HBV core sequence: definition of genotype-specific variability and correlation with geographical origin

There are eight genotypes and nine subtypes of HBV. Small differences in geographical origin are associated with sequence changes in the surface gene. Here, we compared core gene sequences from different genotypes and geographical regions. Specific combinations of 24 amino acid substitutions at nine residues allowed allocation of a sequence to a subtype. Six of these nine residues were located in different T cell epitopes depending on HBV geographical area and/or genotype. Thirty-seven nucleotide changes were associated uniquely with specific genotypes and subtypes. Unique amino acid and nucleotide variants were found in a majority of sequences from specific countries as well as within subtype ayw2 and adr. Specific nucleotide motifs were defined for Korean, Indian, Chinese, Italian and Pacific region isolates. Finally, we observed amino acid motifs that were common to either South-east Asian or Western populations, irrespective of subtype. We believe that HBV strains spread within constrained ethnic groups, result in selection pressures that define sequence variability within each subtype. It suggests that particular T cell epitopes are specific for geographical regions, and thus ethnic groups; this may affect the design of immunomodulatory therapies.

An examination of the relationship between social locations of Chinese immigrants and their ethnic newspaper dependency

This study drew upon media system dependency theory (MSD) and social identity theory to examine the relationship between social locations of Chinese immigrants and their dependency on Chinese ethnic newspapers. Data was obtained from a survey participated by 265 respondents with Chinese origin but currently residing in Australia. Results indicated that among the three indicators of social location, age appeared to be a strong positive predictor of the dependency on ethnic newspapers for information. Respondents who stayed longer in the host country tended to be more frequent readers of ethnic newspapers as well. Education did not appear as a significant predictor of ethnic newspaper dependency. These findings suggested the need for us to further investigate the impact of ethnic print media on ethnic minorities in the age of various information sources offered by new technologies.

Ethnic differences in health related quality of life for patients with type 2 diabetes

Background - The objective of this study was to investigate the association between ethnicity and health related quality of life (HRQoL) in patients with type 2 diabetes. Methods - The EuroQol EQ-5D measure was administered to 1,978 patients with type 2 diabetes in the UK Asian Diabetes Study (UKADS): 1,486 of south Asian origin (Indian, Pakistani, Bangladeshi or other south Asian) and 492 of white European origin. Multivariate regression using ordinary least square (OLS), Tobit, fractional logit and Censored Least Absolutes Deviations estimators was used to estimate the impact of ethnicity on both visual analogue scale (VAS) and utility scores for the EuroQol EQ-5D. Results - Mean EQ-5D VAS and utility scores were lower among south Asians with diabetes compared to the white European population; the unadjusted effect on the mean EQ-5D VAS score was −7.82 (Standard error [SE] = 1.06, p < 0.01) and on the EQ-5D utility score was −0.06 (SE = 0.02, p < 0.01) (OLS estimator). After controlling for socio-demographic and clinical confounders, the adjusted effect on the EQ-5D VAS score was −9.35 (SE = 2.46, p < 0.01) and on the EQ-5D utility score was 0.06 (SE = 0.04), although the latter was not statistically significant. Conclusions - There was a large and statistically significant association between south Asian ethnicity and lower EQ-5D VAS scores. In contrast, there was no significant difference in EQ-5D utility scores between the south Asian and white European sub-groups. Further research is needed to explain the differences in effects on subjective EQ-5D VAS scores and population-weighted EQ-5D utility scores in this context.

Physicochemical properties of water quality of Imeh, Edegelem and Chokocho communities located along Otamiri-oche River in Etche Ethnic Nationality of Rivers State, Nigeria

Some physiochemical properties of water quality of Otamiri-oche River which runs through Imeh, Edegelem and Chokocho Communities in Etche ethnic nationality of Rivers State, Nigeria were investigated. Samples were collected in triplicate from the three different locations along the river in both rainy and dry seasons. Each sampling points is located 500m away from the successive one, and the samples were taken from the open river at the zone extending beyond the shoreline. Samples were stored in ice packs and immediately taken to the laboratory to investigate some selected physico-chemical characteristics. Also, bacteriological study was carried out on the samples. The laboratory results of the selected physico-chemical parameters when compared with the world health organization (WHO) standard showed that all the selected physico-chemical parameters were within the world health organization (WHO) permissible in both rainy and dry season except pH. For rainy season, the pH values were 5.00±0.00, 5.40 ±0.40, and 5.40± 0.30 for Imeh, Edegelem and Chokocho respectively. For the dry season, the pH values were 5.83± 0.01, 5.56±0.01, 5.90±0.01 for Imeh, Edegelem and Chokocho respectively. Also magnesium hardness exceeded the World Health Organization (WHO) permissible limit in rainy season only. The results of bacteriological study showed that all the sampling locations contained high numbers of coliform bacteria in both rainy and dry seasons. The number of coliform bacteria during rainy season was 25.00±0.00, 25.00±0.00, and 35.00±0.00 for Imeh, Edegelem and Chokocho respectively. Those of dry season were 93.00±3.55, 56.66±4.49, and 35.60±4.17 for Imeh, Edegelem and Chokocho respectively. The difference between the rainy and dry season was tested statistically using the t-test. The results of the statistical analyses showed a significant difference (p<0.05) between the rainy and dry seasons.

The Comparison of Under-Five-Children’s Nutrition Status Among Ethnic Groups in North of Iran, 1998 - 2013; Results of a Three Stages Cross-Sectional Study

Background: Despite improvements in child health, malnutrition still remains one of the main public health challenges in Iran. Objectives: The aim of this study was to compare under nutrition among under-five children with regard to ethnicity in rural area in north Iran. Patients and Methods: In three cross-sectional studies 7575 subjects in three time-periods including 2339 children in 1998, 2749 in 2004, and 2487 in 2013, were evaluated. All under-five-children in 20 out of 118 villages were chosen by random sampling and assessed. Under nutrition was defined as underweight, stunting and wasting lower than -2 SD (Z < -2 SD). Results: Generally, stunting was declined 17.1% and underweight and wasting were increased 0.9% and 1%, respectively during 15 years (1998 - 2013). Underweight increased 0.5% in Fars-natives and 3.2% in Turkmans and it was decreased 0.9% in Sistanis. Statistical difference in Turkman children among the three stages of the study was significant (P = 0.001). Stunting has decreased 28.7% in Fars-natives and 35.1% in Sistanis, it was increased 9.3% in Turkman group. Statistical differences among three stages in inter-ethnic groups were significant (P = 0.001 for all). Compared the group with good economic status, the odds ratio was 1.831 in poor economic group (P = 0.001). The risk of under nutrition in Sistanis was 1.754 times more than in Fars-natives (P = 0.001). Conclusions: Under nutrition remains one of the main health problems in under-five-year children in north Iran being more common in Sistani children. Stunting in Sistani children deeply decreased while in Turkman children slightly increased during the 15-year period study. Poor economic status is a risk factor for under nutrition in this area.

Viability of using enamel and dentin from bovine origin as a substitute for human counterparts in an intraoral erosion model

This study ascertained whether under dental erosion models that closely mimics the real-life situation enamel and root dentin from bovine origin would be reliable substitutes for human counterparts. Through a 2x2 crossover design, in a first trial, 14 volunteers wore a palatal device containing slabs of bovine and human enamel. Half of the participants ingested (4x daily, for 10 days) orange juice first, crossing over to mineral water, while the remainder received the reverse sequence. In a second trial, volunteers wore devices with slabs of bovine and human root dentin. Except for the duration of each intraoral phase, which lasted 2 rather 10 days, the experiment with root dentin run exactly as for enamel. Dental substrates were analyzed for surface microhardness. Two-way ANOVAs (α=0.05) indicated no difference between the microhardness values recorded for human and bovine enamel (p=0.1350), but bovine root dentin had lower microhardness compared to its human counterpart (p=0.0432). While bovine enamel can reliably substitute its human counterpart in in situ dental erosion models, bovine root dentin does not seem to be a viable alternative to the corresponding human tissue.

Origin of successive cambia on stem in three species of Menispermaceae

The lianas observed in this study, Abuta convexa (Vell.) Diels, Abuta imene (Mart.) Eichler, and Chondrodendron platiphyllum (A. St.-Hil.) Miers, all have successive cambia in their stems. The terminology applied to stem histology in species with successive cambia is as diverse as the interpretations of the origins of this cambial variant. Therefore, this study specifically investigates the origin of successive cambia through a developmental analysis of the above-mentioned species, including an analysis of the terminology used to describe this cambial variation. For the first time, we have identified several developmental stages giving rise to the origins of successive cambia in this family. First, the pericycle originates in 1-3 layers of conjunctive tissue. After the differentiation of the first ring, the conjunctive tissue undergoes new divisions, developing approximately 10 rows of parenchyma cells. In the middle portion, a layer of sclereids is formed, again subdividing the conjunctive tissue into two parts: internal and external. New cambia originate in the internal part, from which new secondary vascular strands will originate, giving rise to the second successive vascular ring of the stem. The external part remains parenchymatous during the installation of the second ring and will undergo new periclinal division, repeating the entire process. New cambia will originate from the neoformed strands, which will form only rays. In the literature, successive cambia are formed by a meristem called "diffuse lateral meristem."However, based on the species of Menispermaceae studied in this report, it is demonstrated that the diffuse lateral meristem is the pericycle itself.

Vegetable-origin foam employed in dye extraction in tanning and leather processing facilities

This study addressed the use of conventional and vegetable origin polyurethane foams to extract C. I. Acid Orange 61 dye. The quantitative determination of the residual dye was carried out with an UV/Vis absorption spectrophotometer. The extraction of the dye was found to depend on various factors such as pH of the solution, foam cell structure, contact time and dye and foam interactions. After 45 days, better results were obtained for conventional foam when compared to vegetable foam. Despite presenting a lower percentage of extraction, vegetable foam is advantageous as it is considered a polymer with biodegradable characteristics.

Geometric morphometrics of the wing as a tool for assigning genetic lineages and geographic origin to Melipona beecheii (Hymenoptera: Meliponini)

The stingless bee Melipona beecheii presents great variability and is considered a complex of species. In order to better understand this species complex, we need to evaluate its diversity and develop methods that allow geographic traceability of the populations. Here we present a fast, efficient, and inexpensive means to accomplish this using geometric morphometrics of wings. We collected samples from Mexico, Guatemala, El Salvador, Nicaragua, and Costa Rica and we were able to correctly assign 87.1% of the colonies to their sampling sites and 92.4% to their haplotype. We propose that geometric morphometrics of the wing could be used as a first step analysis leaving the more expensive molecular analysis only to doubtful cases.

Mucin pattern reflects the origin of the adenocarcinoma in Barrett's esophagus: a retrospective clinical and laboratorial study

Background: Mucin immunoexpression in adenocarcinoma arising in Barrett's esophagus (BE) may indicate the carcinogenesis pathway. The aim of this study was to evaluate resected specimens of adenocarcinoma in BE for the pattern of mucins and to correlate to the histologic classification. Methods: Specimens were retrospectively collected from thirteen patients who underwent esophageal resection due to adenocarcinoma in BE. Sections were scored for the grade of intestinal metaplasia. The tissues were examined by immunohistochemistry for MUC2 and MUC5AC antibodies. Results: Eleven patients were men. The mean age was 61 years old (varied from 40 to 75 years old). The tumor size had a mean of 4.7 +/- 2.3 cm, and the extension of BE had a mean of 7.7 +/- 1.5 cm. Specialized epithelium with intestinal metaplasia was present in all adjacent mucosas. Immunohistochemistry for MUC2 showed immunoreactivity in goblet cells, while MUC5AC was extensively expressed in the columnar gastric cells, localizing to the surface epithelium and extending to a variable degree into the glandular structures in BE. Tumors were classified according to the mucins in gastric type in 7/13 (MUC5AC positive) and intestinal type in 4/13 (MUC2 positive). Two tumors did not express MUC2 or MUC5AC proteins. The pattern of mucin predominantly expressed in the adjacent epithelium was associated to the mucin expression profile in the tumors, p = 0.047. Conclusion: Barrett's esophagus adenocarcinoma shows either gastric or intestinal type pattern of mucin expression. The two types of tumors developed in Barrett's esophagus may reflect the original cell type involved in the malignant transformation.

Frequency of LCT-13910C > T single nucleotide polymorphism associated with adult-type hypolactasia/lactase persistence among Brazilians of different ethnic groups

Background: Adult-type hypolactasia, the physiological decline of lactase some time after weaning, was previously associated with the LCT -13910C>T polymorphism worldwide except in Africa. Lactase non-persistence is the most common phenotype in humans, except in northwestern Europe with its long history of pastoralism and milking. We had previously shown association of LCT -13910C>T polymorphism with adult-type hypolactasia in Brazilians; thus, we assessed its frequency among different Brazilian ethnic groups. Methods: We investigated the ethnicity-related frequency of this polymorphism in 567 Brazilians [mean age, 42.1 +/- 16.8 years; 157 (27.7%) men]; 399 (70.4%) White, 50 (8.8%) Black, 65 (11.5%) Brown, and 53 (9.3%) Japanese-Brazilian. DNA was extracted from leukocytes; LCT -13910C>T polymorphism was analyzed by PCR-restriction fragment length polymorphism. Results: Prevalence of the CC genotype associated with hypolactasia was similar (57%) among White and Brown groups; however, prevalence was higher among Blacks (80%) and those of Japanese descent (100%). Only 2 (4%) Blacks had TT genotype, and 8 (16%) had the CT genotype. Assuming an association between CC genotype and hypolactasia, and CT and TT genotypes with lactase persistence, 356 (62.8%) individuals had hypolactasia and 211 (37.2%) had lactase persistence. The White and Brown groups had the same hypolactasia prevalence (similar to 57%); nevertheless, was 80% among Black individuals and 100% among Japanese-Brazilians (P < 0.01). Conclusion: The lactase persistence allele, LCT -13910T, was found in about 43% of both White and Brown and 20% of the Black Brazilians, but was absent among all Japanese Brazilians studied.

Genetic Background of Patients from a University Medical Center in Manhattan: Implications for Personalized Medicine

Background: The rapid progress currently being made in genomic science has created interest in potential clinical applications; however, formal translational research has been limited thus far. Studies of population genetics have demonstrated substantial variation in allele frequencies and haplotype structure at loci of medical relevance and the genetic background of patient cohorts may often be complex. Methods and Findings: To describe the heterogeneity in an unselected clinical sample we used the Affymetrix 6.0 gene array chip to genotype self-identified European Americans (N = 326), African Americans (N = 324) and Hispanics (N = 327) from the medical practice of Mount Sinai Medical Center in Manhattan, NY. Additional data from US minority groups and Brazil were used for external comparison. Substantial variation in ancestral origin was observed for both African Americans and Hispanics; data from the latter group overlapped with both Mexican Americans and Brazilians in the external data sets. A pooled analysis of the African Americans and Hispanics from NY demonstrated a broad continuum of ancestral origin making classification by race/ethnicity uninformative. Selected loci harboring variants associated with medical traits and drug response confirmed substantial within-and between-group heterogeneity. Conclusion: As a consequence of these complementary levels of heterogeneity group labels offered no guidance at the individual level. These findings demonstrate the complexity involved in clinical translation of the results from genome-wide association studies and suggest that in the genomic era conventional racial/ethnic labels are of little value.

Report of a chimeric origin of transposable elements in a bovine-coding gene

Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program. Despite the significant number (542) of genes with TE insertions in exons only 14 (2.6%) of them were translated into protein, which we characterized as chimeric genes. From these chimeric genes, only the FAST kinase domains 3 (FASTKD3) gene, present on chromosome BTA 20, is a functional gene and showed evidence of the exaptation event. The genome sequence analysis showed that the last exon coding sequence of bovine FASTKD3 is similar to 85% similar to the ART2A retrotransposon sequence. In addition, comparison among FASTKD3 proteins shows that the last exon is very divergent from those of Homo sapiens, Pan troglodytes and Canis familiares. We suggest that the gene structure of bovine FASTKD3 gene could have originated by several ectopic recombinations between TE copies. Additionally, the absence of TE sequences in all other species analyzed suggests that the TE insertion is clade-specific, mainly in the ruminant lineage.

Origin of primordial magnetic fields

Magnetic fields of intensities similar to those in our galaxy are also observed in high redshift galaxies, where a mean field dynamo would not have had time to produce them. Therefore, a primordial origin is indicated. It has been suggested that magnetic fields were created at various primordial eras: during inflation, the electroweak phase transition, the quark-hadron phase transition (QHPT), during the formation of the first objects, and during reionization. We suggest here that the large-scale fields similar to mu G, observed in galaxies at both high and low redshifts by Faraday rotation measurements (FRMs), have their origin in the electromagnetic fluctuations that naturally occurred in the dense hot plasma that existed just after the QHPT. We evolve the predicted fields to the present time. The size of the region containing a coherent magnetic field increased due to the fusion of smaller regions. Magnetic fields (MFs) similar to 10 mu G over a comoving similar to 1 pc region are predicted at redshift z similar to 10. These fields are orders of magnitude greater than those predicted in previous scenarios for creating primordial magnetic fields. Line-of-sight average MFs similar to 10(-2) mu G, valid for FRMs, are obtained over a 1 Mpc comoving region at the redshift z similar to 10. In the collapse to a galaxy (comoving size similar to 30 kpc) at z similar to 10, the fields are amplified to similar to 10 mu G. This indicates that the MFs created immediately after the QHPT (10(-4) s), predicted by the fluctuation-dissipation theorem, could be the origin of the similar to mu G fields observed by FRMs in galaxies at both high and low redshifts. Our predicted MFs are shown to be consistent with present observations. We discuss the possibility that the predicted MFs could cause non-negligible deflections of ultrahigh energy cosmic rays and help create the observed isotropic distribution of their incoming directions. We also discuss the importance of the volume average magnetic field predicted by our model in producing the first stars and in reionizing the Universe.

Origin of magnetic fields in galaxies

Microgauss magnetic fields are observed in all galaxies at low and high redshifts. The origin of these intense magnetic fields is a challenging question in astrophysics. We show here that the natural plasma fluctuations in the primordial Universe (assumed to be random), predicted by the fluctuation - dissipation theorem, predicts similar to 0.034 mu G fields over similar to 0.3 kpc regions in galaxies. If the dipole magnetic fields predicted by the fluctuation- dissipation theorem are not completely random, microgauss fields over regions greater than or similar to 0.34 kpc are easily obtained. The model is thus a strong candidate for resolving the problem of the origin of magnetic fields in less than or similar to 10(9) years in high redshift galaxies.