Reference-Free Comparative Genomics of 174 Chloroplasts

Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes [1]. We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ∼18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes, from a highly reduced parasitic orchid [2] to a massive algal chloroplast [3], including gnetophytes [4] and cycads [5]. The conservation of this ratio between single copy and duplicated sequence was basal among green plants, independent of photosynthesis and mechanism of genome size change, and different in gymnosperms and lower plants. Major lineages in the angiosperm clade differed in the pattern of shared kmers and de novo contigs. For example, parasitic plants demonstrated an expected accelerated overall rate of evolution, while the hemi-parasitic genomes contained a great deal more novel sequence than holo-parasitic plants, suggesting different mechanisms at different stages of genomic contraction. Additionally, the legumes are diverging more quickly and in different ways than other major families. Small duplicated fragments of the rrn23 genes were deeply conserved among seed plants, including among several species without the IR regions, indicating a crucial functional role of this duplication. Localized de novo assembly of informative kmers greatly reduces the complexity of large comparative analyses by confining the analysis to a small partition of data and genomes relevant to the specific question, allowing direct analysis of next-gen sequence data from previously unstudied genomes and rapid discovery of informative candidate regions.     

Fear Inhibition in High Trait Anxiety

Trait anxiety is recognized as an individual risk factor for the development of anxiety disorders but the neurobiological mechanisms remain unknown. Here we test whether trait anxiety is associated with impaired fear inhibition utilizing the AX+/BX- conditional discrimination procedure that allows for the independent evaluation of startle fear potentiation and inhibition of fear [1]. Sixty undergraduate students participated in the study - High Trait Anxious: n = 28 and Low Trait Anxious: n = 32. We replicated earlier findings that a transfer of conditioned inhibition for startle responses requires contingency awareness. However, contrary to the fear inhibition hypothesis, our data suggest that high trait anxious individuals show a normal fear inhibition of conditioned startle responding. Only at the cognitive level the high trait anxious individuals showed evidence for impaired inhibitory learning of the threat cue. Together with other findings where impaired fear inhibition was only observed in those PTSD patients who were either high on hyperarousal symptoms [2] or with current anxiety symptoms [3], we question whether impaired fear inhibition is a biomarker for the development of anxiety disorders.     

Genetic Diversity of Circulating Rotavirus Strains in Tanzania Prior to the Introduction of Vaccination

Background

Tanzania currently rolls out vaccination against rotavirus-diarrhea, a major cause of child illness and death. As the vaccine covers a limited number of rotavirus variants, this study describes the molecular epidemiology of rotavirus among children under two years in Dar es Salaam, Tanzania, prior to implementation of vaccination.

Methods

Stool specimens, demographic and clinical information, were collected from 690 children admitted to hospital due to diarrhea (cases) and 545 children without diarrhea (controls) during one year. Controls were inpatient or children attending child health clinics. Rotavirus antigen was detected using ELISA and positive samples were typed by multiplex semi-nested PCR and sequencing.

Results

The prevalence of rotavirus was higher in cases (32.5%) than in controls (7.7%, P<0.001). The most common G genotypes were G1 followed by G8, G12, and G4 in cases and G1, G12 and G8 in controls. The Tanzanian G1 variants displayed 94% similarity with the Rotarix vaccine G1 variant. The commonest P genotypes were P[8], P[4] and P[6], and the commonest G/P combination G1 P[8] (n = 123), G8 P[4] and G12 P[6]. Overall, rotavirus prevalence was higher in cool (23.9%) than hot months (17.1%) of the year (P = 0.012). We also observed significant seasonal variation of G genotypes. Rotavirus was most frequently found in the age group of four to six months. The prevalence of rotavirus in cases was lower in stunted children (28.9%) than in non-stunted children (40.1%, P = 0.003) and lower in HIV-infected (15.4%, 4/26) than in HIV-uninfected children (55.3%, 42/76, P<0.001).

Conclusion

This pre-vaccination study shows predominance of genotype G1 in Tanzania, which is phylogenetically distantly related to the vaccine strains. We confirm the emergence of genotype G8 and G12. Rotavirus infection and circulating genotypes showed seasonal variation. This study also suggests that rotavirus may not be an opportunistic pathogen in children infected with HIV.     

Apamin Does Not Inhibit Human Cardiac Na+ Current,L-type Ca2+ Current or Other Major K+ Currents

Background

Apamin is commonly used as a small-conductance Ca²⁺-activated K⁺ (SK) current inhibitor. However, the specificity of apamin in cardiac tissues remains unclear.

Objective

To test the hypothesis that apamin does not inhibit any major cardiac ion currents.

Methods

We studied human embryonic kidney (HEK) 293 cells that expressed human voltage-gated Na⁺, K⁺ and Ca²⁺ currents and isolated rabbit ventricular myocytes. Whole-cell patch clamp techniques were used to determine ionic current densities before and after apamin administration.

Results

Ca²⁺ currents (CACNA1c+CACNB2b) were not affected by apamin (500 nM) (data are presented as median [25^th percentile;75^th percentile] (from –16 [–20;–10] to –17 [–19;–13] pA/pF, P = NS), but were reduced by nifedipine to –1.6 [–3.2;–1.3] pA/pF (p = 0.008). Na⁺ currents (SCN5A) were not affected by apamin (from –261 [–282;–145] to –268 [–379;–132] pA/pF, P = NS), but were reduced by flecainide to –57 [–70;–47] pA/pF (p = 0.018). None of the major K⁺ currents (I _Ks, I _Kr, I _K1 and I _to) were inhibited by 500 nM of apamin (KCNQ1+KCNE1, from 28 [20]; [37] to 23 [18]; [32] pA/pF; KCNH2+KCNE2, from 28 [24]; [30] to 27 [24]; [29] pA/pF; KCNJ2, from –46 [–48;–40] to –46 [–51;–35] pA/pF; KCND3, from 608 [505;748] to 606 [454;684]). Apamin did not inhibit the I _Na or I _CaL in isolated rabbit ventricular myocytes (I _Na, from –67 [–75;–59] to –68 [–71;–59] pA/pF; I _CaL, from –16 [–17;–14] to –14 [–15;–13] pA/pF, P = NS for both).

Conclusions

Apamin does not inhibit human cardiac Na⁺ currents, L-type Ca²⁺ currents or other major K⁺ currents. These findings indicate that apamin is a specific SK current inhibitor in hearts as well as in other organs.     

Epidemiology and Genetic Diversity of Rotavirus Strains in Children with Acute Gastroenteritis in Lahore,Pakistan

Pakistan harbors high disease burden of gastro-enteric infections with majority of these caused by rotavirus. Unfortunately, lack of proper surveillance programs and laboratory facilities have resulted in scarcity of available data on rotavirus associated disease burden and epidemiological information in the country. We investigated 1306 stool samples collected over two years (2008–2009) from hospitalized children under 5 years of age for the presence of rotavirus strains and its genotypic diversity in Lahore. The prevalence rate during 2008 and 2009 was found to be 34% (n = 447 out of 1306). No significant difference was found between different age groups positive for rotavirus (p>0.05). A subset of EIA positive samples was further screened for rotavirus RNA through RT-PCR and 44 (49.43%) samples, out of total 89 EIA positive samples, were found positive. G and P type prevalence was found as follows: G1P [4] = 3(6.81%); G1P [6] = 9(20.45%); G1P [8] = 1(2.27%); G2P [4] = 21(47.72%); G2P [8] = 1(2.27%); G9P [4] = 1(2.27%); G9P [6] = 1(2.27%) and G9P [8] = 7(15.90%). Phylogenetic analysis revealed that the VP7 and VP4 sequences clustered closely with the previously detected strains in the country as well as Belgian rotaviruses. Antigenic characterization was performed by analyzing major epitopes in the immunodominant VP7 and VP4 gene segments. Although the neutralization conferring motifs were found variable between the Pakistani strains and the two recommended vaccines strains (Rotarix™ and RotaTeq™), we validate the use of rotavirus vaccine in Pakistan based on the proven and recognized vaccine efficacy across the globe. Our findings constitute the first report on rotavirus’ genotype diversity, their phylogenetic relatedness and epidemiology during the pre-vaccination era in Lahore, Pakistan and support the immediate introduction of rotavirus vaccine in the routine immunization program of the country.     

What Is a Group? Young Children’s Perceptions of Different Types of Groups and Group Entitativity

To date, developmental research on groups has focused mainly on in-group biases and intergroup relations. However, little is known about children’s general understanding of social groups and their perceptions of different forms of group. In this study, 5- to 6-year-old children were asked to evaluate prototypes of four key types of groups: an intimacy group (friends), a task group (people who are collaborating), a social category (people who look alike), and a loose association (people who coincidently meet at a tram stop). In line with previous work with adults, the vast majority of children perceived the intimacy group, task group, and social category, but not the loose association, to possess entitativity, that is, to be a ‘real group.’ In addition, children evaluated group member properties, social relations, and social obligations differently in each type of group, demonstrating that young children are able to distinguish between different types of in-group relations. The origins of the general group typology used by adults thus appear early in development. These findings contribute to our knowledge about children''s intuitive understanding of groups and group members'' behavior.Young children grow up in a complex social world in which they are constantly flooded with social information. Our social world is composed not only of individuals but of an array of different relationships and social groupings. One challenge for children is to decipher which of these social groupings are meaningful. People can appear to be a group from the outside, for example simply because they are in close proximity to each other, but they can be connected with each other at different levels: they can be kin or friends, be on the same sports or work team, be part of the same national or language group, or they can be associated with each other only briefly and loosely when, for instance, they take the same bus to get to the airport, or line up at a counter at the same time. Determining the type of group to which an association of people belongs is not only crucial for being able to understand individual group members’ behavior but can also be a short-cut to predicting how group members will relate to each other. For example, one can expect kin or friends to be loyal to each other, but one might not expect this about people who happen to be lining up at a counter at the same time. Another important form of predictions that can be drawn from social groupings, but which has been understudied in previous research (see also [1]), regards the grouping as a whole. For example, a friendship is supposed to be a longer-lasting, more coherent entity than a gathering in front of a counter.When it comes to the perception of social groupings, Lickel and colleagues [2] have argued that adults apply a folk typology, in which they intuitively distinguish between four qualitatively different types of groups. In support of this idea, Lickel at el. [3] investigated how adult participants sorted 40 examples of real-life groups, and how they rated each of these groups on a set of eight group characteristics such as shared goals, similarity of group members, interaction among group members, and group size. They found that participants distinguished four basic types of groups: intimacy groups (such as families and friends), task groups (such as work or sports teams), social categories (such as women or U.S. citizens), and loose associations (such as people waiting in line at a counter). Participants associated different group characteristics with each group type, for example a long duration and high levels of interaction for intimacy groups, common goals and interaction in task groups, large size and member similarity for social categories, and short duration and low levels of similarity and common goals for loose associations (for an overview, see [2]). Related research has shown that adults treat some social groupings as entities [4–6]. The extent to which a group appears to be a coherent entity and therefore possesses a quality of “groupness” has been referred to as “entitativity” [2–5, 7]. Lickel and colleagues showed that the four types of groups were perceived by adults to have different levels of entitativity, with the highest level for intimacy groups, followed by task groups, social categories, and loose associations.This group typology has received further support and validation from work in anthropology [8, 9]. Interdisciplinary work has linked these different types of groups to different relational models that are more or less prominent within each group type [10]. For example, communal sharing, a relationship in which I see “what is mine as yours” is more pronounced in intimacy groups than in other types of groups. It has been argued that children do not develop a fully-fledged concept of these different relational models before nine or ten years of age [8, 9].Despite the theoretical importance of this group typology, very little research has investigated its origins in childhood. Instead, developmental research on group cognition in young children has focused mainly on children’s in-group biases, that is, their preference for members of their own group over members of other groups. Research in this tradition has shown that children prefer members of their own group on a variety of implicit and explicit measures [11–14]. Another line of research focuses on the inferences children draw about individuals based on their group membership. For example, 4- to 6-year-old children predict what a person will do, like, or intend on the basis of that person’s gender, race, or ethnicity [15–17]. Children also use information about group membership to make inferences about social interactions: Knowing that two individuals are either from the same or from two different groups influences their prediction about whether those individuals will harm each other (around 4 years; [18]), help each other (from 6 years; [18]), or be friends with each other (from 7 years; [19]).However, this body of research leaves at least three significant gaps in our knowledge about children’s understanding of groups. First, previous research has focused primarily on just one type of group: the one Lickel and colleagues refer to as social categories, thus limiting what we can conclude about children’s understanding of group relations more generally (although see, e.g., [7, 20, 21], for work on preferential behavior towards intimacy and task group members). Second, the main focus of this previous research has been on children’s attitudes and expectations about in-group as compared with out-group members. However, as illustrated in our introductory examples, relationships among members of an in-group may differ in systematic ways depending on the type of in-group to which they belong. Finally, previous work has focused mainly on children’s perceptions of and expectations about individual group members rather than on their perceptions of and expectations about the group as a whole. It is thus important for our understanding of the development of group psychology to ask whether children distinguish different types of social groups and whether they expect relationships within and characteristics of these types of groups to differ from each other.One exception to this general trend is a study conducted by Svirydzenka and colleagues [7]. They found that 10-year-old children intuitively distinguish the same four main types of groups as adults: intimacy groups, task groups, social categories, and loose associations. They also judged the level of entitativity of different group types in similar ways as adults, but their assessments seemed to rely on group characteristics that were more perceptually salient (for example the level of interaction) than adults, who focused on more abstract features such as the importance of the group for its members [22].Inspired by this study and Lickel and colleagues’ work [3], we investigated whether the origins of this folk theory of groups could be seen even in children as young as 5 to 6 years of age. This is an important age in the development of group cognition as 5 to 6 years appears to be just at the border of explicit group understanding. It is at this age that children first show a more general preference for in-group members, even in more abstract and novel groups (in the minimal group paradigm; [21, 23]). Furthermore, it is also at this age that children first become able to predict intergroup relations in third party contexts at least for social categories (e.g., [16, 18]).Thus our objective was to investigate whether, in addition to these preferences and expectations, children of this age also have a more general understanding of groups and different types of group–in other words, an early folk typology of groups. Several prominent theoretical accounts of the origins of intergroup psychology postulate substantial development between the age group in our study and the youngest age, so far, at which a group typology has been found, 10 years [24–26]. However, given their relatively sophisticated abilities in other areas of group cognition, we predicted that already by 5 to 6 years of age, children would be able to make subtle distinctions between different types of groups and use this understanding in order to make inferences about group members’ behaviors within different group types.As a first step, we measured children’s spontaneous definition of a group. We did this to investigate children’s naïve, spontaneous ideas about groups, before presenting them with different group types. We predicted that children would be able to give some appropriate examples of groups and were especially interested in whether they would focus on one particular example or definition when thinking about groups (e.g., mention just one group type), or whether they would be able to give a more abstract definition (covering all group types, such as “a collection of people”). Second, because recent work has shown that 5-year-old children have comparable preferences for two types of group members–task group members and social category members [21]–we investigated which of these two examples (operationalized as people who work together vs. people who are similar to each other) children thought was most representative of a group. Third, we investigated whether preschool children would see an intimacy group, a task group, a social category, and a loose association as qualitatively different.It was impossible, given the young age of our participants, to adopt the exact methods of previous studies, which used complex tasks such as sorting of examples of groups and rating multiple group characteristics for each example. To simplify the procedure so that young children would understand it, we thus created a prototype for each of the four types of groups and asked children to judge these prototypes on entitativity and 12 other group characteristics. These group characteristics were generally inspired by the characteristics Lickel et al. [3] and Svirydzenka et al. [7] chose. However, in addition, we asked about several further characteristics that are important topics in recent work on the developmental origins of group psychology (e.g., [20, 27–29]) and anthropology [8, 9]. There were four main sets of group characteristics. The first three involved judgments and predictions about individual group members and group member relationships (see, e.g., [27]). The first set involved judgments about social obligations and prosocial behaviors among group members (helping, sharing, and loyalty; e.g., [18, 20, 28, 30]). The second involved the quality of group members’ social relationships (liking, familiarity, interdependence, and joint goals; [7, 31]). The third involved properties marking fundamental similarities among group members (group member similarity, shared preferences, and common knowledge; [29, 32, 33]). The fourth set, in contrast, involved traits of the group itself, concerning characteristics that apply to the group as a whole, rather than to individual members (permeability, continuance, and entitativity; [3]). We predicted generally that children’s perceptions of and expectations about groups would be contingent upon the type of group they were presented with and that they would recognize that a loose association was not a real group.     

Determination of 14 Circulating microRNAs in Swedes and Iraqis with and without Diabetes Mellitus Type 2

Background

Recent reports suggest that immigrants from Middle Eastern countries are a high-risk group for type 2 diabetes (T2D) compared with Swedes, and that the pathogenesis of T2D may be ethnicity-specific. Deregulation of microRNA (miRNA) expression has been demonstrated to be associated with T2D but ethnic differences in miRNA have not been investigated. The aim of this study was to explore the ethnic specific expression (Swedish and Iraqi) of a panel of 14 previously identified miRNAs in patients without T2D (including those with prediabetes) and T2D.

Methods

A total of 152 individuals were included in the study (84 Iraqis and 68 Swedes). Nineteen Iraqis and 14 Swedes were diagnosed with T2D. Expression of the 14 selected miRNAs (miR-15a, miR-20, miR-21, miR-24, miR-29b, miR-126, miR-144, miR-150, miR-197, miR-223, miR-191, miR-320a, miR-486-5p, and miR-28-3p) in plasma samples was measured by real-time PCR.

Results

In the whole study population, the expression of miR-24 and miR-29b was significantly different between T2D patients and controls after adjustment for age, sex, waist circumference, family history of T2D, and a sedentary lifestyle. Interestingly, when stratifying the study population according to country of birth, we found that higher expression of miR-144 was significantly associated with T2D in Swedes (OR = 2.43, p = 0.035), but not in Iraqis (OR = 0.54, p = 0.169). The interaction test was significant (p = 0.017).

Conclusion

This study suggests that the association between plasma miR-144 expression and T2D differs between Swedes and Iraqis.     

Community Based Case-Control Study of Rotavirus Gastroenteritis among Young Children during 2008-2010 Reveals Vast Genetic Diversity and Increased Prevalence of G9 Strains in Kolkata

Background

Group A Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children (<5 years) worldwide. Although rotavirus vaccines have been successfully administered in many countries, in India the introduction of rotavirus vaccine in national immunization program was approved in 2014. Since high disease burden and large number of genetic variants have been reported from low income countries including India, monitoring of rotavirus was initiated prior to implementation of the vaccine in the region.

Methods

A total number of 3,582 stool samples were collected from an urban slum community in Kolkata, among which 1,568 samples were obtained from children of ≤5 years of age, with moderate to severe diarrhoea and 2,014 samples were collected from age-sex matched healthy neighbourhood controls. Rotavirus positive samples were typed by multiplex semi-nested PCR and nucleotide sequencing. Circulating strains were phylogenetically analyzed.

Results

Among 1,568 children with diarrhoea, 395 (25.2%), and among 2,014 asymptomatic children, 42 (2%) were rotavirus positive. G1P[8] was identified as the most common strain (32%) followed by G9P[8] (16.9%), G2P[4] (13.5%) and G9P[4] (10.75%). G12 strains with combinations of P[4], P[6] and P[8] comprised 11.9% of total positive strains. The rest (<10%) were rare and uncommon strains like G1P[4], G1P[6], G2P[8] and animal-like strains G4P[6], G6P[14] and G11P[25]. The 42 rotavirus positive samples from asymptomatic children revealed common genotypes like G1, G2 and G9.

Conclusion

This community based case-control study showed increased predominance of genotype G9 in Kolkata. It also confirmed co-circulation of a large number of genetic variants in the community. Asymptomatic rotavirus positive children though low in number can also be a source of dispersal of infection in the community. This study provides background information to the policy makers for implementation of rotavirus vaccines in this region.     

SLC22A1-ABCB1 Haplotype Profiles Predict Imatinib Pharmacokinetics in Asian Patients with Chronic Myeloid Leukemia

Objective

This study aimed to explore the influence of SLC22A1, PXR, ABCG2, ABCB1 and CYP3A5*3 genetic polymorphisms on imatinib mesylate (IM) pharmacokinetics in Asian patients with chronic myeloid leukemia (CML).

Patients and Methods

Healthy subjects belonging to three Asian populations (Chinese, Malay, Indian; n = 70 each) and CML patients (n = 38) were enrolled in a prospective pharmacogenetics study. Imatinib trough (C_0h) and clearance (CL) were determined in the patients at steady state. Haplowalk method was applied to infer the haplotypes and generalized linear model (GLM) to estimate haplotypic effects on IM pharmacokinetics. Association of haplotype copy numbers with IM pharmacokinetics was defined by Mann-Whitney U test.

Results

Global haplotype score statistics revealed a SLC22A1 sub-haplotypic region encompassing three polymorphisms (rs3798168, rs628031 and IVS7+850C>T), to be significantly associated with IM clearance (p = 0.013). Haplotype-specific GLM estimated that the haplotypes AGT and CGC were both associated with 22% decrease in clearance compared to CAC [CL (*10⁻² L/hr/mg): CAC vs AGT: 4.03 vs 3.16, p = 0.017; CAC vs CGC: 4.03 vs 3.15, p = 0.017]. Patients harboring 2 copies of AGT or CGC haplotypes had 33.4% lower clearance and 50% higher C_0h than patients carrying 0 or 1 copy [CL (*10⁻² L/hr/mg): 2.19 vs 3.29, p = 0.026; C_0h (*10⁻⁶ 1/ml): 4.76 vs 3.17, p = 0.013, respectively]. Further subgroup analysis revealed SLC22A1 and ABCB1 haplotypic combinations to be significantly associated with clearance and C_0h (p = 0.002 and 0.009, respectively).

Conclusion

This exploratory study suggests that SLC22A1-ABCB1 haplotypes may influence IM pharmacokinetics in Asian CML patients.     

Inhibition of mTOR by Rapamycin Abolishes Cognitive Deficits and Reduces Amyloid-β Levels in a Mouse Model of Alzheimer's Disease

Background

Reduced TOR signaling has been shown to significantly increase lifespan in a variety of organisms [1], [2], [3], [4]. It was recently demonstrated that long-term treatment with rapamycin, an inhibitor of the mTOR pathway[5], or ablation of the mTOR target p70S6K[6] extends lifespan in mice, possibly by delaying aging. Whether inhibition of the mTOR pathway would delay or prevent age-associated disease such as AD remained to be determined.

Methodology/Principal Findings

We used rapamycin administration and behavioral tools in a mouse model of AD as well as standard biochemical and immunohistochemical measures in brain tissue to provide answers for this question. Here we show that long-term inhibition of mTOR by rapamycin prevented AD-like cognitive deficits and lowered levels of Aβ₄₂, a major toxic species in AD[7], in the PDAPP transgenic mouse model. These data indicate that inhibition of the mTOR pathway can reduce Aβ₄₂ levels in vivo and block or delay AD in mice. As expected from the inhibition of mTOR, autophagy was increased in neurons of rapamycin-treated transgenic, but not in non-transgenic, PDAPP mice, suggesting that the reduction in Aβ and the improvement in cognitive function are due in part to increased autophagy, possibly as a response to high levels of Aβ.

Conclusions/Significance

Our data suggest that inhibition of mTOR by rapamycin, an intervention that extends lifespan in mice, can slow or block AD progression in a transgenic mouse model of the disease. Rapamycin, already used in clinical settings, may be a potentially effective therapeutic agent for the treatment of AD.     

Factors Associated with Lung Function Decline in Patients with Non-Tuberculous Mycobacterial Pulmonary Disease

Background

There is paucity of risk factors on lung function decline among patients with non-tuberculous mycobacteria (NTM) pulmonary disease in literature.

Methods

Patients with NTM pulmonary disease between January 2000 and April 2011 were retrospectively selected. Sixty-eight patients had at least two pulmonary function tests within a mean follow-up period of 47 months.

Results

Sixty-eight patients were included. They had a median age of 65 years and 65% had impaired lung function (Forced expiratory volume in 1 second [FEV₁] <80% of predicted value). The mean FEV₁ decline was 48 ml/year. By linear regression, younger age (beta: 0.472, p<0.001), initial FEV₁>50% of predicted value (beta: 0.349, p = 0.002), male sex (beta: 0.295, p = 0.018), bronchiectasis pattern (beta: 0.232, p = 0.035), and radiographic score >3 (beta: 0.217, p = 0.049) were associated with greater FEV₁ decline. Initial FEV₁>50% of predicted value (beta: 0.263, p = 0.032) was also associated with greater FVC annual decline, whereas M. kansasii pulmonary disease was marginally associated with greater annual FVC decline (beta: 0.227, p = 0.062).

Conclusions

NTM pulmonary disease is associated with greater decline in lung function in patients who are young, male, with bronchiectasis, and with a high radiographic score. Special attention should be given to patients with these risk factors.     

Potential Role for HIV-Specific CD38?/HLA-DR+ CD8+ T Cells in Viral Suppression and Cytotoxicity in HIV Controllers

Background

HIV controllers (HIC) are rare HIV-1-infected patients who exhibit spontaneous viral control. HIC have high frequency of CD38⁻/HLA-DR⁺ HIV-specific CD8⁺ T cells. Here we examined the role of this subset in HIC status.

Materials and Methods

We compared CD38⁻/HLA-DR⁺ CD8⁺ T cells with the classical CD38⁺/HLA-DR⁺ activated phenotype in terms of 1) their activation status, reflected by CD69, CD25, CD71, CD40 and Ki67 expression, 2) functional parameters: Bcl-2 expression, proliferative capacity, and IFN-γ and IL-2 production, and 3) cytotoxic activity. We also investigated how this particular profile is generated.

Results

Compared to CD38⁺/HLA-DR⁺ cells, CD38⁻/HLA-DR⁺ cells exhibited lower expression of several activation markers, better survival capacity (Bcl-2 MFI, 367 [134–462] vs 638 [307–747], P = 0.001), higher frequency of polyfunctional cells (15% [7%–33%] vs 21% [16%–43%], P = 0.0003), greater proliferative capacity (0-fold [0–2] vs 3-fold [2]–[11], P = 0.007), and higher cytotoxicity in vitro (7% [3%–11%] vs 13% [6%–22%], P = 0.02). The CD38⁻/HLA-DR⁺ profile was preferentially generated in response to low viral antigen concentrations.

Conclusions

These data highlight the role of CD38⁻/HLA-DR⁺ HIV-specific CD8⁺ T cell cytotoxicity in HIC status and provide insights into the mechanism by which they are generated. Induction of this protective CD8⁺ subset may be important for vaccine strategies.     

Socioeconomic Predictors of Cognition in Ugandan Children: Implications for Community Interventions

Background

Several interventions to improve cognition in at risk children have been suggested. Identification of key variables predicting cognition is necessary to guide these interventions. This study was conducted to identify these variables in Ugandan children and guide such interventions.

Methods

A cohort of 89 healthy children (45 females) aged 5 to 12 years old were followed over 24 months and had cognitive tests measuring visual spatial processing, memory, attention and spatial learning administered at baseline, 6 months and 24 months. Nutritional status, child''s educational level, maternal education, socioeconomic status and quality of the home environment were also measured at baseline. A multivariate, longitudinal model was then used to identify predictors of cognition over the 24 months.

Results

A higher child''s education level was associated with better memory (p = 0.03), attention (p = 0.005) and spatial learning scores over the 24 months (p = 0.05); higher nutrition scores predicted better visual spatial processing (p = 0.002) and spatial learning scores (p = 0.008); and a higher home environment score predicted a better memory score (p = 0.03).

Conclusion

Cognition in Ugandan children is predicted by child''s education, nutritional status and the home environment. Community interventions to improve cognition may be effective if they target multiple socioeconomic variables.     

Enhancing of Women Functional Status with Metabolic Syndrome by Cardioprotective and Anti-Inflammatory Effects of Combined Aerobic and Resistance Training

These data describe the effects of combined aerobic plus resistance training (CT) with regards to risk factors of metabolic syndrome (MetS), quality of life, functional capacity, and pro- and anti-inflammatory cytokines in women with MetS. In this context, thirteen women (35.4±6.2 yr) completed 10 weeks of CT consisting of three weekly sessions of ∼60 min aerobic training (treadmill at 65–70% of reserve heart rate, 30 min) and resistance training (3 sets of 8–12 repetitions maximum for main muscle groups). Dependent variables were maximum chest press strength; isometric hand-grip strength; 30 s chair stand test; six minute walk test; body mass; body mass index; body adiposity index; waist circumference; systolic (SBP), diastolic and mean blood pressure (MBP); blood glucose; HDL-C; triglycerides; interleukins (IL) 6, 10 and 12, osteoprotegerin (OPG) and serum nitric oxide metabolite (NOx); quality of life (SF-36) and Z-Score of MetS. There was an improvement in muscle strength on chest press (p = 0.009), isometric hand-grip strength (p = 0.03) and 30 s chair stand (p = 0.007). There was a decrease in SBP (p = 0.049), MBP (p = 0.041), Z-Score of MetS (p = 0.046), OPG (0.42±0.26 to 0.38±0.19 ng/mL, p<0.05) and NOx (13.3±2.3 µmol/L to 9.1±2.3 µmol/L; p<0.0005). IL-10 displayed an increase (13.6±7.5 to 17.2±12.3 pg/mL, p<0.05) after 10 weeks of training. Combined training also increased the perception of physical capacity (p = 0.011). This study endorses CT as an efficient tool to improve blood pressure, functional capacity, quality of life and reduce blood markers of inflammation, which has a clinical relevance in the prevention and treatment of MetS.

Trial Registration

Brazilian Clinical Trials Registry (ReBec) - RBR-6gdyvz - http://www.ensaiosclinicos.gov.br/rg/?q=RBR-6gdyvz     

Depletion of Regulatory T Lymphocytes Reverses the Imbalance between Pro- and Anti-Tumor Immunities via Enhancing Antigen-Specific T Cell Immune Responses

Background

The regulatory T cells (Tregs) can actively suppress the immune responses. However, literature about detailed changes of host effective and suppressive immunities before and after depletion of Tregs in ovarian carcinomas, is rare.

Materials and Methods

Ovarian cancer patients and the ascitogenic animal model were employed. Immunologic profiles with flow cytometric analyses, immunohistochemistric staining, RT-PCR, ELISA, and ELISPOT assays were performed. In vivo depletion of Treg cells with the mAb PC61was also performed in the animal model.

Results

The cytokines, including IL-4 (p = 0.017) and TNF-α (p = 0.046), significantly decreased while others such as TGF-β (p = 0.013), IL-6 (p = 0.016), and IL-10 (p = 0.018) were elevated in ascites of ovarian cancer patients, when the disease progressed to advanced stages. The ratio of CD8⁺ T cell/Treg cell in ascites was also lower in advanced diseases than in early diseases (advanced 7.37±0.64 vs. early 14.25±3.11, p = 0.037). The kinetic low-dose CD25 Ab depletion group had significantly lower intra-peritoneal tumor weight (0.20±0.03 g) than the sequential high-dose (0.69±0.06 g) and sequential low-dose (0.67±0.07 g) CD25 Ab deletion groups (p = 0.001) after 49 days of tumor challenge in the animal. The kinetic low-dose CD25 Ab depletion group generated the highest number of IFN-γ-secreting, mesothelin-specific T lymphocytes compared to the other groups (p<0.001).

Conclusions

The imbalance between effective and suppressive immunities becomes more severe as a tumor progresses. The depletion of Treg cells can correct the imbalance of immunologic profiles and generate potent anti-tumor effects. Targeting Treg cells can be a new strategy for the immunotherapy of ovarian carcinoma.     

The Glutathione S-Transferase P1 341C>T Polymorphism and Cancer Risk: A Meta-Analysis of 28 Case-Control Studies

Background

GSTP1, which is one major group of the glutathione S-transferase family, plays an important role in the metabolism of carcinogens and toxins, reducing damage of DNA as a suppressor of carcinogenesis. The 341C>T polymorphism of the GSTP1 has been implicated in cancer risk through cutting down its metabolic detoxification activities. However, results from previous studies remain conflicting rather than conclusive. To clarify the correlation and provide more statistical evidence for detecting the significance of 341C>T, a meta-analysis was conducted.

Methodology/Principal Findings

The relevant studies were identified through searching of PubMed, Embase, ISI Web of Knowledge and China National Knowledge Infrastructure in August 2012, and selected based on the established inclusion criteria for publications, then a meta-analysis was performed to quantitatively summarize the association of GSTP1 341C>T polymorphism with cancer susceptibility. Stratified analyses were employed to identify the source of heterogeneity. Publication bias was evaluated as well as sensitivity analysis. Based on 28 case-control studies with 13249 cases and 16798 controls, the pooled results indicated that the variant genotypes significantly increased the risk of cancer in homozygote comparison (TT versus CC: P = 0.012, OR = 1.40, 95% CI: 1.08–1.81, P _het. = 0.575), and recessive model (TT versus CT/CC: P = 0.012, OR = 1.40, 95% CI: 1.08–1.81, P _het. = 0.562). This was confirmed when stratified analyses were conducted according to ethnicity, source of control, matched control, quality score and cancer types. Moreover, significantly increased risk of cancer was also found in lung cancer (heterozygote comparison and dominant model). The stability of these observations was confirmed by a sensitivity analysis. Begger''s funnel plot and Egger''s test did not reveal any publication bias.

Conclusions/Significance

This meta-analysis suggests that the GSTP1 341C>T polymorphism may contribute to genetic susceptibility to cancer, especially to lung cancer, and in Asian population. Nevertheless, additional well-designed studies focusing on different ethnicity and cancer types are needed to provide a more exact and comprehensive conclusion.     

MTHFR C677T Polymorphism and Risk of Congenital Heart Defects: Evidence from 29 Case-Control and TDT Studies

Background

Methylenetetrahydrofolate reductase (MTHFR) is an important enzyme for folate metabolism in humans; it is encoded by the MTHFR gene. Several studies have assessed the association between MTHFR C677T polymorphism and the risk of congenital heart defects (CHDs), while the results were inconsistent.

Methods and Findings

Multiple electronic databases were searched to identify relevant studies published up to July 22, 2012. Data from case-control and TDT studies were integrated in an allelic model using the Catmap and Metafor software. Twenty-nine publications were included in this meta-analysis. The overall meta-analysis showed significant association between MTHFR C677T polymorphism and CHDs risk in children with heterogeneity (P _{heterogeneity} = 0.000) and publication bias (P _egger = 0.039), but it turned into null after the trim-and-fill method was implemented (OR = 1.12, 95% CI = 0.95–1.31). Nevertheless, positive results were obtained after stratified by ethnicity and sample size in all subgroups except the mixed population. For mothers, there was significant association between the variant and CHDs without heterogeneity (P _{heterogeneity} = 0.150, OR = 1.16, 95% CI = 1.05–1.29) and publication bias (P _egger = 0.981). However, the results varied across each subgroup in the stratified analysis of ethnicity and sample size.

Conclusions

Both infant and maternal MTHFR C677T polymorphisms may contribute to the risk of CHDs.     

Land-Applied Goat Manure as a Source of Human Q-Fever in the Netherlands, 2006–2010

Studies have shown a link between Q-fever positive farms (QFPFs) and community cases of human Q-fever. Our study is the first to investigate the potential role of contaminated land-applied manure in human Q-fever, based on a large set of nationwide notification and farm management data. Time between manure application and disease onset in geographically linked notified human cases coincided with the incubation period of Q-fever. Proximity of contaminated land parcels predicted human cases better than proximity of QFPFs (80% vs. 58%, 0–5 km in 2009). Incidence around QFPFs and contaminated land parcels decreased with distance, but not around non-contaminated land parcels. Incidence was higher around contaminated land parcels than non-contaminated land parcels (RR = [10],95%CI = [7], [1]–[14,2]). Our findings deliver evidence that, apart from QFPFs, land-applied contaminated manure may be another source of human Q-fever.