Applications of biological pores in nanomedicine, sensing, and nanoelectronics

Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics.

Prevention of rapid intracellular degradation of ODC by a carboxyl-terminal truncation

Ornithine decarboxylase (ODC) was converted from a protein with a short intracellular half-life in mammalian cells to a stable protein by truncating 37 residues at its carboxyl terminus. Cells expressing wild-type protein lost ODC activity with a half-life of approximately 1 hour. Cells expressing the truncated protein, however, retained full activity for at least 4 hours. Pulse-chase experiments in which immunoprecipitation and gel electrophoresis were used confirmed the stabilizing effect of the truncation. Thus, a carboxyl-terminal domain is responsible for the rapid intracellular degradation of murine ODC.

Rapid reacquisition in conditioning of the rabbit's nictitating membrane response

Reacquisition after extinction often appears faster than original acquisition. However, data from conditioned suppression studies indicate that this effect may arise from spontaneous recovery and reinstatement of unextinguished contextual stimuli related to the unconditioned stimulus (US). In the present experiments using the rabbit nictitating membrane preparation, spontaneous recovery was eradicated before reaquisition training. US contextual stimuli were controlled by retaining the US during extinction through explicit unpairings of the conditioned stimulus (CS) and US. Attempts were also made to drive the associative strength of the CS into the inhibitory region by differential conditioning and conditioned inhibition procedures. In all cases, reacquisition was very rapid in comparison with a rest control. The results are discussed with respect to their implications for CS and US processing models of conditioning.

A semi-synthetic ion channel platform for detection of phosphatase and protease activity

Sensitive methods to probe the activity of enzymes are important for clinical assays and for elucidating the role of these proteins in complex biochemical networks. This paper describes a semi-synthetic ion channel platform for detecting the activity of two different classes of enzymes with high sensitivity. In the first case, this method uses single ion channel conductance measurements to follow the enzyme-catalyzed hydrolysis of a phosphate group attached to the C-terminus of gramicidin A (gA, an ion channel-forming peptide) in the presence of alkaline phosphatase (AP). Enzymatic hydrolysis of this phosphate group removes negative charges from the entrance of the gA pore, resulting in a product with measurably reduced single ion channel conductance compared to the original gA-phosphate substrate. This technique employs a standard, commercial bilayer setup and takes advantage of the catalytic turnover of enzymes and the amplification characteristics of ion flux through individual gA pores to detect picomolar concentrations of active AP in solution. Furthermore, this technique makes it possible to study the kinetics of an enzyme and provides an estimate for the observed rate constant (k(cat)) and the Michaelis constant (K(M)) by following the conversion of the gA-phosphate substrate to product over time in the presence of different concentrations of AP. In the second case, modification of gA with a substrate for proteolytic cleavage by anthrax lethal factor (LF) afforded a sensitive method for detection of LF activity, illustrating the utility of ion channel-based sensing for detection of a potential biowarfare agent. This ion channel-based platform represents a powerful, novel approach to monitor the activity of femtomoles to picomoles of two different classes of enzymes in solution. Furthermore, this platform has the potential for realizing miniaturized, cost-effective bioanalytical assays that complement currently established assays.

Slugs: potential novel vectors of Escherichia coli O157

Field and laboratory studies were performed to determine whether slugs could act as novel vectors for pathogen (e.g., Escherichia coli O157) transfer from animal feces to salad vegetables. Escherichia coli O157 was isolated from 0.21% of field slugs from an Aberdeenshire sheep farm. These isolates carried the verocytotoxin genes (vt1 and vt2) and the attaching and effacing gene (eae), suggesting that they are potentially pathogenic to humans. Strain typing using multilocus variable number tandem repeats analysis showed that slug and sheep isolates were indistinguishable. Laboratory experiments using an E. coli mutant resistant to nalidixic acid showed that the ubiquitous slug species Deroceras reticulatum could carry viable E. coli on its external surface for up to 14 days. Slugs that had been fed E. coli shed viable bacteria in their feces with numbers showing a short but statistically significant linear log decline. Further, it was found that E. coli persisted for up to 3 weeks in excreted slug feces, and hence, we conclude that slugs have the potential to act as novel vectors of E. coli O157.

Polyamine-mediated regulation of mouse ornithine decarboxylase is posttranslational

The activity of ornithine decarboxylase (ODC) is negatively regulated by intracellular polyamines, which thereby mediate a form of feedback inhibition of the initial enzyme in the pathway of their synthesis. This phenomenon has been believed to result, at least in part, from translational regulation. To investigate this further, we performed four series of experiments. First, we found that a chimeric protein encoded by an mRNA containing the ODC 5' leader sequence did not exhibit polyamine-dependent regulation. Second, we showed that transcripts containing the protein-coding sequence of ODC, but no other ODC-derived sequence information, exhibited regulation. Third, we found that the association of ODC mRNA with ribosomes was not altered when intracellular polyamine levels were modulated under conditions previously deemed to cause translational regulation. Last, we carried out experiments to measure the incorporation of [35S]methionine into ODC in polyamine-starved and polyamine-replete cells. Differential incorporation diminished progressively as pulse-label times were shortened; at the shortest labeling time used (4 min), the difference in favor of ODC in polyamine-starved cells was less than twofold. These findings suggest that it is necessary to reevaluate the question of whether polyamines cause alterations of translation of ODC mRNA.

Structural elements of ornithine decarboxylase required for intracellular degradation and polyamine-dependent regulation

Mammalian ornithine decarboxylase (ODC), a key enzyme in polyamine biosynthesis, is rapidly degraded in cells, an attribute important to the regulation of its activity. Mutant and chimeric ODCs were created to determine the structural requirements for two modes of proteolysis. Constitutive degradation requires the carboxy terminus and is independent of intracellular polyamines. Truncation of five or more carboxy-terminal amino acids prevents this mode of degradation, as do several internal deletions within the 37 carboxy-most amino acids that spare the last five residues. Polyamine-dependent degradation of ODC requires a distinct region outside the carboxy terminus. The ODC of a parasite, Trypanosoma brucei, is structurally very similar to mouse ODC but lacks the carboxy-terminal domain; it is not a substrate for either pathway. The regulatory properties of enzymatically active chimeric proteins incorporating regions of the two ODCs support the conclusion that distinct domains of mouse ODC confer constitutive degradation and polyamine-mediated regulation. Mouse ODC contains two PEST regions. The first was not required for either form of degradation; major deletions within the second ablated constitutive degradation. When mouse and T. brucei ODC RNAs were translated in vitro in a reticulocyte lysate system, the effects of polyamine concentration on ODC protein production and activity were similar for the two mRNAs, which contradicts claims that this system accurately reflects the in vivo effects of polyamines on responsive ODCs.

Rapid reaquisition in conditioning of the rabbit's nictitating membrane response

Reacquisition after extinction often appears faster than original acquisition. However, data from conditioned suppression studies indicate that this effect may arise from spontaneous recovery and reinstatement of unextinguished contextual stimuli related to the unconditioned stimulus (US). In the present experiments using the rabbit nictitating membrane preparation, spontaneous recovery was eradicated before reaquisition training. US contextual stimuli were controlled by retaining the US during extinction through explicit unpairings of the conditioned stimulus (CS) and US. Attempts were also made to drive the associative strength of the CS into the inhibitory region by differential conditioning and conditioned inhibition procedures. In all cases, reacquisition was very rapid in comparison with a rest control. The results are discussed with respect to their implications for CS and US processing models of conditioning.

The ornithine decarboxylase gene of Caenorhabditis elegans: cloning, mapping and mutagenesis

The gene (odc-1) encoding ornithine decarboxylase, a key enzyme in polyamine biosynthesis, was cloned and characterized. Two introns interrupt the coding sequence of the gene. The deduced protein contains 422 amino acids and is homologous to ornithine decarboxylases of other eukaryotic species. In vitro translation of a transcript of the cDNA yielded an enzymatically active product. The mRNA is 1.5 kb in size and is formed by trans-splicing to SL1, a common 5' RNA segment. odc-1 maps to the middle of LG V, between dpy-11 and unc-42 and near a breakpoint of the nDf32 deficiency strain. Enzymatic activity is low in starved stage 1 (L1) larva and, after feeding, rises progressively as the worms develop. Targeted gene disruption was used to create a null allele. Homozygous mutants are normally viable and show no apparent defects, with the exception of a somewhat reduced brood size. In vitro assays for ornithine decarboxylase activity, however, show no detectable enzymatic activity, suggesting that ornithine decarboxylase is dispensible for nematode growth in the laboratory.

Complementation of a polyamine-deficient Escherichia coli mutant by expression of mouse ornithine decarboxylase

Mouse ornithine decarboxylase (ODCase) cDNA was expressed at a high level in an Escherichia coli mutant deficient in polyamine biosynthesis. The expression of mouse ornithine decarboxylase relieved the dependence of the mutant on an exogenous source of polyamines, presumably by providing putrescine, the product of the enzyme. The effect on the enzymatic activity of deletions that removed carboxy-terminal amino acids of the protein was determined.

Diversity of Escherichia coli O157 in a longitudinal farm study using multiple-locus variable-number tandem-repeat analysis

AIMS

To perform a longitudinal study of the diversity of Escherichia coli O157 from a ruminant pasture/stream environment using multiple-locus variable-number tandem-repeat analysis (MLVA).

METHODS AND RESULTS

Samples of faecal droppings from grazing ruminants and from an adjacent stream were tested longitudinally for E. coli O157 by enrichment and immunomagnetic separation (IMS). Using MLVA, 24 different profiles were identified from a total of 231 E. coli O157 isolates, of which 80 were included in a similarity analysis. Four main clusters with several subclusters were observed. Although there was close contact between sheep and cattle during the study period, E. coli O157 was surprisingly not detected from cattle faeces.

CONCLUSIONS

The cluster analysis indicated both unrelated and closely related E. coli O157 strains. The choice of loci to target in MLVA is important for the subtyping result, as loci with high diversities are essential for discriminating between closely related isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

There is a lack of data available on the use of MLVA to describe E. coli O157 diversity and changes over time in the animal reservoirs and the environment. Such data are needed in order to further develop MLVA as a typing method.

Conditioning and reflex modification of the rabbit nictitating membrane response using electrical stimulation in auditory nuclei

Electrical brain stimulation (EBS) was applied to four nuclei in the auditory system, namely, the cochlear nucleus (CN), superior olive (SO), inferior colliculus, and medial geniculate. EBS was also applied to the pontine nuclei, which are the main relays for transmitting auditory conditioned stimuli (CSs) into the cerebellar pathways for conditioning of the nictitating membrane response (NMR). EBS of the CN, but no other site, yielded reflex modification, which was an increase in the unconditioned NMR to an airpuff unconditioned stimulus (US) when preceded by EBS. Throughout the experiment, EBS of the SO produced a distinctive distribution of NMRs, in which a high proportion had latencies less than 50 ms. When EBS was repeatedly paired with the airpuff US, conditioned responses (CRs) were acquired to comparable levels across all sites. At each site, response likelihood was an increasing function of the EBS parameters of pulse amplitude, pulse frequency, and pulse width. Combined with anatomical findings, these results indicate that multiple encodings of an auditory CS are sent to the pathways for the NMR.

Fos-like immunoreactivity in locus coeruleus after classical conditioning of the rabbit's nictitating membrane response

We investigated the changes in Fos-like immunoreactivity in the locus coeruleus (LC) after classical conditioning of the rabbit's nictitating membrane. Specifically, we compared unpaired versus paired presentations of a tone conditioned stimulus (CS) and a tactile unconditioned stimulus (US; near the eye). After two training sessions, only paired presentations resulted in acquisition of a conditioned response. This was associated with comparatively less LC Fos expression than with unpaired presentations. Similar observations have been reported for the ventrolateral medulla which is a major source of afferents to LC. The present results are consistent with a role of LC in attention and learning: activity increases as the animal attends to the CS and US. When the relationship between CS and US has been established, LC activity decreases.

Effects of post-mortem delay on high affinity forskolin binding sites and adenylate cyclase activity in rat and human striatum and cerebral cortex

High affinity [3H]forskolin binding was measured using quantitative autoradiography in the striatum and frontal cortex of rat and human brain. Forskolin binding in rat striatum (310.8 +/- 26.0 pmol/g mean +/- S.E.M.) was approximately 4 times that in the frontal cortex (75.5 +/- 8.4 pmol/g), whereas in post-mortem human brain each region exhibited similar levels of forskolin binding (striatum 51.3 +/- 1.2 and cortex 53.2 +/- 2.1 pmol/g). Basal adenylate cyclase activity was assayed in membranes prepared from striatum and frontal cortex of rat and human; enzyme activity in the rat striatum was approximately 2-fold that in rat frontal cortex whereas enzyme activity in the human striatum was similar to that in the human frontal cortex. To investigate the effect of the interval between death and freezing of the brain, rats were killed by decapitation, then maintained at 37 degrees C for up to 4 hours before freezing and subsequent assay of forskolin binding and adenylate cyclase activity. Striatal forskolin binding declined markedly post-mortem such that 4 h post-mortem it was only 13% of the level in control animals while levels of cortical forskolin binding declined minimally during the immediate post-mortem period. Striatal and cortical adenylate cyclase activity (basal) was minimally influenced by post-mortem delay although in both regions there was a rapid loss of the ability of fluoroaluminate to stimulate adenylate cyclase. The data suggest that the striatum contains a population of high affinity forskolin binding sites which is extremely sensitive to post-mortem delay.(ABSTRACT TRUNCATED AT 250 WORDS)

Distal osteosclerosis

Hyperostosis of the bones of the forearms and lower legs and mild cranial sclerosis were present in five persons in two generations of a South African kindred of mixed ancestry. This disorder, which is clinically innocuous, is inherited as an autosomal dominant trait. Delineation of this disorder to distinguish it from the other inherited sclerosing bone dysplasias permits accurate prognosis and genetic counselling. In view of the unusual anatomical distribution of the abnormalities, the designation "distal osteosclerosis" is proposed for this entity.

Mechanistic insight into gramicidin-based detection of protein-ligand interactions via sensitized photoinactivation

Among the many challenges for the development of ion channel-based sensors is the poor understanding of how to engineer modified transmembrane pores with tailored functionality that can respond to external stimuli. Here, we use the method of sensitized photoinactivation of gramicidin A (gA) channels in planar bilayer lipid membranes to help elucidate the underlying mechanistic details for changes in macroscopic transmembrane ionic current observed upon interaction of C-terminally attached gA ligands with specific proteins in solution. Three different systems were studied: (i) carbonic anhydrase (CA) and gA-sulfonamide, (ii) PSD-95 protein (belonging to the 'PDZ domain-containing protein') and a gA analog carrying the KGGHRRSARYLESSV peptide sequence at the C-terminus, and (iii) an anti-biotin antibody and gA-biotin. The results challenge a previously proposed mechanistic hypothesis suggesting that protein-induced current suppression is due to steric blockage of the ion passage through gA channels, while they reveal new insight for consideration in alternative mechanistic models. Additionally, we demonstrate that the length of a linker between the ligand and the gA channel may be less important for gramicidin-based detection of monovalent compared to multivalent protein-ligand interactions. These studies collectively shed new light on the mechanism of protein-induced current alterations in bilayer recordings of gA derivatives, which may be important in the design of new gramicidin-based sensors.

Real-time processing of serial stimuli in classical conditioning of the rabbit's nictitating membrane response

Real-time models contend that a conditioned stimulus (CS) gives rise to a cascade of hypothetical stimuli that govern conditioned responses (CRs) on a moment-by-moment basis. Experiments with the rabbit nictitating membrane response successfully extended these models to external stimuli. CSs were trained in sequence with an unconditioned stimulus (CSA-CSB-US). When the CSA-CSB interval was shortened, the CR was compressed; when the CSA-CSB interval was lengthened, the CR was broadened. Peaks appeared at 2 places, namely, 1 following CSA by a period equal to its CS-US interval and another following CSB by its CS-US interval. Outside the sequence, the individual CSs evoked CRs located between their respective CS-US intervals. When, however, the 2 CSs were trained separately, the CRs were appropriate to their respective CS-US intervals when tested alone or in sequence. The results are discussed in terms of the J.E. Desmond and J.W. Moore (1988) and S. Grossberg and N.A. Schmajuk (1989) models.

P-FLUX: A phosphorus budget dataset spanning diverse agricultural production systems in the United States and Canada

Quantifying spatial and temporal fluxes of phosphorus (P) within and among agricultural production systems is critical for sustaining agricultural production while minimizing environmental impacts. To better understand P fluxes in agricultural landscapes, P-FLUX, a detailed and harmonized dataset of P inputs, outputs, and budgets, as well as estimated uncertainties for each P flux and budget, was developed. Data were collected from 24 research sites and 61 production systems through the Long-term Agroecosystem Research (LTAR) network and partner organizations spanning 22 U.S. states and 2 Canadian provinces. The objectives of this paper are to (a) present and provide a description of the P-FLUX dataset, (b) provide summary analyses of the agricultural production systems included in the dataset and the variability in P inputs and outputs across systems, and (c) provide details for accessing the dataset, dataset limitations, and an example of future use. P-FLUX includes information on select site characteristics (area, soil series), crop rotation, P inputs (P application rate, source, timing, placement, P in irrigation water, atmospheric deposition), P outputs (crop removal, hydrologic losses), P budgets (agronomic budget, overall budget), uncertainties associated with each flux and budget, and data sources. Phosphorus fluxes and budgets vary across agricultural production systems and are useful resources to improve P use efficiency and develop management strategies to mitigate environmental impacts of agricultural systems. P-FLUX is available for download through the USDA Ag Data Commons (https://doi.org/10.15482/USDA.ADC/1523365).

Methyldopa hypotension and ascending projections from midline serotonin (B3) cells in the medulla

Micro-injection of methyldopa into the area of the midline B3 serotonin cell group in the ventral medulla of spontaneously hypertensive rats, stroke-prone strain (SHRSP), caused a fall in blood pressure of 30-40 mmHg, maximally 2-3 h after administration. This hypotension was abolished by the selective serotonin neurotoxin 5,7-dihydroxytryptamine (5,7-DHT) injected intracerebroventricularly, but it was not affected by intraspinal injection of 5,7-DHT to produce a selective lesion of serotonin nerves descending into the spinal cord, or by injection of 5,7-DHT into the median forebrain bundle, one of the main ascending pathways from the B3 serotonin cells. It seems likely that the midline serotonin B3 cells in the medulla contribute to the hypotensive action of methyldopa through a projection restricted to the caudal brainstem.