Intumescent multilayer nanocoating, made with renewable polyelectrolytes, for flame-retardant cotton

Thin films of fully renewable and environmentally benign electrolytes, cationic chitosan (CH) and anionic phytic acid (PA), were deposited on cotton fabric via layer-by-layer (LbL) assembly in an effort to reduce flammability. Altering the pH of aqueous deposition solutions modifies the composition of the final nanocoating. CH-PA films created at pH 6 were thicker and had 48 wt % PA in the coating, while the thinnest films (with a PA content of 66 wt %) were created at pH 4. Each coating was evaluated at both 30 bilayers (BL) and at the same coating weight added to the fabric. In a vertical flame test, fabrics coated with high PA content multilayers completely extinguished the flame, while uncoated cotton was completely consumed. Microcombustion calorimetry confirmed that all coated fabric reduces peak heat release rate (pkHRR) by at least 50% relative to the uncoated control. Fabric coated with pH 4 solutions shows the greatest reduction in pkHRR and total heat release of 60% and 76%, respectively. This superior performance is believed to be due to high phosphorus content that enhances the intumescent behavior of these nanocoatings. These results demonstrate the first completely renewable intumescent LbL assembly, which conformally coats every fiber in cotton fabric and provides an effective alternative to current flame retardant treatments.     

Genetic and Phenotypic Characterization of Roller Mutants of CAENORHABDITIS ELEGANS

Eighty-eight mutants of C. elegans that display a roller phenotype (a helically twisted body) have been isolated and characterized genetically and phenotypically. The mutations are located in 14 different genes. Most genes contain a number of alleles. Their distribution among the chromosomes appears nonrandom, with seven of the genes being located on linkage group II, some very closely linked. The phenotypes of the mutants suggest that there are five different classes of genes, each class representing a set of similar phenotypic effects: Left Roller (four genes), Right Roller (one gene), Left Squat (one gene), Right Squat (two genes) and Left Dumpy Roller (six genes). The classes of mutants differ with respect to a number of characteristics that include the developmental stages affected and the types of aberrations observed in cuticle structure. A variety of gene interactions were found, arguing that these genes are involved in a common developmental process. The presence of alterations in cuticle morphology strongly suggests that these genes are active in the formation of the nematode cuticle.     

Chronic Obstructive Pulmonary Disease Is Not Associated with KRAS Mutations in Non-Small Cell Lung Cancer

Mutations in epithelial growth factor receptor (EGFR), as well as in the EGFR downstream target KRAS are frequently observed in non-small cell lung cancer (NSCLC). Chronic obstructive pulmonary disease (COPD), an independent risk factor for developing NSCLC, is associated with an increased activation of EGFR. In this study we determined presence of EGFR and KRAS hotspot mutations in 325 consecutive NSCLC patients subjected to EGFR and KRAS mutation analysis in the diagnostic setting and for whom the pulmonary function has been determined at time of NSCLC diagnosis. Information about age at diagnosis, sex, smoking status, forced vital capacity (FVC) and forced expiratory volume in 1 sec (FEV₁) was collected. Chronic obstructive pulmonary disease(COPD) was defined according to 2013 GOLD criteria. Chi-Square, student t-test and multivariate logistic regression were used to analyze the data. A total of 325 NSCLC patients were included, 193 with COPD and 132 without COPD. COPD was not associated with presence of KRAS hotspot mutations, while EGFR mutations were significantly higher in non-COPD NSCLC patients. Both female gender (HR 2.61; 95% CI: 1.56–4.39; p<0.001) and smoking (HR 4.10; 95% CI: 1.14–14.79; p = 0.03) were associated with KRAS mutational status. In contrast, only smoking (HR 0.11; 95% CI: 0.04–0.32; p<0.001) was inversely associated with EGFR mutational status. Smoking related G>T and G>C transversions were significantly more frequent in females (86.2%) than in males (61.5%) (p = 0.008). The exon 19del mutation was more frequent in non-smokers (90%) compared to current or past smokers (36.8%). In conclusion, KRAS mutations are more common in females and smokers, but are not associated with COPD-status in NSCLC patients. EGFR mutations are more common in non-smoking NSCLC patients.     

Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies

Motivation

Next-generation sequencing (NGS) technologies have become much more efficient, allowing whole human genomes to be sequenced faster and cheaper than ever before. However, processing the raw sequence reads associated with NGS technologies requires care and sophistication in order to draw compelling inferences about phenotypic consequences of variation in human genomes. It has been shown that different approaches to variant calling from NGS data can lead to different conclusions. Ensuring appropriate accuracy and quality in variant calling can come at a computational cost.

Results

We describe our experience implementing and evaluating a group-based approach to calling variants on large numbers of whole human genomes. We explore the influence of many factors that may impact the accuracy and efficiency of group-based variant calling, including group size, the biogeographical backgrounds of the individuals who have been sequenced, and the computing environment used. We make efficient use of the Gordon supercomputer cluster at the San Diego Supercomputer Center by incorporating job-packing and parallelization considerations into our workflow while calling variants on 437 whole human genomes generated as part of large association study.

Conclusions

We ultimately find that our workflow resulted in high-quality variant calls in a computationally efficient manner. We argue that studies like ours should motivate further investigations combining hardware-oriented advances in computing systems with algorithmic developments to tackle emerging ‘big data’ problems in biomedical research brought on by the expansion of NGS technologies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0736-4) contains supplementary material, which is available to authorized users.     

Spatial Analysis of Effects of Mowing and Burning on Colony Expansion in Reintroduced Black‐Tailed Prairie Dog (Cynomys ludovicianus)

Factors governing the rate and direction of prairie dog (Cynomys spp.) colony expansion remain poorly understood. However, increased knowledge and ability to control these factors may lead to more effective reintroductions of prairie dogs and restoration of grassland habitats. We present density and directional analyses of the establishment of new burrows on three reintroduced colonies of Black‐tailed prairie dog (Cynomys ludovicianus) in southern New Mexico; the study colonies had been subjected to mow and burn treatments in the second year of the study. Our hypotheses were that prairie dogs will preferentially dig new burrows in the treatment plots versus control plots and that the colonies will expand in the direction of the treatment plots. The results support these hypotheses; analysis of burrow counts by site and treatment shows that prairie dogs preferentially colonized both mow and burn treatments compared to untreated areas at the periphery of the colonies. Directional analysis showed a significant posttreatment orientation of new burrows toward the treatment plots for all colonies. Our results show that the direction of expansion of prairie dog colonies can be manipulated. Effective control of the expansion of prairie dog colonies may lead to more successful reintroductions.     

CNTF variants with increased biological potency and receptor selectivity define a functional site of receptor interaction.

Human CNTF is a neurocytokine that elicits potent neurotrophic effects by activating a receptor complex composed of the ligand-specific alpha-receptor subunit (CNTFR alpha) and two signal transducing proteins, which together constitute a receptor for leukemia inhibitory factor (LIFR). At high concentrations, CNTF can also activate the LIFR and possibly other cross-reactive cytokine receptors in the absence of CNTFR alpha. To gain a better understanding of its structure-function relationships and to develop analogs with increased receptor specificity, the cytokine was submitted to affinity maturation using phage display technology. Variants with greatly increased CNTFR alpha affinity were selected from a phage-displayed library of CNTF variants carrying random amino acid substitutions in the putative D helix. Selected variants contained substitutions of the wild-type Gln167 residue, either alone or in combination with neighboring mutations. These results provide evidence for an important functional role of the mutagenized region in CNTFR alpha binding. Affinity enhancing mutations conferred to CNTF increased potency to trigger biological effects mediated by CNTFR alpha and enhanced neurotrophic activity on chicken ciliary neurons. In contrast, the same mutations did not potentiate the CNTFR alpha-independent receptor actions of CNTF. These CNTF analogs thus represent receptor-specific superagonists, which should help to elucidate the mechanisms underlying the pleiotropic actions of the neurocytokine.     

Somatic CAG expansion in Huntington's disease is dependent on the MLH3 endonuclease domain,which can be excluded via splice redirection

Somatic expansion of the CAG repeat tract that causes Huntington''s disease (HD) is thought to contribute to the rate of disease pathogenesis. Therefore, factors influencing repeat expansion are potential therapeutic targets. Genes in the DNA mismatch repair pathway are critical drivers of somatic expansion in HD mouse models. Here, we have tested, using genetic and pharmacological approaches, the role of the endonuclease domain of the mismatch repair protein MLH3 in somatic CAG expansion in HD mice and patient cells. A point mutation in the MLH3 endonuclease domain completely eliminated CAG expansion in the brain and peripheral tissues of a HD knock-in mouse model (Htt^Q111). To test whether the MLH3 endonuclease could be manipulated pharmacologically, we delivered splice switching oligonucleotides in mice to redirect Mlh3 splicing to exclude the endonuclease domain. Splice redirection to an isoform lacking the endonuclease domain was associated with reduced CAG expansion. Finally, CAG expansion in HD patient-derived primary fibroblasts was also significantly reduced by redirecting MLH3 splicing to the endogenous endonuclease domain-lacking isoform. These data indicate the potential of targeting the MLH3 endonuclease domain to slow somatic CAG repeat expansion in HD, a therapeutic strategy that may be applicable across multiple repeat expansion disorders.     

Comparison of two Ovsynch protocols (GnRH versus LH) for fixed timed insemination in buffalo (Bubalus bubalis)

We evaluated the efficiency of replacing GnRH with LH in the ovulation synchronization protocol in buffaloes. Buffaloes received GnRH on Day 0, (Buserelin; Conceptal, 20 microg), PGF2alpha (Luprostiol; Prosolvin, 15 mg) on Day 7 and GnRH (Buserelin; Conceptal, 10 microg; Group 1) or porcine LH (LH; Lutropin-V, 12.5 mg; Group 2) on Day 9. In Experiment 1, we studied the follicular dynamics of 30 buffaloes (Group 1, n = 15 and Group 2, n = 15). We performed ultrasonography every 12 h from Days 0 to 2, then on Day 7 and then every 6 h from the time of GnRH or LH treatment (Day 9) until the time of ovulation. All females not ovulating by 48 h after the second GnRH or LH injection were considered as nonresponders. In Experiment 2, we evaluated 305 buffaloes (Group 1, n = 154; Group 2, n = 151), using the same two treatments studied in Experiment 1. We also recorded and evaluated aspects like parity, lactational status, the presence of mucus, and uterine tone at the time of artificial insemination (Al). In Experiment 1, ovulation rate after the first GnRH was 86.6% (26/30). Ovulation rates were 93.3% (14/15; Group 1) after the second dose of GnRH and 93.3% (14/15) after LH (Group 2). Ovulation occurred 36.4+/-10.4 h after the first GnRH. The interval for treatment to ovulation was 26.5+/-9.6 h for buffaloes treated with GnRH (Group 1) and 24.4+/-7.9 h for buffaloes treated with LH (Group 2); the time of ovulation did not differ statistically between the two groups (GnRH versus LH; P > 0.05). In Experiment 2, conception rates of the animals AI in the field were 56.5% (Group 1) and 64.2% (Group 2), respectively (P = 0.08). The response to the treatment with LH was not different to the treatment with GnRH; however, multiparous buffaloes had higher conception rates than the primiparous buffaloes in both groups (P > 0.05). Buffaloes with mucus at the time of AI in Group 2 had higher conception rates than the buffaloes that had mucus in Group 1 (P < 0.05). Uterine tone and lactational status did not influence conception rates (P > 0.05). In summary, the results showed that both treatments resulted in synchronization of ovulation and acceptable conception rates. Therefore, the exogenous injection of LH can substitute the GnRH injections in the Ovsynch program in buffaloes.