Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets

Background  

Mass spectrometry is increasingly being used to discover proteins or protein profiles associated with disease. Experimental design of mass-spectrometry studies has come under close scrutiny and the importance of strict protocols for sample collection is now understood. However, the question of how best to process the large quantities of data generated is still unanswered. Main challenges for the analysis are the choice of proper pre-processing and classification methods. While these two issues have been investigated in isolation, we propose to use the classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods.     

Belowground ABA boosts aboveground production of DIMBOA and primes induction of chlorogenic acid in maize

Plants are important mediators between above- and belowground herbivores. Consequently, interactions between root and shoot defenses can have far-reaching impacts on entire food webs. We recently reported that infestation of maize roots by larvae of the beetle Diabrotica virgifera virgifera induced shoot resistance against herbivores and pathogens. Root herbivory also enhanced aboveground DIMBOA and primed for enhanced induction of chlorogenic acid, two secondary metabolites that have been associated with plant stress resistance. Interestingly, the plant hormone abscisic acid (ABA) emerged as a putative long-distance signal in the regulation of these systemic defenses. In this addendum, we have investigated the role of root-derived ABA in aboveground regulation of DIMBOA and the phenolic compounds chlorogenic acid, caffeic and ferulic acid. Furthermore, we discuss the relevance of ABA in relation to defense against the leaf herbivore Spodoptera littoralis. Soil-drench treatment with ABA mimicked root herbivore-induced accumulation of DIMBOA in the leaves. Similarly, ABA mimicked aboveground priming of chlorogenic acid production, causing augmented induction of this compound after subsequent shoot attack by S. littoralis caterpillars. These findings confirm our notion that ABA acts as an important signal in the regulation of aboveground defenses during belowground herbivory. However, based on our previous finding that ABA alone is not sufficient to trigger aboveground resistance against S. littoralis caterpillars, our results also suggest that the ABA-inducible effects on DIMBOA and chlorogenic acid are not solely responsible for root herbivore-induced resistance against S. littoralis.Key words: induced resistance, Spodoptera littoralis, Zea mays, Diabrotica virgifera, DIMBOA, chlorogenic acid, absisic acid, priming     

Biochemical and Structural Characterization of the Interaction between the Siderocalin NGAL/LCN2 (Neutrophil Gelatinase-associated Lipocalin/Lipocalin 2) and the N-terminal Domain of Its Endocytic Receptor SLC22A17

The neutrophil gelatinase-associated lipocalin (NGAL, also known as LCN2) and its cellular receptor (LCN2-R, SLC22A17) are involved in many physiological and pathological processes such as cell differentiation, apoptosis, and inflammation. These pleiotropic functions mainly rely on NGAL''s siderophore-mediated iron transport properties. However, the molecular determinants underlying the interaction between NGAL and its cellular receptor remain largely unknown. Here, using solution-state biomolecular NMR in conjunction with other biophysical methods, we show that the N-terminal domain of LCN2-R is a soluble extracellular domain that is intrinsically disordered and interacts with NGAL preferentially in its apo state to form a fuzzy complex. The relatively weak affinity (≈10 μm) between human LCN2-R-NTD and apoNGAL suggests that the N terminus on its own cannot account for the internalization of NGAL by LCN2-R. However, human LCN2-R-NTD could be involved in the fine-tuning of the interaction between NGAL and its cellular receptor or in a biochemical mechanism allowing the receptor to discriminate between apo- and holo-NGAL.     

Wildlife detector dogs and camera traps: a comparison of techniques for detecting feral cats

A major challenge in controlling overabundant wildlife is monitoring their populations, particularly as they decline to very low density. Camera traps and wildlife detector dogs are increasingly being used for this purpose. We compared the cost-effectiveness of these two approaches for detecting feral cats (Felis catus) on two pastoral properties in Hawke's Bay, North Island, New Zealand. One property was subject to intensive pest removal, while the other had no recent history of pest control. Camera traps and wildlife detector dogs detected cats at similar rates at both sites. The operating costs of each method were also comparable. We identify a number of advantages and disadvantages of each technique, and suggest priorities for further research.     

Bacterial networking

A report of the ESF-EMBO Symposium Bacterial Networks (BacNet08), Sant Feliu de Guixols, Spain, 13-18 September 2008.     

Three-dimensional cancer cell culture in high-yield multiscale scaffolds by shear spinning

Polymeric scaffolds comprising two size scales of microfibers and submicron fibers can better support three-dimensional (3D) cell growth in tissue engineering, making them an important class of healthcare material. However, a major manufacturing barrier hampers their translation into wider practical use: scalability. Traditional production of two-scale scaffolds by electrospinning is slow and costly. For day-to-day cell cultures, the scaffolds need to be affordable, made in high yield to drive down cost. Combining expertise from academia and industry from the United Kingdom and United States, this study uses a new series of high-yield, low-cost scaffolds made by shear spinning for tissue engineering. The scaffolds comprise interwoven submicron fibers and microfibers throughout as observed under scanning electron microscopy and demonstrate good capability to support cell culturing for tumor modeling. Three model human cancer cell lines (HEK293, A549 and MCF-7) with stable expression of GFP were cultured in the scaffolds and found to exhibit efficient cell attachment and sustained 3D growth and proliferation for 30 days. Cryosection and multiphoton fluorescence microscopy confirmed the formation of compact 3D cell clusters throughout the scaffolds. In addition, comparative growth curves of 2D and 3D cultures show significant cell-type-dependent differences. This work applies high-yield shear-spun scaffolds in mammalian tissue engineering and brings practical, affordable applications of multiscale scaffolds closer to reality. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2750, 2019.     

Centrosome defects cause microcephaly by activating the 53BP1‐USP28‐TP53 mitotic surveillance pathway

Mutations in centrosome genes deplete neural progenitor cells (NPCs) during brain development, causing microcephaly. While NPC attrition is linked to TP53‐mediated cell death in several microcephaly models, how TP53 is activated remains unclear. In cultured cells, mitotic delays resulting from centrosome loss prevent the growth of unfit daughter cells by activating a pathway involving 53BP1, USP28, and TP53, termed the mitotic surveillance pathway. Whether this pathway is active in the developing brain is unknown. Here, we show that the depletion of centrosome proteins in NPCs prolongs mitosis and increases TP53‐mediated apoptosis. Cell death after a delayed mitosis was rescued by inactivation of the mitotic surveillance pathway. Moreover, 53BP1 or USP28 deletion restored NPC proliferation and brain size without correcting the upstream centrosome defects or extended mitosis. By contrast, microcephaly caused by the loss of the non‐centrosomal protein SMC5 is also TP53‐dependent but is not rescued by loss of 53BP1 or USP28. Thus, we propose that mutations in centrosome genes cause microcephaly by delaying mitosis and pathologically activating the mitotic surveillance pathway in the developing brain.     

Quirks of dye nomenclature. 7. Gentian violet and other violets

The name, gentian, appeared about 1880. Immediately following its discovery in 1861, this violet dye was known as Violet de Paris or as methyl violet. Initially used as a textile dye, it was soon used to color virtually anything. The names and identity of the components, the varying modes of manufacture, analytical methods and the dye’s significant contribution to biological staining are discussed here. Finally, I discuss the dye’s declining medical use following the revelation of its toxic nature.