Brain mapping: new wave optical imaging

Optical imaging of intrinsic signals is widely used for high-resolution brain mapping in various animal species. A new approach using continuous data acquisition and Fourier decomposition of the signal allows for much faster mapping, opening up the possibility of applying this method to new experimental questions.     

Columnar resolution of blood volume and oximetry functional maps in the behaving monkey; implications for FMRI

The ultimate goal of high-resolution functional brain mapping is single-condition (stimulus versus no-stimulus maps) rather than differential imaging (comparing two "stimulus maps"), because the appropriate ("orthogonal") stimuli are rarely available. This requires some component(s) of activity-dependent hemodynamic signals to closely colocalize with electrical activity, like the early increase in deoxyhemoglobin, shown previously to yield high-quality functional single-condition maps. Conversely, nonlocal vascular responses dominate in cerebral blood volume (CBV)-based single-condition maps. Differential CBV maps are largely restricted to the parenchyma, implying that part of the CBV response does colocalize with electrical activity at fine spatial scale. By removing surface vascular activation from optical imaging data, we document the existence of a capillary CBV response component, regulated at fine spatial scale and yielding single-condition maps exhibiting approximately 100 microm resolution. Blood volume and -flow based single-condition functional mapping at columnar level should thus be feasible, provided that the capillary response component is selectively imaged.     

MRI contrast agents for functional molecular imaging of brain activity

Functional imaging with MRI contrast agents is an emerging experimental approach that can combine the specificity of cellular neural recording techniques with noninvasive whole-brain coverage. A variety of contrast agents sensitive to aspects of brain activity have recently been introduced. These include new probes for calcium and other metal ions that offer high sensitivity and membrane permeability, as well as imaging agents for high-resolution pH and metabolic mapping in living animals. Genetically encoded MRI contrast agents have also been described. Several of the new probes have been validated in the brain; in vivo use of other agents remains a challenge. This review outlines advantages and disadvantages of specific molecular imaging approaches and discusses current or potential applications in neurobiology.     

Genome-Wide High-Resolution Mapping by Recurrent Intermating Using Arabidopsis Thaliana as a Model

We demonstrate a method for developing populations suitable for genome-wide high-resolution genetic linkage mapping, by recurrent intermating among F(2) individuals derived from crosses between homozygous parents. Comparison of intermated progenies to F(2) and ``recombinant inbred' (RI) populations from the same pedigree corroborate theoretical expectations that progenies intermated for four generations harbor about threefold more information for estimating recombination fraction between closely linked markers than either RI-selfed or F(2) individuals (which are, in fact, equivalent in this regard). Although intermated populations are heterozygous, homozygous ``intermated recombinant inbred' (IRI) populations can readily be generated, combining additional information afforded by intermating with the permanence of RI populations. Intermated populations permit fine-mapping of genetic markers throughout a genome, helping to bridge the gap between genetic map resolution and the DNA-carrying capacity of modern cloning vectors, thus facilitating merger of genetic and physical maps. Intermating can also facilitate high-resolution mapping of genes and QTLs, accelerating map-based cloning. Finally, intermated populations will facilitate investigation of other fundamental genetic questions requiring a genome-wide high-resolution analysis, such as comparative mapping of distantly related species, and the genetic basis of heterosis.     

Infantile spasms is associated with deletion of the MAGI2 gene on chromosome 7q11.23-q21.11

Infantile spasms (IS) is the most severe and common form of epilepsy occurring in the first year of life. At least half of IS cases are idiopathic in origin, with others presumed to arise because of brain insult or malformation. Here, we identify a locus for IS by high-resolution mapping of 7q11.23-q21.1 interstitial deletions in patients. The breakpoints delineate a 500 kb interval within the MAGI2 gene (1.4 Mb in size) that is hemizygously disrupted in 15 of 16 participants with IS or childhood epilepsy, but remains intact in 11 of 12 participants with no seizure history. MAGI2 encodes the synaptic scaffolding protein membrane-associated guanylate kinase inverted-2 that interacts with Stargazin, a protein also associated with epilepsy in the stargazer mouse.     

Assessment of single-vessel cerebral blood velocity by phase contrast fMRI

Current approaches to high-field functional MRI (fMRI) provide 2 means to map hemodynamics at the level of single vessels in the brain. One is through changes in deoxyhemoglobin in venules, i.e., blood oxygenation level–dependent (BOLD) fMRI, while the second is through changes in arteriole diameter, i.e., cerebral blood volume (CBV) fMRI. Here, we introduce cerebral blood flow–related velocity-based fMRI, denoted CBFv-fMRI, which uses high-resolution phase contrast (PC) MRI to form velocity measurements of flow. We use CBFv-fMRI in measure changes in blood velocity in single penetrating microvessels across rat parietal cortex. In contrast to the venule-dominated BOLD and arteriole-dominated CBV fMRI signals, CBFv-fMRI is comparable from both arterioles and venules. A single fMRI platform is used to map changes in blood pO₂ (BOLD), volume (CBV), and velocity (CBFv). This combined high-resolution single-vessel fMRI mapping scheme enables vessel-specific hemodynamic mapping in animal models of normal and diseased states and further has translational potential to map vascular dementia in diseased or injured human brains with ultra–high-field fMRI.

This study presents a phase contrast-based, high field MRI-based approach for the functional mapping of cerebral blood velocity in individual cortical arterioles and venules in the rat cortex; this approach can be combined with previously established approaches to map BOLD, CBV, and blood velocity from penetrating microvessels.     

Computer-aided subsite mapping of α-amylases

Subsite mapping is a crucial procedure in the characterization of α-amylases (EC 3.2.1.1), which are extensively used in starch-based industries and in diagnosis of pancreatic and salivary glands disorders. A computer-aided method has been developed for subsite mapping of α-amylases, which substitutes the difficult, expensive, and time-consuming experimental determination of action patterns to crystal structures based energy calculations. Interaction energies between enzymes and carbohydrate substrates were calculated after short energy minimization by a molecular mechanics program. A training set of wild type and mutant amylases with known experimental action patterns of 13 enzymes of wide range of origin was used to set up the procedure. Calculations for training set resulted in good correlation in case of subsite binding energies (r² = 0.827–0.929) and bond cleavage frequencies (r² = 0.727–0.835). A set of eight novel barley amylase 1 mutants was used to test our model. Subsite binding energies were predicted with r² = 0.502 correlation coefficient, while bond cleavage frequency prediction resulted in r² = 0.538. Our computer-aided procedure may supplement the experimental subsite mapping methods to predict and understand characteristic features of α-amylases.     

High-resolution mapping of the Gli3 deletion in the mouse extra-toesH mutant

Extra-toes is a semidominant mutation that affects the Gli3 gene and provokes limb and brain abnormalities. Among the different alleles of this mutation, Xt(H) is due to a deletion that has not yet been fully characterized. Using a PCR-based strategy, we undertook a high-resolution mapping of this deletion and confirmed that Xt(H) is a null allele of Gli3. We further designed a PCR test to identify unequivocally heterozygous and homozygous embryos from their wild-type littermates. Despite the length of the Xt(H) deletion, available data on the mouse genome indicate that no genes other than Gli3 are deleted in Xt(H) mutants. Thus, the Xt(H) mutation can be used as a model for studying the effects that absence of Gli3 function has during development.     

A Three-Dimensional Stereotaxic MRI Brain Atlas of the Cichlid Fish Oreochromis mossambicus

The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system.     

IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains

Intermated Recombinant Inbred Lines (IRILs) in plants, or Advanced Recombinant Inbred Strains in animals, are constructed by carrying out generations of intermating between F2 individuals before starting recurrent inbreeding generations by selfing or sib-mating. IRILs are powerful for high-resolution genetic mapping because they have undergone more recombination than usual Recombinant Inbred Lines (RILs). However, there is no mapping software able to generate actual centiMorgan distances from the segregation data obtained with IRILs. IRILmap software converts genetic distances computed with any linkage mapping program designed for RILs, so that IRIL-derived data can be used to get actual centiMorgan distances, directly comparable to F2, backcross or RIL-derived maps.     

Mapping vocal communication pathways in birds with inducible gene expression

Expression mapping of activity-dependent genes has been very useful to reveal brain activation patterns associated with specific stimuli or behavioral contexts. In addition, activity-induced neuronal gene expression is likely associated with neuronal plasticity and may be part of the mechanism(s) involved in long-term memory formation. Analysis of the immediate-early gene zenk has been used to generate high-resolution maps of brain activation associated with perceptual and motor aspects of vocal communication in songbirds and other avian groups. This molecular approach has generated novel insights into the organization of perceptual and motor control pathways for vocal communication in birds. Its impact on the neurobiology of birdsong will be reviewed here. Emphasis will be given to the caudomedial neostriatum, the area that shows the most robust zenk induction upon presentation of song to songbirds. Another focal point will be the comparative analysis of vocally induced zenk expression patterns across the avian orders that evolved vocal learning (i.e., songbirds, parrots, and hummingbirds). New research directions indicated by this molecular analysis will be discussed throughout.     

Genetic association mapping and genome organization of maize

Association mapping, a high-resolution method for mapping quantitative trait loci based on linkage disequilibrium, holds great promise for the dissection of complex genetic traits. The recent assembly and characterization of maize association mapping panels, development of improved statistical methods, and successful association of candidate genes have begun to realize the power of candidate-gene association mapping. Although the complexity of the maize genome poses several significant challenges to the application of association mapping, the ongoing genome sequencing project will ultimately allow for a thorough genome-wide examination of nucleotide polymorphism-trait association.     

Texture mapping parametric molecular surfaces

Texture mapping is an increasingly popular technique in molecular modeling. It is particularly effective in representing high-resolution surface detail using a low-resolution polygonal model. We describe how texture mapping can be used with parametric molecular surfaces represented as expansions of spherical harmonic functions. We define analytically the texture image and its transformation to a parametric surface. Unlike most methods of texture mapping, this transformation defines a one-to-one correspondence between the surface and the texture; texture coordinates are derived from the location of the surface point and not from physical properties at the surface point. This has advantates for the interactive visualization of surface data. We control the interactive response time by lowering the resolution of the polygon mesh while retaining the high-resolution detail of the texture, or we can lower the resolution of the texture image with the same polygonal model. By using a well-defined convention for texture coordinates, we can use the same image for the original surface or its parametric representation, and we can rapidly switch between images that represent different surface properties without recomputing the texture coordinates. Parametric surfaces allow new flexibility for the visualization of molecular surface data.     

Positional cloning by fast-track SNP-mapping in Drosophila melanogaster

Positional cloning of chemically induced mutations is the rate-limiting step in forward genetic screens in Drosophila. Single-nucleotide polymorphisms (SNPs) are useful markers to locate a mutated region in the genome. Here, we provide a protocol for high-throughput, high-resolution SNP mapping that enables rapid and cost-effective positional cloning in Drosophila. In stage 1 of the protocol, we use highly multiplexed tag-array mini-sequencing assays to map mutations to an interval of 1-2 Mb. In these assays, SNPs are genotyped by primer extension using fluorescently labeled dideoxy-nucleotides. Fluorescent primers are captured and detected on a microarray. In stage 2, we selectively isolate recombinants within the identified 1-2 Mb interval for fine mapping of mutations to about 50 kb. We have previously demonstrated the applicability of this protocol by mapping 14 muscle morphogenesis mutants within 4 months, which represents a significant acceleration compared with other commonly used mapping strategies that may take years.     

Mapping informative clusters in a hierarchical [corrected] framework of FMRI multivariate analysis

Pattern recognition methods have become increasingly popular in fMRI data analysis, which are powerful in discriminating between multi-voxel patterns of brain activities associated with different mental states. However, when they are used in functional brain mapping, the location of discriminative voxels varies significantly, raising difficulties in interpreting the locus of the effect. Here we proposed a hierarchical framework of multivariate approach that maps informative clusters rather than voxels to achieve reliable functional brain mapping without compromising the discriminative power. In particular, we first searched for local homogeneous clusters that consisted of voxels with similar response profiles. Then, a multi-voxel classifier was built for each cluster to extract discriminative information from the multi-voxel patterns. Finally, through multivariate ranking, outputs from the classifiers were served as a multi-cluster pattern to identify informative clusters by examining interactions among clusters. Results from both simulated and real fMRI data demonstrated that this hierarchical approach showed better performance in the robustness of functional brain mapping than traditional voxel-based multivariate methods. In addition, the mapped clusters were highly overlapped for two perceptually equivalent object categories, further confirming the validity of our approach. In short, the hierarchical framework of multivariate approach is suitable for both pattern classification and brain mapping in fMRI studies.     

Mapping Informative Clusters in a Hierarchial Framework of fMRI Multivariate Analysis

Pattern recognition methods have become increasingly popular in fMRI data analysis, which are powerful in discriminating between multi-voxel patterns of brain activities associated with different mental states. However, when they are used in functional brain mapping, the location of discriminative voxels varies significantly, raising difficulties in interpreting the locus of the effect. Here we proposed a hierarchical framework of multivariate approach that maps informative clusters rather than voxels to achieve reliable functional brain mapping without compromising the discriminative power. In particular, we first searched for local homogeneous clusters that consisted of voxels with similar response profiles. Then, a multi-voxel classifier was built for each cluster to extract discriminative information from the multi-voxel patterns. Finally, through multivariate ranking, outputs from the classifiers were served as a multi-cluster pattern to identify informative clusters by examining interactions among clusters. Results from both simulated and real fMRI data demonstrated that this hierarchical approach showed better performance in the robustness of functional brain mapping than traditional voxel-based multivariate methods. In addition, the mapped clusters were highly overlapped for two perceptually equivalent object categories, further confirming the validity of our approach. In short, the hierarchical framework of multivariate approach is suitable for both pattern classification and brain mapping in fMRI studies.