Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocene–Holocene cave deposit on Kangaroo Island, South Australia

Fossils and sediments preserved in caves are an excellent source of information for investigating impacts of past environmental changes on biodiversity. Until recently studies have relied on morphology-based palaeontological approaches, but recent advances in molecular analytical methods offer excellent potential for extracting a greater array of biological information from these sites. This study presents a thorough assessment of DNA preservation from late Pleistocene–Holocene vertebrate fossils and sediments from Kelly Hill Cave Kangaroo Island, South Australia. Using a combination of extraction techniques and sequencing technologies, ancient DNA was characterised from over 70 bones and 20 sediment samples from 15 stratigraphic layers ranging in age from >20 ka to ∼6.8 ka. A combination of primers targeting marsupial and placental mammals, reptiles and two universal plant primers were used to reveal genetic biodiversity for comparison with the mainland and with the morphological fossil record for Kelly Hill Cave. We demonstrate that Kelly Hill Cave has excellent long-term DNA preservation, back to at least 20 ka. This contrasts with the majority of Australian cave sites thus far explored for ancient DNA preservation, and highlights the great promise Kangaroo Island caves hold for yielding the hitherto-elusive DNA of extinct Australian Pleistocene species.

Public engagement in major projects : the Hong Kong experience

Public engagement is an essential process for major municipal infrastructure and construction projects as it serves to identify the interests and concerns of citizens before the planning and design are finalised and thus ensures the schemes are beneficial to all sectors of the community. However, the success of public engagement depends on a number of factors, not least the suitability of the engagement methods used, representativeness and activeness of participants, time pressure, financial constraint and so on. In Hong Kong, the community has experienced discontent with several major projects recently, suggesting the need to examine the effectiveness of its current public engagement mechanism. This paper reports the results of a series of interviews with a variety of stakeholders – indicating the need for a carefully considered public engagement plan to be established at the beginning to drive the process and more experienced people to lead and facilitate the engagement process.

Late Pleistocene stratigraphy of IODP Site U1396 and compiled chronology offshore of south and south west Montserrat, Lesser Antilles

Marine sediments around volcanic islands contain an archive of volcaniclastic deposits, which can be used to reconstruct the volcanic history of an area. Such records hold many advantages over often incomplete terrestrial datasets. This includes the potential for precise and continuous dating of intervening sediment packages, which allow a correlatable and temporally-constrained stratigraphic framework to be constructed across multiple marine sediment cores. Here, we discuss a marine record of eruptive and mass-wasting events spanning ~250 ka offshore of Montserrat, using new data from IODP Expedition 340, as well as previously collected cores. By using a combination of high-resolution oxygen isotope stratigraphy, AMS radiocarbon dating, biostratigraphy of foraminifera and calcareous nannofossils and clast componentry, we identify five major events at Soufriere Hills volcano since 250 ka. Lateral correlation of these events across sediment cores collected offshore of the south and south west of Montserrat, have improved our understanding of the timing, extent and associations between events in this area. Correlations reveal that powerful and potentially erosive density-currents travelled at least 33 km offshore, and demonstrate that marine deposits, produced by eruption-fed and mass-wasting events on volcanic islands, are heterogeneous in their spatial distribution. Thus, multiple drilling/coring sites are needed to reconstruct the full chronostratigraphy of volcanic islands. This multidisciplinary study will be vital to interpreting the chaotic records of submarine landslides at other sites drilled during Expedition 340 and provides a framework that can be applied to the stratigraphic analysis of sediments surrounding other volcanic islands.

Multi-stage collapse events in the South Soufrière Hills, Montserrat as recorded in marine sediment cores

We present new evidence for sector collapses of the South Soufrière Hills (SSH) edifice, Montserrat during the mid-Pleistocene. High-resolution geophysical data provide evidence for sector collapse, producing an approximately 1 km3 submarine collapse deposit to the south of SSH. Sedimentological and geochemical analyses of submarine deposits sampled by sediment cores suggest that they were formed by large multi-stage flank failures of the subaerial SSH edifice into the sea. This work identifies two distinct geochemical suites within the SSH succession on the basis of trace-element and Pb-isotope compositions. Volcaniclastic turbidites in the cores preserve these chemically heterogeneous rock suites. However, the subaerial chemostratigraphy is reversed within the submarine sediment cores. Sedimentological analysis suggests that the edifice failures produced high-concentration turbidites and that the collapses occurred in multiple stages, with an interval of at least 2 ka between the first and second failure. Detailed field and petrographical observations, coupled with SEM image analysis, shows that the SSH volcanic products preserve a complex record of magmatic activity. This activity consisted of episodic explosive eruptions of andesitic pumice, probably triggered by mafic magmatic pulses and followed by eruptions of poorly vesiculated basaltic scoria, and basaltic lava flows.

Design and modification of three-component randomly incorporated copolymers for high performance organic photovoltaic applications

In this study we report the molecular design, synthesis, characterization, and photovoltaic properties of a series of diketopyrrolopyrrole (DPP) and dithienothiophene (DTT) based donor-acceptor random copolymers. The six random copolymers are obtained via Stille coupling polymerization using various concentration ratios of donor to acceptor in the conjugated backbone. Bis(trimethylstannyl)thiophene was used as the bridge block to link randomly with the two comonomers 5-(bromothien-2-yl)-2,5-dialkylpyrrolo[3,4-c]pyrrole-1, 4-dione and 2,6-dibromo-3,5-dipentadecyl-dithieno[3,2-b;2′,3′-d] thiophene. The optical properties of these copolymers clearly reveal a change in the absorption band through optimization of the donor-acceptor ratio in the backbone. Additionally, the solution processability of the copolymers is modified through the attachment of different bulky alkyl chains to the lactam N-atoms of the DPP moiety. Applications of the polymers as light-harvesting and electron-donating materials in solar cells, in conjunction with PCBM as acceptor, show power conversion efficiencies (PCEs) of up to 5.02%.

Characterization and Mapping of Patterned Ground in the Saginaw Lowlands, Michigan: Possible Evidence for Late-Wisconsin Permafrost

We identified, mapped, and characterized a widespread area (gt;1,020 km2) of patterned ground in the Saginaw Lowlands of Michigan, a wet, flat plain composed of waterlain tills, lacustrine deposits, or both. The polygonal patterned ground is interpreted as a possible relict permafrost feature, formed in the Late Wisconsin when this area was proximal to the Laurentide ice sheet. Cold-air drainage off the ice sheet might have pooled in the Saginaw Lowlands, which sloped toward the ice margin, possibly creating widespread but short-lived permafrost on this glacial lake plain. The majority of the polygons occur between the Glacial Lake Warren strandline (~14.8 cal. ka) and the shoreline of Glacial Lake Elkton (~14.3 cal. ka), providing a relative age bracket for the patterned ground. Most of the polygons formed in dense, wet, silt loam soils on flat-lying sites and take the form of reticulate nets with polygon long axes of 150 to 160 m and short axes of 60 to 90 m. Interpolygon swales, often shown as dark curvilinears on aerial photographs, are typically slightly lower than are the polygon centers they bound. Some portions of these interpolygon swales are infilled with gravel-free, sandy loam sediments. The subtle morphology and sedimentological characteristics of the patterned ground in the Saginaw Lowlands suggest that thermokarst erosion, rather than ice-wedge replacement, was the dominant geomorphic process associated with the degradation of the Late-Wisconsin permafrost in the study area and, therefore, was primarily responsible for the soil patterns seen there today.

Binding mechanism of affinity ligands for purification of plasmid DNA

Plasmid DNA for therapeutic and vaccination purposes must be highly purified. The high selectivity of affinity chromatography makes it ideal for the isolation of pDNA from complex biological feed stocks. Affinity chromatography makes use of the biological function and/or individual chemical structure of the interacting molecules. However, the success of any affinity purification protocol is dependent on the availability of suitable ligands. In this study, surface plasmon resonance (SPR) based Biacore system has been employed for the detection and quantification of the binding between lac operon (lacO) sequence contained in a pDNA and synthetic peptides based on the DNA-binding domain of the lac repressor protein, lad. The equilibrium dissociation constant (K D) and association and dissociation rate constants (ka, kd) for the interaction between plasmid DNA and designed peptides were determined.

A novel population balance model for the dilute acid hydrolysis of hemicellulose

Acid hydrolysis is a popular pretreatment for removing hemicellulose from lignocelluloses in order to produce a digestible substrate for enzymatic saccharification. In this work, a novel model for the dilute acid hydrolysis of hemicellulose within sugarcane bagasse is presented and calibrated against experimental oligomer profiles. The efficacy of mathematical models as hydrolysis yield predictors and as vehicles for investigating the mechanisms of acid hydrolysis is also examined. Experimental xylose, oligomer (degree of polymerisation 2 to 6) and furfural yield profiles were obtained for bagasse under dilute acid hydrolysis conditions at temperatures ranging from 110C to 170C. Population balance kinetics, diffusion and porosity evolution were incorporated into a mathematical model of the acid hydrolysis of sugarcane bagasse. This model was able to produce a good fit to experimental xylose yield data with only three unknown kinetic parameters ka, kb and kd. However, fitting this same model to an expanded data set of oligomeric and furfural yield profiles did not successfully reproduce the experimental results. It was found that a ``hard-to-hydrolyse'' parameter, $\alpha$, was required in the model to ensure reproducibility of the experimental oligomer profiles at 110C, 125C and 140C. The parameters obtained through the fitting exercises at lower temperatures were able to be used to predict the oligomer profiles at 155C and 170C with promising results. The interpretation of kinetic parameters obtained by fitting a model to only a single set of data may be ambiguous. Although these parameters may correctly reproduce the data, they may not be indicative of the actual rate parameters, unless some care has been taken to ensure that the model describes the true mechanisms of acid hydrolysis. It is possible to challenge the robustness of the model by expanding the experimental data set and hence limiting the parameter space for the fitting parameters. The novel combination of ``hard-to-hydrolyse'' and population balance dynamics in the model presented here appears to stand up to such rigorous fitting constraints.

Mechanisms underlying the effect of acupuncture on cognitive improvement: A systematic review of animal studies

Acupuncture has been reported to be beneficial in treating cognitive impairment in various pathological conditions. This review describes the effort to understand the signaling pathways that underlie the acupunctural therapeutic effect on cognitive function. We searched the literature in 12 electronic databases from their inception to November 2013, with full text available and language limited to English. Twenty-three studies were identified under the selection criteria. All recruited animal studies demonstrate a significant positive effect of acupuncture on cognitive impairment. Findings suggest acupuncture may improve cognitive function through modulation of signaling pathways involved in neuronal survival and function, specifically, through promoting cholinergic neural transmission, facilitating dopaminergic synaptic transmission, enhancing neurotrophin signaling, suppressing oxidative stress, attenuating apoptosis, regulating glycometabolic enzymes and reducing microglial activation. However, the quality of reviewed studies has room for improvement. Further high-quality animal studies with randomization, blinding and estimation of sample size are needed to strengthen the recognition of group differences.

A preliminary OSL chronology for coastal dunes on Moreton island, Queensland, Australia – Marginal deposits of A large-scale quaternary shelf sediment system

Moreton Island and several other large siliceous sand dune islands and mainland barrier deposits in SE Queensland represent the distal, onshore component of an extensive Quaternary continental shelf sediment system. This sediment has been transported up to 1000 km along the coast and shelf of SE Australia over multiple glacioeustatic sea-level cycles. Stratigraphic relationships and a preliminary Optically Stimulated Luminance (OSL) chronology for Moreton Island indicate a middle Pleistocene age for the large majority of the deposit. Dune units exposed in the centre of the island and on the east coast have OSL ages that indicate deposition occurred between approximately 540 ka and 350 ka BP, and at around 96±10 ka BP. Much of the southern half of the island has a veneer of much younger sediment, with OSL ages of 0.90±0.11 ka, 1.28±0.16 ka, 5.75±0.53 ka and <0.45 ka BP. The younger deposits were partially derived from the reworking of the upper leached zone of the much older dunes. A large parabolic dune at the northern end of the island, OSL age of 9.90±1.0 ka BP, and palaeosol exposures that extend below present sea level suggest the Pleistocene dunes were sourced from shorelines positioned several to tens of metres lower than, and up to few kilometres seaward of the present shoreline. Given the lower gradient of the inner shelf a few km seaward of the island, it seems likely that periods of intermediate sea level (e.g. ~20 m below present) produced strongly positive onshore sediment budgets and the mobilisation of dunes inland to form much of what now comprises Moreton Island. The new OSL ages and comprehensive OSL chronology for the Cooloola deposit, 100 km north of Moreton Island, indicate that the bulk of the coastal dune deposits in SE Queensland were emplaced between approximately 540 ka BP and prior to the Last Interglacial. This chronostratigraphic information improves our fundamental understanding of long-term sediment transport and accumulation on large-scale continental shelf sediment systems.

Understanding past climate variation and environmental change for the future of an iconic landscape – K'gari Fraser Island, Queensland, Australia

The unique combination of landscapes and processes that are present and operate on Fraser Island (K'gari) create a dynamic setting that is capable of recording past environmental events, climate variations and former landscapes. Likewise, its geographic position makes Fraser Island sensitive to those events and processes. Based on optically stimulated luminescence dating, the records archived within the world's largest sand island span a period that has the potential to exceed 750 ka and contain specific records that are of extremely high resolution over the past 40,000 years. This is due to the geographic position of Fraser Island, which lies in the coastal subtropical region of Queensland Australia. Fraser Island is exposed to the open ocean currents of the Coral Sea on the east coast and the waters of Hervey Bay on its western margin and is positioned to receive moisture from the Indo-Australian monsoon, southeast trade winds and experiences occasional tropical and ex-tropical cyclones. We review literature that presents the current level of understanding of sea level change, ecological variation and environmental change on Fraser Island. The previous works illustrate the importance of Fraser Island and may link processes, environments and climates on Fraser Island with global records.

Large variations in the Holocene marine radiocarbon reservoir effect reflect ocean circulation and climatic changes

Accurate radiocarbon dating of marine samples requires knowledge of the marine radiocarbon reservoir effect. This effect for a particular site/region is generally assumed constant through time when calibrating marine 14C ages. However, recent studies have shown large temporal variations of several hundred to a couple of thousand years in this effect for a number of regions during the late Quaternary and Holocene. Here we report marine radiocarbon reservoir correction (ΔRΔR) for Heron Reef and Moreton Bay in southwestern (SW) Pacific for the last 8 ka derived from 14C analysis of 230Th-dated corals. Most of our ΔRΔR for the last ∼5.4 ka agree well with their modern value, but large ΔRΔR variability of ∼410 yr (from trough to peak) with possible decadal/centennial fluctuations is evident for the period ∼5.4–8 ka. The latter time interval also has significant variations with similar features in previously published ΔRΔR values for other sites in the Pacific, including southern Peru–northern Chile in southeastern (SE) Pacific, the South China Sea, Vanuatu and Papua New Guinea, with the largest magnitude of ∼920 yr from SE Pacific. The mechanisms for these large ΔRΔR variations across the Pacific during the mid-Holocene are complex processes involving (1) changes in the quantity and 14C content of upwelled waters in tropical east Pacific (TEP) (frequency and intensity of ocean upwelling in the TEP, and contribution of Subantarctic Mode Water to the upwelled waters, which is influenced by the intensity and position of southern westerly winds), and (2) variations in ocean circulation associated with climate change (La Niña/El Niño conditions, intensity of easterly trade winds, positions of the Intertropical Convergence Zone and the South Pacific Convergence Zone), which control the spreading of the older upwelled surface waters in the TEP to the western sites. Our results imply the need for employing temporal changes in ΔRΔR values, instead of constant (modern) values, for age calibration of Holocene marine samples not only for the SW Pacific sites but also for other tropical and subtropical sites in the Pacific.

VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.