Investigating the poor outcomes of BRAF - mutant advanced colorectal cancer: Analysis from 2530 patients in randomised clinical trials

Background: To improve strategies for the treatment of BRAF-mutant advanced colorectal cancer (aCRC) patients we examined individual data from patients treated with chemotherapy alone in three randomised trials to identify points on the treatment pathway where outcomes differ from BRAF wild-types. Patients and Methods: 2530 aCRC patients were assessed from three randomised trials. End-points were progression free survival (PFS), response rate (RR), disease control rate (DCR), post-progression survival (P-PS) and overall survival (OS). Treatments included first-line oxaliplatin/fluorouracil (OxFU), and second-line irinotecan. Clinicians were unaware of BRAF-status Results 231 patients (9.1%) had BRAF-mutant tumours. BRAF-mutation conferred significantly worse survival independent of associated clinicopathological factors known to be prognostic. Compared with wild-type, BRAF-mutant patients treated with first-line OxFU had similar DCR (59.2% vs 72%; adjusted OR=0.76,p=0.24) and PFS (5.7 vs 6.3 months; adjusted HR=1.14, p=0.26). Following progression on first-line chemotherapy, BRAF-mutant patients had a markedly shorter P-PS (4.2 vs 9.2 months, adjusted HR=1.69,p6 months; OS=24.0 months), however 36.5% progressed rapidly through first-line chemotherapy and thereafter, with OS=4.7 months. Conclusions BRAF-mutant aCRC confers a markedly worse prognosis independent of associated clinicopathological features. Chemotherapy provides meaningful improvements in outcome throughout treatment lines. Post-progression survival is markedly worse and vigilance is required to ensure appropriate delivery of treatment after first-line progression

Stops making sense: translational trade-offs and stop codon reassignment

Background Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences. Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants

Cognitive loading affects motor awareness and movement kinematics but not locomotor trajectories during goal-directed walking in a virtual reality environment.

The primary purpose of this study was to investigate the effects of cognitive loading on movement kinematics and trajectory formation during goal-directed walking in a virtual reality (VR) environment. The secondary objective was to measure how participants corrected their trajectories for perturbed feedback and how participants' awareness of such perturbations changed under cognitive loading. We asked 14 healthy young adults to walk towards four different target locations in a VR environment while their movements were tracked and played back in real-time on a large projection screen. In 75% of all trials we introduced angular deviations of ±5° to ±30° between the veridical walking trajectory and the visual feedback. Participants performed a second experimental block under cognitive load (serial-7 subtraction, counter-balanced across participants). We measured walking kinematics (joint-angles, velocity profiles) and motor performance (end-point-compensation, trajectory-deviations). Motor awareness was determined by asking participants to rate the veracity of the feedback after every trial. In-line with previous findings in natural settings, participants displayed stereotypical walking trajectories in a VR environment. Our results extend these findings as they demonstrate that taxing cognitive resources did not affect trajectory formation and deviations although it interfered with the participants' movement kinematics, in particular walking velocity. Additionally, we report that motor awareness was selectively impaired by the secondary task in trials with high perceptual uncertainty. Compared with data on eye and arm movements our findings lend support to the hypothesis that the central nervous system (CNS) uses common mechanisms to govern goal-directed movements, including locomotion. We discuss our results with respect to the use of VR methods in gait control and rehabilitation

ICMSF Methods Studies. XV. Comparison of Four Media and Methods for Enumerating Staphylococcus aureus in Powdered Milk.

Four media were examined for their usefulness in enumerating Staphylococcus aureus inoculated (a) into milk that was then dried or (b) directly into dried milk powder. In all, seven strains of S. aureus were inoculated individually into each preparation and were enumerated after two periods of storage (18 to 19 d and 60 to 61 d). Fourteen laboratories from twelve countries participated in the comparison which found that direct plating on agar medium in 14-cm petri dishes may be as useful as enrichment followed by streaking. Plating on Baird-Parker medium or on Hauschild pork plasma fibrinogen medium and a MPN method using Giolitti and Cantoni's broth with Tween 80 were equally sensitive for enumerating S. aureus in dried milk powder. The use of Hauschild medium may eliminate the need for supplementary tests to confirm colonies as S. aureus , but in some cases was found to fail in some laboratories. Giolitti and Cantoni's broth without Tween 80 generally was less useful than the three other media for enumerating S. aureus . S. aureus inoculated into milk that was then dried survived longer than when inoculated into dried milk

Amino Acid Metabolic Origin as an Evolutionary Influence on Protein Sequence in Yeast

The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their respective yeast metabolic cycle phases. Typically, the amino acids themselves are most abundant at the end of their precursor’s phase. We show that this metabolic cycling has likely biased the amino acid composition of proteins across the S. cerevisiae genome. In particular, we observed that the metabolic source of amino acids is the single most important source of variation in the amino acid compositions of functionally related proteins and that this signal appears only in (facultative) organisms using both oxidative and reductive metabolism. Periodically expressed proteins are enriched for amino acids generated in the preceding phase of the metabolic cycle. Proteins expressed during the oxidative phase contain more glycolysis-derived amino acids, whereas proteins expressed during the reductive phase contain more respiration-derived amino acids. Rare amino acids (e.g., tryptophan) are greatly overrepresented or underrepresented, relative to the proteomic average, in periodically expressed proteins, whereas common amino acids vary by a few percent. Genome-wide, we infer that 20,000 to 60,000 residues have been modified by this previously unappreciated pressure. This trend is strongest in ancient proteins, suggesting that oscillating endogenous amino acid availability exerted genome-wide selective pressure on protein sequences across evolutionary time

Stimulation of lymphocyte anti-melanoma activity by co-cultured macrophages activated by complex homeopathic medication

<p>Abstract</p> <p>Background</p> <p>Melanoma is the most aggressive form of skin cancer, and the most rapidly expanding cancer in terms of worldwide incidence. Chemotherapeutic approaches to treat melanoma have been uniformly disappointing. A Brazilian complex homeopathic medication (CHM), used as an immune modulator, has been recommended for patients with depressed immune systems. Previous studies in mice have demonstrated that the CHM activates macrophages, induces an increase in the number of leukocytes and improves the murine response against Sarcoma-180.</p> <p>Methods</p> <p>Here we studied the interaction of mouse lymph node lymphocytes, co-cultured <it>in vitro </it>with macrophages in the presence or absence of the CHM, with B16F10 melanoma cells.</p> <p>Results</p> <p>Lymphocytes co-cultured with macrophages in the presence of the CHM had greater anti-melanoma activity, reducing melanoma cell density and increasing the number of lysed tumor cells. There was also a higher proportion of activated (CD25⁺) lymphocytes with increased viability. Overall, lymphocytes activated by treatment destroyed growing cancer cells more effectively than control lymphocytes.</p> <p>Conclusion</p> <p>Co-culture of macrophages with lymphocytes in the presence of the CHM enhanced the anti-cancer performance of lymphocytes against a very aggressive lineage of melanoma cells. These results suggest that non-toxic therapies using CHMs are a promising alternative approach to the treatment of melanomas. In addition, they are attractive combination-therapy candidates, which may enhance the efficacy of conventional medicines by improving the immune response against tumor cells.</p

A complete solution to neutrino mixing

Deviations from expectations have been claimed for solar, atmospheric and high energy prompt neutrinos from charm decay. This information, supplemented only by the existing very good upper limits for oscillations of the $\nu_{\mu}$ at accelerator energies, is used as input to a phenomenological three-flavour analysis of neutrino mixing. The solution found is unique and completely determines the mass eigenstates as well as the mixing matrix relating mass and flavour eigenstates. Assuming the mass eigenstates to follow the hierarchy $m_{1} \ll m_{2} \ll m_{3}$, their values are found to be $m_{1} \ll 10^{-2}$ eV, $m_{2} = (0.18 \pm 0.06)$ eV, $m_{3} = (19.4 \pm 0.7)$ eV. These masses are in agreement with the leptonic quadratic hierarchy of the see-saw model and large enough to render energy-independent any oscillation-induced phenomenon in solar neutrino physics observable on Earth. This possibility is not excluded by the present knowledge of solar neutrino physics. The mixing angles are determined to be $\theta_{12} = 0.55 \pm 0.08$, $\theta_{13} = 0.38 \pm 0.06$, $\theta_{23} < 0.03$. Small values of $\theta_{23}$ are typical of any solution in which $m_{3}$ lies in the cosmological interesting region. The solution found is not in serious contradiction with any of the present limits to the existence of neutrino oscillations. The most relevant implications in particle physics, astrophysics and cosmology are discussed.Comment: 17 pages, 3 figures, to be published in Astroparticle Physic