We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, ...Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph-based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce de novo genome sequence exceeding 99.999% accuracy.
Full text
Available for:
IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Plastic is incredibly abundant in marine environments but little is known about its effects on benthic microbiota and biogeochemical cycling. This study reports the shotgun metagenomic sequencing of ...biofilms fouling plastic and bioplastic microcosms staged at the sediment-water interface of a coastal lagoon. Community composition analysis revealed that plastic biofilms were indistinguishable in comparison to a ceramic biofilm control. By contrast, bioplastic biofilms were distinct and dominated by sulfate-reducing microorganisms (SRM). Analysis of bioplastic gene pools revealed the enrichment of esterases, depolymerases, adenylyl sulfate reductases (
), and dissimilatory sulfite reductases (
). The nearly 20-fold enrichment of a phylogenetically diverse polyhydroxybutyrate (PHB) depolymerase suggests this gene was distributed across a mixed microbial assemblage. The metagenomic reconstruction of genomes identified novel species of
, and
among the abundant SRM, and these genomes contained genes integral to both bioplastic degradation and sulfate reduction. Findings indicate that bioplastic promoted a rapid and significant shift in benthic microbial diversity and gene pools, selecting for microbes that participate in bioplastic degradation and sulfate reduction. If plastic pollution is traded for bioplastic pollution and sedimentary inputs are large, the microbial response could unintentionally affect benthic biogeochemical activities through the stimulation of sulfate reducers.
Medium- to long-range forecasts often guide reservoir release decisions to support water management objectives, including mitigating flood and drought risks. While there is a burgeoning field of ...science targeted at improving forecast products and associated decision support models, data describing how and when forecasts are applied in practice remain undeveloped. This lack of knowledge may prevent hydrological modelers from developing accurate reservoir release schemes for large-scale, distributed hydrology models that are increasingly used to assess the vulnerabilities of large regions to hydrological stress. We address this issue by estimating seasonally varying, regulated inflow forecast horizons used in the operations of more than 300 dams throughout the conterminous United States (CONUS). For each dam, we take actual forward observed inflows (perfect foresight) as a proxy for forecasted flows available to the operator and then identify for each week of the year the forward horizon that best explains the release decisions taken. Resulting “horizon curves” specify for each dam the inferred inflow forecast horizon as a function of the week of the water year. These curves are analyzed for strength of evidence for contribution of medium- to long-range forecasts in decision making. We use random forest classification to estimate that approximately 80 % of large dams and reservoirs in the US (1553±50 out of 1927 dams with at least 10 Mm3 storage capacity) adopt medium- to long-range inflow forecasts to inform release decisions during at least part of the water year. Long-range forecast horizons (more than 6 weeks ahead) are detected in the operations of reservoirs located in high-elevation regions of the western US, where snowpack information likely guides the release. A simulation exercise conducted on four key western US reservoirs indicates that forecast-informed models of reservoir operations may outperform models that neglect the horizon curve – including during flood and drought conditions.
Qualitative research design can be complicated depending upon the level of experience a researcher may have with a particular type of methodology. As researchers, many aspire to grow and expand their ...knowledge and experiences with qualitative design in order to better utilize diversified research paradigms for future investigations. One of the more popular areas of interest in qualitative research design is that of the interview protocol. Interviews provide in-depth information pertaining to participants' experiences and viewpoints of a particular topic. Often times, interviews are coupled with other forms of data collection in order to provide the researcher with a well-rounded collection of information for analyses. This paper explores the effective ways to conduct in-depth, qualitative interviews for novice investigators by employing a step-by-step process for implementation. Key Words: Informal Conversational Interview, General Interview Guide, and Open-Ended Interviews
This study uses an advanced airflow, energy and humidity modelling tool to evaluate the potential for residential mechanical pre-cooling of building thermal mass to shift electricity loads away from ...the peak electricity demand period. The focus of this study is residential buildings with low thermal mass, such as timber-frame houses typical to the US. Simulations were performed for homes in 12 US DOE climate zones. The results show that the effectiveness of mechanical pre-cooling is highly dependent on climate zone and the selected pre-cooling strategy. The expected energy trade-off between cooling peak energy savings and increased off-peak energy use is also shown. The best pre-cooling results (more than 75% energy use shifted away from peak while minimising the total energy penalty) for most climates were obtained using a medium (5 h) pre-cooling time window with a shallow (23.3 °C) pre-cooling set point temperature. All of the pre-cooling strategies investigated caused the annual cooling energy demand of the simulated buildings to increase. Additionally, all of the pre-cooling strategies shifted at least 50% of the on-peak cooling loads away from a peak period window of 4pm–8pm in all climate zones.
•Residential pre-cooling strategies were tested using computer simulation.•Building thermal mass was mechanically pre-cooled using the air conditioner.•Between 50% and 99% of annual peak cooling electricity can be shifted off-peak.•Pre-cooling always increased the total annual cooling electricity use.•The pre-cooling strategies had no significant impact on occupant thermal comfort.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Considerable research effort has recently been directed at improving and operationalising ensemble seasonal streamflow forecasts. Whilst this creates new opportunities for improving the performance ...of water resources systems, there may also be associated risks. Here, we explore these potential risks by examining the sensitivity of forecast value (improvement in system performance brought about by adopting forecasts) to changes in the forecast skill for a range of hypothetical reservoir designs with contrasting operating objectives. Forecast-informed operations are simulated using rolling horizon, adaptive control and then benchmarked against optimised control rules to assess performance improvements. Results show that there exists a strong relationship between forecast skill and value for systems operated to maintain a target water level. But this relationship breaks down when the reservoir is operated to satisfy a target demand for water; good forecast accuracy does not necessarily translate into performance improvement. We show that the primary cause of this behaviour is the buffering role played by storage in water supply reservoirs, which renders the forecast superfluous for long periods of the operation. System performance depends primarily on forecast accuracy when critical decisions are made – namely during severe drought. As it is not possible to know in advance if a forecast will perform well at such moments, we advocate measuring the consistency of forecast performance, through bootstrap resampling, to indicate potential usefulness in storage operations. Our results highlight the need for sensitivity assessment in value-of-forecast studies involving reservoirs with supply objectives.
Drinking water supplies of cities are exposed to potential contamination arising from land use and other anthropogenic activities in local and distal source watersheds. Because water quality sampling ...surveys are often piecemeal, regionally inconsistent, and incomplete with respect to unregulated contaminants, the United States lacks a detailed comparison of potential source water contamination across all of its large cities. Here we combine national-scale geospatial datasets with hydrologic simulations to compute two metrics representing potential contamination of water supplies from point and nonpoint sources for over a hundred U.S. cities. We reveal enormous diversity in anthropogenic activities across watersheds with corresponding disparities in the potential contamination of drinking water supplies to cities. Approximately 5% of large cities rely on water that is composed primarily of runoff from non-pristine lands (e.g., agriculture, residential, industrial), while four-fifths of all large cities that withdraw surface water are exposed to treated wastewater in their supplies.
Fusarium wilt of banana (also known as Panama disease) has been a problem in Australia since 1874. Race 1 of the pathogen (
f. sp.
) is responsible for damage to 'Lady Finger' (AAB, Pome subgroup) ...and other less widely grown cultivars such as 'Ducasse' (Pisang Awak, ABB). Subtropical Race 4 (STR4) also affects these cultivars as well as Cavendish cultivars (AAA) in southern Queensland and northern New South Wales where cold temperature predisposition is involved. Tropical Race 4 (TR4) has led to the demise of the Cavendish industry in the Northern Territory, and its presence was confirmed in a North Queensland plantation in 2015, which warranted destruction of all banana plants on the property; as of this writing (April 2019), TR4 has spread to two adjacent properties. This review, which was commissioned by Biosecurity Queensland in response to the 2015 TR4 outbreak, considers the key epidemiological factors associated with the onset of a Fusarium wilt epidemic. Resistance to TR4, which is mediated by events following entry by the pathogen into the xylem, is not present in any commercially acceptable banana cultivar. Also, there is no effective chemical agent that can be used to manage the disease. Besides prevention, very early recognition and rapid containment of a disease outbreak are necessary to prevent epidemic development. A good understanding of the key factors responsible for disease development is required when devising practical protocols for the destruction of infected plants, treatment of surrounding infested soil, and reduction of inoculum in plant residues and soil.
Human immunodeficiency virus type 1 (HIV-1) infection persists despite years of antiretroviral therapy (ART). To remove the stigma and burden of chronic infection, approaches to eradicate or cure HIV ...infection are desired. Attempts to augment ART with therapies that reverse viral latency, paired with immunotherapies to clear infection, have advanced into the clinic, but the field is still in its infancy. We review foundational studies and highlight new insights in HIV cure research. Together with advances in ART delivery and HIV prevention strategies, future therapies that clear HIV infection may relieve society of the affliction of the HIV pandemic.
Margolis and colleagues review progress and prospects toward developing a true cure for HIV-1 infection, focusing on the biological underpinnings of the “kick and kill” approach to curing HIV-1 infection, which couples reactivation of the latent, integrated provirus with immunotherapies to recognize and kill infected cells.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The abundance of long noncoding RNAs (lncRNAs) and their wide range of functional roles in human cells are fast becoming realized. Importantly, lncRNAs have been identified as epigenetic modulators ...and consequently play a pivotal role in the regulation of gene expression. A human immunodeficiency virus-encoded antisense RNA transcript has recently been reported and we sought to characterize this RNA and determine its potential role in viral transcription regulation. The intrinsic properties of this human immunodeficiency virus-expressed lncRNA were characterized and the data presented here suggest that it functions as an epigenetic brake to modulate viral transcription. Suppression of this long antisense transcript with small single-stranded antisense RNAs resulted in the activation of viral gene expression. This lncRNA was found to localize to the 5′ long-term repeats (LTR) and to usurp components of endogenous cellular pathways that are involved in lncRNA directed epigenetic gene silencing. Collectively, we find that this viral expressed antisense lncRNA is involved in modulating human immunodeficiency virus gene expression and that this regulatory effect is due to an alteration in the epigenetic landscape at the viral promoter.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
PDF
