"Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis

Background Mycobacterium tuberculosis has a global population structure consisting of six main phylogenetic lineages associated with specific geographic regions and human populations. One particular M. tuberculosis genotype known as “Beijing” has repeatedly been associated with drug resistance and has been emerging in some parts of the world. “Beijing” strains are traditionally defined based on a characteristic spoligotyping pattern. We used three alternative genotyping techniques to revisit the phylogenetic classification of M. tuberculosis complex (MTBC) strains exhibiting the typical “Beijing” spoligotyping pattern. Methods and Findings MTBC strains were obtained from an ongoing molecular epidemiological study in Switzerland and Nepal. MTBC genotyping was performed based on SNPs, genomic deletions, and 24-loci MIRU-VNTR. We identified three MTBC strains from patients originating from Tibet, Portugal and Nepal which exhibited a spoligotyping patterns identical to the classical Beijing signature. However, based on three alternative molecular markers, these strains were assigned to Lineage 3 (also known as Delhi/CAS) rather than to Lineage 2 (also known as East-Asian lineage). Sequencing of the RD207 in one of these strains showed that the deletion responsible for this “Pseudo-Beijing” spoligotype was about 1,000 base pairs smaller than the usual deletion of RD207 in classical “Beijing” strains, which is consistent with an evolutionarily independent deletion event in the direct repeat (DR) region of MTBC. Conclusions We provide an example of convergent evolution in the DR locus of MTBC, and highlight the limitation of using spoligotypes for strain classification. Our results indicate that a proportion of “Beijing” strains may have been misclassified in the past. Markers that are more phylogenetically robust should be used when exploring strain-specific differences in experimental or clinical phenotypes.

The ethnolinguistic identity of the domesticators of Asian rice

Linguistic palaeontology permits the identification of two language families whose linguistic ancestors pose the likeliest candidates for the original domesticators of rice, viz. Hmong-Mien and Austroasiatic. In the 2009 model, the ancient Hmong-Mien was identified as the primary domesticators of Asian rice, and the ancient Austroasiatics as the secondary domesticators. Recent rice genetic research leads to the modification of this model for rice domestication, but falls short of identifying the original locus of rice domestication. At the same time, the precise whereabouts of the Austroasiatic homeland remains disputed. Linguistic evidence unrelated to rice agriculture has been adduced to support a southern homeland for Austroasiatic somewhere within the Bay of Bengal littoral. The implications of new rice genetic research are discussed, the linguistic palaeontological evidence is reassessed, and an enduring problem with the archaeology of rice agriculture is highlighted.

Predictors of satisfaction with treatment decision, decision-making preferences, and main treatment goals in patients with advanced cancer

Purpose This study investigated satisfaction with treatment decision (SWTD), decision-making preferences (DMP), and main treatment goals, as well as evaluated factors that predict SWTD, in patients receiving palliative cancer treatment at a Swiss oncology network. Patients and methods Patients receiving a new line of palliative treatment completed a questionnaire 4–6 weeks after the treatment decision. Patient questionnaires were used to collect data on sociodemographics, SWTD (primary outcome measure), main treatment goal, DMP, health locus of control (HLoC), and several quality of life (QoL) domains. Predictors of SWTD (6 = worst; 30 = best) were evaluated by uni- and multivariate regression models. Results Of 480 participating patients in eight hospitals and two private practices, 445 completed all questions regarding the primary outcome measure. Forty-five percent of patients preferred shared, while 44 % preferred doctor-directed, decision-making. Median duration of consultation was 30 (range: 10–200) minutes. Overall, 73 % of patients reported high SWTD (≥24 points). In the univariate analyses, global and physical QoL, performance status, treatment goal, HLoC, prognosis, and duration of consultation were significant predictors of SWTD. In the multivariate analysis, the only significant predictor of SWTD was duration of consultation (p = 0.01). Most patients indicated hope for improvement (46 %), followed by hope for longer life (26 %) and better quality of life (23 %), as their main treatment goal. Conclusion Our results indicate that high SWTD can be achieved in most patients with a 30-min consultation. Determining the patient’s main treatment goal and DMP adds important information that should be considered before discussing a new line of palliative treatment.

The role of chance events in the school-to-work transition: The influence of demographic, personality and career development variables

Chance events are considered important in career development, yet little empirical research is available on their predictors and consequences. The present study investigated socio-demographic (gender, nationality, school-type), personality (openness, locus of control) and career development variables (career decidedness, career planning) in relation to perceived chance events with a retrospective (N = 229, eleventh grade), and 1-year longitudinal prospective study (N = 245, eighth/ninth grade) among Swiss adolescents. The results showed that the majority of both groups reported a significant influence of chance events on their transition from compulsory school to vocational education or high school. Importance of chance events related to socio-demographics and personality but not career preparation. Career preparation and chance events predicted subjective career success in terms of wish correspondence and overall satisfaction with transition outcome among the younger cohort. Implications include the necessity to integrate both thorough career preparation and chance events in theory and counseling practice.

Resistance to Temptation: The Interaction of External and Internal Control on Alcohol Use During Residential Treatment for Alcohol Use Disorder

Background: There is evidence that drinking during residential treatment is related to various factors, such as patients’ general control beliefs and self-efficacy, as well as to external control of alcohol use by program’s staff and situations where there is temptation to drink. As alcohol use during treatment has been shown to be associated with the resumption of alcohol use after discharge from residential treatment, we aimed to investigate how these variables are related to alcohol use during abstinenceoriented residential treatment programs for alcohol use disorders (AUD). Methods: In total, 509 patients who entered 1 of 2 residential abstinence-oriented treatment programs for AUD were included in the study. After detoxification, patients completed a standardized diagnostic procedure including interviews and questionnaires. Drinking was assessed by patients’ selfreport of at least 1 standard drink or by positive breathalyzer testing. The 2 residential programs were categorized as high or low control according to the average number of tests per patient. Results: Regression analysis revealed a significant interaction effect between internal and external control suggesting that patients with high internal locus of control and high frequency of control by staff demonstrated the least alcohol use during treatment (16.7%) while patients with low internal locus of control in programs with low external control were more likely to use alcohol during Treatment (45.9%). No effects were found for self-efficacy and temptation. Conclusions: As alcohol use during treatment is most likely associated with poor treatment outcomes, external control may improve treatment outcomes and particularly support patients with low internal locus of control, who show the highest risk for alcohol use during treatment. High external control may complement high internal control to improve alcohol use prevention while in treatment. Key Words: Alcohol Dependence, Alcohol Use, Locus of Control, Alcohol Testing.

Should I Stay or Should I Go? Career Choice Intentions of Students with Family Business Background

Personal and motivational patterns of intentional founders have been researched in great depth; however, antecedents to career choices of intentional successors have been conspicuously missing in entrepreneurship research. By drawing on theory of planned behavior, we investigate how intentional founders, successors, and employees differ in terms of locus of control and entrepreneurial self-efficacy as well as independence and innovation motives. We find that transitive likelihood of career intent depends on degree of entrepreneurial self-efficacy and the independence motive. Unexpectedly, we see that high levels of internal locus of control lead to a preference of employment, which challenges traditional entrepreneurship research and suggests that the feasibility of an entrepreneurial career path does not automatically make it desirable. Our findings suggest that students with family business background are pessimistic about being in control in an entrepreneurial career, but optimistic about their efficacy to pursue an entrepreneurial career.

Lactate and glucose concentrations in brain interstitial fluid, cerebrospinal fluid, and serum during experimental pneumococcal meningitis

Metabolic abnormalities during bacterial meningitis include hypoglycorrhachia and cerebrospinal fluid (CSF) lactate accumulation. The mechanisms by which these alterations occur within the central nervous system (CNS) are still incompletely delineated. To determine the evolution of these changes and establish the locus of abnormal metabolism during meningitis, glucose and lactate concentrations in brain interstitial fluid, CSF, and serum were measured simultaneously and sequentially during experimental pneumococcal meningitis in rabbits. Interstitial fluid samples were obtained from the frontal cortex and hippocampus by using in situ brain microdialysis, and serum and CSF were directly sampled. There was an increase of CSF lactate concentration, accompanied by increased local production of lactate in the brain, and a decrease of CSF-to-serum glucose ratio that was paralleled by a decrease in cortical glucose concentration. Brain microdialysate lactate concentration was not affected by either systemic lactic acidosis or artificially elevated CSF lactate concentration. These data support the hypothesis that the brain is a locus for anaerobic glycolysis during meningitis, resulting in increased lactate production and perhaps contributing to decreased tissue glucose concentration.

Sonic intelligence as a virtual therapeutic environment

This paper reports on the results of a research project, on comparing one virtual collaborative environment with a first-person visual immersion (first-perspective interaction) and a second one where the user interacts through a sound-kinetic virtual representation of himself (avatar), as a stress-coping environment in real-life situations. Recent developments in coping research are proposing a shift from a trait-oriented approach of coping to a more situation-specific treatment. We defined as real-life situation a target-oriented situation that demands a complex coping skills inventory of high self-efficacy and internal or external "locus of control" strategies. The participants were 90 normal adults with healthy or impaired coping skills, 25-40 years of age, randomly spread across two groups. There was the same number of participants across groups and gender balance within groups. All two groups went through two phases. In Phase I, Solo, one participant was assessed using a three-stage assessment inspired by the transactional stress theory of Lazarus and the stress inoculation theory of Meichenbaum. In Phase I, each participant was given a coping skills measurement within the time course of various hypothetical stressful encounters performed in two different conditions and a control group. In Condition A, the participant was given a virtual stress assessment scenario relative to a first-person perspective (VRFP). In Condition B, the participant was given a virtual stress assessment scenario relative to a behaviorally realistic motion controlled avatar with sonic feedback (VRSA). In Condition C, the No Treatment Condition (NTC), the participant received just an interview. In Phase II, all three groups were mixed and exercised the same tasks but with two participants in pairs. The results showed that the VRSA group performed notably better in terms of cognitive appraisals, emotions and attributions than the other two groups in Phase I (VRSA, 92%; VRFP, 85%; NTC, 34%). In Phase II, the difference again favored the VRSA group against the other two. These results indicate that a virtual collaborative environment seems to be a consistent coping environment, tapping two classes of stress: (a) aversive or ambiguous situations, and (b) loss or failure situations in relation to the stress inoculation theory. In terms of coping behaviors, a distinction is made between self-directed and environment-directed strategies. A great advantage of the virtual collaborative environment with the behaviorally enhanced sound-kinetic avatar is the consideration of team coping intentions in different stages. Even if the aim is to tap transactional processes in real-life situations, it might be better to conduct research using a sound-kinetic avatar based collaborative environment than a virtual first-person perspective scenario alone. The VE consisted of two dual-processor PC systems, a video splitter, a digital camera and two stereoscopic CRT displays. The system was programmed in C++ and VRScape Immersive Cluster from VRCO, which created an artificial environment that encodes the user's motion from a video camera, targeted at the face of the users and physiological sensors attached to the body.

Assessing Difficulties in Career Decision Making Among Swiss Adolescents with the German My Vocational Situation Scale

Assessing problems in career decision making among adolescents is important for career guidance and research. The present study is the first to investigate among Swiss adolescents the factor structure and convergent validity in relation to personality of the German-language adaptation of the My Vocational Situation Scale. Two preliminary studies (N = 217) suggested that using a 5-point Likert scale response format would increase scale reliability. The confirmatory factor analyses in the main study with two cohorts (n = 341, eighth grade; n = 303, eleventh grade) confirmed that four main factors, which assess problems with identity, decision making, information, and perceived barriers, underlie the data. The barriers factor was differentiated into aspired vocation and personal situation. Construct validity was supported by significant relationships between favorable personality characteristics (emotional stability, extraversion, agreeableness, conscientiousness, generalized self-efficacy, and internal locus of control) and fewer problems. The results suggest that the vocational identity and barriers scales can be fruitfully applied to research on and the practice of career counseling with adolescents.

The porcine tumor necrosis factor-encoding genes: sequence and comparative analysis

We have cloned and sequenced a 10.22-kb fragment of the genomic locus of the porcine tumor necrosis factor-encoding genes, TNF-alpha and TNF-beta. A liver genomic DNA library, partially digested with Sau3AI, was cloned into the phage lambda EMBL4 and screened with a porcine TNF-alpha cDNA probe. Analysis showed that both the TNF-alpha and TNF-beta genes were present on the cloned fragment. In addition, the cloned fragment contained about 2 kb of repetitive sequences 5' to the TNF-beta gene. The TNF genes are arranged in a tandem repeat, as is the case for the human, mouse and rabbit TNF genes. The comparison of both genes with their human homologues displayed a considerable degree of conservation (80%), suggesting an equal evolution rate.

Valence and agency influence striatal response to feedback in patients with major depressive disorder

BACKGROUND: Reduced sensitivity to positive feedback is common in patients with major depressive disorder (MDD). However, findings regarding negative feedback are ambiguous, with both exaggerated and blunted responses being reported. The ventral striatum (VS) plays a major role in processing valenced feedback, and previous imaging studies have shown that the locus of controls (self agency v. external agency) over the outcome influences VS response to feedback. We investigated whether attributing the outcome to one's own action or to an external agent influences feedback processing in patients with MDD. We hypothesized that depressed participants would be less sensitive to the feedback attribution reflected by an altered VS response to self-attributed gains and losses. METHODS: Using functional MRI and a motion prediction task, we investigated the neural responses to self-attributed (SA) and externally attributed (EA) monetary gains and losses in unmedicated patients with MDD and healthy controls. RESULTS: We included 21 patients and 25 controls in our study. Consistent with our prediction, healthy controls showed a VS response influenced by feedback valence and attribution, whereas in depressed patients striatal activity was modulated by valence but was insensitive to attribution. This attribution insensitivity led to an altered ventral putamen response for SA - EA losses in patients with MDD compared with healthy controls. LIMITATIONS: Depressed patients with comorbid anxiety disorder were included. CONCLUSION: These results suggest an altered assignment of motivational salience to SA losses in patients with MDD. Altered striatal response to SA negative events may reinforce the belief of not being in control of negative outcomes contributing to a cycle of learned helplessness.

Focused fluid transfer through the mantle above subduction zones

Volcanic arcs above subduction zones are enriched in volatiles and fluid-mobile elements with respect to mid-oceanic ridge basalts. There is general consensus that this particular subduction zone signature is generated by fluid-induced extraction of these elements from subducted oceanic crust and its sedimentary cover. However, how these fluids are transferred through the mantle wedge to the locus of partial melting and what modification the fluids will experience is unresolved. Here we investigate the interaction of slab fluids with the mantle wedge through a series of high-pressure experiments. We explore two end-member processes of focused and porous reactive flow of hydrous slab melts through the mantle. Transfer by porous flow leads to the formation of hydrous minerals that sequester fluid-mobile elements and residual fluids characterized by trace element patterns inconsistent with typical arc lavas. In contrast, no hydrous minerals are formed in the reaction zone of experiments mimicking focused flow, and the typical trace element signature acquired during fluid extraction from the slab is preserved, indicating that this is an efficient process for element transfer through the mantle wedge.

Heterozygous deletion of the PU.1 locus in human AML

The transcription factor PU.1 is essential for myeloid development. Targeted disruption of an upstream regulatory element (URE) decreases PU.1 expression by 80% and leads to acute myeloid leukemia (AML) in mice. Here, we sequenced the URE sequences of PU.1 in 120 AML patients. Four polymorphisms (single nucleotide polymorphisms [SNPs]) in the URE were observed, with homozygosity in all SNPs in 37 patients. Among them, we compared samples at diagnosis and remission, and one patient with cytogenetically normal acute myeloid leukemia M2 was identified with heterozygosity in 3 of the SNPs in the URE at remission. Loss of heterozygosity was further found in this patient at 2 polymorphic sites in the 5' promoter region and in 2 intronic sites flanking exon 4, thus suggesting loss of heterozygosity covering at least 40 kb of the PU.1 locus. Consistently, PU.1 expression in this patient was markedly reduced. Our study suggests that heterozygous deletion of the PU.1 locus can be associated with human AML.

Mapping of a new locus for congenital anomalies of the kidney and urinary tract on chromosome 8q24

Congenital anomalies of the kidney and urinary tract (CAKUT) account for the majority of end-stage renal disease in children (50%). Previous studies have mapped autosomal dominant loci for CAKUT. We here report a genome-wide search for linkage in a large pedigree of Somalian descent containing eight affected individuals with a non-syndromic form of CAKUT.

The mutation causing the black-and-tan pigmentation phenotype of Mangalitza pigs maps to the porcine ASIP locus but does not affect its coding sequence

The gene for agouti signaling protein (ASIP) is centrally involved in the expression of coat color traits in animals. The Mangalitza pig breed is characterized by a black-and-tan phenotype with black dorsal pigmentation and yellow or white ventral pigmentation. We investigated a Mangalitza x Piétrain cross and observed a coat color segregation pattern in the F2 generation that can be explained by virtue of two alleles at the MC1R locus and two alleles at the ASIP locus. Complete linkage of the black-and-tan phenotype to microsatellite alleles at the ASIP locus on SSC 17q21 was observed. Corroborated by the knowledge of similar mouse coat color mutants, it seems therefore conceivable that the black-and-tan pigmentation of Mangalitza pigs is caused by an ASIP allele a(t), which is recessive to the wild-type allele A. Toward positional cloning of the a(t) mutation, a 200-kb genomic BAC/PAC contig of this chromosomal region has been constructed and subsequently sequenced. Full-length ASIP cDNAs obtained by RACE differed in their 5' untranslated regions, whereas they shared a common open reading frame. Comparative sequencing of all ASIP exons and ASIP cDNAs between Mangalitza and Piétrain pigs did not reveal any differences associated with the coat color phenotype. Relative qRT-PCR analyses showed different dorsoventral skin expression intensities of the five ASIP transcripts in black-and-tan Mangalitza. The a(t) mutation is therefore probably a regulatory ASIP mutation that alters its dorsoventral expression pattern.