Neomycin- and spectinomycin-resistance replacement vectors for Bacillus subtilis

A plasmid is described for Bacillus subtilis that facilitates replacement of the widely used neomycin resistance gene (neo) with a spectinomycin resistance (spc_E) gene. A second plasmid is described that facilitates replacement of spc_S, associated with mini-Tn10 mutagenesis in B. subtilis, with neo. These plasmids can also function as integrative vectors for B. subtilis. They expand the scope of strain construction and gene analysis in B. subtilis.     

Evidence for Patterns of Selective Urban Migration in the Greater Indus Valley (2600-1900 BC): A Lead and Strontium Isotope Mortuary Analysis

Just as modern nation-states struggle to manage the cultural and economic impacts of migration, ancient civilizations dealt with similar external pressures and set policies to regulate people’s movements. In one of the earliest urban societies, the Indus Civilization, mechanisms linking city populations to hinterland groups remain enigmatic in the absence of written documents. However, isotopic data from human tooth enamel associated with Harappa Phase (2600-1900 BC) cemetery burials at Harappa (Pakistan) and Farmana (India) provide individual biogeochemical life histories of migration. Strontium and lead isotope ratios allow us to reinterpret the Indus tradition of cemetery inhumation as part of a specific and highly regulated institution of migration. Intra-individual isotopic shifts are consistent with immigration from resource-rich hinterlands during childhood. Furthermore, mortuary populations formed over hundreds of years and composed almost entirely of first-generation immigrants suggest that inhumation was the final step in a process linking certain urban Indus communities to diverse hinterland groups. Additional multi disciplinary analyses are warranted to confirm inferred patterns of Indus mobility, but the available isotopic data suggest that efforts to classify and regulate human movement in the ancient Indus region likely helped structure socioeconomic integration across an ethnically diverse landscape.     

Acyl-CoAs from coenzyme ribozymes.

We describe in vitro selection of two novel ribozymes that mediate coenzyme reactions. The first is a trans-capping ribozyme that attaches coenzyme A (CoA) at the 5' end of any RNA with the proper short terminal sequence, including RNAs with randomized internal sequences. From such a trans-capped CoA-RNA pool, we derive ribozymes that attack biotinyl-AMP using the SH group of CoA. These ribozymes, selected to acylate CoA with the valeryl side chain of biotin, also produce the crucial metabolic intermediates acetyl-CoA and butyryl-CoA with substantial velocities. Thus, we argue that RNAs might have used the chemical functionality offered by coenzymes to support an RNA world metabolism. In particular, we can combine our results with those of other labs to argue that simple chemistry and RNA catalysis suffice to proceed from simple chemicals to catalysis with acyl-CoAs. The trans-capping method can be generalized for production of varied coenzyme ribozymes using a single catalytic RNA subunit. Finally, the long-suggested RNA origin for CoA itself appears to be chemically feasible.     

Recent advances in B-cell epitope prediction methods

Identification of epitopes that invoke strong responses from B-cells is one of the key steps in designing effective vaccines against pathogens. Because experimental determination of epitopes is expensive in terms of cost, time, and effort involved, there is an urgent need for computational methods for reliable identification of B-cell epitopes. Although several computational tools for predicting B-cell epitopes have become available in recent years, the predictive performance of existing tools remains far from ideal. We review recent advances in computational methods for B-cell epitope prediction, identify some gaps in the current state of the art, and outline some promising directions for improving the reliability of such methods.     

Mesenchymal stem cell injection after myocardial infarction improves myocardial compliance

Cellular therapy for myocardial injury has improved ventricular function in both animal and clinical studies, though the mechanism of benefit is unclear. This study was undertaken to examine the effects of cellular injection after infarction on myocardial elasticity. Coronary artery ligation of Lewis rats was followed by direct injection of human mesenchymal stem cells (MSCs) into the acutely ischemic myocardium. Two weeks postinfarct, myocardial elasticity was mapped by atomic force microscopy. MSC-injected hearts near the infarct region were twofold stiffer than myocardium from noninfarcted animals but softer than myocardium from vehicle-treated infarcted animals. After 8 wk, the following variables were evaluated: MSC engraftment and left ventricular geometry by histological methods, cardiac function with a pressure-volume conductance catheter, myocardial fibrosis by Masson Trichrome staining, vascularity by immunohistochemistry, and apoptosis by TdT-mediated dUTP nick-end labeling assay. The human cells engrafted and expressed a cardiomyocyte protein but stopped short of full differentiation and did not stimulate significant angiogenesis. MSC-injected hearts showed significantly less fibrosis than controls, as well as less left ventricular dilation, reduced apoptosis, increased myocardial thickness, and preservation of systolic and diastolic cardiac function. In summary, MSC injection after myocardial infarction did not regenerate contracting cardiomyocytes but reduced the stiffness of the subsequent scar and attenuated postinfarction remodeling, preserving some cardiac function. Improving scarred heart muscle compliance could be a functional benefit of cellular cardiomyoplasty.