Efficient \u3ci\u3eCOI\u3c/i\u3e Barcoding Using High Throughput Single-End 400 bp Sequencing

Background Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current highthroughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (for example, a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system). Results Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5′ and 3′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly, and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%. Conclusions The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications

Efficient COI barcoding using high throughput single-end 400 bp sequencing

Background Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current high-throughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (e.g. a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system). Results Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5′ and 3′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%. Conclusions The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications

The Many Roles of A-to-I RNA Editing in Animals: Functional or Adaptive?

Metazoan adenosine-to-inosine (A-to-I) RNA editing is a highly conserved mechanism that diversifies the transcriptome by post-transcriptionally converting adenosine to inosine. Millions of editing sites have been identified in different species and, based on abnormal editing observed in various disorders, it is intuitive to conclude that RNA editing is both functional and adaptive. In this review, we propose the following major points: (1) “Function/functional” only represents a molecular/phenotypic consequence and is not necessarily connected to “adaptation/adaptive”; (2) Adaptive editing should be judged in the light of evolution and emphasize advantages of temporal-spatial flexibility; (3) Adaptive editing could, in theory, be extended from nonsynonymous sites to all potentially functional sites. This review seeks to conceptually bridge the gap between molecular biology and evolutionary biology and provide a more objective understanding on the biological functions and evolutionary significance of RNA editing

Measurement of PM and its chemical composition in real-world emissions from non-road and on-road diesel vehicles

With the rapid growth in the number of both non-road and on-road diesel vehicles, the adverse effects of particulate matter (PM) and its constituents on air quality and human health have attracted increasing attentions. However, studies on the characteristics of PM and its composition emitted from diesel vehicles are still scarce, especially under real-world driving conditions. In this study, six excavators and five trucks that provided a wide range of emission standards and operation modes were tested, and PM emissions and their constituents - including organic carbon (OC), elemental carbon (EC), water-soluble ions (WSIs), elements, and organic species like polycyclic aromatic hydrocarbons (PAHs), n-alkanes, and hopanes - as well as steranes were analyzed and characterized. The average emission factors for PM (EFPM) from excavator and truck emissions were 829 +/- 806 and 498 +/- 234 mgkg(-1) fuel, respectively. EFPM and PM constituents were significantly affected by fuel quality, operational mode, and emission standards. A significant correlation (R-2 = 0.79, p < 0.01) was found between EFPM for excavators and the sulfur contents in fuel. The highest average EFPM for working excavators was 904 +/- 979 mgkg(-1) fuel as a higher engine load required in this mode. From pre-stage 1 to stage 2, the average EFPM for excavators decreased by 58 %. For trucks, the average nonhighway EFPM at 548 +/- 311 mgkg(-1) fuel was higher than the highway EFPM at 497 +/- 231 mgkg(-1) fuel. Moreover, the reduction rates were 63.5 and 65.6% when switched from China II and III to China IV standards, respectively. Generally, the PM composition emitted from excavators was dominated by OC (39.2 +/- 21.0 %) and EC (33.3 +/- 25.9 %); PM from trucks was dominated by EC (26.9 +/- 20.8 %), OC (9.89 +/- 12 %), and WSIs (4.67 +/- 5.74 %). The average OC/EC ratios for idling and working excavators were 3 to 4 times higher than those for moving excavators. Although the EFPM for excavators and trucks was reduced with the constraint of regulations, the element fractions for excavators increased from 0.49% in pre-stage 1 to 3.03% in stage 2, and the fraction of WSIs for the China IV truck was 5 times higher than the average value of all other-level trucks. Furthermore, as compared with other diesel vehicles, wide ranges were found for excavators of the ratios of benzo[a] anthracene/(benzo[a] anthracene + chrysene) (0.26-0.86), indeno[1,2,3-cd] pyrene/( indeno[1,2,3-cd] pyrene + benzo[ghi] perylene) (0.20-1.0), and fluoranthene = (fluoranthene C pyrene) (0.24-0.87), which might be a result of the complex characteristics of the excavator operation modes. A comparison of our results with those in the literature revealed that on-board measurement data more accurately reflect actual conditions. Although the fractions of the 16 priority PAHs in PM from the excavator and truck emissions were similar, the equivalent concentrations of total benzo[ a] pyrene of excavators were 31 times than that for trucks, implying that more attention should be paid to non-road vehicle emissions

Characterization of Ultrafine Particles and Other Traffic Related Pollutants near Roadways in Beijing

Developing countries, such as China, are facing serious air pollution issues due to fast economic development. In this study, traffic related air pollutants, including number concentration of ultrafine particles (UFPs, diameter &lt; 100 nm), mass concentrations of PM2.5 and black carbon (BC) were measured near the Peking University (PKU) campus in Beijing in December 2011. Data were collected concurrently at a roadway site and on PKU campus. Meteorological data were collected at approximately 40 meters northeast from the roadway sampling site. The traffic density was determined from recorded video footage. Roadside UFP and PM2.5 concentrations were not significantly higher than on campus. A statistically significant Pearson&apos;s correlation of 0.75 was found between BC and PM2.5 mass concentrations. No apparent correlation was found between wind speed and UFP number concentrations, but strong log-decay correlations were found between wind speed and PM2.5 (R-2 = 0.80). There were three days during the measurements when both PM2.5 mass concentrations and UFP number concentrations were higher at the campus site than at the roadway site. This suggests there were potential local emission sources on campus. Temporal profile of UFPs at the campus site peaked around lunch and dinner time, suggesting emissions from the surrounding restaurants and cafeteria that used Chinese-style cooking might have contributed to the observed PM2.5 and UFP levels on campus.National Science Foundation [32525-A6010 AI]; National Natural Science Foundation of China [41121004]; State Key Joint Laboratory of Environment Simulation and Pollution ControlSCI(E)[email protected]; [email protected]

Synthesis, Characterization, and Aqueous Properties of an Amphiphilic Terpolymer with a Novel Nonionic Surfmer

A series of surfactive amphiphilic polymer PAADs were prepared from the copolymerization of sodium acrylate, dodecyl polyoxyethylene acrylate (DPA, a surfmer), and acrylamide under the action of a mixed initiating agent consisting of ammonium persulfate-sodium bisulfite/2,2′-azobis[2-(2-imidazolin-2-yl) propane] dihydrochloride. The aggregative behaviors of PAADs were explored by 13C nuclear magnetic resonance, a viscometer, and a surface tension instrument. It was found that the apparent viscosity and surface activity of PAADs were significantly improved by the increase of average sequence length of hydrophobic micro blocks, strong intermolecular hydrophobic association, or the formation of mixed micelles between hydrophobic micro blocks and micromolecular surface-active agent. The introduction of long-chain alkyls on molecular chains prolonged the average sequence length of hydrophobic micro blocks in molecular chains and enhanced the hydrophobic association between molecular chains and the tight arrangement of molecular chains on water surfaces, thereby increasing the surface activity. Moreover, the anionic monomer sodium acrylate on molecular chains, via electrostatic repulsion, promoted the conversion from intrachain association to intermolecular association and thereby facilitated the formation of dense interfacial films, enhancing the surface activity of water solutions. Then, the anion surfmer sodium dodecylbenzenesulfonate interacted with the hydrophobic micro blocks on the molecular chains to form mixed micelles, which accelerated the interchain association and enhanced the polymer surface activity. The novel polymeric micelle with higher viscosifying ability and surface activity was expected to be a promising oil drive agent for tertiary oil recovery

Regionally-Varying Combustion Sources of the January 2013 Severe Haze Events over Eastern China

Thick haze plagued northeastern China in January 2013, strongly affecting both regional climate and human respiratory health. Here, we present dual carbon isotope constrained (Δ¹⁴C and δ¹³C) source apportionment for combustion-derived black carbon aerosol (BC) for three key hotspot regions (megacities): North China Plain (NCP, Beijing), the Yangtze River Delta (YRD, Shanghai), and the Pearl River Delta (PRD, Guangzhou) for January 2013. BC, here quantified as elemental carbon (EC), is one of the most health-detrimental components of PM_2.5 and a strong climate warming agent. The results show that these severe haze events were equally affected (∼30%) by biomass combustion in all three regions, whereas the sources of the dominant fossil fuel component was dramatically different between north and south. In the NCP region, coal combustion accounted for 66% (46–74%, 95% C.I.) of the EC, whereas, in the YRD and PRD regions, liquid fossil fuel combustion (e.g., traffic) stood for 46% (18–66%) and 58% (38–68%), respectively. Taken together, these findings suggest the need for a regionally-specific description of BC sources in climate models and regionally-tailored mitigation to combat severe air pollution events in East Asia

Molecular characterization of polar organic aerosol constituents in off-road engine emissions using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS): implications for source apportionment

The molecular compositions of polar organic compounds (POCs) in particles emitted from various vessels and excavators were characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and possible molecular structures of POCs were proposed. POCs were extracted with purified water and sorted by elemental composition into three groups: CHO, CHON, and S-containing compounds (CHONS and CHOS). The results show the following. (i) CHO (accounting for 49% of total POCs in terms of peak response) was the most abundant group for all tested off-road engines, followed by CHON (33 %) and CHOS (35 %) for diesel and HFO (heavy-fuel-oil)-fueled off-road engines. (ii) The abundance and structure of the CHON group in water extracts were different in terms of engine type and load. The relative peak response of CHON was the highest for excavator emissions in working mode, compared to the idling and moving modes. Furthermore, dinitrophenol and methyl dinitrophenol were potentially the most abundant emission species for high-rated speed excavators, while nitronaphthol and methyl nitronaphthol were more important for low-rated speed vessels. (iii) The composition and structure of the S-containing compounds were directly influenced by fuel oil characteristics (sulfur content and aromatic ring), with more condensed aromatic rings in the S-containing compounds proposed in HFO-fueled vessel emissions. More abundant aliphatic chains were inferred in diesel equipment emissions. Overall, higher fractions of condensed hydrocarbons and aromatic rings in POCs emitted from vessels using HFO cause strong optical absorption capacity. Different structures in POCs could provide a direction for qualitative and quantitative analysis of organic compounds as tracers to distinguish these emissions from diesel or HFO-fueled off-road engines

Dual-carbon isotope constraints on source apportionment of black carbon in the megacity Guangzhou of the Pearl River Delta region, China for 2018 autumn season

Black carbon (BC) aerosol negatively affects air quality and contributes to climate warming globally. However, little is known about the relative contributions of different source control measures to BC reduction owing to the lack of powerful source-diagnostic tools. We combine the fingerprints of dual-carbon isotope using an optimized Bayesian Markov chain Monte Carlo (MCMC) scheme and for the first time to study the key sources of BC in megacity Guangzhou of the Pearl River Delta (PRD) region, China in 2018 autumn season. The MCMC model-derived source apportionment of BC shows that the dominant contributor is petroleum combustion (39%), followed by coal combustion (34%) and biomass burning (27%). It should be noted that the BC source pattern is highly sensitive to the variations of air masses transported with an enhanced contribution of fossil source from the eastern area, suggesting the important impact of regional atmospheric transportation on the BC source profile in the PRD region. Also, we further found that fossil fuel combustion BC contributed 84% to the total BC reduction during 2013-2018. The response of PM2.5 concentration to the C-14-derived BC source apportionment is successfully fitted (r = 0.90) and the results predicted that it would take similar to 6 years to reach the WHO PM2.5 guideline value (10 mu g m(-3)) for the PRD region if the emission control measures keep same as they are at present. Taken together, our findings suggest that dual-carbon isotope is a powerful tool in constraining the source apportionment of BC for the evaluations of air pollution control and carbon emission measures