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QTL-based evidence for the role of epistasis in evolution.

The extent to which epistasis contributes to adaptation and speciation has been a controversial topic in evolutionary genetics. One experimental approach to study epistasis is based on quantitative trait locus (QTL) mapping using molecular markers. Comparisons can be made among all possible pair-wise combinations of the markers, irrespective of whether an additive QTL is associated with a marker; several software packages have been developed that facilitate this. We review several examples of using this approach to identify epistatic QTLs for traits of evolutionary or ecological interest. While there is variability in the results, the number of epistatic QTL interactions is often greater than or equal to the number of additive QTLs. The magnitude of epistatic effects can be larger than the additive effects. Thus, epistatic interactions seem to be an important part of natural genetic variation. Future studies of epistatic QTLs could lead to descriptions of the genetic networks underlying variation for fitness-related traits.

Animals↗

Facilitator not teacher: a role change for tutors in open learning nursing education.

Open learning is now an established, if rapidly changing, part of post-compulsory education and training in the United Kingdom. It has also developed in significant ways within nurse education. A key role in successful open learning is that of the tutor. Differences between the activities of teaching and facilitation are defined and ways of mapping the tutor's role within these are suggested. Differences in approach can be clustered around the topics of: the locus of control; learning methodology; the learning context and media; and the curriculum. These are discussed in turn to elicit what are the key issues for tutoring in relation to each one.

Curriculum↗

Optimizing drug delivery systems using systematic "design of experiments." Part I: fundamental aspects.

Design of an impeccable drug delivery product normally encompasses multiple objectives. For decades, this task has been attempted through trial and error, supplemented with the previous experience, knowledge, and wisdom of the formulator. Optimization of a pharmaceutical formulation or process using this traditional approach involves changing one variable at a time. Using this methodology, the solution of a specific problematic formulation characteristic can certainly be achieved, but attainment of the true optimal composition is never guaranteed. And for improvement in one characteristic, one has to trade off for degeneration in another. This customary approach of developing a drug product or process has been proved to be not only uneconomical in terms of time, money, and effort, but also unfavorable to fix errors, unpredictable, and at times even unsuccessful. On the other hand, the modern formulation optimization approaches, employing systematic Design of Experiments (DoE), are extensively practiced in the development of diverse kinds of drug delivery devices to improve such irregularities. Such systematic approaches are far more advantageous, because they require fewer experiments to achieve an optimum formulation, make problem tracing and rectification quite easier, reveal drug/polymer interactions, simulate the product performance, and comprehend the process to assist in better formulation development and subsequent scale-up. Optimization techniques using DoE represent effective and cost-effective analytical tools to yield the "best solution" to a particular "problem." Through quantification of drug delivery systems, these approaches provide a depth of understanding as well as an ability to explore and defend ranges for formulation factors, where experimentation is completed before optimization is attempted. The key elements of a DoE optimization methodology encompass planning the study objectives, screening of influential variables, experimental designs, postulation of mathematical models for various chosen response characteristics, fitting experimental data into these model(s), mapping and generating graphic outcomes, and design validation using model-based response surface methodology. The broad topic of DoE optimization methodology is covered in two parts. Part I of the review attempts to provide thought-through and thorough information on diverse DoE aspects organized in a seven-step sequence. Besides dealing with basic DoE terminology for the novice, the article covers the niceties of several important experimental designs, mathematical models, and optimum search techniques using numeric and graphical methods, with special emphasis on computer-based approaches, artificial neural networks, and judicious selection of designs and models.

Drug Delivery Systems↗

The organization of the efferent projections from the pontine parabrachial area to the amygdaloid complex: a Phaseolus vulgaris leucoagglutinin (PHA-L) study in the rat.

The organization of the efferent projections from the pontine parabrachial (pPB) area to the amygdala has been studied in the rat by using microinjections of Phaseolus vulgaris leucoagglutinin (PHA-L), a sensitive and selective anterograde axonal marker, into restricted subregions of the pPB area. The results confirmed that the pPB area primarily projected onto the ipsilateral nucleus centralis of the amygdala (Ce), and to a lesser extent onto the ipsilateral posterior basolateral (BLP), anterior basomedial (BMA), and amygdaloid cortical (ACo) nuclei of the amygdala. Substantial projections were also found in the substantia innominata dorsal/ventral portion of the globus pallidus (SId/GPv), substriatal (SStr), and fondus striatal (FStr) regions which continue the amygdala rostrally. The results demonstrated that the projections of the pPB area onto the Ce were topically organized: 1) The region of the pPB area mainly including the medial subnucleus (pPBm), the waist area (pPBwa), and a thin rostral lamina of the ventral lateral subnucleus (pPBvl) projects primarily to the medial portion of the Ce (CeM). Dense projections were also found in the BLP, BMA, and ACo nuclei of the amygdala, and in the SId/GPv, SStr, and FStr rostral areas. 2) The region of the pPB mainly including the rostral portion of the central lateral subnucleus (pPBcl) and the outer-rostral portion of the external lateral subnucleus (pPBel) projects primarily to the lateral portion of the Ce (CeL). 3) The region of the pPB mainly including the dorsolateral subnucleus (pPBdl), the remaining pPBel, and the external medial (pPBem) subnuclei projects primarily to the lateral capsular portion of the Ce (CeLC) and bilaterally to its rostral portion. Dense projections were also found in the regions which extend the CeLC rostrally and in the SId/GPv, SStr, and FStr rostral areas. The possible role of each of the three parabrachio-amygdaloid pathways described is discussed. It was suggested that the pPB-CeM pathway is mainly implicated in gustatory processes; the pPB-CeL pathway is mainly implicated in visceral and chemosensitive processes; and the pPB-CeLC pathway is mainly implicated in respiratory, cardiovascular, and nociceptive processes.

Afferent Pathways↗

Bases and spaces: resources on the web for accessing the draft human genome.

SUMMARY: Much is expected of the draft human genome sequence, and yet there is no central resource to host the plethora of sequence and mapping information available. Consequently, finding the most useful and reliable human genome data and resources currently available on the web can be challenging, but is not impossible.

Cloning, Molecular↗

Organization and development of brain stem auditory nuclei of the chicken: tonotopic organization of n. magnocellularis and n. laminaris.

Extracellular recordings of responses to tone-burst stimulation were used to determine the tonotopic organization of n. magnocellularis (NM) and n. laminaris (NL) in hatching chickens. NM cells show "primary-like" response patterns to ipsilateral stimulation, and are arranged in dorso-ventral isofrequency columns. Units responding to the highest frequency tones (about 4,100 Hz) are situated at the rostromedial pole of the medial division. Units with lower characteristic frequencies (CF's) are found at successively caudal and lateral sites, until extremely low CF's ( less than 500 Hz) are represented dorsoventrally in the daudolateral tail of the lateral division. No evidence was found of auditory input to the region which receives projections from the macula lagena. NL receives polarized, binaural, excitatory input. Units have similar CF's and thresholds to tones presented to either ear. The tonotopic organization in NL matches that found in NM--high CF's rostromedially and low CF's caudal and lateral. Quantitative procedures were developed for relating CF to the position of a unit within either nucleus. These analyses account for 79% and 89% of the frequency variance found within NM and NL, respectively, and predict the CF of a neuron by its position within each nucleus.

Animals↗

Cytoarchitectonic organization of the human auditory cortex.

A new cytoarchitectonic study of the human auditory cortex was undertaken in the light of recent knowledge concerning the architecture, fiber connectivity, and physiology of this region in the monkey. The survey of three normative human brains (six hemispheres) processed in whole-brain serial sections disclosed a cytoarchitectonic organization of the cortical auditory region similar to that in the macaque. Unlike the monkey, auditory-related cortex was found in parietal operculum and inferior parietal lobule. Similarities in cortical architectonics between human and monkey brains may provide a rationale for the application of knowledge concerning animal physiology and connectivity to man.

Animals↗

Peptide-mass fingerprinting and the ideal covering set for protein characterisation.

The rules that govern the dynamics of protein characterisation by peptide-mass fingerprinting (PMF) were investigated through multiple interrogations of a nonredundant protein database. This was achieved by analysing the efficiency of identifying each entry in the entire database via perfect in silico digestion with a series of 20 pseudo-endoproteinases cutting at the carboxy terminal of each amino acid residue, and the multiple cutters: trypsin, chymotrypsin and Glu-C. The distribution of peptide fragment masses generated by endoproteinase digestion was examined with a view to designing better approaches to protein characterisation by PMF. On average, and for both common and rare cutters, the combination of approximately two fragments was sufficient to identify most database entries. However, the rare cutters left more entries unidentified in the database. Total coverage of the entire database could not be achieved with one enzymatic cutter alone, nor when all 23 cutters were used together. Peptide fragments of > 5000 Da had little effect on the outcome of PMF to correctly characterise database entries, while those with low mass (near to 350 Da in the case of trypsin) were found to be of most utility. The most frequently occurring fragments were also found in this lower mass region. The maximum size of uncut database entries (those not containing a specific amino acid residue) ranged from 52,908 Da to 258,314 Da, while the failure rate for a single cutter in identifying database entries varied from 10,865 (8.4%) to 23,290 (18.1%). PMF is likely to be a mainstay of any high-throughput protein screening strategy for large-scale proteome analysis. A better understanding of the merits and limitations of this technique will allow researchers to optimise their protein characterisation procedures.

Amino Acid Sequence↗

Involvement of the inferior frontal junction in cognitive control: meta-analyses of switching and Stroop studies.

There is growing evidence that a specific region in the posterior frontolateral cortex is involved intimately in cognitive control processes. This region, located in the vicinity of the junction of the inferior frontal sulcus and the inferior precentral sulcus, was termed the inferior frontal junction (IFJ). The IFJ was shown to be involved in the updating of task representations and to be activated commonly in a within-subject investigation of a task-switching paradigm, the Stroop task, and a verbal n-back task. Here, we investigate the involvement of the IFJ in cognitive control by employing a meta-analytic approach. Two quantitative meta-analyses of functional magnetic resonance imaging (fMRI) studies were conducted. One meta-analysis included frontal activations from task-switching, set-shifting, and stimulus-response (S-R) reversal studies, the other included frontal activations from color-word Stroop studies. Results showed highly significant clustering of activations in the IFJ in both analyses. These results provide strong evidence for the consistent involvement of the IFJ in both switching and Stroop paradigms. Furthermore, they support our concept of areal specialization in the frontolateral cortex, which posits that it is not only the middorsolateral part that plays an important role in cognitive control, but also the IFJ. Finally, our results demonstrate how quantitative meta-analyses can be used to test hypotheses about the involvement of specific brain regions in cognitive control.

Brain Mapping↗

Cerebellum and auditory function: an ALE meta-analysis of functional neuroimaging studies.

Over the past two decades neuroimaging data have accumulated showing that the cerebellum, traditionally viewed only as a motor structure, is also active in a wide variety of sensory and cognitive tasks. We have proposed that instead of explicit involvement in any particular motor, sensory, or cognitive task, the cerebellum performs a much more fundamental computation involving the active acquisition of sensory data. We carried out an activation likelihood estimate (ALE) meta-analysis to determine whether neuroimaging results obtained during a wide range of auditory tasks support this proposal. Specifically, we analyzed the coordinates of 231 activation foci obtained in 15 different auditory studies selected through an extensive search of the positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) literature. The studies selected represent a wide variety of purely auditory tasks using highly controlled synthesized acoustic stimuli. The results clearly revealed that in addition to temporal auditory areas of cerebral cortex, specific regions in the cerebellum are activated consistently across studies regardless of the particular auditory task involved. In particular, one area in left lateral crus I area showed the greatest volume and ALE peak value among the extratemporal regions. A subanalysis was carried out that ruled out the specific association of this cerebellar cluster with attentional demand. The results are consistent with the hypothesis that the cerebellum may play a role in purely sensory auditory processing, and are discussed in light of the broader idea of the cerebellum subserving a fundamental sensory function.

Acoustic Stimulation↗

A nonradioactive double detection method for the assignment of spots in two-dimensional blots.

A method for identification of spots on two-dimensional electrophoresis gels by means of immunoblotting is described. This method does not require radioactive-labeled proteins and is based on the dual use of colloidal gold staining to detect the general 2D pattern on the blot and on chemiluminescence to detect the antibody-reactive spot(s). Profit is taken from the fact that the general gold stain produces a background pattern on strong ECL exposures, which allows alignment of the antibody-reactive spot(s) on the general pattern and therefore easy identification of the spot(s) of interest on the two-dimensional maps.

Bacterial Proteins↗

Transcript mapping of the human chromosome 11q12-q13.1 gene-rich region identifies several newly described conserved genes.

Despite the localization of several human diseases to 11q13, the majority of the genes responsible for these disorders have not yet been cloned. Exon amplification and EST mapping were performed using clones derived from an approximately 1.65-Mb P1 artificial chromosome contig encompassing the region that reportedly harbors the gene mutated in the dominantly inherited eye disorder, Best disease. Fifty-eight exons isolated from the region were sequenced, resulting in 41.3% showing weak or no similarity to database sequences. Four exons had exact matches with human ESTs and 2 exons were highly similar to mouse ESTs. The sequence of 1 of these human ESTs was highly similar to that of the rat Rabin3 and mouse Pat-12 genes, which potentially encode Ras-like GTPase binding proteins. Three exon sequences were similar to those of the inner centromere proteins of Gallus gallus and Xenopus laevis, which are mitotic phosphoproteins, and 1 exon sequence had similarity to the epidermal growth factor-like repeat from several proteins. High-resolution mapping of 34 ESTs binned to the 11q12-q13 region by the Human Transcript Mapping Project identified 5 present in the PAC contig, with 1 of these ESTs identifying a human homologue of the rat synaptotagmin VII gene. Database searches identified two overlapping cDNA clones representing almost the entire open reading frame of this human gene and a sequenced cosmid indicating its partial genomic structure. Further database analyses identified another sequenced cosmid from this region that contained both exon-trap and mapped EST sequences. PowerBLAST and GRAIL analysis of this cosmid sequence identified matches with several other ESTs, the previously described FEN1 gene, and a novel evolutionarily conserved gene. These experiments identify candidate genes for disorders that map to this region and indicate that this is a gene-rich region of the human genome.

Amino Acid Sequence↗

Influence of ANOVA design and anatomical standardization on statistical mapping for PET activation.

We have created images of z value, error, and variation components for a PET activation study using various ANOVA designs and anatomical standardization methods. Data were acquired in four PET centers. In each center, CBF was measured on six normal male subjects under resting and covert verb generation, three times for each. The images were anatomically standardized with LINEAR transformation, SPM (Ver. 95), HBA (Karolinska/Tohoku), or MICHIGAN (Minoshima). ANOVA was performed pixel by pixel to compute t (and z) for the task main effect (Verb vs Rest) in four different designs: (i) two way (subject and task) (2W), (ii) two-way with interaction (2WI), (iii) subject considered a random factor (2WI-MX), and (iv) three-way (subject, task, and replication) (3W). A large area extending from the Broca to the left premotor cortex was activated. The localization of the highest peak depended both on the anatomical standardization and on the ANOVA design, the variation ranging 3-4 cm. Smoothing reduced the variation while erasing possible subfoci. The z images of 2W, 2WI, and 3W looked alike, whereas 2WI-MX presented lower peak z values. SPM tended to present higher z values than the other methods. The error was high in the gray and low in the white matter. The root mean square for the subject effect was high on the border of gray matter especially in LINEAR and HBA, revealing intersubject mismatch in the gray matter distribution. The root mean square for the subject-by-task interaction effect revealed individual variation in activation.

Adult↗

Detection of consistently task-related activations in fMRI data with hybrid independent component analysis.

fMRI data are commonly analyzed by testing the time course from each voxel against specific hypothesized waveforms, despite the fact that many components of fMRI signals are difficult to specify explicitly. In contrast, purely data-driven techniques, by focusing on the intrinsic structure of the data, lack a direct means to test hypotheses of interest to the examiner. Between these two extremes, there is a role for hybrid methods that use powerful data-driven techniques to fully characterize the data, but also use some a priori hypotheses to guide the analysis. Here we describe such a hybrid technique, HYBICA, which uses the initial characterization of the fMRI data from Independent Component Analysis and allows the experimenter to sequentially combine assumed task-related components so that one can gracefully navigate from a fully data-derived approach to a fully hypothesis-driven approach. We describe the results of testing the method with two artificial and two real data sets. A metric based on the diagnostic Predicted Sum of Squares statistic was used to select the best number of spatially independent components to combine and utilize in a standard regressional framework. The proposed metric provided an objective method to determine whether a more data-driven or a more hypothesis-driven approach was appropriate, depending on the degree of mismatch between the hypothesized reference function and the features in the data. HYBICA provides a robust way to combine the data-derived independent components into a data-derived activation waveform and suitable confounds so that standard statistical analysis can be performed.

Algorithms↗

Genome mapping by arbitrary amplification of yeast artificial chromosomes.

Several methods have been described for using the polymerase chain reaction (PCR) to isolate fragments of DNA for genome mapping. We have developed an approach for isolating discrete fragments by amplifying DNA with single oligonucleotides (10-mers) with arbitrarily selected sequences. The method is rapid and technically simple. We isolated fragments from a contig of three yeast artificial chromosomes (YACs) from the human Xq28 chromosomal region. We purified YACs yWXD37, yWXD348, and yWXD705 from a preparative pulsed field gel. Amplifications of each YAC were performed with single 10-mers as the PCR primers and the products were visualized on agarose gels. These fragments have been successfully used as hybridization probes against Southern blots containing the YACs and against blots containing human genomic DNA and somatic cell hybrids containing Xq28 as their only human constituent. The results have been concordant with the known order of the YACs. We have also successfully combined 10-mers with primers derived from vector arm sequences to isolate YAC ends. We discuss several uses of this method in comparative mapping and in filling in gaps in physical and genetic maps.

Base Sequence↗

[Neurophysiological and neuroimaging studies for restless legs syndrome and periodic leg movement disorder].

The restless legs syndrome (RLS) is a clinical diagnosis based on the four essential criteria defined by the International Restless Legs Syndrome Study Group (IRLSSG). An idiopathic form can be separated from a symptomatic form. Neurophysiological studies have investigated the pathophysiology of the idiopathic RLS or have been used to exclude a symptomatic cause, in particular polyneuropathy. So far cortical excitability changes, corticomotor, somatosensory and auditory pathways, spinal cord excitability, B-wave rhythm and cycling alternating pattern, as well as reflex mechanisms have been investigated by electroencephalography, evoked potentials, Bereitschaftspotentials, nerve conduction and thermal threshold measurements, electromyography, transcranial Doppler sonography, measurements of the spinal flexor reflex as well as neuroimaging techniques. The etiology of the RLS cannot be revealed by these methods, neurophysiological studies in RLS are, however, useful for a better understanding of the pathophysiology and for exclusion of a polyneuropathy or other symptomatic causes. In addition to neurophysiological investigations, small fiber neuropathy, which seems to be a more common finding in RLS patients than expected to date, may need biopsy for confirmation. This review will focus on investigations of the different systems involved with diverse neurophysiological methods.

Brain↗