Analysis of Hepatitis C Virus Intrahost Diversity across the Coding Region by Ultradeep Pyrosequencing

Hepatitis C virus (HCV) is the leading cause of liver disease worldwide. In this study, we analyzed four treatment-naive patients infected with subtype 1a and performed Roche/454 pyrosequencing across the coding region. We report the presence of low-level drug resistance mutations that would most likely have been missed using conventional sequencing methods. The approach described here is broadly applicable to studies of viral diversity and could help to improve the efficacy of direct-acting antiviral agents (DAA) in the treatment of HCV-infected patients.

Functional markers for gene mapping and genetic diversity studies in sugarcane

Abstract Background The database of sugarcane expressed sequence tags (EST) offers a great opportunity for developing molecular markers that are directly associated with important agronomic traits. The development of new EST-SSR markers represents an important tool for genetic analysis. In sugarcane breeding programs, functional markers can be used to accelerate the process and select important agronomic traits, especially in the mapping of quantitative traits loci (QTL) and plant resistant pathogens or qualitative resistance loci (QRL). The aim of this work was to develop new simple sequence repeat (SSR) markers in sugarcane using the sugarcane expressed sequence tag (SUCEST database). Findings A total of 365 EST-SSR molecular markers with trinucleotide motifs were developed and evaluated in a collection of 18 genotypes of sugarcane (15 varieties and 3 species). In total, 287 of the EST-SSRs markers amplified fragments of the expected size and were polymorphic in the analyzed sugarcane varieties. The number of alleles ranged from 2-18, with an average of 6 alleles per locus, while polymorphism information content values ranged from 0.21-0.92, with an average of 0.69. The discrimination power was high for the majority of the EST-SSRs, with an average value of 0.80. Among the markers characterized in this study some have particular interest, those that are related to bacterial defense responses, generation of precursor metabolites and energy and those involved in carbohydrate metabolic process. Conclusions These EST-SSR markers presented in this work can be efficiently used for genetic mapping studies of segregating sugarcane populations. The high Polymorphism Information Content (PIC) and Discriminant Power (DP) presented facilitate the QTL identification and marker-assisted selection due the association with functional regions of the genome became an important tool for the sugarcane breeding program.

Genetic diversity of the Brazilian Creole cattle Pé-duro assessed by microsatellites and mitochondrial DNA

The objective of this study was to describe the genetic diversity and structure of the largest Pé-duro population by assessing variation at ten autosomal microsatellite (STR) loci and mitochondrial DNA (mtDNA) sequences. The mean expected heterozygosity was 0.755, the mean observed heterozygosity was 0.600 and significant inbreeding coefficient (Fis) and deviations from the Hardy-Weinberg equilibrium in most of analyzed loci demonstrate the impact of inbreeding and homozygosis on this population. A more in-depth genetic analysis could be achieved by expanding the STR list. The analysis of mtDNA provided evidence of ancestral African taurine haplotypes in Pé-duro and excluded maternal Zebuine introgression. In this report, the main Pé-duro population is genetically portrayed by sampling approximately 40% of it. As this herd represents the core of the Pé-duro conservation program, these findings are of outstanding value for the management and preservation of this Brazilian 'native' cattle breed.

Acknowledging linguistic diversity in a multicultural society: the issue of indigenous languages in Colombia.

Nowadays, modern society is gradually becoming multicultural. However, only in the last few years awareness on its importance has been raised. In the case of Colombia, multiculturalism has existed since the pre-Columbian period and today there are more than 80 ethnic groups and 65 indigenous languages in the country. The aim of this work is to illustrate the status of indigenous languages in Colombia and to enlighten about the importance of recognizing, protecting and strengthening the use of these native languages. Subsequent to this, it will be point out that linguistic diversity should be considered a resource and not a barrier to achieve unity in diversity. Finally, ethno-education will be presented as an adequate educational program that may guarantee an equal linguistic representation in the country.

Report to the Provost from the Task Force to Review Dialogues on Diversity

One of the action items arising from the work of the Campus Climate Implementation Team and the President’s Advisory Committee on Diversity was a request from the President to the Provost to review the Dialogues on Diversity course. The Provost instructed this Task Force to review the current Dialogues on Diversity course to determine how it should be continued for optimal impact and to determine whether it is appropriate to add a “Dialogues—Part 2” to the curriculum. The Provost’s charge to the Task Force also asked for recommendations that include details on the following components of the current program: goals and objectives of the revised course administration and recommended department home for the revised course possibility of and need for a second course optimal coordination with other programs/initiatives on campus.

Ethnic/racial diversity, maternal stress, lactation and very low birthweight infants.

OBJECTIVE: (1) To compare maternal characteristics and psychological stress profile among African-American, Caucasian and Hispanic mothers who delivered very low birthweight infants. (2) To investigate associations between psychosocial factors, frequency of milk expression, skin-to-skin holding (STS), and lactation performance, defined as maternal drive to express milk and milk volume. STUDY DESIGN: Self-reported psychological questionnaires were given every 2 weeks after delivery over 10 weeks. Milk expression frequency, STS, and socioeconomic variables were collected. RESULT: Infant birthweight, education, and milk expression frequency differed between groups. Trait anxiety, depression and parental stress in a neonatal intensive care unit (PSS:NICU) were similar. African-American and Caucasian mothers reported the lowest scores in state anxiety and social desirability, respectively. Maternal drive to express milk, measured by maintenance of milk expression, correlated negatively with parental role alteration (subset of PSS:NICU) and positively with infant birthweight and STS. Milk volume correlated negatively with depression and positively with milk expression frequency and STS. CONCLUSION: Differences between groups were observed for certain psychosocial factors. The response bias to self-reported questionnaires between groups may not provide an accurate profile of maternal psychosocial profile. With different factors correlating with maintenance of milk expression and milk volume, lactation performance can be best enhanced with a multi-faceted intervention program, incorporating parental involvement in infant care, close awareness and management of maternal mental health, and encouragement for frequent milk expression and STS.

The impact of communication and cultural diversity in utilizing dental services among Saudi Arabian students in U.S.A.

Objectives: The purpose of this study is to understand the perceived effects of patient-dental staff communication and cultural diversity on the utilization of dental services in the U.S. by Saudi Arabian students who live in the U.S. and enrolled into the King Abdullah Scholarship program. Methods: The study design was an analytical cross-sectional study. Data for this study was obtained from the Saudi Dental Servicers Utilization Survey, a voluntary internet survey available online for one month through Facebook. Ordered logistic regression analyses and multinomial logistic regression analyses were used to measure the relationships between patient-dental staff communication and cultural diversity on the utilization of dental services. Results: Eight hundred and forty-seven responses were analyzed for this study. Overall, the majority of Saudi students reported having excellent communication experience with dental providers in the U.S. More than 58% of respondents reported at least one regular dental visit last year. Factors that influenced the use of regular dental care were: dentist's explanation of treatment plan, response of dental staff to patient's needs, respectful and polite dental staff, dental staff kindness, availability of up-to-date equipment, and overall communication with dentist. However, the utilization of emergency dental care was not associated with any measurement of patient-dental provider communication. Overall future utilization of dental care is associated with all aspects of patient-dental staff communication measured in this survey. Furthermore, more utilization of regular dental care was related to respondent's perception of the importance of trustworthiness dental staff and the importance of a dentist's reputation was only marginally associated. Respondent's perception of dentist's reputation was associated with more use of emergency dental services. Respondents are more likely to anticipate using dental care in the future if they perceived trustworthiness dental staff, and the dentist's reputation as influencing factors to their usage of dental services. Conclusions: Patient-dental staff communication was partially associated with utilization of regular dental care, not associated with utilization of emergency dental care, and broadly associated with anticipated future utilization of dental care. In addition, trustworthy dental staff, and a dentist's reputation were considered to be strong influencing factors towards utilization of dental services.^

Studies of the microbial diversity on analyzed samples from from Peru Margin, Equatorial Pacific, Hydrate Ridge, and Juan de Fuca Ridge

Marine sediments harbor an enormous quantity of microorganisms, including a multitude of novel species. The habitable zone of the marine sediment column begins at the sediment-water interface and probably extends to depths of several thousands of meters. Studies of the microbial diversity in this ecosystem have mostly relied on molecular biological techniques. We used a complementary method - analysis of intact polar membrane lipids - to characterize the in-situ microbial community in sediments covering a wide range of environmental conditions from Peru Margin, Equatorial Pacific, Hydrate Ridge, and Juan de Fuca Ridge. Bacterial and eukaryotic phospholipids were only detected in surface sediments from the Peru Margin. In contrast, deeply buried sediments, independent of their geographic location, were dominated by archaeal diether and tetraether lipids with various polar head groups and core lipids. We compared ring distributions of archaeal tetraether lipids derived from polar glycosidic precursors with those that are present as core lipids. The distributions of these related compound pools were distinct, suggestive of different archaeal sources, i.e., the polar compounds derive from sedimentary communities and the core lipids are fossil remnants from planktonic communities with possible admixtures of decayed sedimentary archaea. This in-situ production of distinct archaeal lipid populations potentially affects applications of the TEX86 paleotemperature proxy as demonstrated by offsets in reconstructed temperatures between both pools. We evaluated how varying cell and lipid stabilities will influence the sedimentary pool by using a box-model. The results are consistent with (i) a requirement of continuous inputs of freshly synthesized lipids in subsurface sediments for explaining the observed distribution of intact polar lipids, and (ii) decreasing lipid inputs with increasing burial depth.

Family diversity in social exclusion situations. Results and reflections on research, teaching and knowledge transfer activities

The purpose of this paper is to characterize the configurations of the families that live in contexts of social exclusion; provide conceptualizations of their operation mode; highlight the formative effects that neighborhood interdisciplinary practices with such families produce in the just graduated psychologists, included on the Extension Program. We wish to contribute to produce systematic knowledge that can account for such family configurations as potential receiver of integration policies. We are also interested on transferring the approach to diversity in the training of young professionals, in order not to be regarded as a deviation from ideal models, but as an expression of different strategies built by members of a community, to resolve children breeding and to bear their existences. This work is the result about reflections on productions inside a research fellowship: The complexities that takes the breeding in families who lives in a social exclusion situation; researches about breeding, carried out from signature Developmental Psychology II, and from de interdisciplinary work with psychologically assisted families in twelve suburbs of the city of La Plata (University Extension Program "Free Legal Offices" (Convention between Law and Social Sciences and Psychology Faculties, U.N.L.P.). From a qualitative methodology and an interdisciplinary participation, the results have arrive at the characterization and proposed conceptualizations of the included families and at the same time determine the benefits that brings with the work that articulates research and extension activities for the training of advanced students and young graduates.

Family diversity in social exclusion situations. Results and reflections on research, teaching and knowledge transfer activities

The purpose of this paper is to characterize the configurations of the families that live in contexts of social exclusion; provide conceptualizations of their operation mode; highlight the formative effects that neighborhood interdisciplinary practices with such families produce in the just graduated psychologists, included on the Extension Program. We wish to contribute to produce systematic knowledge that can account for such family configurations as potential receiver of integration policies. We are also interested on transferring the approach to diversity in the training of young professionals, in order not to be regarded as a deviation from ideal models, but as an expression of different strategies built by members of a community, to resolve children breeding and to bear their existences. This work is the result about reflections on productions inside a research fellowship: The complexities that takes the breeding in families who lives in a social exclusion situation; researches about breeding, carried out from signature Developmental Psychology II, and from de interdisciplinary work with psychologically assisted families in twelve suburbs of the city of La Plata (University Extension Program "Free Legal Offices" (Convention between Law and Social Sciences and Psychology Faculties, U.N.L.P.). From a qualitative methodology and an interdisciplinary participation, the results have arrive at the characterization and proposed conceptualizations of the included families and at the same time determine the benefits that brings with the work that articulates research and extension activities for the training of advanced students and young graduates.

Family diversity in social exclusion situations. Results and reflections on research, teaching and knowledge transfer activities

The purpose of this paper is to characterize the configurations of the families that live in contexts of social exclusion; provide conceptualizations of their operation mode; highlight the formative effects that neighborhood interdisciplinary practices with such families produce in the just graduated psychologists, included on the Extension Program. We wish to contribute to produce systematic knowledge that can account for such family configurations as potential receiver of integration policies. We are also interested on transferring the approach to diversity in the training of young professionals, in order not to be regarded as a deviation from ideal models, but as an expression of different strategies built by members of a community, to resolve children breeding and to bear their existences. This work is the result about reflections on productions inside a research fellowship: The complexities that takes the breeding in families who lives in a social exclusion situation; researches about breeding, carried out from signature Developmental Psychology II, and from de interdisciplinary work with psychologically assisted families in twelve suburbs of the city of La Plata (University Extension Program "Free Legal Offices" (Convention between Law and Social Sciences and Psychology Faculties, U.N.L.P.). From a qualitative methodology and an interdisciplinary participation, the results have arrive at the characterization and proposed conceptualizations of the included families and at the same time determine the benefits that brings with the work that articulates research and extension activities for the training of advanced students and young graduates.

Diversity of abyssal agglutinated foraminifera from Cenomanian to Santonian sediments of the North Atlantic

Benthic foraminiferal assemblages of distinctive taxonomic composition occur at the top of benthic fossil-free black shales which correspond to the anoxic event at the Cenomanian/Turonian boundary in the North Atlantic abyssal DSDP/ODP sites 386, 398, 603 and 641. These assemblages consist of minute, thin-walled agglutinated foraminifera with low specific diversity of 2 to 4 species, variable abundance and dominance of few taxa (Haplophragmoides, Rhizammina and Glomospira). The species are inferred to be opportunistic, able to survive in low-oxygen environments and to be pioneers recolonizing the seafloor after cessation of bottom-water anoxia. Most species are characterized by test morphologies with high surface/volume ratios and single-layered wall structures, with loosely agglutinated grains, and small amounts of organic cement for agglutination. These features are best observed in material from ODP Hole 641A which has exceptional foraminiferai preservation because of its shallow burial depth. The successive appearance of benthic foraminifera after the anoxic event is probably controlled by the continuous reoccurrence of more oxygenated bottom- and interstitial-water conditions. With the final development of oxic bottom-water conditions in the Turonian, a rapid radiation of deep-water agglutinated foraminifera occurred in the North Atlantic.