Type III secretion translocon assemblies that attenuate Yersinia virulence

Type III secretion enables bacteria to intoxicate eukaryotic cells with anti‐host effectors. A class of secreted cargo are the two hydrophobic translocators that form a translocon pore in the host cell plasma membrane through which the translocated effectors may gain cellular entry. In pathogenic Yersinia, YopB and YopD shape this translocon pore. Here, four in cis yopD mutations were constructed to disrupt a predicted α‐helix motif at the C‐terminus. Mutants YopD_I262P and YopD_K267P poorly localized Yop effectors into target eukaryotic cells and failed to resist uptake and killing by immune cells. These defects were due to deficiencies in host‐membrane insertion of the YopD–YopB translocon. Mutants YopD_A263P and YopD_A270P had no measurable in vitro translocation defect, even though they formed smaller translocon pores in erythrocyte membranes. Despite this, all four mutants were attenuated in a mouse infection model. Hence, YopD variants have been generated that can spawn translocons capable of targeting effectors in vitro, yet were bereft of any lethal effect in vivo. Therefore, Yop translocators may possess other in vivo functions that extend beyond being a portal for effector delivery into host cells.     

Estimating animal population density using passive acoustics

Reliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture‐recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast‐developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics‐based density estimation, illustrated with examples from real‐world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic‐based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture‐recapture. The methods are also applicable to other aquatic and terrestrial sound‐producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented here.     

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions

Interactions of proteins regulate signaling, catalysis, gene expression and many other cellular functions. Therefore, characterizing the entire human interactome is a key effort in current proteomics research. This challenge is complicated by the dynamic nature of protein-protein interactions (PPIs), which are conditional on the cellular context: both interacting proteins must be expressed in the same cell and localized in the same organelle to meet. Additionally, interactions underlie a delicate control of signaling pathways, e.g. by post-translational modifications of the protein partners - hence, many diseases are caused by the perturbation of these mechanisms. Despite the high degree of cell-state specificity of PPIs, many interactions are measured under artificial conditions (e.g. yeast cells are transfected with human genes in yeast two-hybrid assays) or even if detected in a physiological context, this information is missing from the common PPI databases. To overcome these problems, we developed a method that assigns context information to PPIs inferred from various attributes of the interacting proteins: gene expression, functional and disease annotations, and inferred pathways. We demonstrate that context consistency correlates with the experimental reliability of PPIs, which allows us to generate high-confidence tissue- and function-specific subnetworks. We illustrate how these context-filtered networks are enriched in bona fide pathways and disease proteins to prove the ability of context-filters to highlight meaningful interactions with respect to various biological questions. We use this approach to study the lung-specific pathways used by the influenza virus, pointing to IRAK1, BHLHE40 and TOLLIP as potential regulators of influenza virus pathogenicity, and to study the signalling pathways that play a role in Alzheimer''s disease, identifying a pathway involving the altered phosphorylation of the Tau protein. Finally, we provide the annotated human PPI network via a web frontend that allows the construction of context-specific networks in several ways.     

Enoxacin inhibits growth of prostate cancer cells and effectively restores microRNA processing

Prostate cancer (PCa) is one of the most incident malignancies worldwide. Although efficient therapy is available for early-stage PCa, treatment of advanced disease is mainly ineffective and remains a clinical challenge. microRNA (miRNA) dysregulation is associated with PCa development and progression. In fact, several studies have reported a widespread downregulation of miRNAs in PCa, which highlights the importance of studying compounds capable of restoring the global miRNA expression. The main aim of this study was to define the usefulness of enoxacin as an anti-tumoral agent in PCa, due to its ability to induce miRNA biogenesis in a TRBP-mediated manner. Using a panel of five PCa cell lines, we observed that all of them were wild type for the TARBP2 gene and expressed TRBP protein. Furthermore, primary prostate carcinomas displayed normal levels of TRBP protein. Remarkably, enoxacin was able to decrease cell viability, induce apoptosis, cause cell cycle arrest, and inhibit the invasiveness of cell lines. Enoxacin was also effective in restoring the global expression of miRNAs. This study is the first to show that PCa cells are highly responsive to the anti-tumoral effects of enoxacin. Therefore, enoxacin constitutes a promising therapeutic agent for PCa.     

Lifestyle Regularity Measured by The Social Rhythm Metric in Parkinson's Disease

Parkinson's disease (PD) is a chronic progressive motor disorder that may present with a spectrum of symptoms and disease severity. Therapy is frequently associated with motor fluctuations and dyskinesias; therefore, monitoring of motor fluctuations and daily abilities is important for adequate management. The Social Rhythm Metric (SRM) is a diary‐like questionnaire that quantifies the extent to which a person's life is regular vs. irregular on a daily basis with respect to event timing. Lifestyle regularity has been assessed by the SRM in other clinical situations. The aim of this study was to evaluate lifestyle regularity in a population with PD using the SRM and its relationship to clinical and therapeutic factors. Twenty‐eight consecutive patients with PD and 14 control subjects were studied. Severity of motor dysfunction was evaluated with the Unified Parkinson's Disease Rating Scale (UPDRS). Depressive symptoms were assessed with the Montgomery Asberg Depressive Rating Scale (MADRS), sleep quality with the Pittsburgh Sleep Quality Index (PSQI), and subjective daytime sleepiness with the Epworth sleepiness scale. Daily lifestyle regularity was assessed by the SRM for 2 weeks. Patients with PD had lower SRM scores than controls, and those with motor fluctuations had even lower scores (p=0.04). Patients with motor fluctuations showed more clinical disability (p=0.01), a worse quality of sleep (p=0.02), and more depressive symptoms (p=0.02). SRM results were correlated with PSQI values (p=0.016). Our findings show that the regularity of daily activities as measured by the SRM is disorganized in patients with PD and that this irregularity is related to sleep quality.     

Assessing road effects on bats: the role of landscape, road features, and bat activity on road-kills

Recent studies suggest that roads can significantly impact bat populations. Though bats are one of the most threatened groups of European vertebrates, studies aiming to quantify bat mortality and determine the main factors driving it remain scarce. Between March 16 and October 31 of 2009, we surveyed road-killed bats daily along a 51-km-long transect that incorporates different types of roads in southern Portugal. We found 154 road-killed bats of 11 species. The two most common species in the study area, Pipistrellus kuhlii and P. pygmaeus, were also the most commonly identified road-kill, representing 72 % of the total specimens collected. About two-thirds of the total mortality occurred between mid July and late September, peaking in the second half of August. We also recorded casualties of threatened and rare species, including Miniopterus schreibersii, Rhinolophus ferrumequinum, R. hipposideros, Barbastella barbastellus, and Nyctalus leisleri. These species were found mostly in early autumn, corresponding to the mating and swarming periods. Landscape features were the most important variable subset for explaining bat casualties. Road stretches crossing or in the vicinity of high-quality habitats for bats—including dense Mediterranean woodland (“montado”) areas, water courses with riparian gallery, and water reservoirs—yielded a significantly higher number of casualties. Additionally, more road-killed bats were recorded on high-traffic road stretches with viaducts, in areas of higher bat activity and near known roosts.     

The importance of remnants of natural vegetation for maintaining ant diversity in Brazilian agricultural landscapes

Brazil is one of the leading producers of soybeans and other annual crops, and in several regions landowners are required by law to maintain 20 % of their lands with natural vegetation (i.e. as “legal reserves”). However, there is a growing concern that some of these reserves will be subject to increased levels of disturbance or even be lost as a result of the ongoing legislation reforms. In this sense, studies that evaluate the conservation potential of retaining natural habitats within agricultural areas are of great importance. We assessed the efficiency with which remnants of natural vegetation conserve the native ant fauna in a context of intensive agriculture. We compared the structure of ground-dwelling ant assemblages between crop fields and reserves located in different farms. Ant species richness was much higher in the reserves than in the crops, and this pattern was consistent in spite of variations in the type of crop planted in each field, and in the size (39–149 ha) and vegetation (open or closed savanna) of the reserves. From 41.4 to 76.4 % of all species recorded within each farm were exclusively found in the reserves. Differences in species composition were strong not only because the reserves had much more species, but also because the species that were present in both habitats showed contrasting patterns of abundance in each habitat. Overall, our results highlight that even small remnants of natural vegetation can have a significant potential to maintain a higher diversity of ants within an agriculturally dominated landscape.     

Calcium-Binding Capacity of Centrin2 Is Required for Linear POC5 Assembly but Not for Nucleotide Excision Repair

Centrosomes, the principal microtubule-organising centres in animal cells, contain centrins, small, conserved calcium-binding proteins unique to eukaryotes. Centrin2 binds to xeroderma pigmentosum group C protein (XPC), stabilising it, and its presence slightly increases nucleotide excision repair (NER) activity in vitro. In previous work, we deleted all three centrin isoforms present in chicken DT40 cells and observed delayed repair of UV-induced DNA lesions, but no centrosome abnormalities. Here, we explore how centrin2 controls NER. In the centrin null cells, we expressed centrin2 mutants that cannot bind calcium or that lack sites for phosphorylation by regulatory kinases. Expression of any of these mutants restored the UV sensitivity of centrin null cells to normal as effectively as expression of wild-type centrin. However, calcium-binding-deficient and T118A mutants showed greatly compromised localisation to centrosomes. XPC recruitment to laser-induced UV-like lesions was only slightly slower in centrin-deficient cells than in controls, and levels of XPC and its partner HRAD23B were unaffected by centrin deficiency. Interestingly, we found that overexpression of the centrin interactor POC5 leads to the assembly of linear, centrin-dependent structures that recruit other centrosomal proteins such as PCM-1 and NEDD1. Together, these observations suggest that assembly of centrins into complex structures requires calcium binding capacity, but that such assembly is not required for centrin activity in NER.     

DNA damage in peripheral blood of patients with chronic obstructive pulmonary disease (COPD)

Chronic obstructive pulmonary disease (COPD) is a condition characterized by chronic airway inflammation and remodeling, lung parenchymal inflammation, and destruction resulting in expiratory airflow obstruction, hyperinflation of the lung with loss of elastic recoil, and impairment of gas exchange. Skeletal muscles in individuals with COPD generate free radicals at rest, and production increases during contractile activity. Overproduction of free radicals may result in oxidant-antioxidant imbalance in favor of oxidants. This study evaluated the levels of genetic damage in peripheral blood of patients with COPD using the cytokinesis-blocked micronucleus (CBMN) and the comet assays. The study was conducted with 25 patients with COPD and 25 controls matched for age and sex. Results of both comet and CBMN assays showed an increase in the level of DNA damage. In the group of patients with COPD, the mean frequency of binucleate cells with micronuclei was 6.72+/-3.02, and in the control group, 4.20+/-2.08 (p=0.00233). Mean comet value was 26.84+/-19.61 in patients with COPD and 7.25+/-7.57 in the control group (p=0.00004). The increased frequency of micronuclei in patients with COPD was primarily assigned to clastogenic events and DNA amplification because the frequency of nucleoplasmic bridges and buds was also increased. Oxidative stress in lung cells is a constant source of free radicals that damage genetic material of both lung and circulating cells.