Human Genomic Diversity Where the Mediterranean Joins the Atlantic.

Throughout the past few years, a lively debate emerged about the timing and magnitude of the human migrations between the Iberian Peninsula and the Maghreb. Several pieces of evidence, including archaeological, anthropological, historical, and genetic data, have pointed to a complex and intermingled evolutionary history in the western Mediterranean area. To study to what extent connections across the Strait of Gibraltar and surrounding areas have shaped the present-day genomic diversity of its populations, we have performed a screening of 2.5 million single-nucleotide polymorphisms in 142 samples from southern Spain, southern Portugal, and Morocco. We built comprehensive data sets of the studied area and we implemented multistep bioinformatic approaches to assess population structure, demographic histories, and admixture dynamics. Both local and global ancestry inference showed an internal substructure in the Iberian Peninsula, mainly linked to a differential African ancestry. Western Iberia, from southern Portugal to Galicia, constituted an independent cluster within Iberia characterized by an enriched African genomic input. Migration time modeling showed recent historic dates for the admixture events occurring both in Iberia and in the North of Africa. However, an integrative vision of both paleogenomic and modern DNA data allowed us to detect chronological transitions and population turnovers that could be the result of transcontinental migrations dating back from Neolithic times. The present contribution aimed to fill the gaps in the modern human genomic record of a key geographic area, where the Mediterranean and the Atlantic come together.

Genetic variation patterns of ß-thalassemia in Western Andalusia (Spain) reveal a structure of specific mutations within the Iberian Peninsula.

BACKGROUND: Analyses of the genomic variation in the western Mediterranean population are being used to reveal its evolutionary history and to understand the molecular basis of particular diseases. AIM: To observe the ß-thalassemia mutational spectrum in western Andalusia, Spain, in the context of the Mediterranean. In addition, associations between disease and neutral gene variants within the ß-globin gene (HBB) were also evaluated. SUBJECTS AND METHODS: This study included 63 unrelated individuals diagnosed with ß-thalassemia. In addition, 97 unrelated, healthy subjects of the same territory were also analysed as proxies of the normal genetic background. Allele associations and population genetic structure analyses were performed using different methodologies. RESULTS: Data have revealed a rather restricted spectrum of ß-thalassemia mutations in the analysed sample. Although the detected variants fit well with the Mediterranean pattern, certain singularities support a structure of some specific ß-thalassemia alleles. The IVSI-1 (G > A) shows a strong regionalisation. The spatial correlogram revealed a typically narrow wave structure, presumably linked to genetic isolation and genetic drift. CONCLUSIONS: The long history of endemic malaria in the study territory, the rather high consanguinity rates among its autochthonous population, and other demographic features have been used here to understand the western Andalusian ß-thalassemia molecular portrait.

Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world.

BACKGROUND: The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components. AIM: To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages. SUBJECT AND METHODS: Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed. RESULTS: Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages. CONCLUSION: The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.

Purcell effect in photonic crystal microcavities embedding InAs/InP quantum wires.

The spontaneous emission rate and Purcell factor of self-assembled quantum wires embedded in photonic crystal micro-cavities are measured at 80 K by using micro-photoluminescence, under transient and steady state excitation conditions. The Purcell factors fall in the range 1.1 - 2 despite the theoretical prediction of ≈15.5 for the figure of merit. We explain this difference by introducing a polarization dependence on the cavity orientation, parallel or perpendicular with respect to the wire axis, plus spectral and spatial detuning factors for the emitters and the cavity modes, taking in account the finite size of the quantum wires.

Characterization of B-cell and T-cell responses to a tetravalent dengue purified inactivated vaccine in healthy adults.

The increasing global impact of dengue underscores the need for a dengue virus (DENV) vaccine. We assessed B-cell and T-cell responses following vaccination with four formulations of a tetravalent dengue purified inactivated vaccine (DPIV) in dengue-primed and dengue-naive adults from two studies (NCT01666652, NCT01702857). Frequencies of DPIV-induced memory B cells specific to each DENV serotype remained high up to 12 months post-vaccination, and were higher in the dengue-primed than dengue-naive adults. A subsequent DPIV booster dose induced strong anamnestic B-cell responses. Multifunctional CD4+ T cells (predominantly expressing IL-2) were induced by DPIV, with higher frequencies in dengue-primed adults. DPIV-induced CD4+ T cells also demonstrated in vitro proliferative capacity and antigen-specific production of GM-CSF, IFN-γ, and IL-13. CD8+ T-cell responses were undetectable in dengue-naive adults and low in dengue-primed individuals. B- and T-cell responses persisted up to 12 months post-vaccination in both dengue-primed and dengue-naive adults.

Cell-Mediated Immunity Generated in Response to a Purified Inactivated Vaccine for Dengue Virus Type 1.

Dengue is the most prevalent arboviral disease afflicting humans, and a vaccine appears to be the most rational means of control. Dengue vaccine development is in a critical phase, with the first vaccine licensed in some countries where dengue is endemic but demonstrating insufficient efficacy in immunologically naive populations. Since virus-neutralizing antibodies do not invariably correlate with vaccine efficacy, other markers that may predict protection, including cell-mediated immunity, are urgently needed. Previously, the Walter Reed Army Institute of Research developed a monovalent purified inactivated virus (PIV) vaccine candidate against dengue virus serotype 1 (DENV-1) adjuvanted with alum. The PIV vaccine was safe and immunogenic in a phase I dose escalation trial in healthy, flavivirus-naive adults in the United States. From that trial, peripheral blood mononuclear cells obtained at various time points pre- and postvaccination were used to measure DENV-1-specific T cell responses. After vaccination, a predominant CD4+ T cell-mediated response to peptide pools covering the DENV-1 structural proteins was observed. Over half (13/20) of the subjects produced interleukin-2 (IL-2) in response to DENV peptides, and the majority (17/20) demonstrated peptide-specific CD4+ T cell proliferation. In addition, analysis of postvaccination cell culture supernatants demonstrated an increased rate of production of cytokines, including gamma interferon (IFN-γ), IL-5, and granulocyte-macrophage colony-stimulating factor (GM-CSF). Overall, the vaccine was found to have elicited DENV-specific CD4+ T cell responses as measured by enzyme-linked immunosorbent spot (ELISpot), intracellular cytokine staining (ICS), lymphocyte proliferation, and cytokine production assays. Thus, together with antibody readouts, the use of a multifaceted measurement of cell-mediated immune responses after vaccination is a useful strategy for more comprehensively characterizing immunity generated by dengue vaccines.IMPORTANCE Dengue is a tropical disease transmitted by mosquitoes, and nearly half of the world's population lives in areas where individuals are at risk of infection. Several vaccines for dengue are in development, including one which was recently licensed in several countries, although its utility is limited to people who have already been infected with one of the four dengue viruses. One major hurdle to understanding whether a dengue vaccine will work for everyone-before exposure-is the necessity of knowing which marker can be measured in the blood to signal that the individual has protective immunity. This report describes an approach measuring multiple different parts of immunity in order to characterize which signals one candidate vaccine imparted to a small number of human volunteers. This approach was designed to be able to be applied to any dengue vaccine study so that the data can be compared and used to inform future vaccine design and/or optimization strategies.

Safety and Immunogenicity of Different Formulations of a Tetravalent Dengue Purified Inactivated Vaccine in Healthy Adults from Puerto Rico: Final Results after 3 Years of Follow-Up from a Randomized, Placebo-Controlled Phase I Study.

Four formulations of an investigational tetravalent dengue purified inactivated vaccine, administered as two doses one month (M) apart, were previously shown to be immunogenic and well-tolerated up to M13 of the phase I study NCT01702857. Here, we report results of the follow-up from M14 to year (Y) 3. One hundred healthy Puerto Rican adults, predominantly dengue virus (DENV)-primed, were randomized 1:1:1:1:1 to receive placebo or vaccine formulations: 1 µg/serotype/dose adjuvanted with aluminum, AS01E or AS03B, or aluminum-adjuvanted 4 µg/serotype/dose. No serious adverse events occurred. Two medically-attended potential immune-mediated disease cases, vaccination unrelated, were reported (groups 1 µg+Alum and 1 µg+AS03B). Of 14 instances of suspected dengue, none were laboratory confirmed. Geometric mean neutralizing antibody titers against DENV 1-4 waned from M14, but remained above pre-vaccination levels for DENV 1-3, with the highest values for group 1 µg+AS03B: 1220.1, 920.5, 819.4, and 940.5 (Y2), and 1329.3, 1169.2, 1219.8, and 718.9 (Y3). All formulations appeared to be safe and immunogenic during the 3-year follow-up.

Phase I Randomized Study of a Tetravalent Dengue Purified Inactivated Vaccine in Healthy Adults from Puerto Rico.

The safety and immunogenicity of four adjuvanted formulations of an investigational tetravalent dengue purified inactivated vaccine (DPIV) were evaluated in a predominantly dengue-primed population in Puerto Rico. In this placebo-controlled, randomized, observer-blind, phase I trial, 100 healthy adults were randomized 1:1:1:1:1 to receive DPIV at Day (D)0 and D28 (1 µg per dengue virus [DENV] type 1-4 adjuvanted with either alum, AS01E or AS03B, or 4 µg per DENV type adjuvanted with alum) or saline placebo. Functional antibody responses were assessed using a microneutralization assay at D56, Month (M)7, and M13. All DPIV formulations were well tolerated and no safety signals were identified through M13. The M13 according-to-protocol (ATP) immunogenicity cohort included 83 participants. The ATP analysis of immunogenicity was performed only on the 78 subjects seropositive for ≥ 1 DENV type at baseline: 69 tetravalent, three trivalent, two bivalent, and four monovalent. In all DPIV groups, geometric mean antibody titers (GMTs) increased from D0 to D56 and waned modestly through M13, while remaining well above prevaccination levels. The 4 µg + alum and the AS01E- and AS03B-adjuvanted formulations were highly immunogenic, with M13-neutralizing antibody GMTs against all four DENV types above 1,000. M13/D0 GMT ratios were highest in the 1 µg + AS03B group (ranging 3.2-3.7 depending on the DENV type). These results encourage continued clinical development of DPIV (ClinicalTrials.gov: NCT01702857).

Theoretical and experimental study of the Suzuki-phase photonic crystal lattice by angle-resolved photoluminescence spectroscopy.

A complete theoretical and experimental analysis of the photonic band structure for the Suzuki-phase lattice is presented. The band diagrams were calculated by two-dimensional plane wave expansion and three-dimensional guided-mode expansion methods. Angle resolved photoluminescence spectroscopy has been used to measure the emission of the photonic crystal structure realized in active InAsP/InP slabs. Photonic bands with a very low group velocity along an entire direction of the reciprocal lattice have been measured, which may have important applications on future photonic devices. The experimentally determined dispersion is in very good agreement with the calculated photonic bands. The presence of defect modes produced by microcavities in the Suzuki-phase lattice has also been established.

Dengue Virus Exposures Among Deployed U.S. Military Personnel.

AbstractDengue virus infections have adversely impacted U.S. military operations since the Spanish-American War. The erosion of mission capabilities and lost duty days are underestimated. Appreciating the incidence and prevalence of dengue infections in U.S. military personnel is important to inform disease prevention strategies. Banked pre- and post-deployment serum samples from 1,000 U.S. military personnel with a single deployment to a dengue-endemic region were tested using a screening microneutralization assay to detect anti-dengue-virus-neutralizing antibodies. A total of 76 (7.6%) post-deployment samples were positive and 15 of the pre-deployment samples were negative. These figures represent an infection incidence of 1.5% and total of 17.6 seroconversions per 10,000 deployment months. These data represent a deploying military population with a relatively high background rate of dengue seropositivity, a low level of infection during deployment compared with background infection rates in the local populations, and the potential for worsening clinical attack rates with increased frequency of deployment. Additional studies are required to more clearly elucidate the dengue infection and disease risk in U.S. military personnel.

Phase 1 Randomized Study of a Tetravalent Dengue Purified Inactivated Vaccine in Healthy Adults in the United States.

AbstractThe safety and immunogenicity of four formulations of an investigational tetravalent dengue purified inactivated vaccine (DPIV), formulated at 1 or 4 µg with aluminum hydroxide (alum) or at 1 µg with an adjuvant system (AS01E or AS03B), were evaluated in a first-time-in-human, placebo-controlled, randomized, observer-blind, phase 1 trial in the continental United States. Two doses of vaccine or placebo were administered intramuscularly 4 weeks apart to 100 healthy adults 18-39 years of age, randomized 1:1:1:1:1 to receive one of four DPIV formulations or saline placebo. The response to a third dose was evaluated in a subset of nine participants remote from primary vaccination. Humoral immunogenicity was assessed using a 50% microneutralization assay. All DPIV formulations were well tolerated. No vaccine-related serious adverse events were observed through 12 months after the second vaccine dose. In all DPIV groups, geometric mean antibody titers peaked at Day 56, waned through 6 months after the second vaccine dose, and then stabilized. In the nine subjects where boosting was evaluated, a strong anamnestic response was observed. These results support continuation of the clinical development of this dengue vaccine candidate (clinicaltrials.gov: NCT01666652).

Mechanisms of H2O2-induced oxidative stress in endothelial cells.

Hydrogen peroxide, produced by inflammatory and vascular cells, induces oxidative stress that may contribute to endothelial dysfunction. In smooth muscle cells, H(2)O(2) induces production of O(2)*(-) by activating NADPH oxidase. However, the mechanisms whereby H(2)O(2) induces oxidative stress in endothelial cells are poorly understood. We examined the effects of H(2)O(2) on O(2)*(-) levels on porcine aortic endothelial cells (PAEC). Treatment with 60 micromol/L H(2)O(2) markedly increased intracellular O(2)*(-) levels (determined by conversion of dihydroethidium to hydroxyethidium) and produced cytotoxicity (determined by propidium iodide staining) in PAEC. Overexpression of human manganese superoxide dismutase in PAEC reduced O(2)*(-) levels and attenuated cytotoxicity resulting from treatment with H(2)O(2). L-NAME, an inhibitor of nitric oxide synthase (NOS), and apocynin, an inhibitor of NADPH oxidase, reduced O(2)*(-) levels in PAEC treated with H(2)O(2), suggesting that both NOS and NADPH oxidase contribute to H(2)O(2)-induced O(2)*(-) in PAEC. Inhibition of NADPH oxidase using apocynin and NOS rescue with L-sepiapterin together reduced O(2)*(-) levels in PAEC treated with H(2)O(2) to control levels. This suggests interaction-distinct NOS and NADPH oxidase pathways to superoxide. We conclude that H(2)O(2) produces oxidative stress in endothelial cells by increasing intracellular O(2)*(-) levels through NOS and NADPH oxidase. These findings suggest a complex interaction between H(2)O(2) and oxidant-generating enzymes that may contribute to endothelial dysfunction.

16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles.

BACKGROUND: Sample storage conditions, extraction methods, PCR primers, and parameters are major factors that affect metagenomics analysis based on microbial 16S rRNA gene sequencing. Most published studies were limited to the comparison of only one or two types of these factors. Systematic multi-factor explorations are needed to evaluate the conditions that may impact validity of a microbiome analysis. This study was aimed to improve methodological options to facilitate the best technical approaches in the design of a microbiome study. Three readily available mock bacterial community materials and two commercial extraction techniques, Qiagen DNeasy and MO BIO PowerSoil DNA purification methods, were used to assess procedures for 16S ribosomal DNA amplification and pyrosequencing-based analysis. Primers were chosen for 16S rDNA quantitative PCR and amplification of region V3 to V1. Swabs spiked with mock bacterial community cells and clinical oropharyngeal swabs were incubated at respective temperatures of -80°C, -20°C, 4°C, and 37°C for 4 weeks, then extracted with the two methods, and subjected to pyrosequencing and taxonomic and statistical analyses to investigate microbiome profile stability. RESULTS: The bacterial compositions for the mock community DNA samples determined in this study were consistent with the projected levels and agreed with the literature. The quantitation accuracy of abundances for several genera was improved with changes made to the standard Human Microbiome Project (HMP) procedure. The data for the samples purified with DNeasy and PowerSoil methods were statistically distinct; however, both results were reproducible and in good agreement with each other. The temperature effect on storage stability was investigated by using mock community cells and showed that the microbial community profiles were altered with the increase in incubation temperature. However, this phenomenon was not detected when clinical oropharyngeal swabs were used in the experiment. CONCLUSIONS: Mock community materials originated from the HMP study are valuable controls in developing 16S metagenomics analysis procedures. Long-term exposure to a high temperature may introduce variation into analysis for oropharyngeal swabs, suggestive of storage at 4°C or lower. The observed variations due to sample storage temperature are in a similar range as the intrapersonal variability among different clinical oropharyngeal swab samples.

The seroprevalence and seroincidence of dengue virus infection in western Kenya.

Epidemics of dengue fever have been documented throughout the African continent over the past several decades, however little is known about the prevalence or incidence of dengue virus infection in the absence of an outbreak. No studies have analyzed the prevalence of dengue infection in western Kenya to date. This study describes the seroincidence and seroprevalence of dengue infection in western Kenya. Banked sera obtained from 354 healthy, afebrile children ages 12-47 months from Kisumu District, Kenya, were analyzed for antibodies to dengue virus using an IgG indirect ELISA. We found a seroprevalence of 1.1% (4 of 354 samples) and incidence of 8.5 seroconversions per 1000 persons per year in this study population. This appears to be similar to that previously reported in coastal regions of the country outside of known epidemic periods. Since there has never been a reported dengue epidemic in western Kenya, continued investigation and evaluation in a patient population presenting with fever is necessary to further confirm this finding.

Study of short- and long-term storage of teeth and its influence on DNA.

DNA degradation can interfere with the resolution of forensic cases. Allelic dropout often reduces the opportunity for adequate comparisons between degraded and reference samples. This study analyzed DNA degradation in 24 extracted teeth after storage at room temperature for 0, 2, 5, and 10 years. DNA concentration, quantified by dot-blot hybridization, declined significantly for the first 2 years, but there was no significant further degradation from the second to the tenth year of storage. COfiler analysis was used and the allelic dropout ratio for the amelogenin locus relative to CSF1PO locus was also estimated. Statistically significant differences were found between fresh teeth and teeth from the 2- and 5-year groups but not from the 10-year group. Under our storage conditions most of the DNA degradation occurred during the first 2 years. Further research is needed to control for individual and external factors that could affect DNA.

Q fever: epidemiology, diagnosis, and treatment.

Q fever, a zoonosis caused by Coxiella burnetii, is seen throughout the world. Recent reports suggest that its incidence in the United States is increasing, with more than 30 cases reported in the US military. The disease has many acute and chronic manifestations. Endocarditis is the most common form of chronic disease, and recent studies have led to substantial changes in the approach to its diagnosis and treatment. Military and civilian health care professionals need to consider Q fever when evaluating patients with appropriate geographic exposures and clinical presentations to prevent delays in diagnosis and treatment.

Ehrlichiosis: making the diagnosis in the acute setting.

Human monocytic ehrlichiosis (HME) is a tick-borne disease transmitted during the summer months in the mid-Atlantic, southeastern and south-central United States. A large proportion of patients presenting with ehrlichiosis must be hospitalized because of the severity of their presenting signs, symptoms and lab abnormalities. We report a case of HME presenting with negative serologies and positive DNA PCR for Ehrlichia chaffeensis during the acute illness. The patient was empirically treated with doxycycline before the availability of diagnostic test results and had a rapid recovery. This report summarizes the common findings of ehrlichiosis on presentation, diagnostic strategies, and treatment options. This case emphasizes the importance of considering tick-borne diseases in the differential diagnosis for patients presenting with nonspecific febrile syndromes in endemic areas and using the clinical scenario to determine whether empiric treatment for a tick-borne disease is necessary. Delaying treatment while awaiting confirmatory tests is unnecessary, and may result in a less favorable patient outcome.