Functional diversity can facilitate the collapse of an undesirable ecosystem state

Biodiversity may increase ecosystem resilience. However, we have limited understanding if this holds true for ecosystems that respond to gradual environmental change with abrupt shifts to an alternative state. We used a mathematical model of anoxic–oxic regime shifts and explored how trait diversity in three groups of bacteria influences resilience. We found that trait diversity did not always increase resilience: greater diversity in two of the groups increased but in one group decreased resilience of their preferred ecosystem state. We also found that simultaneous trait diversity in multiple groups often led to reduced or erased diversity effects. Overall, our results suggest that higher diversity can increase resilience but can also promote collapse when diversity occurs in a functional group that negatively influences the state it occurs in. We propose this mechanism as a potential management approach to facilitate the recovery of a desired ecosystem state.     

In Vitro Selection for Salt Tolerance in Brassica juncea L. Using Cotyledon Explants, Callus and Cell Suspension Cultures

Salt-tolerant Brassica juncea L. cell lines or plants have beenselected by screening callus pieces, cell suspension culturesand cotyledon explants in vitro on high concentrations of NaCl.Callus-based selection was unsatisfactory, as only two out ofseven isolated clones retained tolerance after 3 months of subcultureon NaCl-free medium. Selections made via plated cell suspensionswere found to be more stable for salt-tolerance. AH selectedtolerant cell lines, however, failed to regenerate plantlets.A third selection method, employing cotyledon explants was basedon their high potential for regenerating multiple shoots. Outof a total of 2620 explants cultured on high salt media, threesurvived, showed sustained callus proliferation and each regeneratedone shoot. The salt-selected shoots withstood the stabilitytest after 3 months of growth and axillary bud multiplicationon NaCl-free medium. While one of these somaclones was morphologicallyabnormal and sterile, the other two could be reared to maturitywith normal seed set. Brassica juncea, tissue culture, in vitro selection, salt-tolerance, plant regeneration     

Discovery and Validation of Clinical Biomarkers of Cancer: A Review Combining Metabolomics and Proteomics

Early detection and diagnosis of cancer can allow timely medical intervention, which greatly improves chances of survival and enhances quality of life. Biomarkers play an important role in assisting clinicians and health care providers in cancer diagnosis and treatment follow‐up. In spite of years of research and the discovery of thousands of candidate cancer biomarkers, only a few have transitioned to routine usage in the clinic. This review highlights advances in proteomics technologies that have enabled high rates of discovery of candidate cancer biomarkers and evaluates integration with other omics technologies to improve their progress through to validation and clinical translation. Furthermore, it gauges the role of metabolomics technology in cancer biomarker research and assesses it as a complementary tool in aiding cancer biomarker discovery and validation.     

Metal ion-mediated reduction in surface entropy improves diffraction quality of crystals of the IRAK-4 death domain.

Interleukin-1 receptor-associated kinase-4 (IRAK-4) is an essential component of innate immunity in mice and humans. IRAK-4 is a bipartite protein composed of a death domain (DD) that mediates molecular recognition, and a catalytic kinase domain. Structure determination of the proteolytically stable, soluble IRAK-4 DD was hampered by poor diffraction quality. Addition of manganese (II) chloride to the crystallization solution produced significant improvements in diffraction, and the structure has been determined to 1.7-Angstrom resolution. Examination of the IRAK-4 DD crystal structure reveals a single manganese ion coordinated to surface residues lysine-21 and aspartate-24. Coordination of the manganese ion resulted in a reduction in the surface entropy at this region of the molecule, by generating a contact-forming and conformationally homogenous surface patch. Prior studies have shown that surface entropy reduction by mutation of surface residues with large flexible side chains (i.e., Lys and Glu) to smaller side chains results in the production of diffraction-quality crystals. The intrinsic high surface entropy of Lys residues can also be decreased by reductive methylation. Our results suggest that screening of manganese ions as a crystallization additive may also facilitate ordered crystallization by reduction of surface entropy. Given the quick and inexpensive nature of screening, this technique is likely to be amenable to high-throughput methods such as those employed by Protein Structure Initiatives.