Rewiring Riboswitches to Create New Genetic Circuits in Bacteria.

Riboswitches are RNA elements that control the expression of genes through a variety of mechanisms in response to the specific binding of small-molecule ligands. Since their discovery, riboswitches have shown promise for the artificial control of transcription or translation of target genes, be it for industrial biotechnology, protein expression, metabolic engineering, antimicrobial target validation, or gene function discovery. However, natural riboswitches are often unsuitable for these purposes due to their regulation by small molecules which are already present within the cell. For this reason, research has focused on creating riboswitches that respond to alternative biologically inert ligands or to molecules which are of interest for biosensing. Here we present methods for the development of artificial riboswitches in Gram-negative and Gram-positive bacteria. These methods are based on reengineering natural aptamers to change their ligand specificity toward molecules which do not bind the original aptamer (ie, that are orthogonal to the original). The first approach involves targeted mutagenesis of native riboswitches to change their specificity toward rationally designed synthetic ligand analogs. The second approach involves the fusion of previously validated orthogonal aptamers with native expression platforms to create novel chimeric riboswitches for the microbial target. We establish the applicability of these methods both for the control of exogenous genes as well as for the control of native genes.

Pseudocollinia brintoni gen. nov., sp. nov. (Apostomatida: Colliniidae), a parasitoid ciliate infecting the euphausiid Nyctiphanes simplex.

A novel parasitoid ciliate, Pseudocollinia brintoni gen. nov., sp. nov. was discovered infecting the subtropical sac-spawning euphausiid Nyctiphanes simplex off both coasts of the Baja California peninsula, Mexico. We used microscopic, and genetic information to describe this species throughout most of its life cycle. Pseudocollinia is distinguished from other Colliniidae genera because it exclusively infects euphausiids, has a polymorphic life cycle, and has a small cone-shaped oral cavity whose left wall has a field of ciliated kinetosomes and whose opening is surrounded on the left and right by 2 'oral' kineties (or ciliary rows) that terminate at its anterior border. Two related species that infect different euphausiid species from higher latitudes in the northeastern Pacific Ocean, Collinia beringensis Capriulo and Small, 1986, briefly redescribed herein, and Collinia oregonensis Gómez-Gutiérrez, Peterson, and Morado, 2006, are transferred to the genus Pseudocollinia. P. brintoni has between 12 and 18 somatic kineties, and its oral cavity has only 2 oral kineties, while P. beringensis comb. nov. has more somatic kineties, including 3 oral kineties. P. oregonensis comb. nov. has an intermediate number of somatic kineties. P. beringensis comb. nov. also infects Thysanoessa raschi (a new host species). SSU rRNA and cox1 gene sequences demonstrated that Pseudocollinia ciliates are apostome ciliates and that P. brintoni is different from P. beringensis comb. nov. High densities of rod-shaped bacteria (1.7 µm length, 0.2 to 0.5 µm diameter) were associated with P. brintoni. After euphausiid rupture, high concentrations of P. brintoni and bacteria cluster to form 3 to 6 cm long filaments where tomites encyst and transform to the phoront stage; this is a novel place for encystation. P. brintoni may complete its life cycle when the euphausiids feed on these filaments.

Biological activity of EDQM CRS for Interferon alfa-2a and Interferon alfa-2b - assessment in two in vitro bioassays.

The European Directorate for the Quality of Medicines (EDQM) supplies Chemical Reference Substances (CRS) for Interferon (IFN) alfa-2a (CRS I0320300) and for IFN alfa-2b (CRS I0320301) for specified physicochemical tests. However, no information is provided as to their biological activity. In contrast, the World Health Organization (WHO) provides the 2nd International Standards (IS) for IFN alfa-2a (code 95/650) and for IFN alfa-2b (code 95/566), with activity defined in International Units (IU) for calibration of biological activity of preparations of IFN. We have compared the EDQM CRSs with the WHO ISs in two bioassay systems, one measuring the anti-proliferative activity in the Daudi cell line and the other measuring a reporter gene activation in an A549 cell line. In each of these assay systems, the CRSs gave dose - response relations, which were similar to those for the WHO ISs. Estimates of relative activity for each CRS, in terms of the respective IS, showed specific biological activity for the CRSs of the same order as the nominal specific activity for the ISs. However, the estimates of relative activity were not consistent between the two assays systems, emphasizing the need for calibration within each system, if the CRS were to be used as a working standard for bioassays. For structure-activity studies, both physicochemical and biological activity characterisation are required for the same biopharmaceutical preparation. CRS I0320300 and CRS I0320301 may prove useful as working standards for some bioassay systems.

Factors affecting reaction times to short anterior postural disturbances.

One source of falls in the elderly may be an inability to sufficiently adjust to transient postural perturbations or slips. Identifying useful predictors of fall potential, as well as factors that affect the ability of an individual to detect a movement of the standing support surface may provide insight into postural stability and methods to increase stability in elders. The effects of acceleration, displacement, neurological status, and age on movement detection reaction times were studied in 25 individuals--1 young adults, seven neurologically intact elderly adults, and six elders with (diabetic) peripheral neuropathy. Acceleration detection thresholds for anterior perturbations of 1, 4, and 16 mm of the support surface was previously determined for each subject via a two-alternative forced choice (2AFC) protocol, with longer (16 mm) moves yielding lower 2AFC thresholds (12-39 mm/s(2)) that varied by group. Using the acceleration threshold value determined, and 125% of that threshold (suprathreshold), reaction times to the start of the platform movement were determined for all three displacements. Reaction times to an additional superthreshold movement (4 mm at 100 mm/s(2)) were also measured. Lower acceleration values over longer moves required longer reaction times for motion detection. Reaction times were also influenced by peak energy imparted to the subject through the move. The higher prevalence of falls in the elderly and elderly diabetic may be due to slowing reaction times compounded by larger amounts of imparted energy needed for detection of a slipping event.

Using electrostatic self-assembled gradient nanosensor phantoms for calibration of an optical intrinsic signal imaging system.

Wide-field optical intrinsic signal (OIS) imaging has been used in functional cortex mapping for its excellent spatial resolution. To compensate for its low temporal resolution, extrinsic dye signals have been introduced. Fluorescence spectroscopy in the form of nanoengineered sensors has also been used to detect biochemical signals of molecular interactions. In this paper, oxygen-sensitive dye Ru(dpp)/sub 3//sup 2+/ was immobilized into nano-sized spheres by electrostatic layer-by-layer (LbL) self-assembly, and then deposited on glass slides as intensity gradients. By comparing gradient ratios and ratios of function dye Ru(dpp)/sub 3//sup 2+/ and reference dye between epi-fluorescence microscope and an OIS imaging system, the feasibility and efficiency of nano-sized oxygen sensors in OIS imaging were studied.

Acceleration threshold detection during short anterior and posterior perturbations on a translating platform.

Balance control systems have usually been studied under two conditions, during quiet standing or under large postural perturbations of a magnitude that requires a postural adjustment to prevent falling. Between these two extremes lie perturbations that can be repeated and measured while not forcing adaptive strategies from the postural control system. Unlike other studies of postural control, we employed very short translations with varying accelerations at the edge of psychophysical detectability. These perturbations were vibration-free anterior or posterior translations of the platform on which a subject stood. Using a full Latin-square design set of perturbations in the forward or backward direction, with a smooth or jerk acceleration profile, and of length 4 or 20 mm, were presented to five subjects. Perceptual peak acceleration thresholds were determined by an iterative psychophysical method that forced the subjects to choose in which of two sequential intervals that they perceived a stimulus to have been presented. The only factor found that significantly correlated with detection was perturbation length. The 4 mm peak thresholds averaged 14.51 mm/s2 while 20 mm thresholds averaged 8.55 mm/s2. For the short perturbations employed in this study, detection of motion thus was dependent upon the magnitude of the acceleration, but it was independent of the acceleration profile (jerk versus smooth) or movement direction. By understanding the influences on the ability to perceptually detect motion underfoot, we can begin to understand what elements of the postural control system might be involved in the second-to-second control of balance.

International Standards for hepatocyte growth factor/scatter factor: initial assessment of candidate materials and their evaluation by multicentre collaborative study.

Hepatocyte growth factor/scatter factor (HGF/SF) is a potent paracrine growth factor with motogenic, mitogenic and morphogenic activities, and a potential therapeutic role in hepatic and renal disease, as well as diagnostic and prognostic applications. It is synthesised as an inactive, single-chain precursor that is cleaved by serine proteases to give a biologically active, heterodimeric form. To develop World Health Organization (WHO) International Standards (IS) for HGF/SF, candidate preparations of the two forms were assessed in a multicentre study in which they were compared with local standards by bioassay and immunoassay. Among laboratories, there was a wide variation in the estimates of potencies of the candidate standards in terms of in-house reference preparations, but between-assay and within-assay variabilities were low within laboratories. In some assay systems, the precursor and heterodimer showed different responses. Since both molecular forms are widely used in current assay systems, this suggested that a reference preparation was required for each form of the HGF/SF molecule. Accordingly, the Expert Committee on Biological Standardization of WHO established the heterodimeric material (96/564) as the first IS for HGF/SF, human, recombinant, with an assigned unitage of 4000 IU/ampoule and, for the purpose of immunoassay calibration, a nominal HGF/SF content of 4 microg/ampoule. The precursor preparation (96/556) was established as the first IS for HGF/SF (precursor) with an assigned unitage of 2000 IU/ampoule and, for the purpose of immunoassay calibration, a nominal HGF/SF (precursor) content of 4 microg/ampoule. The preparations can be obtained upon written request to the National Institute for Biological Standards and Control (NIBSC, PO Box 1193), by e-mail (standards@nibsc.ac.uk) or ordered at http://www.nibsc.ac.uk.

The first international standard for human leptin and the first international standard for mouse leptin: comparison of candidate preparations by in vitro bioassays and immunoassays.

In an international collaborative study, two preparations of human sequence recombinant leptin and two preparations of mouse sequence recombinant leptin were evaluated, using in vitro bioassays and immunoassays, by eight laboratories, in three countries, for their suitability to serve as the international standard (IS) for human and mouse leptin respectively. The bioassays detected the human and mouse leptin with similar potency, while the immunoassays showed a greater response to the leptin of the species against which the antibody preparation had been raised. Comparison of the candidate standards with the various preparations of leptin of the same species currently assayed in the participating laboratories showed that immunoassay measurements cannot be used to predict the biological potency. On the basis of the results reported here, in October 1999 the Expert Committee on Biological Standardization of the World Health Organization established the preparation coded 97/594 as the first IS for human leptin, with an assigned unitage of 4000 IU/ampoule, and the preparation coded 97/626 as the first IS for mouse leptin, with an assigned unitage of 4000 IU/ampoule. The ISs for leptin are distributed by the National Institute for Biological Standards and Control, UK, http://www.nibsc.ac.uk.

Inactivation of JNK activity by mitogen-activated protein kinase phosphatase-2 in EAhy926 endothelial cells is dependent upon agonist-specific JNK translocation to the nucleus.

We have investigated the termination of agonist-stimulated mitogen-activated protein (MAP) kinase activity in EAhy926 cells by MAP kinase phosphatase-2 (MKP-2). In cells expressing either wild-type (WT) or catalytically inactive (CI)-MKP-2, there was no significant differences in TNFalpha-stimulated JNK or p38 MAP kinase activity, however hydrogen peroxide (H2O2)-stimulated JNK activity was substantially reduced in WT-MKP-2 expressing clones and enhanced in cells expressing CI-MKP-2. Consistent with these findings, we observed substantial nuclear translocation of JNK occurred in response to H2O2 but not TNFalpha. Using a phosphospecific anti-JNK antibody, we found that TNFalpha-stimulated JNK activity was associated principally with the cytosol while in response to H2O2, JNK activity was found within the nucleus. These results show that the role of MKP-2 in terminating JNK activity is determined by the translocation of JNK to the nucleus, which is under agonist-specific regulation and not a universal cellular response to stimulation.

The splice variants of vascular endothelial growth factor (VEGF) and their receptors.

Vascular endothelial growth factor (VEGF) is a secreted mitogen highly specific for cultured endothelial cells. In vivo VEGF induces microvascular permeability and plays a central role in both angiogenesis and vasculogenesis. VEGF is a promising target for therapeutic intervention in certain pathological conditions that are angiogenesis dependent, most notably the neovascularisation of growing tumours. Through alternative mRNA splicing, a single gene gives rise to several distinct isoforms of VEGF, which differ in their expression patterns as well as their biochemical and biological properties. Two VEGF receptor tyrosine kinases (VEGFRs) have been identified, VEGFR-1 (Flt-1) and VEGFR-2 (KDR/Flk-1). VEGFR-2 seems to mediate almost all observed endothelial cell responses to VEGF, whereas roles for VEGFR-1 are more elusive. VEGFR-1 might act predominantly as a ligand-binding molecule, sequestering VEGF from VEGFR-2 signalling. Several isoform-specific VEGF receptors exist that modulate VEGF activity. Neuropilin-1 acts as a co-receptor for VEGF(165), enhancing its binding to VEGFR-2 and its bioactivity. Heparan sulphate proteoglycans (HSPGs), as well as binding certain VEGF isoforms, interact with both VEGFR-1 and VEGFR-2. HSPGs have a wide variety of functions, such as the ability to partially restore lost function to damaged VEGF(165) and thereby prolonging its biological activity.

Expanding the scope of the IEEE Transactions on Rehabilitation Engineering to explicitly include Neural Engineering.

The original scope of this Transactions implicitly gave it wide latitude to include all aspects of biologically based Neural Engineering. The Transactions now has an additional explicit charter to target Neural Engineering and its links to rehabilitation, from the very basic science to the highly engineered design application. This Transactions will become a prime repository for the emerging field of Neural Engineering, without losing its rehabilitation roots.

Brain-computer interface technology: a review of the first international meeting.

Over the past decade, many laboratories have begun to explore brain-computer interface (BCI) technology as a radically new communication option for those with neuromuscular impairments that prevent them from using conventional augmentative communication methods. BCI's provide these users with communication channels that do not depend on peripheral nerves and muscles. This article summarizes the first international meeting devoted to BCI research and development. Current BCI's use electroencephalographic (EEG) activity recorded at the scalp or single-unit activity recorded from within cortex to control cursor movement, select letters or icons, or operate a neuroprosthesis. The central element in each BCI is a translation algorithm that converts electrophysiological input from the user into output that controls external devices. BCI operation depends on effective interaction between two adaptive controllers, the user who encodes his or her commands in the electrophysiological input provided to the BCI, and the BCI which recognizes the commands contained in the input and expresses them in device control. Current BCI's have maximum information transfer rates of 5-25 b/min. Achievement of greater speed and accuracy depends on improvements in signal processing, translation algorithms, and user training. These improvements depend on increased interdisciplinary cooperation between neuroscientists, engineers, computer programmers, psychologists, and rehabilitation specialists, and on adoption and widespread application of objective methods for evaluating alternative methods. The practical use of BCI technology depends on the development of appropriate applications, identification of appropriate user groups, and careful attention to the needs and desires of individual users. BCI research and development will also benefit from greater emphasis on peer-reviewed publications, and from adoption of standard venues for presentations and discussion.

Multimicroelectrode stimulation within the cat L6 spinal cord: influences of electrode combinations and stimulus interleave time on knee joint extension torque.

During multimicroelectrode stimulation within the cat L6 spinal cord, the number of electrodes activated, their separation distance, and the stimulus interleave time all influenced isometric knee joint extension torque. The torque evoked by stimulation with a three electrode combination could be enhanced or suppressed when compared with that evoked by single or paired electrode stimulation. A similar difference was noted when comparing two electrode combination versus single electrode stimulation. Relative fatigue was not improved significantly by interleaving the stimuli from two or three microelectrodes. Compared with the extension torque response evoked by noninterleaved stimulation, torque evoked by interleaved stimulation with the two microelectrode combination was decreased when the electrode distance was 2.0 mm or less and increased when the electrode distance was 3.0 mm. Designing an optimal stimulation strategy for multimicroelectrode spinal cord stimulation will be challenging and complex if a suppression effect among these electrodes is to be avoided. To reduce muscle fatigue, an asynchronous, interleaved strategy of stimulation may be required.

Role of citrate synthase in aldosterone-mediated sodium reabsorption.

Aldosterone and other mineralocorticoids increase citrate synthase activity in the kidney and enhance renal sodium reabsorption, but it is unclear whether the increased citrate synthase activity is involved in renal sodium transport. We used the Wistar-Furth rat, an inbred strain found to be deficient in renal citrate synthase activity, as an experimental model to investigate this issue. We confirmed that renal citrate synthase activity from adrenalectomized Wistar-Furth rats was decreased compared with that from control Wistar rats (by 28%). Similarly, urinary citrate excretion was 23% lower in Wistar-Furth rats. Subnormal citrate formation in Wistar-Furth rats could not be accounted for by differences in systemic pH or circulating potassium levels. Because renal citrate synthase activity was reduced in Wistar-Furth rats, we hypothesized that renal sodium excretory responses to mineralocorticoids would be reduced as well. Four-hour sodium excretion after intraperitoneal injection of 5 microg of aldosterone was reduced by 56% in adrenalectomized Wistar rats and by 52% in adrenalectomized Wistar-Furth rats (both P<0.01 compared with vehicle injection). Similarly, the pattern of urinary sodium excretion in response to subcutaneous injections of deoxycorticosterone acetate over a 2-week period was similar in adrenalectomized Wistar and Wistar-Furth rats. In summary, acute and chronic antinatriuretic responses to mineralocorticoids are maintained in Wistar-Furth rats at the level of Wistar rats, despite the marked reduction in citrate synthase activity. These findings are not consistent with an important role for citrate synthase activity in mineralocorticoid-mediated renal sodium transport.

A commentary: the impact of the IEEE TRANSACTIONS ON REHABILITATION ENGINEERING on the field of rehabilitation engineering and science.

The IEEE TRANSACTIONS ON REHABILITATION ENGINEERING, founded 8.5 years ago, has survived, thrived, been of high quality, attracted the best authors in its field and related fields, been the publication of choice for manuscript submission in the rehabilitation engineering and related science area, possessed a wide and international distribution and loyal readership, been oft-cited, been financially sound, and made a marked impact on the field of Rehabilitation Engineering.

Bioassays for growth factors.

Growth factors have a wide variety of actions in living systems, providing a range of potentially quantifiable responses for measurement of their biological activity. The biological activity has to be assessed by bioassay as it cannot be predicted from physicochemical data alone. Bioassay systems range from in vivo responses to changes in receptor binding and in early components of signal transduction pathways. The most commonly used systems are based on the measurement of responses of immortalized cell lines, which although not as functionally relevant as in vivo assays, are easier to use. Most growth factors have multiple actions on multiple targets, and can show differential changes in their different activities, so use of the biological activity measured in one bioassay system to predict biological activity in another system must be rigorously validated. Since the bioassay systems are themselves inherently variable, measurement of the growth factor's activity must be made relative to a common, stable, reference preparation to permit valid inter-assay and inter-laboratory comparisons.

Production of type 2 cytokines by CD8+ lung cells is associated with greater decline in pulmonary function in patients with systemic sclerosis.

OBJECTIVE: This study addresses the hypothesis that a profibrotic pattern of cytokines is produced in the lungs of patients with systemic sclerosis (SSc) and causes fibrosis. METHODS: Using a reverse transcriptase-polymerase chain reaction technique, interleukin-4 (IL-4), IL-5, and interferon-gamma (IFNgamma) messenger RNA (mRNA) were measured in unseparated CD8+ and CD4+ bronchoalveolar lavage (BAL) cells from SSc patients and healthy controls. To confirm the results, CD8+ T cells were cloned from BAL fluids, and the pattern of cytokine mRNA made by these cells was determined. Serial pulmonary function tests were done. RESULTS: BAL cells from healthy controls made IFNgamma mRNA, with no or little IL-4 or IL-5 mRNA. In contrast, BAL cells from the majority of SSc patients made IL-4 and/or IL-5 mRNA, with or without approximately equal amounts of IFNgamma mRNA. This pattern of cytokines was made by CD8+ T cells, which were increased in the lungs of these SSc patients. Patients whose BAL cells made this type 2 pattern of cytokine mRNA had a significant decline in forced vital capacity over time after the BAL, whereas patients whose BAL cells made IFNgamma mRNA alone did not. Both wild-type and an alternative splice variant of IL-4 mRNA were increased in BAL cells from SSc patients. Both forms of IL-4 stimulated alpha2(I) collagen mRNA in human dermal and lung fibroblasts. CONCLUSION: The type 2 pattern of cytokine mRNA produced by BAL cells from SSc patients differs from unopposed IFNgamma production found in healthy BAL cells. This production of type 2 cytokine mRNA by CD8+ T cells is associated with a significant decline in lung function over time, which suggests a pathologic role for these T cells in interstitial fibrosis in SSc.

Isometric torque about the knee joint generated by microstimulation of the cat L6 spinal cord.

Isometric torque was generated about the knee joint by microstimulation of the cat L6 spinal cord using a single microelectrode. The torque responses varied with microstimulation location. Appreciable extension torque was generated by microstimulation in ventrolateral locations of the L6 spinal cord. Stimulation parameters (intensity, frequency and pulse-width) also influenced the extension torque. Specific stimulation parameters (100 microA intensity, 40 Hz frequency and 0.20 ms pulse-width) appear best suited for mapping the spinal cord based on knee joint torque responses. Low levels of cocontraction of the extensor and flexor could be achieved when extension torque was produced, but also varied with the stimulation locations. There are locations in the L6 ventral horn where microstimulation could evoke sustained extension for at least 4 min with only a slight change in torque. This study suggests the possibility of restoring lower limb function in patients with spinal cord injury above the lumbar level.