Statistical evaluation of the Predictive Toxicology Challenge 2000-2001

MOTIVATION: The development of in silico models to predict chemical carcinogenesis from molecular structure would help greatly to prevent environmentally caused cancers. The Predictive Toxicology Challenge (PTC) competition was organized to test the state-of-the-art in applying machine learning to form such predictive models. RESULTS: Fourteen machine learning groups generated 111 models. The use of Receiver Operating Characteristic (ROC) space allowed the models to be uniformly compared regardless of the error cost function. We developed a statistical method to test if a model performs significantly better than random in ROC space. Using this test as criteria five models performed better than random guessing at a significance level p of 0.05 (not corrected for multiple testing). Statistically the best predictor was the Viniti model for female mice, with p value below 0.002. The toxicologically most interesting models were Leuven2 for male mice, and Kwansei for female rats. These models performed well in the statistical analysis and they are in the middle of ROC space, i.e. distant from extreme cost assumptions. These predictive models were also independently judged by domain experts to be among the three most interesting, and are believed to include a small but significant amount of empirically learned toxicological knowledge. AVAILABILITY: PTC details and data can be found at: http://www.predictive-toxicology.org/ptc/.     

Binding specificity and mRNA targets of a C. elegans PUF protein, FBF-1

Sequence-specific RNA-protein interactions underlie regulation of many mRNAs. Here we analyze the RNA sequence specificity of Caenorhabditis elegans FBF-1, a founding member of the PUF protein family. Like other PUF proteins, FBF-1 binds to the 3' UTR of target mRNAs and decreases expression of those target genes. Here, we show that FBF-1 and its close relative, FBF-2, bind with similar affinity to multiple RNA sites. We use mutagenesis and in vivo selection experiments to identify nucleotides that are essential for FBF-1 binding. The binding elements comprise a "core" central region and flanking sequences. The core region is similar but distinct from the binding sites of other PUF proteins. We combine the identification of binding elements with informatics to predict new FBF-1 binding sites in a C. elegans 3' UTR database. These data identify a set of new candidate mRNA targets of FBF-1 and FBF-2.     

Genotype, phenotype and cancer: Role of low penetrance genes and environment in tumour susceptibility

Role of heredity and lifestyle in sporadic cancers is well documented. Here we focus on the influence of low penetrance genes and habits, with emphasis on tobacco habit in causing head and neck cancers. Role of such gene-environment interaction can be well studied in individuals with multiple primary cancers. Thus such a biological model may elucidate that cancer causation is not solely due to genetic determinism but also significantly relies on lifestyle of the individual.     

Anti-infection silver nanoparticle immobilized biomaterials facilitated by argon plasma grafting technology

Many research groups have attained slow, persistent, continuous release of silver ions through careful experimental design using existing methods. Such methods effectively kill planktonic bacteria and therefore prevent surface adhesion of pathogens. However, the resultant modified coatings cannot provide long-term antibacterial efficacy due to sustained anti-microbial release. In this study, the anti-infection activity of AgNP immobilized biomaterials was evaluated, facilitated by argon plasma grafting technology and activated by bacterial colonization. The modified materials generated in this study showed excellent specificity and were active against both Gram-positive and Gram-negative biofilm forming bacteria, including methicillin-resistant Staphylococcus aureus, Staphylococcus epidermidis, and Escherichia coli. The anti-infection biomaterials developed in this study demonstrate several attractive advantages in comparison to traditional anti-bacterial surfaces loaded with antibiotics or other types of antibacterial agents and include (1) broad spectrum of activity against antibiotic resistant bacteria, (2) the unlikelihood of bacterial resistance, (3) specificity, (4) biocompatibility, and (5) stability.     

Burst Firing in Bee Gustatory Neurons Prevents Adaptation

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Translation acrobatics: how cancer cells exploit alternate modes of translational initiation

Recent work has brought to light many different mechanisms of translation initiation that function in cells in parallel to canonical cap‐dependent initiation. This has important implications for cancer. Canonical cap‐dependent translation initiation is inhibited by many stresses such as hypoxia, nutrient limitation, proteotoxic stress, or genotoxic stress. Since cancer cells are often exposed to these stresses, they rely on alternate modes of translation initiation for protein synthesis and cell growth. Cancer mutations are now being identified in components of the translation machinery and in cis‐regulatory elements of mRNAs, which both control translation of cancer‐relevant genes. In this review, we provide an overview on the various modes of non‐canonical translation initiation, such as leaky scanning, translation re‐initiation, ribosome shunting, IRES‐dependent translation, and m⁶A‐dependent translation, and then discuss the influence of stress on these different modes of translation. Finally, we present examples of how these modes of translation are dysregulated in cancer cells, allowing them to grow, to proliferate, and to survive, thereby highlighting the importance of translational control in cancer.     

Advances in 3D printing of composite scaffolds for the repairment of bone tissue associated defects

The conventional methods of using autografts and allografts for repairing defects in bone, the osteochondral bone, and the cartilage tissue have many disadvantages, like donor site morbidity and shortage of donors. Moreover, only 30% of the implanted grafts are shown to be successful in treating the defects. Hence, exploring alternative techniques such as tissue engineering to treat bone tissue associated defects is promising as it eliminates the above-mentioned limitations. To enhance the mechanical and biological properties of the tissue engineered product, it is essential to fabricate the scaffold used in tissue engineering by the combination of various biomaterials. Three-dimensional (3D) printing, with its ability to print composite materials and with complex geometry seems to have a huge potential in scaffold fabrication technique for engineering bone associated tissues. This review summarizes the recent applications and future perspectives of 3D printing technologies in the fabrication of composite scaffolds used in bone, osteochondral, and cartilage tissue engineering. Key developments in the field of 3D printing technologies involves the incorporation of various biomaterials and cells in printing composite scaffolds mimicking physiologically relevant complex geometry and gradient porosity. Much recently, the emerging trend of printing smart scaffolds which can respond to external stimulus such as temperature, pH and magnetic field, known as 4D printing is gaining immense popularity and can be considered as the future of 3D printing applications in the field of tissue engineering.