Comparison of species classification models of mass spectrometry data : kernel discriminant analysis vs. random forest : a case study of Afrormosia (Pericopsis elata (Harms) Meeuwen)

Rationale: The genus Pericopsis includes four tree species of which only Pericopsis elata (Harms) Meeuwen is of commercial interest. Enforcement officers might have difficulties discerning this CITES-listed species from some other tropical African timber species. Therefore, we tested several methods to separate and identify these species rapidly in order to enable customs officials to uncover illegal trade. In this study, two classification methods using Direct Analysis in Real Time (DART) ionization coupled with Time-of-Flight Mass Spectrometry (DART-TOFMS) data to discern between several species are presented. Methods: Metabolome profiles were collected using DART ionization coupled with TOFMS analysis of heartwood specimens of all four Pericopsis species and Haplormosia monophylla (Harms) Harms, Dalbergia melanoxylon Guill. & Perr. Harms, and Milicia excelsa (Welw.) C.C. Berg. In total, 95 specimens were analysed and the spectra evaluated. Kernel Discriminant Analysis (KDA) and Random Forest classification were used to discern the species. Results: DART-TOFMS spectra obtained from wood slivers and post-processing analysis using KDA and Random Forest classification separated Pericopsis elata from the other Pericopsis taxa and its lookalike timbers Haplormosia monophylla, Milicia excelsa, and Dalbergia melanoxylon. Only 50 ions were needed to achieve the highest accuracy. Conclusions: DART-TOFMS spectra of the taxa were reproducible and the results of the chemometric analysis provided comparable accuracy. Haplormosia monophylla was visually distinguished based on the heatmap and was excluded from further analysis. Both classification methods, KDA and Random Forest, were capable of distinguishing Pericopsis elata from the other Pericopsis taxa, Milicia excelsa, and Dalbergia melanoxylon, timbers that are commonly traded

Repetitive, Marker-Free, Site-Specific Integration as a Novel Tool for Multiple Chromosomal Integration of DNA

We present a tool for repetitive, marker-free, site-specific integration in Lactococcus lactis, in which a nonreplicating plasmid vector (pKV6) carrying a phage attachment site (attP) can be integrated into a bacterial attachment site (attB). The novelty of the tool described here is the inclusion of a minimal bacterial attachment site (attB(min)), two mutated loxP sequences (lox66 and lox71) allowing for removal of undesirable vector elements (antibiotic resistance marker), and a counterselection marker (oroP) for selection of loxP recombination on the pKV6 vector. When transformed into L. lactis expressing the phage TP901-1 integrase, pKV6 integrates with high frequency into the chromosome, where it is flanked by attL and attR hybrid attachment sites. After expression of Cre recombinase from a plasmid that is not able to replicate in L. lactis, loxP recombinants can be selected for by using 5-fluoroorotic acid. The introduced attB(min) site can subsequently be used for a second round of integration. To examine if attP recombination was specific to the attB site, integration was performed in strains containing the attB, attL, and attR sites or the attL and attR sites only. Only attP-attB recombination was observed when all three sites were present. In the absence of the attB site, a low frequency of attP-attL recombination was observed. To demonstrate the functionality of the system, the xylose utilization genes (xylABR and xylT) from L. lactis strain KF147 were integrated into the chromosome of L. lactis strain MG1363 in two steps

Six versus 12 months' adjuvant trastuzumab in patients with HER2-positive early breast cancer: the PERSEPHONE non-inferiority RCT

Background The addition of adjuvant trastuzumab to chemotherapy has significantly improved outcomes in human epidermal growth factor receptor 2 (HER2) positive early, potentially curable breast cancer. Twelve months’ trastuzumab tested in the registration trials was adopted for standard adjuvant treatment in 2006. Subsequently similar outcomes were demonstrated using 9 weeks trastuzumab. Shorter durations were therefore tested for non-inferiority. Objectives To establish whether 6 months’ adjuvant trastuzumab is non-inferior to 12 months in HER2-positive early breast cancer using a primary endpoint of 4-year disease-free-survival (DFS). Design Phase III randomised, controlled, non-inferiority trial. Setting 152 NHS Hospitals. Participants 4088 patients with HER2-positive early breast cancer planned to receive both chemotherapy and trastuzumab. Intervention Randomisation (1:1) between six months’ or twelve months’ trastuzumab. Main outcomes Primary endpoint was DFS four years after diagnosis. Secondary endpoints were overall survival (OS), cost effectiveness, and cardiac function during trastuzumab. Assuming a 4-year DFS rate of 80% with 12 months, 4000 patients were required to demonstrate non-inferiority of 6-months (5% 1-sided significance, 85% power), defining the non-inferiority limit as no worse than 3% below the standard arm. Costs and quality-adjusted life years (QALYs) were estimated by within-trial analysis and a lifetime decision-analytic model. Results Between 4th October 2007 and 31st July 2015, 2045 patients were randomised to 12-months’ trastuzumab and 2043 to 6-months. Sixty-nine percent had ER-positive disease; 90% received anthracyclines (49% with taxanes; 41% without taxanes); 10% received taxanes without anthracyclines; 54% had trastuzumab sequentially after chemotherapy; 85% received adjuvant chemotherapy (58% were node negative). At 6.1 years median follow-up with 389 (10%) deaths, and 566 (14%) DFS events, 4-year DFS rates for the 4088 patients were 89.5% (95% CI, 88.1-90.8) in the 6-month group and 90.3% (95% CI 88.9- 91.5) in the 12-month group (Hazard Ratio 1.10; 90% CI 0.96–1.26, non-inferiority p=0.01), demonstrating non-inferiority of 6-months’ trastuzumab. Congruent results were found for OS (non-inferiority p=0.0003), and landmark analyses 6 months from starting trastuzumab (non-inferiority p=0.03 (DFS) and p=0.006 (OS)). 6-months’ trastuzumab resulted in fewer patients reporting adverse events of severe grade (365/1929 (19%) versus 460/1935 (24%) 12-month patients, p=0.0003) or stopping early because of cardiotoxicity (61/1977 (3%) versus 146/1941 (8%) 12-month patients, p<0.0001). Health economic analysis showed significantly lower lifetime costs and similar lifetime QALYs, and thus a high probability that 6 months is cost-effective compared to 12 months. Patient reported experiences on the trial highlighted fatigue, and aches and pains most frequently. Limitations The type of chemotherapy and timing of trastuzumab changed through the recruitment phase of the study as standard practice altered. Conclusions PERSEPHONE demonstrated that in HER2-positive early breast cancer 6 months’ adjuvant trastuzumab was non-inferior to 12 months. There was significantly less cardiac toxicity and fewer severe adverse events with 6 months’ treatment. Future work On-going translational work investigates patient and tumour genetic determinants of toxicity, and trastuzumab efficacy. An individual patient data meta-analysis with PHARE and other trastuzumab duration trials is planned. Trial registration ISRCTN 52968807 Funding National Institute for Health Research, Health Technology Assessment Programme (HTA Project: 06/303/98).National Institute for Health Research, Health Technology Assessment Programme (HTA Project: 06/303/98)

A Functional Gene Array for Detection of Bacterial Virulence Elements

Emerging known and unknown pathogens create profound threats to public health. Platforms for rapid detection and characterization of microbial agents are critically needed to prevent and respond to disease outbreaks. Available detection technologies cannot provide broad functional information about known or novel organisms. As a step toward developing such a system, we have produced and tested a series of high-density functional gene arrays to detect elements of virulence and antibiotic resistance mechanisms. Our first generation array targets genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for gene family detection and discrimination. When tested with organisms at varying phylogenetic distances from the four target strains, the array detected orthologs for the majority of targeted gene families present in bacteria belonging to the same taxonomic family. In combination with whole-genome amplification, the array detects femtogram concentrations of purified DNA, either spiked in to an aerosol sample background, or in combinations from one or more of the four target organisms. This is the first report of a high density NimbleGen microarray system targeting microbial antibiotic resistance and virulence mechanisms. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples

The Eocene-Oligocene boundary climate transition: An Antarctic perspective

Antarctica underwent a complex evolution over the course of the Cenozoic, which influenced the history of the Earth’s climate system. The Eocene-Oligocene boundary is a divide of this history when the ice-free ‘greenhouse world’ transitioned to the ‘icehouse’ with the glaciation of Antarctica. Prior to this, Antarctica experienced warm climates, peaking during Early Eocene when tropical-like conditions existed at the margins of the continent where geological evidence is present. Climate signals in the geological record show that the climate then cooled, but not enough to allow the existence of significant ice until the latest Eocene. Glacial deposits from several areas around the continental margin indicate that ice was present by the earliest Oligocene. This matches the major oxygen isotope positive shift captured by marine records. On land, vegetation was able to persist, but the thermophylic plants of the Eocene were replaced by shrubby vegetation with the southern beech Nothofagus, mosses and ferns, which survived in tundra-like conditions. Coupled climate–ice sheet modelling indicates that changing levels of atmospheric CO2 controlled Antarctica’s climate and the onset of glaciation. Factors such as mountain uplift, vegetation changes, ocean gateway opening and orbital forcing all played a part in cooling the polar climate, but only when CO2 levels reached critical thresholds was Antarctica tipped into an icy glacial world

Growth and retreat of the last British–Irish Ice Sheet, 31 000 to 15 000 years ago: the BRITICE-CHRONO reconstruction

The BRITICE-CHRONO consortium of researchers undertook a dating programme to constrain the timing of advance, maximum extent and retreat of the British–Irish Ice Sheet between 31 000 and 15 000 years before present. The dating campaign across Ireland and Britain and their continental shelves, and across the North Sea included 1500 days of field investigation yielding 18 000 km of marine geophysical data, 377 cores of sea floor sediments, and geomorphological and stratigraphical information at 121 sites on land; generating 690 new geochronometric ages. These findings are reported in 28 publications including synthesis into eight transect reconstructions. Here we build ice sheet-wide reconstructions consistent with these findings and using retreat patterns and dates for the inter-transect areas. Two reconstructions are presented, a wholly empirical version and a version that combines modelling with the new empirical evidence. Palaeoglaciological maps of ice extent, thickness, velocity, and flow geometry at thousand-year timesteps are presented. The maximum ice volume of 1.8 m sea level equivalent occurred at 23 ka. A larger extent than previously defined is found and widespread advance of ice to the continental shelf break is confirmed during the last glacial. Asynchrony occurred in the timing of maximum extent and onset of retreat, ranging from 30 to 22 ka. The tipping point of deglaciation at 22 ka was triggered by ice stream retreat and saddle collapses. Analysis of retreat rates leads us to accept our hypothesis that the marine-influenced sectors collapsed rapidly. First order controls on ice-sheet demise were glacio-isostatic loading triggering retreat of marine sectors, aided by glaciological instabilities and then climate warming finished off the smaller, terrestrial ice sheet. Overprinted on this signal were second order controls arising from variations in trough topographies and with sector-scale ice geometric readjustments arising from dispositions in the geography of the landscape. These second order controls produced a stepped deglaciation. The retreat of the British–Irish Ice Sheet is now the world’s most well-constrained and a valuable data-rich environment for improving ice-sheet modelling.publishedVersio

Acetate Kinase Isozymes Confer Robustness in Acetate Metabolism

Acetate kinase (ACK) (EC no: 2.7.2.1) interconverts acetyl-phosphate and acetate to either catabolize or synthesize acetyl-CoA dependent on the metabolic requirement. Among all ACK entries available in UniProt, we found that around 45% are multiple ACKs in some organisms including more than 300 species but surprisingly, little work has been done to clarify whether this has any significance. In an attempt to gain further insight we have studied the two ACKs (AckA1, AckA2) encoded by two neighboring genes conserved in Lactococcus lactis (L. lactis) by analyzing protein sequences, characterizing transcription structure, determining enzyme characteristics and effect on growth physiology. The results show that the two ACKs are most likely individually transcribed. AckA1 has a much higher turnover number and AckA2 has a much higher affinity for acetate in vitro. Consistently, growth experiments of mutant strains reveal that AckA1 has a higher capacity for acetate production which allows faster growth in an environment with high acetate concentration. Meanwhile, AckA2 is important for fast acetate-dependent growth at low concentration of acetate. The results demonstrate that the two ACKs have complementary physiological roles in L. lactis to maintain a robust acetate metabolism for fast growth at different extracellular acetate concentrations. The existence of ACK isozymes may reflect a common evolutionary strategy in bacteria in an environment with varying concentrations of acetate