Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains

Background  

Homologous recombination mediated by the λ-Red genes is a common method for making chromosomal modifications in Escherichia coli. Several protocols have been developed that differ in the mechanisms by which DNA, carrying regions homologous to the chromosome, are delivered into the cell. A common technique is to electroporate linear DNA fragments into cells. Alternatively, DNA fragments are generated in vivo by digestion of a donor plasmid with a nuclease that does not cleave the host genome. In both cases the λ-Red gene products recombine homologous regions carried on the linear DNA fragments with the chromosome. We have successfully used both techniques to generate chromosomal mutations in E. coli K-12 strains. However, we have had limited success with these λ-Red based recombination techniques in pathogenic E. coli strains, which has led us to develop an enhanced protocol for recombineering in such strains.     

Mutations in H5N1 Influenza Virus Hemagglutinin that Confer Binding to Human Tracheal Airway Epithelium

The emergence in 2009 of a swine-origin H1N1 influenza virus as the first pandemic of the 21st Century is a timely reminder of the international public health impact of influenza viruses, even those associated with mild disease. The widespread distribution of highly pathogenic H5N1 influenza virus in the avian population has spawned concern that it may give rise to a human influenza pandemic. The mortality rate associated with occasional human infection by H5N1 virus approximates 60%, suggesting that an H5N1 pandemic would be devastating to global health and economy. To date, the H5N1 virus has not acquired the propensity to transmit efficiently between humans. The reasons behind this are unclear, especially given the high mutation rate associated with influenza virus replication. Here we used a panel of recombinant H5 hemagglutinin (HA) variants to demonstrate the potential for H5 HA to bind human airway epithelium, the predominant target tissue for influenza virus infection and spread. While parental H5 HA exhibited limited binding to human tracheal epithelium, introduction of selected mutations converted the binding profile to that of a current human influenza strain HA. Strikingly, these amino-acid changes required multiple simultaneous mutations in the genomes of naturally occurring H5 isolates. Moreover, H5 HAs bearing intermediate sequences failed to bind airway tissues and likely represent mutations that are an evolutionary “dead end.” We conclude that, although genetic changes that adapt H5 to human airways can be demonstrated, they may not readily arise during natural virus replication. This genetic barrier limits the likelihood that current H5 viruses will originate a human pandemic.     

Use of stable isotopes to measure the metabolic activity of the human intestinal microbiota

The human intestinal microbiota is a complex biological system comprising a vast repertoire of microbes with considerable metabolic activity relevant to both bacterial growth and host health. Greater strides have been made in the analysis of microbial diversity than in the measurement of functional activity, particularly in vivo. Stable isotope probing offers a new approach by coupling measurements of metabolic activity with microbial identification. Using a low-enrichment labeling strategy in vitro, this study has identified metabolically active bacterial groups via magnetic-bead capture methodology and stable isotope ratio analysis. Using five probes (EUB338, Bac303, Bif164, EREC482, and Clep866), changes in the activities of key intestinal microbial groups were successfully measured by exploiting tracers of de novo RNA synthesis. Perturbation of the nutrient source with oligofructose generated changes in the activity of bifidobacteria as expected, but also in the Bacteroides-Prevotella group, the Eubacterium rectale-Clostridium coccoides group, and the Clostridium leptum subgroup. Changes in activity were also observed in response to the medium type. This study suggests that changes in the functional activity of the gut microbiota can be assessed using tracers of de novo nucleic acid synthesis combined with measurement of low isotopic enrichment in 16S rRNA. Such tracers potentially limit substrate bias because they are universally available to bacteria. This low-enrichment labeling approach does not depend on the commercial availability of specific labeled substrates and can be easily translated to in vivo probing experiments of the functional activity of the microbiota in the human gut.     

Non-ideal effects in indentation testing of soft tissues

Indentation has several advantages as a loading mode for determining constitutive behavior of soft, biological tissues. However, indentation induces a complex, spatially heterogeneous deformation field that creates analytical challenges for the calculation of constitutive parameters. As a result, investigators commonly assume small indentation depths and large sample thicknesses to simplify analysis and then restrict indentation depth and sample geometry to satisfy these assumptions. These restrictions limit experimental resolution in some fields, such as brain biomechanics. However, recent experimental evidence suggests that conventionally applied limits are in fact excessively conservative. We conducted a parametric study of indentation loading with various indenter geometries, surface interface conditions, sample compressibility, sample geometry and indentation depth to quantitatively describe the deviation from previous treatments that results from violation of the assumptions of small indentation depth and large sample thickness. We found that the classical solution was surprisingly robust to violation of the assumption of small strain but highly sensitive to violation of the assumption of large sample thickness, particularly if the indenter was cylindrical. The ramifications of these findings for design of indentation experiments are discussed and correction factors are presented to allow future investigators to account for these effects without recreating our finite element models.     

Local competition sparks concerns for fairness in the ultimatum game

Humans reject uneven divisions of resources, even at personal cost. This is observed in countless experiments using the ultimatum game, where a proposer offers to divide a resource with a responder who either accepts the division or rejects it (whereupon both earn zero). Researchers debate why humans evolved a psychology that is so averse to inequity within partnerships. We suggest that the scale of competition is crucial: under local competition with few competitors, individuals reject low offers, because they cannot afford to be disadvantaged relative to competitors. If one competes against the broader population (i.e. global competition), then it pays to accept low offers to increase one''s absolute pay-off. We support this intuition with an illustrative game-theoretical model. We also conducted ultimatum games where participants received prizes based on pay-offs relative to immediate partners (local competition) versus a larger group (global competition). Participants demanded higher offers under local competition, suggesting that local competition increases people''s demands for fairness and aversion to inequality.     

The antioxidant activity of alpha-tocopherol-bovine serum albumin complex in micellar and liposome autoxidations

A comparison is made of the antioxidant activity of a water-soluble form of alpha-tocopherol complexed with bovine serum albumin (alpha-T X BSA) with that of micellar alpha-tocopherol and aqueous 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylate (Trolox) to inhibit autoxidation of linoleic acid in sodium dodecyl sulfate micelles. The peroxyl radical trapping ability of alpha-T X BSA compares favorably with that of alpha-tocopherol and Trolox, and all three can be used in quantitative measurements of the susceptibility of the micellar substrate to undergo autoxidation: the oxidizability, for reactions initiated in the micellar phase by di-tertbutylhyponitrite (DBHN) or in the aqueous phase by azobisamidinopropane hydrochloride (ABAP). alpha-Tocopherol and Trolox are also effective antioxidants to inhibit DBHN- or ABAP-initiated autoxidations of dilinoleoylphosphatidylcholine (DLPC) liposomes prepared as multilamellar or unilamellar bilayers characterized by 31P NMR spectra. The oxidizability of DLPC liposomes is determined by various combinations of water-soluble and lipid-soluble initiators and the antioxidants, alpha-tocopherol and Trolox. In contrast, alpha-T X BSA does not effectively trap peroxyl radicals when it is added after initiation of autoxidation in the lipid phase (DBHN) or in the aqueous phase (ABAP). The radical trapping ability of alpha-T X BSA becomes evident if it is mixed with the DLPC for some hours before initiation. This result is interpreted in terms of diffusion of alpha-tocopherol from the bound alpha-T X BSA form to the liposome before it exhibits antioxidant activity.