based on these results of nematicidal activity, this strain can be evaluated in the field as an alternative in the biocontrol of Nacobbus aberrans in chili cultivation

An original Eurasian haplotype, HLA-DRB1*14:54-DQB1*05:03, influences the susceptibility to idiopathic achalasia

<div><p>Idiopathic achalasia is a relatively infrequent esophageal motor disorder for which major histocompatibility complex (MHC) genes are well-identified risk factors. However, no information about HLA-achalasia susceptibility in Mexicans has previously been reported. We studied a group of 91 patients diagnosed with achalasia and 234 healthy controls with Mexican admixed ancestry. HLA alleles and conserved extended haplotypes were analyzed using high-resolution HLA typing based on Sanger and next-generation sequencing technologies. Admixture estimates were determined using HLA-B and short tandem repeats. Results were analyzed by non-parametric statistical analysis and Bonferroni correction. P-values < 0.05 were considered significant. Patients with achalasia had 56.7% Native American genes, 24.7% European genes, 16.5% African genes and 2.0% Asian genes, which was comparable with the estimates in the controls. Significant increases in the frequencies of alleles DRB1*14:54 and DQB1*05:03 and the extended haplotypes DRB1*14:54-DQB1*05:03 and DRB1*11:01-DQB1*03:01, even after Bonferroni correction (<i>p</i>C<0.05), were found in the achalasia group compared to those in the controls. Concluding, the HLA class II alleles HLA-DRB1*14:54:01 and DQB1*05:03:01 and the extended haplotype are risk factors for achalasia in mixed-ancestry Mexican individuals. These results also suggest that the HLA-DRB1*14:54-DQB1*05:03 haplotype was introduced by admixture with European and/or Asian populations.</p></div

Gene frequencies of HLA-DRB1 in achalasia patients and healthy controls.

<p>Gene frequencies of HLA-DRB1 in achalasia patients and healthy controls.</p

Most frequent HLA-A/-B/-C/-DRB1/-DQB1 conserved extended haplotypes in Achalasia patients and healthy controls.

<p>Most frequent HLA-A/-B/-C/-DRB1/-DQB1 conserved extended haplotypes in Achalasia patients and healthy controls.</p

HLA-B/-C/-DRB1/-DQB1 conserved extended haplotypes in achalasia patients and healthy controls.

<p>HLA-B/-C/-DRB1/-DQB1 conserved extended haplotypes in achalasia patients and healthy controls.</p

Gene frequencies of HLA-DQB1 in achalasia patients and healthy controls.

<p>Gene frequencies of HLA-DQB1 in achalasia patients and healthy controls.</p