Predicting the Proteins of Angomonas deanei, Strigomonas culicis and Their Respective Endosymbionts Reveals New Aspects of the Trypanosomatidae Family

Endosymbiont-bearing trypanosomatids have been considered excellent models for the study of cell evolution because the host protozoan co-evolves with an intracellular bacterium in a mutualistic relationship. Such protozoa inhabit a single invertebrate host during their entire life cycle and exhibit special characteristics that group them in a particular phylogenetic cluster of the Trypanosomatidae family, thus classified as monoxenics. in an effort to better understand such symbiotic association, we used DNA pyrosequencing and a reference-guided assembly to generate reads that predicted 16,960 and 12,162 open reading frames (ORFs) in two symbiont-bearing trypanosomatids, Angomonas deanei (previously named as Crithidia deanei) and Strigomonas culicis (first known as Blastocrithidia culicis), respectively. Identification of each ORF was based primarily on TriTrypDB using tblastn, and each ORF was confirmed by employing getorf from EMBOSS and Newbler 2.6 when necessary. the monoxenic organisms revealed conserved housekeeping functions when compared to other trypanosomatids, especially compared with Leishmania major. However, major differences were found in ORFs corresponding to the cytoskeleton, the kinetoplast, and the paraflagellar structure. the monoxenic organisms also contain a large number of genes for cytosolic calpain-like and surface gp63 metalloproteases and a reduced number of compartmentalized cysteine proteases in comparison to other TriTryp organisms, reflecting adaptations to the presence of the symbiont. the assembled bacterial endosymbiont sequences exhibit a high A+T content with a total of 787 and 769 ORFs for the Angomonas deanei and Strigomonas culicis endosymbionts, respectively, and indicate that these organisms hold a common ancestor related to the Alcaligenaceae family. Importantly, both symbionts contain enzymes that complement essential host cell biosynthetic pathways, such as those for amino acid, lipid and purine/pyrimidine metabolism. These findings increase our understanding of the intricate symbiotic relationship between the bacterium and the trypanosomatid host and provide clues to better understand eukaryotic cell evolution.Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)ERC AdG SISYPHEUniv Fed Rio de Janeiro, Inst Biofis Carlos Chagas Filho, Lab Ultraestrutura Celular Hertha Meyer, BR-21941 Rio de Janeiro, BrazilUniv Fed Rio de Janeiro, Inst Biofis Carlos Chagas Filho, Lab Metab Macromol Firmino Torres de Castro, BR-21941 Rio de Janeiro, BrazilLab Bioinformat, Lab Nacl Computacao Cient, Rio de Janeiro, BrazilINRIA Grenoble Rhone Alpes, BAMBOO Team, Villeurbanne, FranceUniv Lyon 1, CNRS, UMR5558, Lab Biometrie & Biol Evolut, F-69622 Villeurbanne, FranceUniv Estadual Campinas, Inst Biol, Dept Genet Evolucao & Bioagentes, São Paulo, BrazilUniv São Paulo, Fac Ciencias Farmaceut Ribeirao Preto, Dept Ciencias Farmaceut, São Paulo, BrazilLab Nacl Ciencia & Tecnol Bioetano, São Paulo, BrazilUniv Fed Minas Gerais, Inst Ciencias Biol, Dept Bioquim & Imunol, Belo Horizonte, MG, BrazilUniv Fed Goias, Inst Ciencias Biol, Mol Biol Lab, Goiania, Go, BrazilFundacao Oswaldo Cruz, Inst Carlos Chagas, Lab Biol Mol Tripanossomatideos, Curitiba, Parana, BrazilFundacao Oswaldo Cruz, Inst Carlos Chagas, Lab Genom Func, Curitiba, Parana, BrazilUniv Estadual Campinas, Ctr Pluridisciplinar Pesquisas Quim Biol & Agr, São Paulo, BrazilUniv Fed Minas Gerais, Inst Ciencias Biol, Dept Parasitol, Belo Horizonte, MG, BrazilUniv Fed Santa Catarina, Dept Microbiol Imunol & Parasitol, Ctr Ciencias Biol, Lab Protozool & Bioinformat, Florianopolis, SC, BrazilUniv Fed Vicosa, Dept Bioquim & Biol Mol, Ctr Ciencias Biol & Saude, Vicosa, MG, BrazilInst Butantan, Lab Especial Ciclo Celular, São Paulo, BrazilUniv São Paulo, Dept Biol, Fac Filosofia Ciencias & Letras Ribeirao Preto, São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Microbiol Imunol & Parasitol, São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Microbiol Imunol & Parasitol, São Paulo, BrazilWeb of Scienc

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Variation of metabolic profiles in developing maize kernels up- and down-regulated for the hda101 gene

To shed light on the specific contribution of HDA101 in modulating metabolic pathways in the maize seed, changes in the metabolic profiles of kernels obtained from hda101 mutant plants have been investigated by a metabonomic approach. Dynamic properties of chromatin folding can be mediated by enzymes that modify DNA and histones. The enzymes responsible for the steady-state of histone acetylation are histone acetyltransferase and histone deacetylase (HDA). Therefore, it is interesting to evaluate the effects of up- and down-regulation of a Rpd-3 type HDA on the development of maize seeds in terms of metabolic changes. This has been reached by analysing nuclear magnetic resonance spectra by different chemometrician approaches, such as Orthogonal Projection to Latent Structure-Discriminant Analysis, Parallel Factors Analysis, and Multi-way Partial Least Squares-Discriminant Analysis (N-PLS-DA). In particular, the latter approaches were chosen because they explicitly take time into account, organizing data into a set of slices that refer to different steps of the developing process. The results show the good discriminating capabilities of the N-PLS-DA approach, even if the number of samples ought be increased to obtain better predictive capabilities. However, using this approach, it was possible to show differences in the accumulation of metabolites during development and to highlight the changes occuring in the modified seeds. In particular, the results confirm the role of this gene in cell cycle control

A genomic storm in critically injured humans

Critical injury in humans induces a genomic storm with simultaneous changes in expression of innate and adaptive immunity genes

ADDITIONAL LANGUAGES AT HIGH SCHOOL: FROM THE ZONE OF (IN)DIFFERENCE TO THE ZONE OF TRANSFORMATION

In the present paper, we argue that traditional stereotypes related to the language learners such as non-native speaker; prejudices regarding the way communicative practices across languages take place may darken the communicative practices that arise locally. Such situated practices, as long as recognized, have the potential to become resources for the organization of learning and to broaden one’s participation in various domains of everyday life. It is noteworthy that any possibility of widening participation is mediated by locally situated interaction, which is open to interpretation. We understand that, in an additional language, people may be able to use situated communicative practices to participate in experiences with the emerging language and thus achieve their social goals. We conclude that failure to recognize the wealth of heterogeneity that may arise locally is a great loss and in order to recognize and interpret it in real time there is a need to overcome the conception of language as a modern and static object. Based on the principles of Critical Applied Linguistics and Sociocultural Studies, we seek to present a theoretical discussion about the need for understanding communicative practices at school beyond the traditional standards, which are grounded on essentialized structures and on a monolingual ideology

Additional languages at high school from the zone of difference to the zone of transformation

Resumo: No presente artigo argumentamos que os tradicionais estereótipos referentes ao aprendiz de línguas, como a denominação de falante não nativo, os estigmas em relação à língua adicional emergente e os estilos de avaliação que enfocam apenas conteúdos e habilidades sem considerar as múltiplas experiências dos educandos podem obscurecer as práticas de linguagem que, ao surgirem localmente, quando reconhecidas, têm o potencial de tornar-se recursos para a organização da aprendizagem e para ampliar as formas de participação nas várias esferas da lida cotidiana. Importa esclarecer que qualquer possibilidade de ampliação é mediada por comunicações localmente situadas e que estão abertas a interpretações. Entendemos que, em uma língua adicional, as pessoas teriam sim possibilidades de lançar mão de práticas de linguagem “diferenciadas” para participar de experiências com a língua emergente e, assim, alcançar seus objetivos sociais. Concluímos que deixar de reconhecer a riqueza da heterogeneidade que surge localmente é um grande prejuízo, porém reconhecê-la e interpretá-la em tempo real não é uma aspiração trivial.We argue that traditional stereotypes of languages learners, such as non-native speakers, prejudices against the developing (additional) language and evaluation styles that focus only on content and skills, but fail to consider how people develop through their multiple experiences, can darken language practices that arise locally. These practices, when recognized, can become resources for the organization of learning and for the transformation in forms of participation in various contexts of everyday life. We note that transformations are mediated by locally situated communications and are open to interpretations. We also take the perspective that people can make use of “differentiated” language practices to participate in experiences with their emerging language and thus achieve their social objectives. We conclude that failure to recognize heterogeneity as a wealth is a great loss, but to recognize it and interpret it in real time is not a trivial accomplishment

A case of intoxication with tea made from Digitalis purpurea

We present the case of a 34-year-old woman with recurrent depressive disorder who ingested purple foxglove with suicidal intent. She bought a foxglove plant (Digitalis purpurea) over the internet and used all of its leaves to make a tea that she then drank over a period of a few hours. Seventeen hours later, she developed abdominal pain, emesis and bradycardia and was admitted via the emergency department to the intensive care unit for further treatment and monitoring. The plasma digoxin concentration measured 3.53 nmol/l (therapeutic reference range 0.77-1.50 nmol/l) 21 hours after ingestion of the tea. She remained heamodynamically and neurologically stable, was treated with antiemetics and simple analgesia and did not require digoxin-specific antibodies. Despite normal renal function, her plasma digoxin half-life was prolonged (estimated 76 h), reflecting the long half-life of the parent compound digitoxin which is the main cardiac glycoside in Digitalis purpurea. She was transferred to psychiatric care 48 h after admission. In this report, we compare this case to other similar cases, which to date have only been rarely reported in the literature.</jats:p

Fungal-bacterial associations in urban allotment garden soils

The soil microbiome in urban agriculture has not received much attention to date despite its important role in soil functionality. In this work, we evaluated the composition and diversity of fungal and bacterial communities through DNA extraction and ITS/16S marker gene sequencing in 40 soil samples collected from 10 urban allotment garden areas in the city of Santiago de Compostela (northwestern Spain). Despite anthropogenic activities are expected to affect negatively the microbial diversity, the richness of both fungal and bacterial communities was comparable to that of soils from other urban land-use categories with lower anthropogenic influence, i.e., urban forests, urban grasslands, and urban agricultural fields. However, the deterministic effect of soil properties and geographical distances was almost negligible in the surveyed allotment gardens. Neutral community models confirmed that the fungal and bacterial communities followed a random distribution (pseudo-R2fungi|bacteria = 0.653 | 0.898) and that they were more random (tNSTfungi|bacteria = 0.54 | 0.74) compared to the other abovementioned land-use categories (tNSTfungi|bacteria = 0.46 | 0.67, p ≪ 0.001). Network analysis showed that in contrast to natural soils with lower anthropogenic influence, microbial associations formed very small modules; and frequently, microbial units remained unconnected. Taken together, our findings provide evidence that the soil microbial communities in the studied urban allotment gardens comprised a random assortment of microbes and their interactions, thereby supporting potential implications of anthropogenic activity for soil health and ultimately ecosystem functionalityDr. Paradelo and Dr. Gómez-Brandón thank the Spanish State Agency for Research (AEI) for their Ramón y Cajal grants RYC-2016-19286 and RYC-2016-21231, funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future”. This research has been funded by the Xunta de Galicia regional government (grant number ED431F 2018/04)S

Influence of land use on the microbiological properties of urban soils

Advancing towards sustainable cities needs a better understanding of all components of urban ecosystems, including soils, but the biological component of urban soils remains poorly studied compared to natural and agricultural soils. With the objective of advancing knowledge in this aspect, we studied the microbiological properties in 61 soils of the city of Santiago de Compostela (NW Spain), under several land uses (urban grassland, urban forest, urban garden, and periurban arable land). We determined thirteen extracellular enzymatic activities as a proxy of microbial community functioning, along with measures of microbial activity (basal respiration), microbial abundance (DNA extraction and real-time PCR), and the composition of microbial communities (Illumina MiSeq sequencing on 16S rRNA and ITS marker regions). Results showed a high variability in all of the microbiological variables among soils, reflecting the typical spatial heterogeneity of urban soils. Respiration and enzymatic activities were highly correlated to soil organic matter contents but not affected by land use within the city, with the exception of alkaline phosphomonoesterase activity, which was higher in urban garden soils and correlated positively to pH and availability of phosphorus and nitrogen. Unlike fungal abundance, we recorded a higher bacterial abundance in the urban grasslands than in the other land uses. While the composition of bacterial communities was structured in a more homogeneous, land use-dependent manner (33% variance, pAdonis = 0.001), the respective fungal communities were more heterogeneous and less influenced by group-dependent characteristics (18%, pAdonis = 0.001). Soil pH had a larger influence on the bacterial community composition (28% variance) compared to the fungal composition (8.5% variance). Overall, these findings provide evidence that the typically high soil heterogeneity of urban ecosystems is the main driving force for the urban soil microbiome, with soil organic matter determining largely microbial activityDr. Paradelo and Dr. Gómez-Brandón thank the Spanish State Agency for Research (AEI) for their Ramón y Cajal grants RYC-2016-19286 and RYC-2016-21231, funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future”. This research has been funded by the Xunta de Galicia regional government (grant number ED431F 2018/04)S