Genetic context and mobilization of class 1 integrons in Pseudomonas aeruginosa : are plasmids redundant?

University of Technology, Sydney. Faculty of Science.Antibiotic resistance is a global problem with some predicting a return to the pre antibiotic era where a bacterial infection was commonly fatal. Pseudomonas aeruginosa is one example of this problem. This bacterium is a major cause of infection especially in cystic fibrosis sufferers and in burns victims. The rising rates of adverse outcomes are partly a consequence of strains commonly displaying multi-drug resistance (MDR) profiles. MDR is driven by a number of intrinsic mechanisms in P. aeruginosa clinical isolates as well as by the capture of diverse resistance-mediating genes by Lateral Gene Transfer (LGT). LGT and intrinsic factors often act cooperatively to generate complex MDR phenotypes. While these complex interactions have been examined in a small number of isolates there has not been a comprehensive survey of strains on a global scale. Thus it is not clear what mechanisms and genes may be important in influencing the evolution of MDR at regional or global levels. Also, in some isolates, resistance profiles cannot always be explained by identifying the common resistance determining pathways, suggesting that additional mechanisms of resistance may be emerging in P. aeruginosa. The focus of this project was to comprehensively study the major mechanisms responsible for antibiotic resistance in P. aeruginosa strains from diverse geographical areas. Pathogenic P. aeruginosa isolates from four countries (Australia and three South American countries) were characterized by PCR to identify mobile elements and their genetic context. Also, quantitative expression analysis for activity of several pathways that influence antibiotic resistance was assessed and culture experiments were conducted to test how random movement of mobile elements during growth may influence resistance to some antibiotics. Data presented in this thesis indicated that, in most strains, antibiotic resistance was being driven by changes in multiple pathways (including overexpression of AmpC and two efflux pumps) and by the presence or absence of genes acquired by Lateral Gene Transfer (LGT). Class 1 integrons, elements important in the spread of antibiotic resistance genes in Gram-negative bacteria, were most frequently recovered in South American countries. Many class 1 integrons were mapped to a specific location within the genome. Regardless of country of origin all these mapped integrons were found to be in the chromosome, often in Genomic islands, and not on a plasmid despite data in the literature implying the opposite. The association of class 1 integrons with genomic islands may be an important mechanism driving LGT in P. aeruginosa. Also, a newly emerging mechanism involving the insertion sequence IS26 was identified that is capable of mobilizing resistance and other genes. This IS26-mediated mechanism may allow phenotype switching in clonal lines in a way that is likely to further exacerbate the treatment of infections mediated by P. aeruginosa. Data presented here suggested that P. aeruginosa strains are evolving to become multidrug resistant in increasingly complex ways. This is occurring by single strains acquiring changes in numerous known pathways as well as by newly emerging resistance mechanisms in this species

Terminal investment induced by a bacteriophage in a rhizosphere bacterium.

Despite knowledge about microbial responses to abiotic stress, few studies have investigated stress responses to antagonistic species, such as competitors, predators and pathogens. While it is often assumed that interacting populations of bacteria and phage will coevolve resistance and exploitation strategies, an alternative is that individual bacteria tolerate or evade phage predation through inducible responses to phage presence. Using the microbial model Pseudomonas fluorescens SBW25 and its lytic DNA phage SBW25Φ2, we demonstrate the existence of an inducible response in the form of a transient increase in population growth rate, and found that the response was induced by phage binding. This response was accompanied by a decrease in bacterial cell size, which we propose to be an associated cost. We discuss these results in the context of bacterial ecology and phage-bacteria co-evolution

Towards a robotic personal trainer for the elderly

The use of robots in the environment of the elderly has grown significantly in recent years. The idea is to try to increase the comfort and well-being of older people through the employment of some kind of automated processes that simplify daily work. In this paper we present a prototype of a personal robotic trainer which, together with a non-invasive sensor, allows caregivers to monitor certain physical activities in order to improve their performance. In addition, the proposed system also takes into account how the person feels during the performance of the physical exercises and thus, determine more precisely if the exercise is appropriate or not for a specific person.This work was partly supported by the Spanish Government (RTI2018-095390-B-C31) and FCT—Fundação para a Ciência e Tecnologia through the Post-Docscholarship SFRH/BPD/102696/2014 (A. Costa) and UID/CEC/00319/2019

Parkinson disease-linked GBA mutation effects reversed by molecular chaperones in human cell and fly models

GBA gene mutations are the greatest cause of Parkinson disease (PD). GBA encodes the lysosomal enzyme glucocerebrosidase (GCase) but the mechanisms by which loss of GCase contributes to PD remain unclear. Inhibition of autophagy and the generation of endoplasmic reticulum (ER) stress are both implicated. Mutant GCase can unfold in the ER and be degraded via the unfolded protein response, activating ER stress and reducing lysosomal GCase. Small molecule chaperones that cross the blood brain barrier help mutant GCase refold and traffic correctly to lysosomes are putative treatments for PD. We treated fibroblast cells from PD patients with heterozygous GBA mutations and Drosophila expressing human wild-type, N370S and L444P GBA with the molecular chaperones ambroxol and isofagomine. Both chaperones increased GCase levels and activity, but also GBA mRNA, in control and mutant GBA fibroblasts. Expression of mutated GBA in Drosophila resulted in dopaminergic neuronal loss, a progressive locomotor defect, abnormal aggregates in the ER and increased levels of the ER stress reporter Xbp1-EGFP. Treatment with both chaperones lowered ER stress and prevented the loss of motor function, providing proof of principle that small molecule chaperones can reverse mutant GBA-mediated ER stress in vivo and might prove effective for treating PD

Linear advancing actions followed by deceleration and turn are the most common movements preceding goals in male professional soccer

Data were collected through time-motion analysis from soccer players participating in the English Premier League using a modified version of the Bloomfield Movement Classification with differences analysed through chi-square. The most common individual movement preceding a goal was a linear advancing motion (32.4 ± 1%), followed by deceleration (20.2 ± 0.9%) and turn (19.8 ± 0.9%). Actions also involved were change in angle run (cut and arc run), ball blocking, lateral advancing motion (crossover and shuffle) and jumps. Although players followed similar trends there were dissimilarities based on the role, with attackers (assistant and scorer) performing more linear actions, subtle turns and cuts and defenders (defender of assistant and defender of scorer) more ball blockings, lateral movements and arc runs. In 82.9 ± 1.5% of player involvements there was at least 1 high intensity (HI) movement with assistant showing the lowest percentage and defender of scorer the highest. This study shows the multidirectional nature and context specificity of soccer during goal scoring situations, with linear actions such as sprints being the most common movements, followed by decelerations and turns. Moreover, it highlights the recurrent application of these at HI, and so, training strategies should prioritize the development of player’s explosiveness

Relevance of Fc Gamma Receptor Polymorphisms in Cancer Therapy With Monoclonal Antibodies

Therapeutic monoclonal antibodies (mAbs), including immune checkpoint inhibitors (ICIs), are an important breakthrough for the treatment of cancer and have dramatically changed clinical outcomes in a wide variety of tumours. However, clinical response varies among patients receiving mAb-based treatment, so it is necessary to search for predictive biomarkers of response to identify the patients who will derive the greatest therapeutic benefit. The interaction of mAbs with Fc gamma receptors (Fc gamma R) expressed by innate immune cells is essential for antibody-dependent cellular cytotoxicity (ADCC) and this binding is often critical for their in vivo efficacy. Fc gamma RIIa (H131R) and Fc gamma RIIIa (V158F) polymorphisms have been reported to correlate with response to therapeutic mAbs. These polymorphisms play a major role in the affinity of mAb receptors and, therefore, can exert a profound impact on antitumor response in these therapies. Furthermore, recent reports have revealed potential mechanisms of ICIs to modulate myeloid subset composition within the tumour microenvironment through Fc gamma R-binding, optimizing their anti-tumour activity. The purpose of this review is to highlight the clinical contribution of Fc gamma R polymorphisms to predict response to mAbs in cancer patients

Detection of curved lines with B-COSFIRE filters: A case study on crack delineation

The detection of curvilinear structures is an important step for various computer vision applications, ranging from medical image analysis for segmentation of blood vessels, to remote sensing for the identification of roads and rivers, and to biometrics and robotics, among others. %The visual system of the brain has remarkable abilities to detect curvilinear structures in noisy images. This is a nontrivial task especially for the detection of thin or incomplete curvilinear structures surrounded with noise. We propose a general purpose curvilinear structure detector that uses the brain-inspired trainable B-COSFIRE filters. It consists of four main steps, namely nonlinear filtering with B-COSFIRE, thinning with non-maximum suppression, hysteresis thresholding and morphological closing. We demonstrate its effectiveness on a data set of noisy images with cracked pavements, where we achieve state-of-the-art results (F-measure=0.865). The proposed method can be employed in any computer vision methodology that requires the delineation of curvilinear and elongated structures.Comment: Accepted at Computer Analysis of Images and Patterns (CAIP) 201

Topological Analysis of Metabolic Networks Integrating Co-Segregating Transcriptomes and Metabolomes in Type 2 Diabetic Rat Congenic Series

Background: The genetic regulation of metabolic phenotypes (i.e., metabotypes) in type 2 diabetes mellitus is caused by complex organ-specific cellular mechanisms contributing to impaired insulin secretion and insulin resistance. Methods: We used systematic metabotyping by 1H NMR spectroscopy and genome-wide gene expression in white adipose tissue to map molecular phenotypes to genomic blocks associated with obesity and insulin secretion in a series of rat congenic strains derived from spontaneously diabetic Goto-Kakizaki (GK) and normoglycemic Brown-Norway (BN) rats. We implemented a network biology strategy approach to visualise shortest paths between metabolites and genes significantly associated with each genomic block. Results: Despite strong genomic similarities (95-99%) among congenics, each strain exhibited specific patterns of gene expression and metabotypes, reflecting metabolic consequences of series of linked genetic polymorphisms in the congenic intervals. We subsequently used the congenic panel to map quantitative trait loci underlying specific metabotypes (mQTL) and genome-wide expression traits (eQTL). Variation in key metabolites like glucose, succinate, lactate or 3-hydroxybutyrate, and second messenger precursors like inositol was associated with several independent genomic intervals, indicating functional redundancy in these regions. To navigate through the complexity of these association networks we mapped candidate genes and metabolites onto metabolic pathways and implemented a shortest path strategy to highlight potential mechanistic links between metabolites and transcripts at colocalized mQTLs and eQTLs. Minimizing shortest path length drove prioritization of biological validations by gene silencing. Conclusions: These results underline the importance of network-based integration of multilevel systems genetics datasets to improve understanding of the genetic architecture of metabotype and transcriptomic regulations and to characterize novel functional roles for genes determining tissue-specific metabolism

Neutrophil to lymphocyte ratio and breast cancer risk: analysis by subtype and potential interactions

Multiple studies have found the neutrophil to lymphocyte ratio (NLR) to be associated with adverse breast cancer (BC) prognosis and survival. Very limited data exist on the role of NLR and risk of BC. The BREOGAN study is a population-based case-control study conducted in Galicia, Spain. We examined the WBC- and NLR-BC relationships. The risk of BC increased with increasing levels of neutrophils percentage (NE%) (multivariable OR for the highest category (95% CI) = 2.14 (1.39-3.32), P-trend < 0.001) and of the NLR (multivariable OR for the highest category (95% CI) = 1.93 (1.26-2.97), P-trend < 0.001). Lymphocytes absolute (L#) and percentage (L%) were associated with a decreased risk of BC (multivariable OR for the highest category (95% CI) = 0.54 (0.35-0.83), and 0.51 (0.33-0.79), P-trend = 0.001 and < 0.001, respectively). The NLR-BC association was more pronounced among Luminal A BC (multivariable OR for the highest category (95% CI) = 2.00 (1.17-3.45), P-trend < 0.001), HER2-negative BC (multivariable OR for the highest category (95% CI) = 1.87 (1.16-3.02), P-trend < 0.001), and those with high total cholesterol and low H2O2 levels