[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 300 additional molecules important in different areas of atmospheric science have been added to the database. The compilation can be accessed through www.hitran.org. Most of the HITRAN data have now been cast into an underlying relational database structure that offers many advantages over the long-standing sequential text-based structure. The new structure empowers the user in many ways. It enables the incorporation of an extended set of fundamental parameters per transition, sophisticated line-shape formalisms, easy user-defined output formats, and very convenient searching, filtering, and plotting of data. A powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.

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The HITRAN 2008 molecular spectroscopic database

Nitrogen is a key element controlling the species composition, diversity, dynamics, and functioning of many terrestrial, freshwater, and marine ecosystems. Many of the original plant species living in these ecosystems are adapted to, and function optimally in, soils and solutions with low levels of available nitrogen. The growth and dynamics of herbivore populations, and ultimately those of their predators, also are affected by N. Agriculture, combustion of fossil fuels, and other human activities have altered the global cycle of N substantially, generally increasing both the availability and the mobility of N over large regions of Earth. The mobility of N means that while most deliberate applications of N occur locally, their influence spreads regionally and even globally. Moreover, many of the mobile forms of N themselves have environmental consequences. Although most nitrogen inputs serve human needs such as agricultural production, their environmental conse- quences are serious and long term. Based on our review of available scientific evidence, we are certain that human alterations of the nitrogen cycle have: 1) approximately doubled the rate of nitrogen input into the terrestrial nitrogen cycle, with these rates still increasing; 2) increased concentrations of the potent greenhouse gas N 2O globally, and increased concentrations of other oxides of nitrogen that drive the formation of photochemical smog over large regions of Earth; 3) caused losses of soil nutrients, such as calcium and potassium, that are essential for the long-term maintenance of soil fertility; 4) contributed substantially to the acidification of soils, streams, and lakes in several regions; and 5) greatly increased the transfer of nitrogen through rivers to estuaries and coastal oceans. In addition, based on our review of available scientific evidence we are confident that human alterations of the nitrogen cycle have: 6) increased the quantity of organic carbon stored within terrestrial ecosystems; 7) accelerated losses of biological diversity, especially losses of plants adapted to efficient use of nitrogen, and losses of the animals and microorganisms that depend on them; and 8) caused changes in the composition and functioning of estuarine and nearshore ecosystems, and contributed to long-term declines in coastal marine fisheries.

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Human alteration of the global nitrogen cycle: sources and consequences

The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.

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The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

The supply of blood, blood products and components in the UK, as elsewhere, is safe, although there is no cause for complacency. Use of blood, blood products and components is not without risk of morbidity and mortality. Transfusion-transmitted infections (TTIs) continue to occur and may severely affect the health and welfare of recipients. As indicated by recent and current inquiries, public interest in these TTIs is huge. The risk of TTI can be mitigated but not abolished. Measures to reduce risk include screening of donors, testing of donations and, where appropriate, treatment of donations. The introduction of newer screening tests might identify some infectious donations but come at a cost, which could exceed a justifiable limit. Thus, the recognition, detection, reporting and investigation of cases of possible TTIs need to be improved. Recipients of blood should understand that, although transfusion in the UK is safe, it is not free of risk and so should be provided with full information so that properly informed consent can be given.

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Challenges for the maintaining the microbiological safety of the UK blood supply.

Objectives: Human rhinovirus (HRV) is associated with pulmonary exacerbations in patients with CF. With sensitive RT-PCR techniques HRV is readily detected and new strains are being identified. In asthma, children with HRV group C have been shown to have more severe exacerbations. The aim of this project was to establish the frequency of each HRV group during exacerbations and to assess whether any HRV group is more pathogenic. Methods: Viral throat swabs were taken on all adult exacerbations between Dec 2008 and May 2011. Positive HRV samples were stored and typed in more detail. Date matched non-CF samples positive for HRV were used as community controls. To allow typing the extracted viral RNA was transcribed into cDNA. The resulting cDNA underwent two rounds of nested PCR reaction to produce amplicons of the VP4/VP2 region. This was then sequenced to allow genetic typing of the specimens. The HRV groups were then compared using demographic and clinical data obtained from patient records. Conclusion: HRV was identified in 7% of pulmonary exacerbations. 126 positive samples were stored and typing was possible in 104 of the isolates. HRV group A was identied in 57 (55%) of isolates, group B in 23 (22%), and group C in 24 (23%). The frequency of HRV group A was higher than that seen in community (55% vs 40%). Some patients had viral persistence for several weeks with the same serotype. Virus associated exacerbations had significantly greater impact on lung function, length of treatment, and time to next exacerbation compared to matched patients without a virus. However, no individual HRV group appeared more pathogenic and the detrimental effects were seen with all groups.

https://erj.ersjournals.com/content/erj/42/Suppl_57/P3603.full.pdf

Frequency and pathogenicity of rhinovirus associated pulmonary exacerbations in patients with cystic fibrosis

Abstract Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the level of pathogen detection within a species, or risk of spillover to other species. Micro-organisms that occur in healthy animals can be an important model for understanding and predicting the dynamics of pathogens of greater health concern, which are hard to study in wild populations due to their relative rarity. We therefore used a metagenomic approach to jointly characterise viral and prokaryotic carriage in faeces collected from a healthy wild bird population ( Cygnus olor ; mute swan) that has been subject to long-term study. Using 223 samples from known individuals allowed us to compare differences in prokaryotic and eukaryotic viral carriage between adults and juveniles at an unprecedented level of detail. We discovered and characterised 77 novel virus species, of which 21% belong putatively to bird-infecting families, and described the core prokaryotic microbiome of C. olor . Whilst no difference in microbiota diversity was observed between juveniles and adult individuals, 50% (4/8) of bird-infecting virus families (picornaviruses, astroviruses, adenoviruses and bornaviruses) and 3.4% (9/267) of prokaryotic families (including Helicobacteraceae , Spirochaetaceae and Flavobacteriaceae families) were differentially abundant and/or prevalent between juveniles and adults. This indicates that perturbations that affect population age-structures of wildlife could alter circulation dynamics and spillover risk of microbes, potentially including pathogens. 

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Impact of host age on viral and bacterial communities in a waterbird population

5122 POSTER Effect of Synchronous Chemo-radiation on Quality of Life: Results From the SECRAB Trial (ISRCTN: 84214355) Presented on Behalf of the SECRAB Steering Committee

Peter Simmonds

Papers

Challenges for the maintaining the microbiological safety of the UK blood supply.

Frequency and pathogenicity of rhinovirus associated pulmonary exacerbations in patients with cystic fibrosis

Impact of host age on viral and bacterial communities in a waterbird population

5122 POSTER Effect of Synchronous Chemo-radiation on Quality of Life: Results From the SECRAB Trial (ISRCTN: 84214355) Presented on Behalf of the SECRAB Steering Committee

Clinical significance of the detection of GBV-C virus in the serum of patients with acute liver failure of unknown aetiology.