Validating a measure for eco-anxiety in Portuguese young adults and exploring its associations with environmental action.

BACKGROUND: Worsening environmental conditions may amplify people's emotional responses to an environmental crisis (eco-anxiety). In Portugal, young people seem to be especially concerned about climate change. However, this phenomenon needs to be interpreted using accurate instruments. Thus, this study aimed to validate the Portuguese version of the Hogg Eco-Anxiety Scale (HEAS) in young adults and examine the associations among eco-anxiety, sociodemographic characteristics, and pro-environmental behaviours. METHODS: A survey was administered to 623 Portuguese university students aged between 18 and 25 years. The survey included our Portuguese translation of the HEAS (obtained through a back-translation and pretesting process), a sociodemographic assessment, and questions related to pro-environmental behaviours. Confirmatory factor analysis was conducted to assess the construct validity of the Portuguese version of the HEAS, and global fit indices were used to assess whether the original four-dimensional structure of the scale was reproduced. The reliability of the Portuguese version of the HEAS was evaluated by Cronbach's alpha and the intraclass correlation coefficient. Measurement invariance examined sex differences in scale interpretation. Linear regressions were used to detect whether sociodemographic variables predict eco-anxiety and whether eco-anxiety predicts pro-environmental behaviours. RESULTS: The factorial structure of the original scale was replicated in the Portuguese version of the HEAS, showing good internal consistency, reliability over time and strict invariance between men and women. A higher paternal education level predicted greater eco-anxiety in children. Two dimensions of eco-anxiety-namely, rumination and anxiety about personal impacts on the environment-predicted higher engagement in pro-environmental behaviours. CONCLUSIONS: The translated scale is an appropriate tool to measure eco-anxiety in the Portuguese context and should be used to collect evidence to drive environmental and health policies. An individual's education level should be considered a determinant of their emotional response to environmental conditions. Importantly, eco-anxiety can act as a protective emotional response to preserving the planet.

Systematic Review of Patient-Reported Outcome Measures for Patients with Exercise-Induced Leg Pain.

Background and Objectives: To determine the most commonly used patient-reported outcome measures (PROMs) in exercise-induced leg pain (EILP) and to identify specific PROMs for EILP in order to evaluate their psychometric properties and methodological quality. Materials and Methods: A strategic search was performed in different databases to identify and extract the characteristics of studies based on the use of PROMs in patients with EILP. Specific PROMs were evaluated according to the Terwee et al. and COSMIN criteria. Results: Fifty-six studies were included in the review. The Medial Tibial Stress Syndrome Score (MTSSS), Lower Extremity Functional Scale (LEFS) and Exercise-Induced Leg Pain Questionnaire (EILP-Q) were identified as specific PROMs for EILP. The Visual Analog Scale (VAS) was the most widely used instrument in the assessment of EILP. The methodological quality assessment showed six positive values for the LEFS, four for the MTSSS and three for the EILP-Q for the eight psychometric properties analyzed according to the COSMIN criteria. The evaluation of the nine psychometric properties according to Terwee showed five positive values for the LEFS and MTSSS, and three for the EILP-Q. Conclusions: The overall methodological quality of the PROMs used was low. The VAS was the most widely used instrument in the assessment of EILP, and the LEFS was the highest quality PROM available for EILP, followed by the MTSSS and EILP-Q, respectively.

Morph-agronomic characterization of watermelon accessions with resistance to Fusarium Wilt.

Fifty-five watermelon accessions were inoculated in pots using Fusarium oxysporum f. sp. niveum chlamydospores in a completely randomized design with five replications. Among the 42 accessions that were resistant, twelve accessions with a mean score ≤1 were selected for morpho-agronomic characterization. 'Sugar Baby' and 'Charleston Gray' were used as controls. Field research was conducted over two production cycles in a randomized block design with three replications and five plants per plot. For the characterization 13 quantitative agronomic traits were used. The dissimilarity measures were obtained by the sum of the matrices of standardized mean Euclidean distance. Coefficients of variation ranged from 5.33% (number of days until 50% of plants with at least one female flower) and 17.20% (mass of characterized fruit). In the second cycle, a reduction in days was observed for the flowering. For soluble solids content, the accession BGH-UNIVASF 40 was statistically equal to the commercial cultivars in the second cycle. Accessions were grouped similarly using two grouping methods, Tocher and the farthest neighbor method. The most promising accessions were BGH-UNIVASF 40, 169, 177 and 210 for use in future hybridizations. BGH-UNIVASF 76, 128 and 185 (Citrullus lanatus var. citroides) can be used as resistant Fusarium wilt rootstocks.

Memory illusions and category malleability: False recognition for goal-derived reorganizations of common categories.

Four studies explore semantic memory intrusions for goal-derived subcategories (e.g., "sports good for backache") embedded in taxonomic categories (e.g., "sports"). Study 1 presented hybrid lists (composed of typical items from both representations: taxonomic categories and subcategories) together with names of subcategories, names of taxonomic categories, or with no names. Subcategory names produced levels of false recognitions for critical lures from subcategories comparable with critical lures from taxonomic categories. Study 2 presented lists of exemplars either from taxonomic categories or subcategories (between participants). Lists of subcategories paired with their names produced higher levels of false recognition for subcategories lures compared with taxonomic lures. Study 3 replicated this result and showed that even though distinctiveness of taxonomic lures in a subcategory context (i.e., subcategory list with a subcategory name) may facilitate rejection of these lures, subcategory lures were still more falsely recognized than were taxonomic lures when retrieval monitoring was hindered through speeded recognition. Study 4 replicated the results with lists in which production frequency was better controlled and with a larger sample allowing for increased power of the test. Although confirming the critical role of preexistent categorical structures in the generation of false memories, results show that false memories for goal-derived subcategories can occur with the same frequency as false memories stemming from better established taxonomic categories. Such results broaden the scope of occurrence of false memories to goal-derived semantic organizations, which are often closer to categorizations used in real-world environments.

Hybrid oncocytic/chromophobe renal cell tumor: An integrated genetic and epigenetic characterization of a case.

INTRODUCTION: Hybrid oncocytic/chromophobe tumor (HOCT) is a renal cell neoplasm displaying overlapping cellular and architectural features of both renal oncocytoma (RO) and chromophobe renal cell carcinoma (chRCC). It has been described in the context of oncocytosis, Birt-Hogg-Dubé syndrome, and also sporadically. Thus far, HOCT immunohischemical profile and cytogenetic alterations have been reported, but not epigenetic alterations. Herein, we characterize a HOCT case, including microRNA expression, comparing it to sporadic RO and chRCC. METHODS: An HOCT was entirely submitted. Representative paraffin blocks were selected for histochemical, immunohistochemical and FISH analyses. MicroRNAs were extracted from the two components separately and selected microRNA expression was performed. RESULTS: This 4 cm HOCT, from a 69 year-old female, was composed mainly by oncocytic cells with an insular distribution (RO-like) and areas of larger clarified cells (chRCC-like). The two areas displayed different features: RO-like areas showed negative colloidal iron staining, multifocal CD15, negative CK7, focal multiple tetrasomies, and higher miR21 expression; chRCC-like areas showed colloidal iron diffuse staining with moderate intensity, focal CD15 and CK7, no numeric chromosomic alterations, and higher miR141 and miR200b expression. CONCLUSION: microRNA expression in the two HOCT components is similar to its sporadic tumors counterparts. Morphologic, immunohistochemical, cytogenetic and epigenetic data on this case suggest either two independent pathogenic pathways or an early pathogenic divergence for RO-like and chRCC-like components of HOCT.

Insights from tissue-specific transcriptome sequencing analysis of Triatoma infestans.

Triatoma infestans is an insect of subfamily Triatominae (Hemiptera: Reduviidae) and an important vector of Trypanosoma cruzi, the etiologic agent of human Chagas disease. In this work we reported a transcriptome assembly and annotation of T. infestans heads obtained by Next Generation Sequencing (NGS) technologies.

Immunoinformatics Features Linked to Leishmania Vaccine Development: Data Integration of Experimental and In Silico Studies.

Leishmaniasis is a wide-spectrum disease caused by parasites from Leishmania genus. There is no human vaccine available and it is considered by many studies as apotential effective tool for disease control. To discover novel antigens, computational programs have been used in reverse vaccinology strategies. In this work, we developed a validation antigen approach that integrates prediction of B and T cell epitopes, analysis of Protein-Protein Interaction (PPI) networks and metabolic pathways. We selected twenty candidate proteins from Leishmania tested in murine model, with experimental outcome published in the literature. The predictions for CD4⁺ and CD8⁺ T cell epitopes were correlated with protection in experimental outcomes. We also mapped immunogenic proteins on PPI networks in order to find Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with them. Our results suggest that non-protective antigens have lowest frequency of predicted T CD4⁺ and T CD8⁺ epitopes, compared with protective ones. T CD4⁺ and T CD8⁺ cells are more related to leishmaniasis protection in experimental outcomes than B cell predicted epitopes. Considering KEGG analysis, the proteins considered protective are connected to nodes with few pathways, including those associated with ribosome biosynthesis and purine metabolism.

Genome analysis reveals insights of the endophytic Bacillus toyonensis BAC3151 as a potentially novel agent for biocontrol of plant pathogens.

Diseases caused by phytopathogenic microorganisms account for enormous losses for agribusiness. Although Bacillus species are recognized as being antimicrobial producers and some may provide benefits to plants, the association between Bacillus toyonensis and plants has not been studied. In this study, the whole-genome sequenced endophytic B. toyonensis BAC3151, which has demonstrated antimicrobial activity and quorum sensing inhibition of phytopathogenic bacteria, was investigated for its potential for the production of compounds for biocontrol of plant pathogens. Four whole-genome sequenced B. toyonensis strains shared 3811 protein-coding DNA sequences (CDSs), while strain-specific CDSs, such as biosynthetic gene clusters of antimicrobials, were associated with specific chromosomal regions and mobile genetic elements of the strains. B. toyonensis strains had a higher frequency of putative bacteriocins gene clusters than that of Bacillus species traditionally used for the production of antimicrobials. In addition, gene clusters potentially involved in the production of novel bacteriocins were found in BAC3151, as well as biosynthetic genes of several other compounds, including non-ribosomal peptides, N-acyl homoserine lactonase and chitinases, revealing a genetic repertoire for antimicrobial synthesis greater than that of other Bacillus strains that have demonstrated effective activity against phytopathogens. This study showed for the first time that B. toyonensis has potential to produce various antimicrobials, and the analyses performed indicated that the endophytic strain BAC3151 can be useful for the development of new strategies to control microbial diseases in plants that are responsible for large damages in agricultural crops.

Molecular characterization of lipoamide dehydrogenase gene in Trypanosoma cruzi populations susceptible and resistant to benznidazole.

Lipoamide dehydrogenase (LipDH) is a flavin-containing disulfide oxidoreductase from the same group of thioredoxin reductase, glutathione reductase and trypanothione reductase. This enzyme is found in the mitochondria of all aerobic organisms where it takes part in at least three important multienzyme complexes from the citric acid cycle. In this study, we performed a phylogenetic analysis comparing the amino acid sequence of the LipDH from Trypanosoma cruzi (TcLipDH) with the LipDH from other organisms. Subsequently, the copy number of the TcLipDH gene, the mRNA and protein levels, and the enzymatic activity of the LipDH were determined in populations and strains of T. cruzi that were either resistant or susceptible to benznidazole (BZ). In silico analysis showed the presence of two TcLipDH alleles in the T. cruzi genome. It also showed that TcLipDH protein has less than 55% of identity in comparison to the human LipDH, but the active site is conserved in both of them. Southern blot results suggest that the TcLipDH is a single copy gene in the genome of the T. cruzi samples analyzed. Northern blot assays showed one transcript of 2.4 kb in all T. cruzi populations. Northern blot and Real Time RT-PCR data revealed that the TcLipDH mRNA levels were 2-fold more expressed in the BZ-resistant T. cruzi population (17LER) than in its susceptible pair (17WTS). Western blot results revealed that the TcLipDH protein level is 2-fold higher in 17LER sample in comparison to 17WTS sample. In addition, LipDH activity was higher in the 17LER population than in the 17WTS. Sequencing analysis revealed that the amino acid sequences of the TcLipDH from 17WTS and 17LER populations are identical. Our findings show that one of the mechanisms associated with in vitro-induced BZ resistance to T. cruzi correlates with upregulation of LipDH enzyme.

Comparative genomic analysis of three Leishmania species that cause diverse human disease.

Leishmania parasites cause a broad spectrum of clinical disease. Here we report the sequencing of the genomes of two species of Leishmania: Leishmania infantum and Leishmania braziliensis. The comparison of these sequences with the published genome of Leishmania major reveals marked conservation of synteny and identifies only approximately 200 genes with a differential distribution between the three species. L. braziliensis, contrary to Leishmania species examined so far, possesses components of a putative RNA-mediated interference pathway, telomere-associated transposable elements and spliced leader-associated SLACS retrotransposons. We show that pseudogene formation and gene loss are the principal forces shaping the different genomes. Genes that are differentially distributed between the species encode proteins implicated in host-pathogen interactions and parasite survival in the macrophage.

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes.

Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides.

Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis.

BACKGROUND: The fungal genus Sporothrix includes at least four human pathogenic species. One of these species, S. brasiliensis, is the causal agent of a major ongoing zoonotic outbreak of sporotrichosis in Brazil. Elsewhere, sapronoses are caused by S. schenckii and S. globosa. The major aims on this comparative genomic study are: 1) to explore the presence of virulence factors in S. schenckii and S. brasiliensis; 2) to compare S. brasiliensis, which is cat-transmitted and infects both humans and cats with S. schenckii, mainly a human pathogen; 3) to compare these two species to other human pathogens (Onygenales) with similar thermo-dimorphic behavior and to other plant-associated Sordariomycetes. RESULTS: The genomes of S. schenckii and S. brasiliensis were pyrosequenced to 17x and 20x coverage comprising a total of 32.3 Mb and 33.2 Mb, respectively. Pair-wise genome alignments revealed that the two species are highly syntenic showing 97.5% average sequence identity. Phylogenomic analysis reveals that both species diverged about 3.8-4.9 MYA suggesting a recent event of speciation. Transposable elements comprise respectively 0.34% and 0.62% of the S. schenckii and S. brasiliensis genomes and expansions of Gypsy-like elements was observed reflecting the accumulation of repetitive elements in the S. brasiliensis genome. Mitochondrial genomic comparisons showed the presence of group-I intron encoding homing endonucleases (HE's) exclusively in S. brasiliensis. Analysis of protein family expansions and contractions in the Sporothrix lineage revealed expansion of LysM domain-containing proteins, small GTPases, PKS type1 and leucin-rich proteins. In contrast, a lack of polysaccharide lyase genes that are associated with decay of plants was observed when compared to other Sordariomycetes and dimorphic fungal pathogens, suggesting evolutionary adaptations from a plant pathogenic or saprobic to an animal pathogenic life style. CONCLUSIONS: Comparative genomic data suggest a unique ecological shift in the Sporothrix lineage from plant-association to mammalian parasitism, which contributes to the understanding of how environmental interactions may shape fungal virulence. . Moreover, the striking differences found in comparison with other dimorphic fungi revealed that dimorphism in these close relatives of plant-associated Sordariomycetes is a case of convergent evolution, stressing the importance of this morphogenetic change in fungal pathogenesis.

Description of Post-discharge Outcomes of Patients with COVID-19 in a Tertiary Referral Center in the Philippines.

Background and Objectives: The immediate post-discharge period of COVID-19 patients is a vulnerable state due to several complications that may arise during this time. Some patients get readmitted shortly after being discharged while others report persistence of symptoms, develop specialized needs, or observe a decline from their baseline functional capacity. Information on the outcomes of post-COVID discharge patients in our institution is currently lacking. This study described the outcomes of patients with COVID-19 after their discharge from the service areas of Philippine General Hospital. Methods: This study is a retrospective chart review involving charts of all adult patients discharged from the PGH COVID service areas last August 2021 to October 2021. Data from their follow up consults at 1 week, 1 month, and 3 months post-discharge were reviewed. Baseline characteristics and post-discharge outcomes including post-COVID symptoms, special care needs, mortality, rehospitalization, emergency consult, level of dependence, and ability to return to work were assessed. Results: A total of 171 patient charts were included. The mean age of patients was 53.7 years. Most were male (60.2%), unemployed (59.7%), non-smoker (55%), hypertensive (57.9%), diabetic (50.2%), and obese (50.2%). Most of them were oxygen requiring (80%) and with severe to critical COVID infection (72.5%) during admission. At 3 months post-discharge, 113 (66%) were stable and able to complete the follow up, 8 (4.6%) died, 9 (5.2%) got readmitted, and 41 (23.9%) were lost to follow up. Among those who were able to follow up after 3 months, 84 (74%) were asymptomatic. Among those who remained symptomatic, the most common symptoms were dyspnea, fatigue, and cough. After 3 months, 100 (88%) did not require special care needs, 100 (88%) were fully independent, and 45 (39.8%) were able to return to baseline work. Conclusions: Despite the majority of patients having severe to critical COVID infection during admission, most were asymptomatic within 3 months post-discharge. In those who developed persistent symptoms, dyspnea, cough, and fatigue were the most common symptoms identified regardless of COVID severity. Majority did not require special care needs.

MicroRNA profile: a promising ancillary tool for accurate renal cell tumour diagnosis.

BACKGROUND: Renal cell tumours (RCTs) are clinically, morphologically and genetically heterogeneous. Accurate identification of renal cell carcinomas (RCCs) and its discrimination from normal tissue and benign tumours is mandatory. We, thus, aimed to define a panel of microRNAs that might aid in the diagnostic workup of RCTs. METHODS: Fresh-frozen tissues from 120 RCTs (clear-cell RCC, papillary RCC, chromophobe RCC (chRCC) and oncocytomas: 30 cases each), 10 normal renal tissues and 60 cases of ex-vivo fine-needle aspiration biopsies from RCTs (15 of each subtype validation set) were collected. Expression levels of miR-21, miR-141, miR-155, miR-183 and miR-200b were assessed by quantitative reverse transcription-PCR. Receiver operator characteristic curves were constructed and the areas under the curve were calculated to assess diagnostic performance. Disease-specific survival curves and a Cox regression model comprising all significant variables were computed. RESULTS: Renal cell tumours displayed significantly lower expression levels of miR-21, miR-141 and miR-200b compared with that of normal tissues, and expression levels of all miRs differed significantly between malignant and benign RCTs. Expression analysis of miR-141 or miR-200b accurately distinguished RCTs from normal renal tissues, oncocytoma from RCC and chRCC from oncocytoma. The diagnostic performance was confirmed in the validation set. Interestingly, miR-21, miR-141 and miR-155 expression levels showed prognostic significance in a univariate analysis. CONCLUSION: The miR-141 or miR-200b panel accurately distinguishes RCC from normal kidney and oncocytoma in tissue samples, discriminating from normal kidney and oncocytoma, whereas miR-21, miR-141 and miR-155 convey prognostic information. This approach is feasible in fine-needle aspiration biopsies and might provide an ancillary tool for routine diagnosis.

Role of NorR-like transcriptional regulators under nitrosative stress of the δ-proteobacterium, Desulfovibrio gigas.

NorR protein was shown to be responsible for the transcriptional regulation of flavorubredoxin and its associated oxidoreductase in Escherichia coli. Since Desulfovibrio gigas has a rubredoxin:oxygen oxidoreductase (ROO) that is involved in both oxidative and nitrosative stress response, a NorR-like protein was searched in D. gigas genome. We have found two putative norR coding units in its genome. To study the role of the protein designated as NorR1-like (NorR1L) in the presence of nitrosative stress, a norR1L null mutant of D. gigas was created and a phenotypic analysis was performed under the nitrosating agent GSNO. We show that under these conditions, the growth of both D. gigas mutants Δroo and ΔnorR1-like is impaired. In order to confirm that D. gigas NorR1-like may play identical function as the NorR of E. coli, we have complemented the E. coli ΔnorR mutant strain with the norR1-like gene and have evaluated growth when nitrosative stress was imposed. The growth phenotype of E. coli ΔnorR mutant strain was recovered under these conditions. We also found that induction of roo gene expression is completely abolished in the norR1L mutant strain of D. gigas subjected to nitrosative stress. It is identified in δ-proteobacteria, for the first time a transcription factor that is involved in nitrosative stress response and regulates the rd-roo gene expression.

An assessment on epitope prediction methods for protozoa genomes.

BACKGROUND: Epitope prediction using computational methods represents one of the most promising approaches to vaccine development. Reduction of time, cost, and the availability of completely sequenced genomes are key points and highly motivating regarding the use of reverse vaccinology. Parasites of genus Leishmania are widely spread and they are the etiologic agents of leishmaniasis. Currently, there is no efficient vaccine against this pathogen and the drug treatment is highly toxic. The lack of sufficiently large datasets of experimentally validated parasites epitopes represents a serious limitation, especially for trypanomatids genomes. In this work we highlight the predictive performances of several algorithms that were evaluated through the development of a MySQL database built with the purpose of: a) evaluating individual algorithms prediction performances and their combination for CD8+ T cell epitopes, B-cell epitopes and subcellular localization by means of AUC (Area Under Curve) performance and a threshold dependent method that employs a confusion matrix; b) integrating data from experimentally validated and in silico predicted epitopes; and c) integrating the subcellular localization predictions and experimental data. NetCTL, NetMHC, BepiPred, BCPred12, and AAP12 algorithms were used for in silico epitope prediction and WoLF PSORT, Sigcleave and TargetP for in silico subcellular localization prediction against trypanosomatid genomes. RESULTS: A database-driven epitope prediction method was developed with built-in functions that were capable of: a) removing experimental data redundancy; b) parsing algorithms predictions and storage experimental validated and predict data; and c) evaluating algorithm performances. Results show that a better performance is achieved when the combined prediction is considered. This is particularly true for B cell epitope predictors, where the combined prediction of AAP12 and BCPred12 reached an AUC value of 0.77. For T CD8+ epitope predictors, the combined prediction of NetCTL and NetMHC reached an AUC value of 0.64. Finally, regarding the subcellular localization prediction, the best performance is achieved when the combined prediction of Sigcleave, TargetP and WoLF PSORT is used. CONCLUSIONS: Our study indicates that the combination of B cells epitope predictors is the best tool for predicting epitopes on protozoan parasites proteins. Regarding subcellular localization, the best result was obtained when the three algorithms predictions were combined. The developed pipeline is available upon request to authors.

Anatomy and evolution of telomeric and subtelomeric regions in the human protozoan parasite Trypanosoma cruzi.

BACKGROUND: The subtelomeres of many protozoa are highly enriched in genes with roles in niche adaptation. T. cruzi trypomastigotes express surface proteins from Trans-Sialidase (TS) and Dispersed Gene Family-1 (DGF-1) superfamilies which are implicated in host cell invasion. Single populations of T. cruzi may express different antigenic forms of TSs. Analysis of TS genes located at the telomeres suggests that chromosome ends could have been the sites where new TS variants were generated. The aim of this study is to characterize telomeric and subtelomeric regions of T. cruzi available in TriTrypDB and connect the sequences of telomeres to T. cruzi working draft sequence. RESULTS: We first identified contigs carrying the telomeric repeat (TTAGGG). Of 49 contigs identified, 45 have telomeric repeats at one end, whereas in four contigs the repeats are located internally. All contigs display a conserved telomeric junction sequence adjacent to the hexamer repeats which represents a signature of T. cruzi chromosome ends. We found that 40 telomeric contigs are located on T. cruzi chromosome-sized scaffolds. In addition, we were able to map several telomeric ends to the chromosomal bands separated by pulsed-field gel electrophoresis.The subtelomeric sequence structure varies widely, mainly as a result of large differences in the relative abundance and organization of genes encoding surface proteins (TS and DGF-1), retrotransposon hot spot genes (RHS), retrotransposon elements, RNA-helicase and N-acetyltransferase genes. While the subtelomeric regions are enriched in pseudogenes, they also contain complete gene sequences matching both known and unknown expressed genes, indicating that these regions do not consist of nonfunctional DNA but are instead functional parts of the expressed genome. The size of the subtelomeric regions varies from 5 to 182 kb; the smaller of these regions could have been generated by a recent chromosome breakage and telomere healing event. CONCLUSIONS: The lack of synteny in the subtelomeric regions suggests that genes located in these regions are subject to recombination, which increases their variability, even among homologous chromosomes. The presence of typical subtelomeric genes can increase the chance of homologous recombination mechanisms or microhomology-mediated end joining, which may use these regions for the pairing and recombination of free ends.

When Type 2 Processing Misfires: The Indiscriminate Use of Statistical Thinking about Reasoning Problems.

Research on dual-process theories of judgment makes abundant use of reasoning problems that present a conflict between Type 1 intuitive responses and Type 2 rule-based responses. However, in many of these reasoning tasks, there is no way to discriminate between the adequate and inadequate use of rules based on logical or probabilistic principles. To experimentally discriminate between the two, we developed a new set of problems: rule-inadequate versions of standard base-rate problems (where base rates are made irrelevant). Across four experiments, we observed conflict sensitivity (measured in terms of response latencies and response confidence) in responses to standard base-rate problems but also in responses to rule-inadequate versions of these problems. This failure to discriminate between real and merely apparent (or spurious) conflict suggests that participants often misuse statistical information and draw conclusions based on irrelevant base rates. We conclude that inferring the sound use of statistical rules from normatively correct responses to standard conflict problems may be unwarranted when this kind of reasoning bias is not controlled for.

Expression Profile of Genes Related to the Th17 Pathway in Macrophages Infected by Leishmania major and Leishmania amazonensis: The Use of Gene Regulatory Networks in Modeling This Pathway.

Leishmania amazonensis and Leishmania major are the causative agents of cutaneous and mucocutaneous diseases. The infections' outcome depends on host-parasite interactions and Th1/Th2 response, and in cutaneous form, regulation of Th17 cytokines has been reported to maintain inflammation in lesions. Despite that, the Th17 regulatory scenario remains unclear. With the aim to gain a better understanding of the transcription factors (TFs) and genes involved in Th17 induction, in this study, the role of inducing factors of the Th17 pathway in Leishmania-macrophage infection was addressed through computational modeling of gene regulatory networks (GRNs). The Th17 GRN modeling integrated experimentally validated data available in the literature and gene expression data from a time-series RNA-seq experiment (4, 24, 48, and 72 h post-infection). The generated model comprises a total of 10 TFs, 22 coding genes, and 16 cytokines related to the Th17 immune modulation. Addressing the Th17 induction in infected and uninfected macrophages, an increase of 2- to 3-fold in 4-24 h was observed in the former. However, there was a decrease in basal levels at 48-72 h for both groups. In order to evaluate the possible outcomes triggered by GRN component modulation in the Th17 pathway. The generated GRN models promoted an integrative and dynamic view of Leishmania-macrophage interaction over time that extends beyond the analysis of single-gene expression.

Complete genome sequence of type strain Campylobacter fetus subsp. venerealis NCTC 10354T.

Campylobacter fetus subsp. venerealis is the etiologic agent of bovine genital campylobacteriosis, a sexually transmitted disease of cattle that is of worldwide importance. The complete sequencing and annotation of the genome of the type strain C. fetus subsp. venerealis NCTC 10354(T) are reported.