Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori

Helicobacter pylori colonizes the gastric mucosa of half of the human population, causing gastritis, ulcers, and cancer. H. pylori is naturally competent for transformation by exogenous DNA, and recombination during mixed infections of one stomach with multiple H. pylori strains generates extensive allelic diversity. We developed an in vitro transformation protocol to study genomic imports after natural transformation of H. pylori. The mean length of imported fragments was dependent on the combination of donor and recipient strain and varied between 1294 bp and 3853 bp. In about 10% of recombinant clones, the imported fragments of donor DNA were interrupted by short interspersed sequences of the recipient (ISR) with a mean length of 82 bp. 18 candidate genes were inactivated in order to identify genes involved in the control of import length and generation of ISR. Inactivation of the antimutator glycosylase MutY increased the length of imports, but did not have a significant effect on ISR frequency. Overexpression of mutY strongly increased the frequency of ISR, indicating that MutY, while not indispensable for ISR formation, is part of at least one ISR-generating pathway. The formation of ISR in H. pylori increases allelic diversity, and contributes to the uniquely low linkage disequilibrium characteristic of this pathogen

The Capaciousness of No: Affective Refusals as Literacy Practices

© 2020 The Authors. Reading Research Quarterly published by Wiley Periodicals, Inc. on behalf of International Literacy Association The authors considered the capacious feeling that emerges from saying no to literacy practices, and the affective potential of saying no as a literacy practice. The authors highlight the affective possibilities of saying no to normative understandings of literacy, thinking with a series of vignettes in which children, young people, and teachers refused literacy practices in different ways. The authors use the term capacious to signal possibilities that are as yet unthought: a sense of broadening and opening out through enacting no. The authors examined how attention to affect ruptures humanist logics that inform normative approaches to literacy. Through attention to nonconscious, noncognitive, and transindividual bodily forces and capacities, affect deprivileges the human as the sole agent in an interaction, thus disrupting measurements of who counts as a literate subject and what counts as a literacy event. No is an affective moment. It can signal a pushback, an absence, or a silence. As a theoretical and methodological way of thinking/feeling with literacy, affect proposes problems rather than solutions, countering solution-focused research in which the resistance is to be overcome, co-opted, or solved. Affect operates as a crack or a chink, a tiny ripple, a barely perceivable gesture, that can persist and, in doing so, hold open the possibility for alternative futures

Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families

Our understanding of basic evolutionary processes in bacteria is still very limited. For example, multiple recent dating estimates are based on a universal inter-species molecular clock rate, but that rate was calibrated using estimates of geological dates that are no longer accepted. We therefore estimated the short-term rates of mutation and recombination in Helicobacter pylori by sequencing an average of 39,300 bp in 78 gene fragments from 97 isolates. These isolates included 34 pairs of sequential samples, which were sampled at intervals of 0.25 to 10.2 years. They also included single isolates from 29 individuals (average age: 45 years) from 10 families. The accumulation of sequence diversity increased with time of separation in a clock-like manner in the sequential isolates. We used Approximate Bayesian Computation to estimate the rates of mutation, recombination, mean length of recombination tracts, and average diversity in those tracts. The estimates indicate that the short-term mutation rate is 1.4×10−6 (serial isolates) to 4.5×10−6 (family isolates) per nucleotide per year and that three times as many substitutions are introduced by recombination as by mutation. The long-term mutation rate over millennia is 5–17-fold lower, partly due to the removal of non-synonymous mutations due to purifying selection. Comparisons with the recent literature show that short-term mutation rates vary dramatically in different bacterial species and can span a range of several orders of magnitude

Normalizing biomedical terms by minimizing ambiguity and variability

<p>Abstract</p> <p>Background</p> <p>One of the difficulties in mapping biomedical named entities, e.g. genes, proteins, chemicals and diseases, to their concept identifiers stems from the potential variability of the terms. Soft string matching is a possible solution to the problem, but its inherent heavy computational cost discourages its use when the dictionaries are large or when real time processing is required. A less computationally demanding approach is to normalize the terms by using heuristic rules, which enables us to look up a dictionary in a constant time regardless of its size. The development of good heuristic rules, however, requires extensive knowledge of the terminology in question and thus is the bottleneck of the normalization approach.</p> <p>Results</p> <p>We present a novel framework for discovering a list of normalization rules from a dictionary in a fully automated manner. The rules are discovered in such a way that they minimize the ambiguity and variability of the terms in the dictionary. We evaluated our algorithm using two large dictionaries: a human gene/protein name dictionary built from BioThesaurus and a disease name dictionary built from UMLS.</p> <p>Conclusions</p> <p>The experimental results showed that automatically discovered rules can perform comparably to carefully crafted heuristic rules in term mapping tasks, and the computational overhead of rule application is small enough that a very fast implementation is possible. This work will help improve the performance of term-concept mapping tasks in biomedical information extraction especially when good normalization heuristics for the target terminology are not fully known.</p

OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature

<p>Abstract</p> <p>Background</p> <p>Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required.</p> <p>Results</p> <p>Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes <url>http://ibi.imim.es/osirisform.html</url>. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, <url>http://ibi.imim.es/OSIRISv1.2.html</url>) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented.</p> <p>Conclusion</p> <p>OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.</p

Cerebellar astrocytes co-express several ADP receptors. Presence of functional P2Y13-like receptors

Astrocytes exhibit a form of excitability based on variations of intracellular Ca2+ concentration in response to various stimuli, including ADP, ATP, UTP and dinucleotides. Here, we investigate the presence of the recently cloned ADP-sensitive receptors, P2Y12 and P2Y13 subtypes, which are negatively coupled to adenylate cyclase, in cerebellar astrocytes. We checked the effect of specific agonists, 2-methylthioadenosine diphosphate (2MeSADP) and ADP, on adenylate cyclase stimulation induced by isoproterenol. Both agonists significantly reduced the cAMP accumulation induced by isoproterenol. The inhibitory effect was concentration-dependent with IC50 values of 46 ± 13 and 23 ± 14 nM for 2MeSADP and ADP, respectively. The experiments were carried out in the presence of MRS-2179, a specific antagonist of P2Y1 receptor, to avoid any contribution of this receptor. Using fura-2 microfluorimetry we also proved that astrocytes responded to 2MeSADP stimulations with calcium responses in the absence and also in the presence of MRS-2179. Both effects, inhibition of adenylate cyclase and intracellular calcium mobilization, were not modified by 2MeSAMP, an antagonist of P2Y12 receptor, suggesting that were mediated by P2Y13-like receptors

Abnormal increase in urinary aquaporin-2 excretion in response to hypertonic saline in essential hypertension

<p>Abstract</p> <p>Background</p> <p>Dysregulation of the expression/shuttling of the aquaporin-2 water channel (AQP2) and the epithelial sodium channel (ENaC) in renal collecting duct principal cells has been found in animal models of hypertension. We tested whether a similar dysregulation exists in essential hypertension.</p> <p>Methods</p> <p>We measured urinary excretion of AQP2 and ENaC β-subunit corrected for creatinine (u-AQP2_CR, u-ENaC_β-CR), prostaglandin E2 (u-PGE₂) and cyclic AMP (u-cAMP), fractional sodium excretion (FE_Na), free water clearance (C_H2O), as well as plasma concentrations of vasopressin (AVP), renin (PRC), angiotensin II (Ang II), aldosterone (Aldo), and atrial and brain natriuretic peptide (ANP, BNP) in 21 patients with essential hypertension and 20 normotensive controls during 24-h urine collection (baseline), and after hypertonic saline infusion on a 4-day high sodium (HS) diet (300 mmol sodium/day) and a 4-day low sodium (LS) diet (30 mmol sodium/day).</p> <p>Results</p> <p>At baseline, no differences in u-AQP2_CRor u-ENaC_β-CRwere measured between patients and controls. U-AQP2_CRincreased significantly more after saline in patients than controls, whereas u-ENaC_β-CRincreased similarly. The saline caused exaggerated natriuretic increases in patients during HS intake. Neither baseline levels of u-PGE₂, u-cAMP, AVP, PRC, Ang II, Aldo, ANP, and BNP nor changes after saline could explain the abnormal u-AQP2_CRresponse.</p> <p>Conclusions</p> <p>No differences were found in u-AQP2_CRand u-ENaC_β-CRbetween patients and controls at baseline. However, in response to saline, u-AQP2_CRwas abnormally increased in patients, whereas the u-ENaC_β-CRresponse was normal. The mechanism behind the abnormal AQP2 regulation is not clarified, but it does not seem to be AVP-dependent.</p> <p>Clinicaltrial.gov identifier</p> <p><a href="http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=00345124">NCT00345124</a>.</p