High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

<p>Abstract</p> <p>Background</p> <p>Knowledge of the origins, distribution, and inheritance of variation in the malaria parasite (<it>Plasmodium falciparum</it>) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenges to high-throughput sequencing technologies. We explore the viability of the Roche 454 Genome Sequencer FLX (GS FLX) high throughput sequencing technology for both whole genome sequencing and fine-resolution characterization of genetic exchange in malaria parasites.</p> <p>Results</p> <p>We present a scheme to survey recombination in the haploid stage genomes of two sibling parasite clones, using whole genome pyrosequencing that includes a sliding window approach to predict recombination breakpoints. Whole genome shotgun (WGS) sequencing generated approximately 2 million reads, with an average read length of approximately 300 bp. <it>De novo </it>assembly using a combination of WGS and 3 kb paired end libraries resulted in contigs ≤ 34 kb. More than 8,000 of the 24,599 SNP markers identified between parents were genotyped in the progeny, resulting in a marker density of approximately 1 marker/3.3 kb and allowing for the detection of previously unrecognized crossovers (COs) and many non crossover (NCO) gene conversions throughout the genome.</p> <p>Conclusions</p> <p>By sequencing the 23 Mb genomes of two haploid progeny clones derived from a genetic cross at more than 30× coverage, we captured high resolution information on COs, NCOs and genetic variation within the progeny genomes. This study is the first to resequence progeny clones to examine fine structure of COs and NCOs in malaria parasites.</p

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

Perspectives on the use of transcriptomics to advance biofuels

As a field within the energy research sector, bioenergy is continuously expanding. Although much has been achieved and the yields of both ethanol and butanol have been improved, many avenues of research to further increase these yields still remain. This review covers current research related with transcriptomics and the application of this high-throughput analytical tool to engineer both microbes and plants with the penultimate goal being better biofuel production and yields. The initial focus is given to the responses of fermentative microbes during the fermentative production of acids, such as butyric acid, and solvents, including ethanol and butanol. As plants offer the greatest natural renewable source of fermentable sugars within the form of lignocellulose, the second focus area is the transcriptional responses of microbes when exposed to plant hydrolysates and lignin-related compounds. This is of particular importance as the acid/base hydrolysis methods commonly employed to make the plant-based cellulose available for enzymatic hydrolysis to sugars also generates significant amounts of lignin-derivatives that are inhibitory to fermentative bacteria and microbes. The article then transitions to transcriptional analyses of lignin-degrading organisms, such as Phanerochaete chrysosporium, as an alternative to acid/base hydrolysis. The final portion of this article will discuss recent transcriptome analyses of plants and, in particular, the genes involved in lignin production. The rationale behind these studies is to eventually reduce the lignin content present within these plants and, consequently, the amount of inhibitors generated during the acid/base hydrolysis of the lignocelluloses. All four of these topics represent key areas where transcriptomic research is currently being conducted to identify microbial genes and their responses to products and inhibitors as well as those related with lignin degradation/formation.clos

Traffic light labelling could prevent mortality from noncommunicable diseases in Canada: A scenario modelling study

Background:&nbsp;Traffic-light labelling (TLL) is a promising front-of-pack system to help consumers make informed dietary choices. It has been shown that adopting TLL in Canada, through an optimistic scenario of avoiding, if possible, foods with red traffic lights, could effectively reduce Canadians&rsquo; intakes of energy, total fat, saturated fat, and sodium by 5%, 13%, 14% and 6%, respectively. However, the potential health impact of adopting TLL has not been determined in the North American context. Objective:&nbsp;This study modelled the potential impact of adopting TLL on mortality from noncommunicable diseases (NCDs) in Canada, due to the previously predicted improved nutrient intakes. Methods:&nbsp;Investigators used data from adults (n&nbsp;= 19,915) in the 2004 nationally representative Canadian Community Health Survey (CCHS)-Cycle 2.2. Nutrient amounts in foods consumed by CCHS respondents were profiled using the 2013 United Kingdom&rsquo;s TLL criteria. Whenever possible, foods assigned at least one red light (non-compliant foods) were replaced with similar, but compliant, foods identified from a Canadian brand-specific food database. Respondents&rsquo; nutrient intakes were calculated under the original CCHS scenario and the counterfactual TLL scenario, and entered in the Preventable Risk Integrated ModEl (PRIME) to estimate the health impact of adopting TLL. The primary outcome was the number of deaths attributable to diet-related NCDs that could be averted or delayed based on the TLL scenario compared with the baseline scenario. Results:&nbsp;PRIME estimated that 11,715 deaths (95% CI 10,500&ndash;12,865) per year due to diet-related NCDs, among which 72% are specifically related to cardiovascular diseases, could be prevented if Canadians avoided foods labelled with red traffic lights. The reduction in energy intakes would by itself save 10,490 deaths (9,312&ndash;11,592; 90%). Conclusions:&nbsp;This study, although depicting an idealistic scenario, suggests that TLL (if used to avoid red lights when possible) could be an effective population-wide intervention to improve NCD outcomes in Canada.</p