Gene expression study in the non-model organism Botryllus schlosseri through SOLiD RNA-seqs

Botryllus schlosseri is a colonial ascidian widespread in temperate, shallow seas of the world. The organism is widely used for the study, in an evolutionary perspective, of a variety of biological processes ranging from sexual and asexual reproduction to regeneration, allorecognition and immune responses. However, despite its importance as model organism, no sequenced genome is available today. We undertook the analysis of the transcriptome of B. schlosseri in various colonial developmental phases and during tunic regeneration. The asexual reproduction by continuous palleal budding and the vascular system regeneration were the target of our RNA-seq experiments. In the first experiment, 3 different phases of the colonial blastogenetic cycle were considered: the mid-cycle, where colonies are metabolically very active; a phase immediately before the generation change (take-over), where colonies are getting ready to the generation change, and the take-over phase where adult zooids die and are replaced by buds which reach adulthood. Total RNA was extracted from various colonies for each of considered experimental condition. In the second experiment, the tunic of some colonies was cut and let to regenerate for 2 days. After tunic regeneration, total RNA was extracted. cDNA libraries were built according to SOLiD protocols and they were sequenced using SOLiD 4 and SOLID 5500 sequencers. In the absence of a reference genome, the gene expression analysis requires a de novo assembly of RNA-seq experiments. In this thesis a method to assemble RNAseq reads produced by SOLiD sequencers is described for the first time. The analysis of simulated data allowed us to improves the overall method. Gene expression data and gene annotation have been stored in a database and they can be managed in a compact structure which is directly and quickly accessed by a developed Web interface. The Web interface makes possible the analysis of many experimental conditions and their comparison, to highlight expression differences, through a common Web browser. Many thousands of differentially expressed transcripts were found and some of these are involved in natural apoptosis. This biological process was described in details using morphological studies: during take-over, tissues of adult zooids undergo apoptosis and zooids are replaced by primary buds that grow to become the new adult generation

Transcriptome dynamics in the asexual cycle of the chordate Botryllus schlosseri

Background: We performed an analysis of the transcriptome during the blastogenesis of the chordate Botryllus schlosseri, focusing in particular on genes involved in cell death by apoptosis. The tunicate B. schlosseri is an ascidian forming colonies characterized by the coexistence of three blastogenetic generations: filter-feeding adults, buds on adults, and budlets on buds. Cyclically, adult tissues undergo apoptosis and are progressively resorbed and replaced by their buds originated by asexual reproduction. This is a feature of colonial tunicates, the only known chordates that can reproduce asexually. Results: Thanks to a newly developed web-based platform (http://botryllus.cribi.unipd.it), we compared the transcriptomes of the mid-cycle, the pre-take-over, and the take-over phases of the colonial blastogenetic cycle. The platform is equipped with programs for comparative analysis and allows to select the statistical stringency. We enriched the genome annotation with 11,337 new genes; 581 transcripts were resolved as complete open reading frames, translated in silico into amino acid sequences and then aligned onto the non-redundant sequence database. Significant differentially expressed genes were classified within the gene ontology categories. Among them, we recognized genes involved in apoptosis activation, de-activation, and regulation. Conclusions: With the current work, we contributed to the improvement of the first released B. schlosseri genome assembly and offer an overview of the transcriptome changes during the blastogenetic cycle, showing up- and down-regulated genes. These results are important for the comprehension of the events underlying colony growth and regression, cell proliferation, colony homeostasis, and competition among different generations

Polymer mechanochemistry-enabled pericyclic reactions

Over the past decades, it became clear that next to heat and light, pericyclic reactions can be induced mechanochemically when the reacting motifs are embedded as latent force-responsive groups (mechanophores) into polymer architectures. Not only does this enable a variety of functions and applications on a material level, but moreover grants access to symmetry-forbidden reaction products with respect to the Woodward-Hoffmann rules. The latter indicates that polymer mechanochemistry follows its own set of rules that, however, regarding underlying mechanisms and design rationales is far from being holistically understood. Here we review the existing body of literature and identify common structural features and substitution prerequisites to the polymer framework shining light on the differences between polymer mechanochemical pericyclic reactions and their traditional counterparts. By this, we believe to contribute to the major challenge of not only retrospectively describing force-induced reactivity but eventually finding a common molecular design guideline. © The Royal Society of Chemistry 2020

Successful smoking cessation with electronic cigarettes in smokers with a documented history of recurring relapses: a case series

<p>Abstract</p> <p>Introduction</p> <p>Smoking cessation programs are useful in helping smokers to quit, but smoking is a very difficult addiction to break and the need for novel and effective approaches to smoking cessation interventions is unquestionable. The E-cigarette is a battery-powered electronic nicotine delivery device that may help smokers to remain abstinent during their quit attempt. We report for the first time objective measures of smoking cessation in smokers who experimented with the E-cigarette.</p> <p>Case presentation</p> <p>Three Caucasian smokers (two men aged 47 and 65 years and one woman aged 38 years) with a documented history of recurring relapses were able to quit and to remain abstinent for at least six months after taking up an E-cigarette.</p> <p>Conclusions</p> <p>This is the first time that objective measures of smoking cessation are reported for smokers who quit successfully after using an E-cigarette. This was accomplished in smokers who repeatedly failed in previous attempts with professional smoking cessation assistance using the usual nicotine dependence treatments and smoking cessation counselling.</p

Effect of an electronic nicotine delivery device (e-Cigarette) on smoking reduction and cessation: a prospective 6-month pilot study

BACKGROUND: Cigarette smoking is a tough addiction to break. Therefore, improved approaches to smoking cessation are necessary. The electronic-cigarette (e-Cigarette), a battery-powered electronic nicotine delivery device (ENDD) resembling a cigarette, may help smokers to remain abstinent during their quit attempt or to reduce cigarette consumption. Efficacy and safety of these devices in long-term smoking cessation and/or smoking reduction studies have never been investigated. METHODS: In this prospective proof-of-concept study we monitored possible modifications in smoking habits of 40 regular smokers (unwilling to quit) experimenting the 'Categoria' e-Cigarette with a focus on smoking reduction and smoking abstinence. Study participants were invited to attend a total of five study visits: at baseline, week-4, week-8, week-12 and week-24. Product use, number of cigarettes smoked, and exhaled carbon monoxide (eCO) levels were measured at each visit. Smoking reduction and abstinence rates were calculated. Adverse events and product preferences were also reviewed. RESULTS: Sustained 50% reduction in the number of cig/day at week-24 was shown in 13/40(32.5%) participants; their median of 25 cigs/day decreasing to 6 cigs/day (p < 0.001). Sustained 80% reduction was shown in 5/40(12.5%) participants; their median of 30 cigs/day decreasing to 3 cigs/day (p = 0.043). Sustained smoking abstinence at week-24 was observed in 9/40(22.5%) participants, with 6/9 still using the e-Cigarette by the end of the study. Combined sustained 50% reduction and smoking abstinence was shown in 22/40 (55%) participants, with an overall 88% fall in cigs/day. Mouth (20.6%) and throat (32.4%) irritation, and dry cough (32.4%) were common, but diminished substantially by week-24. Overall, 2 to 3 cartridges/day were used throughout the study. Participants' perception and acceptance of the product was good. CONCLUSION: The use of e-Cigarette substantially decreased cigarette consumption without causing significant side effects in smokers not intending to quit (http://ClinicalTrials.gov number NCT01195597)

PABS: An online platform to assist BAC-by-BAC sequencing projects

Genome sequencing projects are either based on whole genome shotgun (WGS) or on a BAC-by-BAC strategy. Although WGS is in most cases the preferred choice, sometimes the BAC-by-BAC approach may be better because it requires a much simpler assembly process. Furthermore, when the study is limited to specific regions of the genome, the WGS would require an unjustified effort, making the BAC-by-BAC the only feasible strategy. In this paper we describe an informatics pipeline called PABS (Platform Assisted BAC-by-BAC Sequencing) that we developed to provide a tool to optimize the BAC-by-BAC sequencing strategy. PABS has two main functions: (i) PABS-Select, to choose suitable overlapping clones; and (ii) PABS-Validate, to verify whether a BAC under analysis is actually overlapping the neighboring BAC

An update on lateral flow immunoassay for the rapid detection of SARS-CoV-2 antibodies

Over the last three years, after the outbreak of the COVID-19 pandemic, an unprecedented number of novel diagnostic tests have been developed. Assays to evaluate the immune response to SARS-CoV-2 have been widely considered as part of the control strategy. The lateral flow immunoassay (LFIA), to detect both IgM and IgG against SARS-CoV-2, has been widely studied as a point-of-care (POC) test. Compared to laboratory tests, LFIAs are faster, cheaper and user-friendly, thus available also in areas with low economic resources. Soon after the onset of the pandemic, numerous kits for rapid antibody detection were put on the market with an emergency use authorization. However, since then, scientists have tried to better define the accuracy of these tests and their usefulness in different contexts. In fact, while during the first phase of the pandemic LFIAs for antibody detection were auxiliary to molecular tests for the diagnosis of COVID-19, successively these tests became a tool of seroprevalence surveillance to address infection control policies. When in 2021 a massive vaccination campaign was implemented worldwide, the interest in LFIA reemerged due to the need to establish the extent and the longevity of immunization in the vaccinated population and to establish priorities to guide health policies in low-income countries with limited access to vaccines. Here, we summarize the accuracy, the advantages and limits of LFIAs as POC tests for antibody detection, highlighting the efforts that have been made to improve this technology over the last few years

The climate in the European Union and the enlarged European Region is a determinant of the COVID-19 case fatality ratio

Climate could influence the COVID-19 pandemic, but while no evidence has been advanced on the influence of colder climates, some studies have provided data to support a possible heat-related protective factor. The objective is to verify whether areas with a Cold Temperate Climate (TC) have a higher Case Fatality Ratio (CFR) for COVID-19 than areas with a Cold Climate (CC) or with a Mediterranean Climate (MC) in the European Union and the Enlarged European Region. Countries or regions were subdivided into 3 groups according to the Köppen climate classification system: TC (Cfa, Cfb and Cfc in the Köppen system); MC (Csa, Csb); CC (D and E in the Köppen system). The total number of cases and the total number of deaths were detected on 13 August 2020 on the COVID-19 Map-Johns Hopkins Coronavirus Resource Center-the CFR was thus calculated by area. Living in TC areas is strongly associated with risk of a high Case Fatality Ratio for COVID-19, OR for MC =0.42, IC 95% 0.41-0.43; OR for CC=0.33, IC 95% 0.33-0.35. The results are confirmed in the EU, OR per MC=0.85, CI 95% 0.84-0.87; OR per CC=0.63, IC 95% 0.61-0.65.The study found that the IC in a humid temperate climate is associated with higher CFR with respect to the coldest and warmest temperate climates in Europe. This does not appear to be the only determinant of the pandemic

Is the Inversion in the Trend of the Lethality of the COVID-19 in the Two Hemispheres due to the Difference in Seasons and Weather?

The climate has an influence on the COVID-19 virus lethality. The aim of this study is to verify if the summer weather coincided with the decrease of the Case Fatality Ratio (CFR) in Europe and if, on the contrary, an inverse trend was observed in Australia and New Zealand. To verify our hypothesis, we considered the largest European countries (Germany, UK, France, Italy, and Spain), plus Belgium and the Netherlands. Furthermore, we compared these countries with Australia and New Zealand. For each country considered, we have calculated the CFR from the beginning of the pandemic to May 6th and from May 6th to September 21st (late summer in Europe, late winter in the southern hemisphere). The CFRs were calculated from the John Hopkins University database. According to the results, in all European countries, a progressive decrease in CFR is observed. A diametrically opposite result is found in Australia where, on the contrary, the CFR is much higher at the end of September (at the end of winter) than on May 6th (mid-autumn), and the risk of dying if we count the infection is higher in September. In New Zealand, there are no statistically significant differences between the two surveys. The present study was based on public access macro data

Evaluation of humoral and cellular response to third dose of BNT162b2 mRNA COVID-19 vaccine in patients treated with B-cell depleting therapy

Objective: to investigate the responses to mRNA COVID-19 vaccines in a cohort of immunosuppressed patients affected by immune-mediated inflammatory diseases (IMID). Methods: we have measured humoral and cellular immunity using quantitative IgG anti-SARS-CoV-2 Spike antibody (anti-S-IgG), neutralization assays and specific interferon-gamma (IFN-g) release assay (IGRA) before and after the third dose of BNT162b2. The response of those on anti-CD20 (n = 18) was then compared with healthy controls (HC, n = 18) and IMID naïve to anti-CD20 drugs (n = 13). Results: a third BNT162b2 dose is highly immunogenic in IMID patients naïve to anti-CD20, as 100% of the subjects seroconverted compared to the 55% in anti-CD20. The rate of IGRA response was of 79% in anti-CD20, 50% in IMID naïve to anti-CD20, 100% in HC. Among those who have seroconverted, IMID patients had significantly reduced anti-S-IgG and neutralization titers compared to HC, whereas no significant difference was observed when comparing anti-CD20 and HC. Furthermore, 13% of anti-CD20 and 7.7% of IMID were simultaneously negative for both neutralizing antibodies and IGRA after three doses. Conclusion: these data draw attention to the immunogenicity of COVID-19 vaccination in treated IMID, taking specific groups into consideration for vaccination program