A quantitative assessment of distributions and sources of tropospheric halocarbons measured in Singapore.

This work reports the first ground-based atmospheric measurements of 26 halocarbons in Singapore, an urban-industrial city-state in Southeast (SE) Asia. A total of 166 whole air canister samples collected during two intensive 7 Southeast Asian Studies (7SEAS) campaigns (August-October 2011 and 2012) were analyzed for C1-C2 halocarbons using gas chromatography-electron capture/mass spectrometric detection. The halocarbon dataset was supplemented with measurements of selected non-methane hydrocarbons (NMHCs), C1-C5 alkyl nitrates, sulfur gases and carbon monoxide to better understand sources and atmospheric processes. The median observed atmospheric mixing ratios of CFCs, halons, CCl4 and CH3CCl3 were close to global tropospheric background levels, with enhancements in the 1-17% range. This provided the first measurement evidence from SE Asia of the effectiveness of Montreal Protocol and related national-scale regulations instituted in the 1990s to phase-out ozone depleting substances (ODS). First- and second-generation CFC replacements (HCFCs and HFCs) dominated the atmospheric halocarbon burden with HFC-134a, HCFC-22 and HCFC-141b exhibiting enhancements of 39-67%. By combining near-source measurements in Indonesia with receptor data in Singapore, regionally transported peat-forest burning smoke was found to impact levels of several NMHCs (ethane, ethyne, benzene, and propane) and short-lived halocarbons (CH3I, CH3Cl, and CH3Br) in a subset of the receptor samples. The strong signatures of these species near peat-forest fires were potentially affected by atmospheric dilution/mixing during transport and by mixing with substantial urban/regional backgrounds at the receptor. Quantitative source apportionment was carried out using positive matrix factorization (PMF), which identified industrial emissions related to refrigeration, foam blowing, and solvent use in chemical, pharmaceutical and electronics industries as the major source of halocarbons (34%) in Singapore. This was followed by marine and terrestrial biogenic activity (28%), residual levels of ODS from pre-Montreal Protocol operations (16%), seasonal incidences of peat-forest smoke (13%), and fumigation related to quarantine and pre-shipment (QPS) applications (7%)

Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome

<p>Abstract</p> <p>Background</p> <p>Infection of cattle with <it>Mycobacterium avium </it>subspecies <it>paratuberculosis </it>(<it>M. ap</it>) causes severe economic losses to the dairy industry in the USA and worldwide. In an effort to better examine diversity among <it>M. ap </it>strains, we used optical mapping to profile genomic variations between strains of <it>M. ap </it>K-10 (sequenced strain) and <it>M. ap </it>ATCC 19698 (type strain).</p> <p>Results</p> <p>The assembled physical restriction map of <it>M. ap </it>ATCC 19698 showed a genome size of 4,839 kb compared to the sequenced K-10 genome of 4,830 kb. Interestingly, alignment of the optical map of the <it>M. ap </it>ATCC 19698 genome to the complete <it>M. ap </it>K-10 genome sequence revealed a 648-kb inversion around the origin of replication. However, Southern blotting, PCR amplification and sequencing analyses of the inverted region revealed that the genome of <it>M. ap </it>K-10 differs from the published sequence in the region starting from 4,197,080 bp to 11,150 bp, spanning the origin of replication. Additionally, two new copies of the coding sequences > 99.8% were identified, identical to the MAP0849c and MAP0850c genes located immediately downstream of the MAP3758c gene.</p> <p>Conclusion</p> <p>The optical map of <it>M. ap </it>ATCC 19698 clearly indicated the miss-assembly of the sequenced genome of <it>M. ap </it>K-10. Moreover, it identified 2 new genes in <it>M. ap </it>K-10 genome. This analysis strongly advocates for the utility of physical mapping protocols to complement genome sequencing projects.</p

Recurrent slope failure enhancing source rock burial depth and seal unit competence in the Pearl River Mouth Basin, offshore South China Sea

High-quality 3-D seismic data are used to assess the significance of mass-transport deposits (MTDs) to the evolution of the Pearl River Mouth Basin (South China Sea). Basal shear surfaces and lateral margins of seven recurrent MTDs are mapped to reveal a general NE-SW transport direction throughout the Late Miocene-Quaternary. A key result of our analysis is the perceived relationship between the recurrence of slope instability in the study area and the Dongsha Tectonic Event. Using borehole data to constrain the ages of interpreted MTDs, we show that tectonic uplift in the northern South China Sea led to slope oversteepening in the Late Miocene (between 10.5 Ma and 5.5 Ma), preconditioning it to fail recurrently for more than 10 Ma. Interpreted MTDs are shown to enhance burial depths of source and reservoir units, and improve seal competence in lower-slope areas. Conversely, upper slope regions record important erosion and reduced sealing capacity in Late Cenozoic strata. As a result, we postulate that the thickness variations imposed by MTDs on Late Miocene-Quaternary strata have important implications to petroleum plays in the South China Sea

Prolonged post-rift magmatism on highly extended crust of divergent continental margins (Baiyun Sag, South China Sea)

Three-dimensional (3D) seismic, borehole and geochemical data reveal a prolonged phase of post-rift magmatism on highly extended crust of the Baiyun Sag, South China Sea. Two volcanic complexes are identified and described in the context of continental rifting and diachronous continental breakup of the South China Sea. Biostratigraphic data from exploration wells BY7-1 and BY2, complemented by K–Ar datings from core samples, confirm that magmatic activity in the Baiyun Sag occurred in two main stages: (1) a first episode at the base of the Miocene (23.8 Ma); and (2) a second episode occurring at the end of the Early Miocene (17.6 Ma). The relative location of volcanic complexes in the Baiyun Sag, and their stratigraphic position, reveals prolonged magmatism inboard of the ocean–continent transition zone during continental breakup. We suggest that magmatism in the Baiyun Sag reflects progressive continental breakup in the South China Sea, with the last volcanic episode marking the end of a breakup sequence representing the early post-rift tectonic events associated with the continental breakup process. Seismic and borehole data from this breakup sequence records diachronous magma emplacement and complex changes in depositional environments during continental breakup

Distribution patterns of dinoflagellate communities along the Songhua River

Background Dinoflagellates have the potential to pose severe ecological and economic damages to aquatic ecosystems. It is therefore largely needed to understand the causes and consequences of distribution patterns of dinoflagellate communities in order to manage potential environmental problems. However, a majority of studies have focused on marine ecosystems, while the geographical distribution patterns of dinoflagellate communities and associated determinants in freshwater ecosystems remain unexplored, particularly in running water ecosystems such as rivers and streams. Methods Here we utilized multiple linear regression analysis and combined information on species composition recovered by high-throughput sequencing and spatial and environmental variables to analyze the distribution patterns of dinoflagellate communities along the Songhua River. Results After high-throughput sequencing, a total of 490 operational taxonomic units (OTUs) were assigned to dinoflagellates, covering seven orders, 13 families and 22 genera. Although the sample sites were grouped into three distinctive clusters with significant difference (p  0.05). Among all 24 environmental factors, two environmental variables, including NO3-N and total dissolved solids (TDS), were selected as the significantly influential factors (p < 0.05) on the distribution patterns of dinoflagellate communities based on forward selection. The redundancy analysis (RDA) model showed that only a small proportion of community variation (6.1%) could be explained by both environmental (NO3-N and TDS) and dispersal predictors (watercourse distance) along the River. Variance partitioning revealed a larger contribution of local environmental factors (5.85%) than dispersal (0.50%) to the total variation of dinoflagellate communities. Discussion Our findings indicated that in addition to the two quantifiable processes in this study (species sorting and dispersal), more unquantifiable stochastic processes such as temporal extinction and colonization events due to rainfall may be responsible for the observed geographical distribution of the dinoflagellate community along the Songhua River. Results obtained in this study suggested that deeper investigations covering different seasons are needed to understand the causes and consequences of geographical distribution patterns of dinoflagellate biodiversity in river ecosystems

Change detection of land use and land cover in an urban region with SPOT-5 images and partial Lanczos extreme learning machine

Satellite remote sensing technology and the science associated with evaluation of land use and land cover (LULC) in an urban region makes use of the wide range images and algorithms. Improved land management capacity is critically dependent on real-time or near real-time monitoring of land-use/land cover change (LUCC) to the extent to which solutions to a whole host of urban/rural interface development issues may be well managed promptly. Yet previous processing with LULC methods is often time-consuming, laborious, and tedious making the outputs unavailable within the required time window. This paper presents a new image classification approach based on a novel neural computing technique that is applied to identify the LULC patterns in a fast growing urban region with the aid of 2.5-meter resolution SPOT-5 image products. The classifier was constructed based on the partial Lanczos extreme learning machine (PL-ELM), which is a novel machine learning algorithm with fast learning speed and outstanding generalization performance. Since some different classes of LULC may be linked with similar spectral characteristics, texture features and vegetation indexes were extracted and included during the classification process to enhance the discernability. A validation procedure based on ground truth data and comparisons with some classic classifiers prove the credibility of the proposed PL-ELM classification approach in terms of the classification accuracy as well as the processing speed. A case study in Dalian Development Area (DDA) with the aid of the SPOT-5 satellite images collected in the year of 2003 and 2007 and PL-ELM fully supports the monitoring needs and aids in the rapid change detection with respect to both urban expansion and coastal land reclamations

Recurrent failure of the continental slope as a key factor controlling reservoir potential in the South China Sea (Qiongdongnan Basin, South Hainan Island)

High-resolution multi-beam bathymetry, 3D and 2D seismic reflection profiles from the South China Sea are used to investigate the morphology, characteristics, origin and implications to petroleum systems of recurrent slope failure in the Qiongdongnan Basin, northern South China Sea. Seven Late Miocene-Holocene mass-transport deposits (MTDs) and numerous submarine canyons were identified on the continental slope and rise. Providing new insights on the evolution of an enigmatic region of the South China Sea, this paper defends that the interpreted MTDs were caused by a combination of high sedimentation rates and local tectonic uplift. By comparing the stratigraphy of the study area with local sea-level curves, we show that a significant portion of shelf-edge deposits effectively bypassed most of the continental slope during the Miocene-Quaternary to accumulate as large MTDs on its lower part (i.e. on the 'basin-floor'), independently of sea-level changes. Our work has implications to the current sequence stratigraphic models for continental margins, and sheds new light on the reservoir potential of Miocene units in the South China Sea. Hence, regions where base-of-slope fans are expected to occur are, in the study area, occupied by large-scale recurrent MTDs sourced from the shelf edge. Stratigraphically, recurrent slope instability resulted: a) in abrupt episodes of accommodation space creation on the shelf-edge, b) on a moderate reduction in accommodation space at the base of the continental slope, and c) in a complete separation between shelf and distal slope depositional systems, with most stratigraphic markers on 3D seismic data being diachronous across the continental margin. As MTDs also comprise the bulk of channel-fill deposits in large submarine canyons, we propose that the reservoir potential of channel-fill deposits in the South China Sea is closely dependent on the nature of the sediment (i.e. net-to-gross ratio) eroded and transported by these same MTDs

The Baiyun Slide Complex, South China Sea: a modern example of slope instability controlling submarine-channel incision on continental slopes

The Baiyun Slide Complex is one of the largest submarine landslides on the northern margin of the South China Sea. Newly acquired high-resolution bathymetric data, 2D and 3D seismic data permitted the systematic investigation of the Baiyun Slide Complex in terms of its seafloor morphology and associated sedimentary processes. The headwall region of the Baiyun Slide Complex, located at a water depth between 1000 m and 1700 m, is U-shaped and opens towards the east. It was efficiently and almost completely evacuated, generating pronounced headwall and sidewall scarps. Submarine channels, sediment waves, migrating channels, sediment drifts and moats are observed within and around the headwall region, illustrating the effects of both downslope and along-slope sedimentary processes. Submarine channels are 16–37 km-long 800-1500 m-wide, and 20 to 50 m-deep. As a modern example of the interplay between slope instability and subsequent incision, submarine channels were generated after the formation of the Baiyun Slide scar to suggest intensified downslope sedimentary processes after the slope collapsed. The initiation and formation of these submarine channels result from the evacuation of the Baiyun Slide scar, which provided the necessary space of the continental slope to accommodate subsequent turbidity and mass wasting flows. Our results are an important example of how submarine landslides can influence erosional and depositional processes on continental margins

Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association

<p>Abstract</p> <p>Background</p> <p>The genome of <it>Mycobacterium avium </it>subspecies <it>paratuberculosis </it>(<it>MAP</it>) is remarkably homogeneous among the genomes of bovine, human and wildlife isolates. However, previous work in our laboratories with the bovine K-10 strain has revealed substantial differences compared to sheep isolates. To systematically characterize all genomic differences that may be associated with the specific hosts, we sequenced the genomes of three U.S. sheep isolates and also obtained an optical map.</p> <p>Results</p> <p>Our analysis of one of the isolates, <it>MAP </it>S397, revealed a genome 4.8 Mb in size with 4,700 open reading frames (ORFs). Comparative analysis of the <it>MAP </it>S397 isolate showed it acquired approximately 10 large sequence regions that are shared with the human <it>M. avium </it>subsp. <it>hominissuis </it>strain 104 and lost 2 large regions that are present in the bovine strain. In addition, optical mapping defined the presence of 7 large inversions between the bovine and ovine genomes (~ 2.36 Mb). Whole-genome sequencing of 2 additional sheep strains of <it>MAP </it>(JTC1074 and JTC7565) further confirmed genomic homogeneity of the sheep isolates despite the presence of polymorphisms on the nucleotide level.</p> <p>Conclusions</p> <p>Comparative sequence analysis employed here provided a better understanding of the host association, evolution of members of the <it>M. avium </it>complex and could help in deciphering the phenotypic differences observed among sheep and cattle strains of <it>MAP</it>. A similar approach based on whole-genome sequencing combined with optical mapping could be employed to examine closely related pathogens. We propose an evolutionary scenario for <it>M. avium </it>complex strains based on these genome sequences.</p

Incision of submarine channels over pockmark trains in the South China Sea

The genesis of submarine channels is often controlled by gravity flows, but channels can also be formed by oceanographic processes. Using multibeam bathymetry and two-dimensional seismic data from the western South China Sea, this study reveals how pockmarks can ultimately form channels under the effect of bottom currents and gravity-driven sedimentary processes. We demonstrate that alongslope and across-slope channels were initiated by pockmark trains on the seafloor. Discrete pockmarks were elongated due to the erosion of gravity-driven sedimentary processes and bottom currents, and later coalesced to form immature channels with irregular thalwegs. These gradually evolved into mature channels with continuous overbanks and smooth thalwegs. Submarine channel evolution was significantly influenced by seafloor topography since the Late Miocene. The evolutionary model documented here is a key to understanding how channels are formed in deep-water environments