Patch Clamp and Perfusion Techniques for Studying Ion Channels Expressed in Xenopus oocytes

The protocol presented here is designed to study the activation of the large conductance, voltage- and Ca²⁺-activated K⁺ (BK) channels. The protocol may also be used to study the structure-function relationship for other ion channels and neurotransmitter receptors¹. BK channels are widely expressed in different tissues and have been implicated in many physiological functions, including regulation of smooth muscle contraction, frequency tuning of inner hair cells and regulation of neurotransmitter release^2-6. BK channels are activated by membrane depolarization and by intracellular Ca²⁺ and Mg^2+6-9. Therefore, the protocol is designed to control both the membrane voltage and the intracellular solution. In this protocol, messenger RNA of BK channels is injected into Xenopus laevis oocytes (stage V-VI) followed by 2-5 days of incubation at 18°C^10-13. Membrane patches that contain single or multiple BK channels are excised with the inside-out configuration using patch clamp techniques^10-13. The intracellular side of the patch is perfused with desired solutions during recording so that the channel activation under different conditions can be examined. To summarize, the mRNA of BK channels is injected into Xenopus laevis oocytes to express channel proteins on the oocyte membrane; patch clamp techniques are used to record currents flowing through the channels under controlled voltage and intracellular solutions.Download video file.^{(62M, mov)}     

Common minor histocompatibility antigen discovery based upon patient clinical outcomes and genomic data

Background

Minor histocompatibility antigens (mHA) mediate much of the graft vs. leukemia (GvL) effect and graft vs. host disease (GvHD) in patients who undergo allogeneic stem cell transplantation (SCT) [1], [2], [3], [4]. Therapeutic decision making and treatments [5] based upon mHAs will require the evaluation of multiple candidate mHAs and the selection of those with the potential to have the greatest impact on clinical outcomes. We hypothesized that common, immunodominant mHAs, which are presented by HLA-A, B, and C molecules, can mediate clinically significant GvL and/or GvHD, and that these mHAs can be identified through association of genomic data with clinical outcomes.

Methodology/Principal Findings

Because most mHAs result from donor/recipient cSNP disparities, we genotyped 57 myeloid leukemia patients and their donors at 13,917 cSNPs [6]. We correlated the frequency of genetically predicted mHA disparities with clinical evidence of an immune response and then computationally screened all peptides mapping to the highly associated cSNPs for their ability to bind to HLA molecules. As proof-of-concept, we analyzed one predicted antigen, T4A, whose mHA mismatch trended towards improved overall and disease free survival in our cohort. T4A mHA mismatches occurred at the maximum theoretical frequency for any given SCT. T4A-specific CD8+ T lymphocytes (CTLs) were detected in 3 of 4 evaluable post-transplant patients predicted to have a T4A mismatch.

Conclusions/Significance

Our method is the first to combine clinical outcomes data with genomics and bioinformatics methods to predict and confirm a mHA. Refinement of this method should enable the discovery of clinically relevant mHAs in the majority of transplant patients and possibly lead to novel immunotherapeutics [5].     

Using ultraviolet light for improved antifouling performance on ship hull coatings

Abstract

A two-part study was designed to investigate the efficacy of using UVC to prevent biofouling in the context of ship hull coatings. The first study determined the frequency of UVC required for a coating that does not have any additives (epoxy). It was found that 1?min/day was effective at preventing hard fouling but not biofilm development. The second study addressed several variables: coating type (epoxy, copper, fouling release), frequency of UVC (no exposure, continuous exposure, 1min/6h, 1?min/day), and distance from the lamp (25 and 50?mm). Continuous UVC exposure resulted in no biofouling settlement but it did damage the copper coating. Intermittent UVC exposure was effective at preventing biofouling recruitment to both the copper and the fouling release coatings. Variations were observed with regards to the fouling composition, especially biofilms, sedimentary tubeworms and barnacles, suggesting tolerances within the community.     

The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations

Microbial communities associated with agricultural animals are important for animal health, food safety, and public health. Here we combine high-throughput sequencing (HTS), quantitative-PCR assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2–4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples), significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were potentially metabolically active and encountered in on-farm samples. Network analysis was focused on the foodborne pathogen Campylobacter and revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. These data represent the first use of HTS to characterize the poultry microbiome across a series of farm-to-fork samples and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.     

Spatial patterns of DNA replication, protein synthesis, and oxygen concentration within bacterial biofilms reveal diverse physiological states

It has long been suspected that microbial biofilms harbor cells in a variety of activity states, but there have been few direct experimental visualizations of this physiological heterogeneity. Spatial patterns of DNA replication and protein synthetic activity were imaged and quantified in staphylococcal biofilms using immunofluorescent detection of pulse-labeled DNA and also an inducible green fluorescent protein (GFP) construct. Stratified patterns of DNA synthetic and protein synthetic activity were observed in all three biofilm systems to which the techniques were applied. In a colony biofilm system, the dimensions of the zone of anabolism at the air interface ranged from 16 to 38 microm and corresponded with the depth of oxygen penetration measured with a microelectrode. A second zone of activity was observed along the nutrient interface of the biofilm. Much of the biofilm was anabolically inactive. Since dead cells constituted only 10% of the biofilm population, most of the inactive cells in the biofilm were still viable. Collectively, these results suggest that staphylococcal biofilms contain cells in at least four distinct states: growing aerobically, growing fermentatively, dead, and dormant. The variety of activity states represented in a biofilm may contribute to the special ecology and tolerance to antimicrobial agents of biofilms.     

Successful artificial insemination in the corn snake,Elaphe gutatta,using fresh and cooled semen

The design and implementation of assisted reproductive technology to improve genetic diversity and augment captive populations is an important but rarely applied research field in reptiles. Using the corn snake (Elaphe gutatta) as a model, the Henry Doorly Zoo recently produced offspring born as a result of artificial insemination using both fresh, diluted semen, and diluted semen stored at refrigeration for 3 days. Semen was collected noninvasively from sexually mature male corn snakes using a gentle massaging technique, extended in medium then inseminated into the oviducts of adult females. Using molecular genetic techniques to confirm or refute the success of the insemination using primers developed for the black rat snake, Elaphe obsolete, all possible parents and offspring genotypes were evaluated. A paternity‐by‐exclusion analysis verified that the offspring were in fact a result of artificial insemination. Zoo Biol 26:363–369, 2007. © 2007 Wiley‐Liss, Inc.