Sources and processes that control the submicron organic aerosol composition in an urban Mediterranean environment (Athens): a high temporal-resolution chemical composition measurement study

Submicron aerosol chemical composition was studied during a year-long period (26 July 2016–31 July 2017) and two wintertime intensive campaigns (18 December 2013–21 February 2014 and 23 December 2015–17 February 2016), at a central site in Athens, Greece, using an Aerosol Chemical Speciation Monitor (ACSM). Concurrent measurements included a particle-into-liquid sampler (PILS-IC), a scanning mobility particle sizer (SMPS), an AE-33 Aethalometer, and ion chromatography analysis on 24 or 12&thinsp;h filter samples. The aim of the study was to characterize the seasonal variability of the main submicron aerosol constituents and decipher the sources of organic aerosol (OA). Organics were found to contribute almost half of the submicron mass, with 30&thinsp;min resolution concentrations during wintertime reaching up to 200&thinsp;µg&thinsp;m−3. During winter (all three campaigns combined), primary sources contributed about 33&thinsp;% of the organic fraction, and comprised biomass burning (10&thinsp;%), fossil fuel combustion (13&thinsp;%), and cooking (10&thinsp;%), while the remaining 67&thinsp;% was attributed to secondary aerosol. The semi-volatile component of the oxidized organic aerosol (SV-OOA; 22&thinsp;%) was found to be clearly linked to combustion sources, in particular biomass burning; part of the very oxidized, low-volatility component (LV-OOA; 44&thinsp;%) could also be attributed to the oxidation of emissions from these primary combustion sources. These results, based on the combined contribution of biomass burning organic aerosol (BBOA) and SV-OOA, indicate the importance of increased biomass burning in the urban environment of Athens as a result of the economic recession. During summer, when concentrations of fine aerosols are considerably lower, more than 80&thinsp;% of the organic fraction is attributed to secondary aerosol (SV-OOA 31&thinsp;% and LV-OOA 53&thinsp;%). In contrast to winter, SV-OOA appears to result from a well-mixed type of aerosol that is linked to fast photochemical processes and the oxidation of primary traffic and biogenic emissions. Finally, LV-OOA presents a more regional character in summer, owing to the oxidation of OA over the period of a few days.</p

Evaluation of the CO2 Storage Capacity in Sandstone Formations from the Southeast Mesohellenic trough (Greece)

This study investigates the capability of the Southeast Mesohellenic Trough (SE MHT) sandstone formations to serve as a potential reservoir for CO2 storage in response to the emerging climate change issues by promoting environmentally friendly mineral sequestration applications. Sandstone samples, for the first time, were evaluated for their petrographic characteristics, mineral chemistry, geochemical properties, as well as their petrophysical and gas adsorption properties through tests. The sandstones were tested and classified into distinct groups. The most promising site to be considered for pilot CO2 storage testing is the Pentalofos Formation locality since its sandstones display specific mineral phases with the proper modal composition to conceivably react with injected CO2, leading to the development of newly formed and stable secondary mineral phases. The gas adsorption results are also more encouraging for sandstones from this sedimentary formation. All the measured UCS (uniaxial compressive strength), Ei (bending stiffness), and ν (Poisson’s ratio) results are above those dictated by international standards to perform CO2 storage practices safely. Furthermore, the specified targeted locality from the Pentalofos Formation holds the geological advantage of being overlaid by an impermeable cap-rock formation, making it suitable for deploying CO2 mineralization practices. The demarcated area could permanently store a calculated amount of ~50 × 105 tons of CO2 within the geological reservoir by reacting with the specified mineral phases, as specified through the proposed petrographic PrP index (potential reactive phases)

The use of premature chromosome condensation to study in interphase cells the influence of environmental factors on human genetic material

Nowadays, there is a constantly increasing concern regarding the mutagenic and carcinogenic potential of a variety of harmful environmental factors to which humans are exposed in their natural and anthropogenic environment. These factors exert their hazardous potential in humans' personal (diet, smoking, pharmaceuticals, cosmetics) and occupational environment that constitute part of the anthropogenic environment. It is well known that genetic damage due to these factors has dramatic implications for human health. Since most of the environmental genotoxic factors induce arrest or delay in cell cycle progression, the conventional analysis of chromosomes at metaphase may underestimate their genotoxic potential. Premature Chromosome Condensation (PCC) induced either by means of cell fusion or specific chemicals, enables the microscopic visualization of interphase chromosomes whose morphology depends on the cell cycle stage, as well as the analysis of structural and numerical aberrations at the G1 and G2 phases of the cell cycle. The PCC has been successfully used in problems involving cell cycle analysis, diagnosis and prognosis of human leukaemia, assessment of interphase chromosome malformations resulting from exposure to radiation or chemicals, as well as elucidation of the mechanisms underlying the conversion of DNA damage into chromosomal damage. In this report, particular emphasis is given to the advantages of the PCC methodology used as an alternative to conventional metaphase analysis in answering questions in the fields of radiobiology, biological dosimetry, toxicogenetics, clinical cytogenetics and experimental therapeutics

Multi-year chemical composition of the fine-aerosol fraction in Athens, Greece, with emphasis on the contribution of residential heating in wintertime

In an attempt to take effective action towards mitigating pollution episodes in Athens, precise knowledge of PM2.5 composition and its sources is a prerequisite. Thus, a 2-year chemical composition dataset from aerosol samples collected in an urban background site in central Athens from December 2013 to March 2016 has been obtained and a positive matrix factorization (PMF) was applied in order to identify and apportion fine aerosols to their sources. A total of 850 aerosol samples were collected on a 12 to 24&thinsp;h basis and analyzed for major ions, trace elements, and organic and elemental carbon, allowing us to further assess the impact of residential heating as a source of air pollution over Athens.The ionic and carbonaceous components were found to constitute the major fraction of the PM2.5 aerosol mass. The annual contribution of the ion mass (IM), particulate organic mass (POM), dust, elemental carbon (EC), and sea salt (SS) was calculated at 31&thinsp;%, 38&thinsp;%, 18&thinsp;%, 8&thinsp;%, and 3&thinsp;%, respectively, and exhibited considerable seasonal variation. In winter, the share of IM was estimated down to 23&thinsp;%, with POM&thinsp;+ EC being the dominant component accounting for 52&thinsp;% of the PM2.5 mass, while in summer, IM (42&thinsp;%) and carbonaceous aerosols (41&thinsp;%) contributed almost equally.Results from samples collected on a 12&thinsp;h basis (day and night) during the three intensive winter campaigns indicated the impact of heating on the levels of a series of compounds. Indeed, PM2.5, EC, POM, NO3−, C2O42−, non sea salt (nss) K+ and selected trace metals including Cd and Pb were increased by up to a factor of 4 in the night compared to the day, highlighting the importance of heating on air quality in Athens. Furthermore, in order to better characterize wintertime aerosol sources and quantify the impact of biomass burning on PM2.5 levels, source apportionment was performed. The data can be interpreted on the basis of six sources, namely biomass burning (31&thinsp;%), vehicular emissions (19&thinsp;%), heavy oil combustion (7&thinsp;%), regional secondary (21&thinsp;%), marine aerosols (9&thinsp;%), and dust particles (8&thinsp;%). Regarding night-to-day patterns their contributions shifted from 19&thinsp;%, 19&thinsp;%, 8&thinsp;%, 31&thinsp;%, 12&thinsp;%, and 10&thinsp;% of the PM2.5 mass during day to 39&thinsp;%, 19&thinsp;%, 6&thinsp;%, 14&thinsp;%, 7&thinsp;%, and 7&thinsp;% during the night, underlining the significance of biomass burning as the main contributor to fine particle levels during nighttime in winter.</p

Genomic characteristics and clinical effect of the emergent SARS-CoV-2 B.1.1.7 lineage in London, UK: a whole-genome sequencing and hospital-based cohort study

BACKGROUND: Emergence of variants with specific mutations in key epitopes in the spike protein of SARS-CoV-2 raises concerns pertinent to mass vaccination campaigns and use of monoclonal antibodies. We aimed to describe the emergence of the B.1.1.7 variant of concern (VOC), including virological characteristics and clinical severity in contemporaneous patients with and without the variant. METHODS: In this cohort study, samples positive for SARS-CoV-2 on PCR that were collected from Nov 9, 2020, for patients acutely admitted to one of two hospitals on or before Dec 20, 2020, in London, UK, were sequenced and analysed for the presence of VOC-defining mutations. We fitted Poisson regression models to investigate the association between B.1.1.7 infection and severe disease (defined as point 6 or higher on the WHO ordinal scale within 14 days of symptoms or positive test) and death within 28 days of a positive test and did supplementary genomic analyses in a cohort of chronically shedding patients and in a cohort of remdesivir-treated patients. Viral load was compared by proxy, using PCR cycle threshold values and sequencing read depths. FINDINGS: Of 496 patients with samples positive for SARS-CoV-2 on PCR and who met inclusion criteria, 341 had samples that could be sequenced. 198 (58%) of 341 had B.1.1.7 infection and 143 (42%) had non-B.1.1.7 infection. We found no evidence of an association between severe disease and death and lineage (B.1.1.7 vs non-B.1.1.7) in unadjusted analyses (prevalence ratio [PR] 0·97 [95% CI 0·72-1·31]), or in analyses adjusted for hospital, sex, age, comorbidities, and ethnicity (adjusted PR 1·02 [0·76-1·38]). We detected no B.1.1.7 VOC-defining mutations in 123 chronically shedding immunocompromised patients or in 32 remdesivir-treated patients. Viral load by proxy was higher in B.1.1.7 samples than in non-B.1.1.7 samples, as measured by cycle threshold value (mean 28·8 [SD 4·7] vs 32·0 [4·8]; p=0·0085) and genomic read depth (1280 [1004] vs 831 [682]; p=0·0011). INTERPRETATION: Emerging evidence exists of increased transmissibility of B.1.1.7, and we found increased virus load by proxy for B.1.1.7 in our data. We did not identify an association of the variant with severe disease in this hospitalised cohort. FUNDING: University College London Hospitals NHS Trust, University College London/University College London Hospitals NIHR Biomedical Research Centre, Engineering and Physical Sciences Research Council

Favourable antibody responses to human coronaviruses in children and adolescents with autoimmune rheumatic diseases

Background: Differences in humoral immunity to coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), between children and adults remain unexplained and the impact of underlying immune dysfunction or suppression unknown. Here, we sought to examine the antibody immune competence of children and adolescents with prevalent inflammatory rheumatic diseases, juvenile idiopathic arthritis (JIA), juvenile dermatomyositis (JDM) and juvenile systemic lupus erythematosus (JSLE), against the seasonal human coronavirus (HCoV)-OC43 that frequently infects this age group. // Methods: Sera were collected from JIA (n=118), JDM (n=49) and JSLE (n=30) patients, and from healthy control (n=54) children and adolescents, prior to the coronavirus disease-19 (COVID-19) pandemic. We employed sensitive flow cytometry-based assays to determine titres of antibodies that reacted with the spike and nucleoprotein of HCoV-OC43 and cross-reacted with the spike and nucleoprotein of SARS-CoV-2, and compared with respective titres in sera from patients with multisystem inflammatory syndrome in children and adolescents (MIS-C). // Findings: Despite immune dysfunction and immunosuppressive treatment, JIA, JDM and JSLE patients maintained comparable or stronger humoral responses than healthier peers, dominated by IgG antibodies to HCoV-OC43 spike, and harboured IgG antibodies that cross-reacted with SARS-CoV-2 spike. In contrast, responses to HCoV-OC43 and SARS-CoV-2 nucleoproteins exhibited delayed age-dependent class-switching and were not elevated in JIA, JDM and JSLE patients, arguing against increased exposure. // Conclusions: Consequently, autoimmune rheumatic diseases and their treatment were associated with a favourable ratio of spike to nucleoprotein antibodies

Preexisting and de novo humoral immunity to SARS-CoV-2 in humans

Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detect preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable by a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the IgG class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies, targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. Notably, SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection

Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism

7-carboxy-7-deazaguanine synthase (QueE) catalyzes a key S-adenosyl-L-methionine (AdoMet)- and Mg[superscript 2+]-dependent radical-mediated ring contraction step, which is common to the biosynthetic pathways of all deazapurine-containing compounds. QueE is a member of the AdoMet radical superfamily, which employs the 5′-deoxyadenosyl radical from reductive cleavage of AdoMet to initiate chemistry. To provide a mechanistic rationale for this elaborate transformation, we present the crystal structure of a QueE along with structures of pre- and post-turnover states. We find that substrate binds perpendicular to the [4Fe-4S]-bound AdoMet, exposing its C6 hydrogen atom for abstraction and generating the binding site for Mg[superscript 2+], which coordinates directly to the substrate. The Burkholderia multivorans structure reported here varies from all other previously characterized members of the AdoMet radical superfamily in that it contains a hypermodified ([β [subscript 6] over α [subscript 3]]) protein core and an expanded cluster-binding motif, CX[subscript 14]CX[subscript 2]C.United States. Dept. of Energy. Office of Biological and Environmental ResearchUnited States. Dept. of Energy. Office of Basic Energy SciencesNational Center for Research Resources (U.S.) (P41RR012408)National Institute of General Medical Sciences (U.S.) (P41GM103473)National Center for Research Resources (U.S.) (5P41RR015301-10)National Institute of General Medical Sciences (U.S.) (8 P41 GM 103403-10)United States. Dept. of Energy (Contract DE-AC02-06CH11357

hElp3 Directly Modulates the Expression of HSP70 Gene in HeLa Cells via HAT Activity

Human Elongator complex, which plays a key role in transcript elongation in vitro assay, is incredibly similar in either components or function to its yeast counterpart. However, there are only a few studies focusing on its target gene characterization in vivo. We studied the effect of down-regulation of the human elongation protein 3 (hELP3) on the expression of HSP70 through antisense strategy. Transfecting antisense plasmid p1107 into HeLa cells highly suppressed hELP3 expression, and substantially reduced expression of HSP70 mRNA and protein. Furthermore, chromatin immunoprecipitation assay (ChIP Assay) revealed that hElp3 participates in the transcription elongation of HSPA1A in HeLa cells. Finally, complementation and ChIP Assay in yeast showed that hElp3 can not only complement the growth and slow activation of HSP70 (SSA3) gene transcription, but also directly regulates the transcription of SSA3. On the contrary, these functions are lost when the HAT domain is deleted from hElp3. These data suggest that hElp3 can regulate the transcription of HSP70 gene, and the HAT domain of hElp3 is essential for this function. These findings now provide novel insights and evidence of the functions of hELP3 in human cells

The International Virus Bioinformatics Meeting 2020.

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting