Metabolomic Analysis of Rat Brain by High Resolution Nuclear Magnetic Resonance Spectroscopy of Tissue Extracts

Studies of gene expression on the RNA and protein levels have long been used to explore biological processes underlying disease. More recently, genomics and proteomics have been complemented by comprehensive quantitative analysis of the metabolite pool present in biological systems. This strategy, termed metabolomics, strives to provide a global characterization of the small-molecule complement involved in metabolism. While the genome and the proteome define the tasks cells can perform, the metabolome is part of the actual phenotype. Among the methods currently used in metabolomics, spectroscopic techniques are of special interest because they allow one to simultaneously analyze a large number of metabolites without prior selection for specific biochemical pathways, thus enabling a broad unbiased approach. Here, an optimized experimental protocol for metabolomic analysis by high-resolution NMR spectroscopy is presented, which is the method of choice for efficient quantification of tissue metabolites. Important strengths of this method are (i) the use of crude extracts, without the need to purify the sample and/or separate metabolites; (ii) the intrinsically quantitative nature of NMR, permitting quantitation of all metabolites represented by an NMR spectrum with one reference compound only; and (iii) the nondestructive nature of NMR enabling repeated use of the same sample for multiple measurements. The dynamic range of metabolite concentrations that can be covered is considerable due to the linear response of NMR signals, although metabolites occurring at extremely low concentrations may be difficult to detect. For the least abundant compounds, the highly sensitive mass spectrometry method may be advantageous although this technique requires more intricate sample preparation and quantification procedures than NMR spectroscopy. We present here an NMR protocol adjusted to rat brain analysis; however, the same protocol can be applied to other tissues with minor modifications.     

Quality control in manufacturing oligo arrays: a combinatorial design approach.

The advent of the DNA microarray technology has brought with it the exciting possibility of simultaneously observing the expression levels of all genes in an organism. One such microarray technology, called "oligo arrays," manufactures short single strands of DNA (called probes) onto a glass surface using photolithography. An altered or missed step in such a manufacturing protocol can adversely affect all probes using this failed step and is in general impossible to disentangle from experimental variation when using such a defective array. The idea of designing special quality control probes to detect a failed step was first formulated by Hubbell and Pevzner (1999). We consider an alternative formulation of this problem and use a combinatorial design approach to solve it. Our results improve over prior work in guaranteeing coverage of all protocol steps and in being able to tolerate a greater number of unreliable probe intensities.     

The randomized controlled trial in studies using biomarkers

The randomized controlled trial (RCT) is a scientific experiment during which observations on the effects of therapy or a preventive action are conducted by the researcher under rigorous control. The purpose of the experiment is to clear the uncertainties surrounding a clinical/research issue and involves isolating the 'treatment' and 'end result' variables from external influences. RCTs therefore make use of scientific method standards: measuring, which includes the possibility of reproducing observations; controlling factors unconnected to the cause-effect relationship of interest; and the external verification or 'falsification' of the cause-effect relationship. Many RCTs are now including biomarkers to answer scientific questions in a more accurate way. In the present methodological paper, the main aspects involved in the design and conduction of a trial are discussed, with special emphasis on the use of biomarkers. Aspects that are often overlooked by scientists involved in the design of trials include multiple comparisons, subgroup analysis, the duration of the observations, the use of surrogate endpoints, and ethical issues. This review summarizes the main issues that should be addressed in a protocol, and illustrates these with an example.     

A special theory of biphasic mixtures and experimental results for human annulus fibrosus tested in confined compression

A finite deformation mixture theory is used to quantify the mechanical properties of the annulus fibrosus using experimental data obtained from a confined compression protocol. Certain constitutive assumptions are introduced to derive a special mixture of an elastic solid and an inviscid fluid, and the constraint of intrinsic incompressibility is introduced in a manner that is consistent with results obtained for the special theory. Thirty-two annulus fibrosus specimens oriented in axial (n = 16) and radial (n = 16) directions were obtained from the middle-lateral portion of intact intervertebral discs from human lumbar spines and tested in a stress-relaxation protocol. Material constants are determined by fitting the theory to experimental data representing the equilibrium stress versus stretch and the surface stress time history curves. No significant differences in material constants due to orientation existed, but significant differences existed due to the choice of theory used to fit the data. In comparison with earlier studies with healthy annular tissue, we report a lower aggregate modulus and a higher initial permeability constant. These differences are explained by the choice of reference configuration for the experimental studies.     

The randomized controlled trial in studies using biomarkers

The randomized controlled trial (RCT) is a scientific experiment during which observations on the effects of therapy or a preventive action are conducted by the researcher under rigorous control. The purpose of the experiment is to clear the uncertainties surrounding a clinical/research issue and involves isolating the 'treatment' and 'end result' variables from external influences. RCTs therefore make use of scientific method standards: measuring, which includes the possibility of reproducing observations; controlling factors unconnected to the cause-effect relationship of interest; and the external verification or 'falsification' of the cause-effect relationship. Many RCTs are now including biomarkers to answer scientific questions in a more accurate way. In the present methodological paper, the main aspects involved in the design and conduction of a trial are discussed, with special emphasis on the use of biomarkers. Aspects that are often overlooked by scientists involved in the design of trials include multiple comparisons, subgroup analysis, the duration of the observations, the use of surrogate endpoints, and ethical issues. This review summarizes the main issues that should be addressed in a protocol, and illustrates these with an example.     

Inferring the effect of therapy on tumors showing stochastic Gompertzian growth

The present work deals with a Gompertz-type diffusion process, which includes in the drift term a time-dependent function C(t) representing the effect of a therapy able to modify the dynamics of the underlying process. However, in experimental studies is not immediate to deduce the functional form of C(t) from a treatment protocol. So a statistical approach is proposed in order to estimate this function when a control group and one or more treated groups are observed. In order to validate the proposed strategy a simulation study for several interesting functional forms of C(t) has been carried out. Finally, an application to infer the net effect of cisplatin and doxorubicin+cyclophosphamide in actual murine models is presented.     

A Note on the Balance between Random Sampling and Population Size (on the 30th Anniversary of G. Malécot''s Paper)

Wright's model for the effects of random fluctuations in gene frequency in a population of fixed size is generalized to randomly fluctuating population size, and treated from the viewpoint of G. Malécot, using a martingale convergence theorem. The gene frequency approaches a limit, whose value depends on the actual realization, or history, of the process; that is, convergence is with probability one (or: almost surely) in statistical language. The limit does not necessarily represent a state of fixation of either allele; in particular, the limiting probability distribution is not necessarily trivial. For the special case of deterministically varying population size, a necessary and sufficient condition for such non-triviality is given.     

Effectiveness of a short-term treatment with progesterone injections on synchrony of lambing and fertility in tropical hair sheep

The efficacy of using a low cost system for delivering progesterone as part of an estrous synchronization protocol in sheep was evaluated. In experiment 1, Barbados Black Belly ewes (n=34) and ewe lambs (n=35; 37.5±0.9 kg) were assigned to be untreated, control animals (C), or to receive PGF(2α) on d0 (PG), or receive two injections of progesterone (200mg, i.m. each) on D -5 and on D -2.5, prior to PGF(2α), on D 0 (2PPG). Treatment with 2PPG increased the proportion of animals lambing to the first service (P<0.05), an effect that was greater in ewe lambs than ewes (treatment × parity; P<0.05). The interval from ram introduction to lambing and the mean lambing day was less (P=0.04) in the 2PPG-treated animals compared to control animals. In Experiment 2, lactating ewes from experiment 1 (n=61) 60-85 days postpartum were assigned within parity and number of lambs reared to remain nursing (S; n=29) or weaned (W; n=32) 3 weeks prior to treatment with the 2PPG protocol. There was no effect of treatment on the proportion of animals lambing to the first service or overall, interval from ram introduction to lambing and lambing interval. An 8-month lambing interval was observed in ewes in which estrus was synchronized regardless of physiological state. In conclusion, the two-progesterone injection synchronization protocol may be used as a practical low cost and efficient method of synchronizing estrus to reduce the lambing interval and maximize productivity in tropical breeds of sheep.     

Cognitive auditory evoked potentials in children with special language impairment

Perception and discrimination of auditory and speech stimuli in children aged 7-9 years with either receptive (n=6) or expressive (n=5) type of special language impairment and 7 healthy age-matched controls was investigated using evoked potential technique. The measurements were performed with a 32-channel Neuroscan electroencephalographic system. Two types of stimuli were applied, pure tones (1 kHz and 2 kHz) and double syllabi consisting of one consonant and one vocal characteristic of Croatian language. The stimuli were presented in an oddball paradigm, requiring a conscious reaction for the subjects. Latencies and amplitudes of P1, N1, P2, N2, P3, N4, and SW waves were analized, as well as the reaction time and number of responses. There were found no statistically significant difference between children with special language impairment and the control group in average response time and number of responses to tone burst or double syllable. Analysis of variance of all used variables showed a statistically significant difference in P3 and Sw wave latencies after double syllable stimulation, P3 and N4 waves latencies after target stimulation, P2 and Sw wave amplitude; and in N1 wave amplitude after pure tone stimulation. Our study showed that children with speech and language disorder take longer time to perceive and discriminate between either tonal or speech auditory stimuli than children with typical speech and language development.     

Electrophysiological Evidence for Domain-General Inhibitory Control during Bilingual Language Switching

This paper presents an experiment that explored the role of domain–general inhibitory control on language switching. Reaction times (RTs) and event–related brain potentials (ERPs) were recorded when low–proficient bilinguals with high and low inhibitory control (IC) switched between overt picture naming in both their L1 and L2. Results showed that the language switch costs of bilinguals with high–IC were symmetrical, while that of bilinguals with low–IC were not. The N2 component failed to show a significant interaction between group, language and task, indicating that inhibition may not comes into play during the language task schema competition phase. The late positive component (LPC), however, showed larger amplitudes for L2 repeat and switch trials than for L1 trials in the high–IC group, indicating that inhibition may play a key role during the lexical response selection phase. These findings suggest that domain–general inhibitory control plays an important role in modulating language switch costs and its influence can be specified in lexical selection phase.     

Effect of the Initial Synaptic State on the Probability to Induce Long-Term Potentiation and Depression

Long-term potentiation (LTP) and long-term depression (LTD) are the two major forms of long-lasting synaptic plasticity in the mammalian neurons, and are directly related to higher brain functions such as learning and memory. Experimentally, they are characterized by a change in the strength of a synaptic connection induced by repetitive and properly patterned stimulation protocols. Although many important details of the molecular events leading to LTP and LTD are known, experimenters often report problems in using standard induction protocols to obtain consistent results, especially for LTD in vivo. We hypothesize that a possible source of confusion in interpreting the results, from any given experiment on synaptic plasticity, can be the intrinsic limitation of the experimental techniques, which cannot take into account the actual state and peak conductance of the synapses before the conditioning protocol. In this article, we investigate the possibility that the same experimental protocol may result in different consequences (e.g., LTD instead of LTP), according to the initial conditions of the stimulated synapses, and can generate confusing results. Using biophysical models of synaptic plasticity and hippocampal CA1 pyramidal neurons, we study how, why, and to what extent the phenomena observed at the soma after induction of LTP/LTD reflects the actual (local) synaptic state. The model and the results suggest a physiologically plausible explanation for why LTD induction is experimentally difficult to obtain. They also suggest experimentally testable predictions on the stimulation protocols that may be more effective.     

The strong-inference protocol: not just for grant proposals

The strong-inference protocol puts into action the important concepts in Platt's often-assigned, classic paper on the strong-inference method (10). Yet, perhaps because students are frequently performing experiments with known outcomes, the protocols they write as undergraduates are usually little more than step-by-step instructions for performing the experiment. The strong-inference protocol, however, includes an explicit statement of possible experimental outcomes and the interpretation that would follow from each. This approach encourages thorough planning, enhances the efficiency of experimental designs, and increases the power of statistical analysis by explicitly stating a priori predictions as well as the statistical methods that will be used to test them. A sample protocol for an experiment investigating temperature-metabolism relations in chicken embryos is provided to illustrate the important components of the strong-inference protocol and to encourage instructors to incorporate this powerful research tool into undergraduate laboratory courses.     

Engineering Platform and Experimental Protocol for Design and Evaluation of a Neurally-controlled Powered Transfemoral Prosthesis

To enable intuitive operation of powered artificial legs, an interface between user and prosthesis that can recognize the user''s movement intent is desired. A novel neural-machine interface (NMI) based on neuromuscular-mechanical fusion developed in our previous study has demonstrated a great potential to accurately identify the intended movement of transfemoral amputees. However, this interface has not yet been integrated with a powered prosthetic leg for true neural control. This study aimed to report (1) a flexible platform to implement and optimize neural control of powered lower limb prosthesis and (2) an experimental setup and protocol to evaluate neural prosthesis control on patients with lower limb amputations. First a platform based on a PC and a visual programming environment were developed to implement the prosthesis control algorithms, including NMI training algorithm, NMI online testing algorithm, and intrinsic control algorithm. To demonstrate the function of this platform, in this study the NMI based on neuromuscular-mechanical fusion was hierarchically integrated with intrinsic control of a prototypical transfemoral prosthesis. One patient with a unilateral transfemoral amputation was recruited to evaluate our implemented neural controller when performing activities, such as standing, level-ground walking, ramp ascent, and ramp descent continuously in the laboratory. A novel experimental setup and protocol were developed in order to test the new prosthesis control safely and efficiently. The presented proof-of-concept platform and experimental setup and protocol could aid the future development and application of neurally-controlled powered artificial legs.     

Language comprehension in the balance: the robustness of the action-compatibility effect (ACE)

How does language comprehension interact with motor activity? We investigated the conditions under which comprehending an action sentence affects people''s balance. We performed two experiments to assess whether sentences describing forward or backward movement modulate the lateral movements made by subjects who made sensibility judgments about the sentences. In one experiment subjects were standing on a balance board and in the other they were seated on a balance board that was mounted on a chair. This allowed us to investigate whether the action compatibility effect (ACE) is robust and persists in the face of salient incompatibilities between sentence content and subject movement. Growth-curve analysis of the movement trajectories produced by the subjects in response to the sentences suggests that the ACE is indeed robust. Sentence content influenced movement trajectory despite salient inconsistencies between implied and actual movement. These results are interpreted in the context of the current discussion of embodied, or grounded, language comprehension and meaning representation.     

Effect of body condition on reproductive efficiency of lactating dairy cows receiving a timed insemination

Body condition may influence pregnancy rates to a timed insemination (Ovsynch/TAI) protocol and affect the economical performance of dairy farms. The objectives were to compare pregnancy rates using the Ovsynch/TAI protocol for the first service of lactating dairy cows with body condition scores < 2.5 (scale: 1 to 5, low BCS group) versus > or = 2.5 (control group) and to estimate the economic impact of the effect of body condition on reproductive performance. At 63 +/- 3 d post partum, cows were assigned to 2 experimental groups (low BCS = 81; control = 126), and were treated with GnRH at d 0 and with PGF2alpha 7 d later. At 48 h after PGF2alpha, cows received an injection of GnRH and were inseminated 16 h later. Pregnancy rates to the Ovsynch/TAI protocol were lower for the low BCS group than for the control group at 27 d (18.1 +/- 6.1% < 33.8 +/- 4.5%; P<0.02) and at 45 d (11.1 +/- 5.4% < 25.6 +/- 4.1%; P<0.02) after insemination. Economic analysis indicated that reducing the percentage of the herd in low body condition increases net revenues per cow per year. Body condition influenced pregnancy rates to the Ovsynch/TAI protocol.     

Whole Retinal Explants from Chicken Embryos for Electroporation and Chemical Reagent Treatments

The retina is a good model for the developing central nervous system. The large size of the eye and most importantly the accessibility for experimental manipulations in ovo/in vivo makes the chicken embryonic retina a versatile and very efficient experimental model. Although the chicken retina is easy to target in ovo by intraocular injections or electroporation, the effective and exact concentration of the reagents within the retina may be difficult to fully control. This may be due to variations of the exact injection site, leakage from the eye or uneven diffusion of the substances. Furthermore, the frequency of malformations and mortality after invasive manipulations such as electroporation is rather high.This protocol describes an ex ovo technique for culturing whole retinal explants from chicken embryos and provides a method for controlled exposure of the retina to reagents. The protocol describes how to dissect, experimentally manipulate, and culture whole retinal explants from chicken embryos. The explants can be cultured for approximately 24 hr and be subjected to different manipulations such as electroporation. The major advantages are that the experiment is not dependent on the survival of the embryo and that the concentration of the introduced reagent can be varied and controlled in order to determine and optimize the effective concentration. Furthermore, the technique is rapid, cheap and together with its high experimental success rate, it ensures reproducibleresults. It should be emphasized that it serves as an excellent complement to experiments performed in ovo.     

Promising perspectives for ruminal protection of polyunsaturated fatty acids through polyphenol-oxidase-mediated crosslinking of interfacial protein in emulsions

Previously, polyunsaturated fatty acids (PUFA) from linseed oil were effectively protected (>80%) against biohydrogenation through polyphenol-oxidase-mediated protein crosslinking of an emulsion, prepared with polyphenol oxidase (PPO) extract from potato tuber peelings. However, until now, emulsions of only 2 wt% oil have been successfully protected, which implies serious limitations both from a research perspective (e.g. in vivo trials) as well as for further upscaling toward practical applications. Therefore, the aim of this study was to increase the oil/PPO ratio. In the original protocol, the PPO extract served both an emulsifying function as well as a crosslinking function. Here, it was first evaluated whether alternative protein sources could replace the emulsifying function of the PPO extract, with addition of PPO extract and 4-methylcatechol (4MC) to induce crosslinking after emulsion preparation. This approach was then further used to evaluate protection of emulsions with higher oil content. Five candidate emulsifiers (soy glycinin, gelatin, whey protein isolate (WPI), bovine serum albumin and sodium caseinate) were used to prepare 10 wt% oil emulsions, which were diluted five times (w/w) with PPO extract (experiment 1). As a positive control, 2 wt% oil emulsions were prepared directly with PPO extract according to the original protocol. Further, emulsions of 2, 4, 6, 8 and 10 wt% oil were prepared, with 80 wt% PPO extract (experiment 2), or with 90, 80, 70, 60 and 50 wt% PPO extract, respectively (experiment 3) starting from WPI-stabilized emulsions. Enzymatic crosslinking was induced by 24-h incubation with 4MC. Ruminal protection efficiency was evaluated by 24-h in vitro batch simulation of the rumen metabolism. In experiment 1, protection efficiencies were equal or higher than the control (85.5% to 92.5% v. 81.3%). In both experiments 2 and 3, high protection efficiencies (>80%) were achieved, except for emulsions containing 10 wt% oil emulsions (<50% protection), which showed oiling-off after enzymatic crosslinking. This study demonstrated that alternative emulsifier proteins can be used in combination with PPO extract to protect emulsified PUFA-rich oils against ruminal biohydrogenation. By applying the new protocol, 6.5 times less PPO extract was required.     

A class of exact solutions for biomacromolecule diffusion-reaction in live cells

A class of novel explicit analytic solutions for a system of n+1 coupled partial differential equations governing biomolecular mass transfer and reaction in living organisms are proposed, evaluated, and analyzed. The solution process uses Laplace and Hankel transforms and results in a recursive convolution of an exponentially scaled Gaussian with modified Bessel functions. The solution is developed for wide range of biomolecular binding kinetics from pure diffusion to multiple binding reactions. The proposed approach provides solutions for both Dirac and Gaussian laser beam (or fluorescence-labeled biomacromolecule) profiles during the course of a Fluorescence Recovery After Photobleaching (FRAP) experiment. We demonstrate that previous models are simplified forms of our theory for special cases. Model analysis indicates that at the early stages of the transport process, biomolecular dynamics is governed by pure diffusion. At large times, the dominant mass transfer process is effective diffusion. Analysis of the sensitivity equations, derived analytically and verified by finite difference differentiation, indicates that experimental biologists should use full space-time profile (instead of the averaged time series) obtained at the early stages of the fluorescence microscopy experiments to extract meaningful physiological information from the protocol. Such a small time frame requires improved bioinstrumentation relative to that in use today. Our mathematical analysis highlights several limitations of the FRAP protocol and provides strategies to improve it. The proposed model can be used to study biomolecular dynamics in molecular biology, targeted drug delivery in normal and cancerous tissues, motor-driven axonal transport in normal and abnormal nervous systems, kinetics of diffusion-controlled reactions between enzyme and substrate, and to validate numerical simulators of biological mass transport processes in vivo.     

Controlling behavioral experiments with a new programming language (SORCA) for microcomputer systems

A new programming language SORCA has been defined and a compiler has been written for Z80-based microcomputer systems with CP/M operating system. The language was developed to control behavioral experiments by external stimuli and by time schedule in real-time. Eight binary hardware input lines are sampled cyclically by the computer and can be used to sense switches, level detectors and other binary information, while 8 binary hardware output lines, that are cyclically updated, can be used to control relays, lamps, generate tones or for other purposes. The typical reaction time (cycle time) of a SORCA-program is 500 microseconds to 1 ms. All functions can be programmed as often as necessary. Included are the basic logic functions, counters, timers, majority gates and other complex functions. Parameters can be given as constants or as a result of a step function or of a random process (with Gaussian or equal distribution). Several tasks can be performed simultaneously. In addition, results of an experiment (e.g., number of reactions or latencies) can be measured and printed out on request or automatically. The language is easy to learn and can also be used for many other control purposes.