MIDICHLORIA MITOCHONDRII AS AN EMERGING INFECTIOUS AGENT: MOLECULAR AND IMMUNOLOGICAL STUDIES ON THE INTRA-MITOCHONDRIAL SYMBIONT OF THE HARD TICK IXODES RICINUS

M. mitochondrii is an alpha proteobacteria belonging to the order Rickettsiales. It is an intracellular bacterium present in different tick species and in particular it is studied in the hard tick I. ricinus. The prevalence of M. mitochondrii in I. ricinus is 100% in females and around 40% in males. The recently sequenced genome of M. mitochondrii revealed the presence of 26 putative flagellar genes. Open questions are whether these genes are expressed and whether they possess the domains expected for the flagellar function. To answer to these questions, a putative flagellar protein has been produced in recombinant form, purified and used for the production of polyclonal antibodies. These were used for immunostainig and immunogold detection of M. mitochondrii in I. ricinus ovary. Furthermore, the expression of seven flagellar genes has been evaluated and the proteins codified by the 26 genes have been analyzed for the presence of domains specific for flagellar proteins. In I. ricinus, M. mitochondrii is observed in the oocytes and in other cells of the ovary, where the symbiont is present in the cell cytoplasm and inside the mitochondria. No studies have so far investigated whether M. mitochondrii is present in the salivary glands of the tick and whether it is transmitted to vertebrates during the tick blood meal. To address the above questions, we used a recombinant antigen of M. mitochondrii (to screen vertebrate sera) and antibodies against this antigen (for the staining of the symbiont in the salivary glands). In conclusion, the obtained results provide evidences that: 1) M. mitochondrii is the first rickettsiales that posses a flagellar structure; 2) M. mitochondrii, detected in the salivary glands of I. ricinus, could be transmitted to the vertebrate host during the tick bite; 3) vertebrate hosts develop an antigenic response against a recombinant protein of M. mitochondrii suggesting the possibility that M. mitochondrii is infectious to vertebrates

What's in a Name? Understanding Profile Name Reuse on Twitter

Users on Twitter are commonly identified by their profile names. These names are used when directly addressing users on Twitter, are part of their profile page URLs, and can become a trademark for popular accounts, with people referring to celebrities by their real name and their profile name, interchangeably. Twitter, however, has chosen to not permanently link profile names to their corresponding user accounts. In fact, Twitter allows users to change their profile name, and afterwards makes the old profile names available for other users to take. In this paper, we provide a large-scale study of the phenomenon of profile name reuse on Twitter. We show that this phenomenon is not uncommon, investigate the dynamics of profile name reuse, and characterize the accounts that are involved in it. We find that many of these accounts adopt abandoned profile names for questionable purposes, such as spreading malicious content, and using the profile name's popularity for search engine optimization. Finally, we show that this problem is not unique to Twitter (as other popular online social networks also release profile names) and argue that the risks involved with profile-name reuse outnumber the advantages provided by this feature

Shortage of Albendazole and Its Consequences for Patients with Cystic Echinococcosis Treated at a Referral Center in Italy

Albendazole (ABZ) is the best drug available to treat cystic echinococcosis (CE), a neglected tropical disease. Cystic echinococcosis patients often receive a continuous course of the drug for 6-12 months. In Italy, ABZ shortages occur almost on a yearly basis. We searched clinical records at the World Health Organization Collaborating Center for the Clinical Management of CE in Pavia, Italy, to estimate the amount of ABZ prescribed to patients between January 2012 and February 2017. The cost of ABZ was estimated at €2.25 per tablet based on the current market price in Italy. Patients to whom ABZ had been prescribed were contacted to determine if they had experienced difficulties in purchasing the drug and to assess how such problems affected their treatment. Of 348 identified CE patients, 127 (36.5%) were treated with ABZ for a total of 20,576 days. This led to an estimated cost of €92,592. Seventy-five patients were available for follow-up, 42 (56%) reported difficulties in obtaining ABZ. Of these patients, four (9.5%) had to search out of their region and 10 (23.8%) had to go out of the country. A total of 27 patients (64%) had to visit more than five pharmacies to locate the drug and 10 patients (23.8%) interrupted treatment because of ABZ nonavailability. Shortages in ABZ distribution can disrupt CE treatment schedules and jeopardize patient health

The Italian registry of cystic echinococcosis (RIEC): the first prospective registry with a European future

n/

Extracellular non-coding RNA signatures of the metacestode stage of Echinococcus multilocularis

Extracellular RNAs (ex-RNAs) are secreted by cells through different means that may involve association with proteins, lipoproteins or extracellular vesicles (EV). In the context of parasitism, ex-RNAs represent new and exciting communication intermediaries with promising potential as novel biomarkers. In the last years, it was shown that helminth parasites secrete ex-RNAs, however, most work mainly focused on RNA secretion mediated by EV. Ex-RNA study is of special interest in those helminth infections that still lack biomarkers for early and/or follow-up diagnosis, such as echinococcosis, a neglected zoonotic disease caused by cestodes of the genus Echinococcus. In this work, we have characterised the ex-RNA profile secreted by in vitro grown metacestodes of Echinococcus multilocularis, the casuative agent of alveolar echinococcosis. We have used high throughput RNA-sequencing together with RT-qPCR to characterise the ex-RNA profile secreted towards the extra- and intra-parasite milieus in EV-enriched and EV-depleted fractions. We show that a polarized secretion of small RNAs takes place, with microRNAs mainly secreted to the extra-parasite milieu and rRNA- and tRNA-derived sequences mostly secreted to the intra-parasite milieu. In addition, we show by nanoparticle tracking analyses that viable metacestodes secrete EV mainly into the metacestode inner vesicular fluid (MVF); however, the number of nanoparticles in culture medium and MVF increases > 10-fold when metacestodes show signs of tegument impairment. Interestingly, we confirm the presence of host miRNAs in the intra-parasite milieu, implying their internalization and transport through the tegument towards the MVF. Finally, our assessment of the detection of Echinococcus miRNAs in patient samples by RT-qPCR yielded negative results suggesting the tested miRNAs may not be good biomarkers for this disease. A comprehensive study of the secretion mechanisms throughout the life cycle of these parasites will help to understand parasite interaction with the host and also, improve current diagnostic tools

Proteomic analysis of plasma exosomes from cystic echinococcosis patients provides in vivo support for distinct immune response profiles in active vs inactive infection and suggests potential biomarkers

The reference diagnostic method of human abdominal Cystic Echinococcosis (CE) is imaging, particularly ultrasound, supported by serology when imaging is inconclusive. However, current diagnostic tools are neither optimal nor widely available. The availability of a test detecting circulating biomarkers would considerably improve CE diagnosis and cyst staging (active vs inactive), as well as treatments and follow-up of patients. Exosomes are extracellular vesicles involved in intercellular communication, including immune system responses, and are a recognized source of biomarkers. With the aim of identifying potential biomarkers, plasma pools from patients infected by active or inactive CE, as well as from control subjects, were processed to isolate exosomes for proteomic label-free quantitative analysis. Results were statistically processed and subjected to bioinformatics analysis to define distinct features associated with parasite viability. First, a few parasite proteins were identified that were specifically associated with either active or inactive CE, which represent potential biomarkers to be validated in further studies. Second, numerous identified proteins of human origin were common to active and inactive CE, confirming an overlap of several immune response pathways. However, a subset of human proteins specific to either active or inactive CE, and central in the respective protein-protein interaction networks, were identified. These include the Src family kinases Src and Lyn, and the immune-suppressive cytokine TGF-β in active CE, and Cdc42 in inactive CE. The Src and Lyn Kinases were confirmed as potential markers of active CE in totally independent plasma pools. In addition, insights were obtained on immune response profiles: largely consistent with previous evidence, our observations hint to a Th1/Th2/regulatory immune environment in patients with active CE and a Th1/inflammatory environment with a component of the wound healing response in the presence of inactive CE. Of note, our results were obtained for the first time from the analysis of samples obtained in vivo from a well-characterized, large cohort of human subjects

Ex-Ray: Detection of History-Leaking Browser Extensions

Web browsers have become the predominant means for developing and deploying applications, and thus they often handle sensitive data such as social interactions or financial credentials and information. As a consequence, defensive measures such as TLS, the Same-Origin Policy (SOP), and Content Security Policy (CSP) are critical for ensuring that sensitive data remains in trusted hands. Browser extensions, while a useful mechanism for allowing third-party extensions to core browser functionality, pose a security risk in this regard since they have access to privileged browser APIs that are not necessarily restricted by the SOP or CSP. Because of this, they have become a major vector for introducing malicious code into the browser. Prior work has led to improved security models for isolating and sandboxing extensions, as well as techniques for identifying potentially malicious extensions. The area of privacy-violating browser extensions has so far been covered by manual analysis and systems performing search on specific text on network traffic. However, comprehensive content-agnostic systems for identifying tracking behavior at the network level are an area that has not yet received significant attention. In this paper, we present a dynamic technique for identifying privacy-violating extensions in Web browsers that relies solely on observations of the network traffic patterns generated by browser extensions. We then present Ex-Ray, a prototype implementation of this technique for the Chrome Web browser, and use it to evaluate all extensions from the Chrome store with more than 1,000 installations (10,691 in total). Our evaluation finds new types of tracking behavior not covered by state of the art systems. Finally, we discuss potential browser improvements to prevent abuse by future user-tracking extensions

The P-Loop Domain of Yeast Clp1 Mediates Interactions Between CF IA and CPF Factors in Pre-mRNA 3′ End Formation

Cleavage factor IA (CF IA), cleavage and polyadenylation factor (CPF), constitute major protein complexes required for pre-mRNA 3′ end formation in yeast. The Clp1 protein associates with Pcf11, Rna15 and Rna14 in CF IA but its functional role remained unclear. Clp1 carries an evolutionarily conserved P-loop motif that was previously shown to bind ATP. Interestingly, human and archaean Clp1 homologues, but not the yeast protein, carry 5′ RNA kinase activity. We show that depletion of Clp1 in yeast promoted defective 3′ end formation and RNA polymerase II termination; however, cells expressing Clp1 with mutant P-loops displayed only minor defects in gene expression. Similarly, purified and reconstituted mutant CF IA factors that interfered with ATP binding complemented CF IA depleted extracts in coupled in vitro transcription/3′ end processing reactions. We found that Clp1 was required to assemble recombinant CF IA and that certain P-loop mutants failed to interact with the CF IA subunit Pcf11. In contrast, mutations in Clp1 enhanced binding to the 3′ endonuclease Ysh1 that is a component of CPF. Our results support a structural role for the Clp1 P-loop motif. ATP binding by Clp1 likely contributes to CF IA formation and cross-factor interactions during the dynamic process of 3′ end formation

Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>Several large-scale gene co-expression networks have been constructed successfully for predicting gene functional modules and cis-regulatory elements in Arabidopsis (<it>Arabidopsis thaliana</it>)<it>.</it> However, these networks are usually constructed and analyzed in an <it>ad hoc</it> manner. In this study, we propose a completely parameter-free and systematic method for constructing gene co-expression networks and predicting functional modules as well as cis-regulatory elements.</p> <p>Results</p> <p>Our novel method consists of an automated network construction algorithm, a parameter-free procedure to predict functional modules, and a strategy for finding known cis-regulatory elements that is suitable for consensus scanning without prior knowledge of the allowed extent of degeneracy of the motif. We apply the method to study a large collection of gene expression microarray data in Arabidopsis. We estimate that our co-expression network has ~94% of accuracy, and has topological properties similar to other biological networks, such as being scale-free and having a high clustering coefficient. Remarkably, among the ~300 predicted modules whose sizes are at least 20, 88% have at least one significantly enriched functions, including a few extremely significant ones (ribosome, <it>p</it> < 1E-300, photosynthetic membrane, <it>p</it> < 1.3E-137, proteasome complex, <it>p</it> < 5.9E-126). In addition, we are able to predict cis-regulatory elements for 66.7% of the modules, and the association between the enriched cis-regulatory elements and the enriched functional terms can often be confirmed by the literature. Overall, our results are much more significant than those reported by several previous studies on similar data sets. Finally, we utilize the co-expression network to dissect the promoters of 19 Arabidopsis genes involved in the metabolism and signaling of the important plant hormone gibberellin, and achieved promising results that reveal interesting insight into the biosynthesis and signaling of gibberellin.</p> <p>Conclusions</p> <p>The results show that our method is highly effective in finding functional modules from real microarray data. Our application on Arabidopsis leads to the discovery of the largest number of annotated Arabidopsis functional modules in the literature. Given the high statistical significance of functional enrichment and the agreement between cis-regulatory and functional annotations, we believe our Arabidopsis gene modules can be used to predict the functions of unknown genes in Arabidopsis, and to understand the regulatory mechanisms of many genes.</p