Reduced-field of view three-dimensional MR acoustic radiation force imaging with a low-rank reconstruction for targeting transcranial focused ultrasound.

PURPOSE: To rapidly image and localize the focus in MR-guided focused ultrasound (FUS) while maintaining a low ultrasound duty cycle to minimize tissue effects. METHODS: MR-acoustic radiation force imaging (ARFI) is key to targeting FUS procedures such as neuromodulation, and works by encoding ultrasound-induced displacements into the phase of MR images. However, it can require long scan times to cover a volume of tissue, especially when minimizing the FUS dose during targeting is paramount. To simultaneously minimize scan time and the FUS duty cycle, a 2-min three-dimensional (3D) reduced-FOV spin echo ARFI scan with two-dimensional undersampling was implemented at 3T with a FUS duty cycle of 0.85%. The 3D k-space sampling scheme incorporated uniform undersampling in one phase-encoded axis and partial Fourier (PF) sampling in the other. The scan interleaved FUS-on and FUS-off data collection to improve displacement map quality via a joint low-rank image reconstruction. Experiments in agarose and graphite phantoms and living macaque brains for neuromodulation and blood-brain barrier opening studied the effects of the sampling and reconstruction strategy on the acquisition, and evaluated its repeatability and accuracy. RESULTS: In the phantom, the distances between displacement centroids of 10 prospective reconstructions and a fully sampled reference were below 1 mm. In in vivo brain, the distances between centroids ranged from 1.3 to 2.1 mm. Results in phantom and in vivo brain both showed that the proposed method can recover the FUS focus compared to slower fully sampled scans. CONCLUSION: The proposed 3D MR-ARFI reduced-FOV method enables rapid imaging of the FUS focus while maintaining a low FUS duty cycle.

Characterization of Pingliang xiaoheidou (ZDD 11047), a soybean variety with resistance to soybean cyst nematode Heterodera glycines.

KEY MESSAGE: A novel QTL (qSCN-PL10) for SCN resistance and related candidate genes were identified in the soybean variety Pingliang xiaoheidou, and plant basal immunity seems to contribute to the SCN resistance. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating soybean pests worldwide. The development of host plant resistance represents an effective strategy to control SCN. However, owing to the lack of diversity of resistance genes in soybean varieties, further investigation is necessary to identify new SCN resistance genes. By analyzing the resistance phenotypes of soybean variety Pingliang xiaoheidou (Pingliang, ZDD 11047), we found that it exhibited the different resistance phenotypes from PI 88788 and Peking varieties. Because Pingliang variety contains the Rhg1-a (low copy) haplotype and lacks the resistant Rhg4 haplotype, novel quantitative trait locus might account for their SCN resistance. After sequencing parental lines (Magellan and Pingliang) and 200 F2:3 progenies, a high-density genetic map was constructed using the specific length amplified fragment sequencing method and qSCN-PL10 was identified as a novel locus for SCN resistance. Candidate genes were predicted by RNA sequencing (RNA-seq) in the qSCN-PL10 locus region. The RNA-seq analysis performed also indicated that plant basal immunity plays an important role in the resistance of Pingliang to SCN. These results lay a foundation for the use of marker-assisted breeding to enhance the resistance to SCN.

RNA-Seq analysis of nodule development at five different developmental stages of soybean (Glycine max) inoculated with Bradyrhizobium japonicum strain 113-2.

Nodule development directly affects nitrogen fixation efficiency during soybean growth. Although abundant genome-based information related to nodule development has been released and some studies have reported the molecular mechanisms that regulate nodule development, information on the way nodule genes operate in nodule development at different developmental stages of soybean is limited. In this report, notably different nodulation phenotypes in soybean roots inoculated with Bradyrhizobium japonicum strain 113-2 at five developmental stages (branching stage, flowering stage, fruiting stage, pod stage and harvest stage) were shown, and the expression of nodule genes at these five stages was assessed quantitatively using RNA-Seq. Ten comparisons were made between these developmental periods, and their differentially expressed genes were analysed. Some important genes were identified, primarily encoding symbiotic nitrogen fixation-related proteins, cysteine proteases, cystatins and cysteine-rich proteins, as well as proteins involving plant-pathogen interactions. There were no significant shifts in the distribution of most GO functional annotation terms and KEGG pathway enrichment terms between these five development stages. A cystatin Glyma18g12240 was firstly identified from our RNA-seq, and was likely to promote nodulation and delay nodule senescence. This study provides molecular material for further investigations into the mechanisms of nitrogen fixation at different soybean developmental stages.

Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions.

BACKGROUND: Soybean is an important crop that provides valuable proteins and oils for human use. Because soybean growth and development is extremely sensitive to water deficit, quality and crop yields are severely impacted by drought stress. In the face of limited water resources, drought-responsive genes are therefore of interest. Identification and analysis of dehydration- and rehydration-inducible differentially expressed genes (DEGs) would not only aid elucidation of molecular mechanisms of stress response, but also enable improvement of crop stress tolerance via gene transfer. Using Digital Gene Expression Tag profiling (DGE), a new technique based on Illumina sequencing, we analyzed expression profiles between two soybean genotypes to identify drought-responsive genes. RESULTS: Two soybean genotypes - drought-tolerant Jindou21 and drought-sensitive Zhongdou33 - were subjected to dehydration and rehydration conditions. For analysis of DEGs under dehydration conditions, 20 cDNA libraries were generated from roots and leaves at two different time points under well-watered and dehydration conditions. We also generated eight libraries for analysis under rehydration conditions. Sequencing of the 28 libraries produced 25,000-33,000 unambiguous tags, which were mapped to reference sequences for annotation of expressed genes. Many genes exhibited significant expression differences among the libraries. DEGs in the drought-tolerant genotype were identified by comparison of DEGs among treatments and genotypes. In Jindou21, 518 and 614 genes were differentially expressed under dehydration in leaves and roots, respectively, with 24 identified both in leaves and roots. The main functional categories enriched in these DEGs were metabolic process, response to stresses, plant hormone signal transduction, protein processing, and plant-pathogen interaction pathway; the associated genes primarily encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significantly expressed (|log2 ratio| ≥ 8) genes - Glyma15g03920, Glyma05g02470, Glyma15g15010, Glyma05g09070, Glyma06g35630, Glyma08g12590, and Glyma11g16000 - are more likely to determine drought stress tolerance. The expression patterns of eight randomly-selected genes were confirmed by quantitative RT-PCR; the results of QRT-PCR analysis agreed with transcriptional profile data for 96 out of 128 (75%) data points. CONCLUSIONS: Many soybean genes were differentially expressed between drought-tolerant and drought-sensitive genotypes. Based on GO functional annotation and pathway enrichment analysis, some of these genes encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significant DEGs are candidates for improving soybean drought tolerance. These findings will be helpful for analysis and elucidation of molecular mechanisms of drought tolerance; they also provide a basis for cultivating new varieties of drought-tolerant soybean.

Intrinsic horizontal connections process global tactile features in the primary somatosensory cortex: neuroanatomical evidence.

To understand manual tactile functions in primates, it is essential to explore the interactions between the finger pad representations in somatosensory cortex. To this end, we used optical imaging and electrophysiological mapping to guide neuroanatomical tracer injections into distal digit tip representations of Brodmann area 3b in the squirrel monkey. Retrogradely labeled cell densities and anterogradely labeled fibers and terminal patches in somatosensory areas were plotted and quantified with respect to tangential distribution. Within area 3b, reciprocal patchy distribution of anterograde and retrograde labeling spanned the representation of the distal pad of multiple digits, indicating strong cross-digit connectivity. Inter-areal connections revealed bundles of long-range fibers projecting anteroposteriorly, connecting area 3b with clusters of labeled neurons and terminal axon arborizations in area 1. Inter-areal linkage appeared to be largely confined to the representation of the injected finger. These findings provide the neuroanatomical basis for the interaction between distal finger pad representations observed by recent electrophysiological studies. We propose that intra-areal connectivity may be heavily involved in interdigit integration such as shape discrimination, whereas long-range inter-areal connections may subserve active touch in a digit-specific manner.

Functional magnetic resonance imaging of awake monkeys: some approaches for improving imaging quality.

Functional magnetic resonance imaging (fMRI) at high magnetic field strength can suffer from serious degradation of image quality because of motion and physiological noise, as well as spatial distortions and signal losses due to susceptibility effects. Overcoming such limitations is essential for sensitive detection and reliable interpretation of fMRI data. These issues are particularly problematic in studies of awake animals. As part of our initial efforts to study functional brain activations in awake, behaving monkeys using fMRI at 4.7 T, we have developed acquisition and analysis procedures to improve image quality with encouraging results. We evaluated the influence of two main variables on image quality. First, we show how important the level of behavioral training is for obtaining good data stability and high temporal signal-to-noise ratios. In initial sessions, our typical scan session lasted 1.5 h, partitioned into short (<10 min) runs. During reward periods and breaks between runs, the monkey exhibited movements resulting in considerable image misregistrations. After a few months of extensive behavioral training, we were able to increase the length of individual runs and the total length of each session. The monkey learned to wait until the end of a block for fluid reward, resulting in longer periods of continuous acquisition. Each additional 60 training sessions extended the duration of each session by 60 min, culminating, after about 140 training sessions, in sessions that last about 4 h. As a result, the average translational movement decreased from over 500 µm to less than 80 µm, a displacement close to that observed in anesthetized monkeys scanned in a 7-T horizontal scanner. Another major source of distortion at high fields arises from susceptibility variations. To reduce such artifacts, we used segmented gradient-echo echo-planar imaging (EPI) sequences. Increasing the number of segments significantly decreased susceptibility artifacts and image distortion. Comparisons of images from functional runs using four segments with those using a single-shot EPI sequence revealed a roughly twofold improvement in functional signal-to-noise-ratio and 50% decrease in distortion. These methods enabled reliable detection of neural activation and permitted blood-oxygenation-level-dependent-based mapping of early visual areas in monkeys using a volume coil. In summary, both extensive behavioral training of monkeys and application of segmented gradient-echo EPI sequence improved signal-to-noise ratio and image quality. Understanding the effects these factors have is important for the application of high field imaging methods to the detection of submillimeter functional structures in the awake monkey brain.

Reorganization of somatosensory cortical areas 3b and 1 after unilateral section of dorsal columns of the spinal cord in squirrel monkeys.

An incomplete lesion of the ascending afferents from the hand in the dorsal columns of the spinal cord in monkeys is followed after weeks of recovery by a reactivation of much of the territory of the hand representations in primary somatosensory cortex (area 3b). However, the relationship between the extent of the dorsal column lesion and the amount of cortical reactivation has not been clear. Largely, this is due to the uncertainties about axon sparing after spinal cord lesions. Here, we unilaterally sectioned dorsal column afferents in the cervical spinal cord (C4-C6) in adult squirrel monkeys. After weeks of recovery, cholera toxin subunit B (CTB) was injected into the distal phalanges to label normal and surviving afferents to the cuneate nuclei representing the hands. Days later, the responsiveness of neurons in cortical areas 3b and 1 to tactile stimulation on the hand was evaluated in a microelectrode mapping session. The sizes and densities of CTB-labeled patches in the cuneate nuclei of both sides were quantified and compared. The results indicate that extensive reactivations of the hand representations in cortical areas 3b and 1 occur contralateral to the spinal cord lesion, even when <1% of labeled dorsal column terminations in the cuneate nucleus remained. These results raise the possibilities that secondary afferents from innervated neurons in the spinal cord contribute to the reactivation, and that the reactivation of area 1 is not completely dependent on inputs from area 3b.

High-resolution functional magnetic resonance imaging mapping of noxious heat and tactile activations along the central sulcus in New World monkeys.

This study mapped the fine-scale functional representation of tactile and noxious heat stimuli in cortical areas around the central sulcus of anesthetized squirrel monkeys by using high-resolution blood oxygen level-dependent (BOLD) fMRI at 9.4T. Noxious heat (47.5°C) stimulation of digits evoked multiple spatially distinct and focal BOLD activations. Consistent activations were observed in areas 3a, 3b, 1, and 2, whereas less frequent activation was present in M1. Compared with tactile activations, thermal nociceptive activations covered more area and formed multiple foci within each functional area. In general, noxious heat activations in area 3b did not colocalize with tactile responses. The spatial relationships of heat and tactile activations in areas 3a and 1/2 varied across animals. Subsequent electrophysiological mapping confirmed that the evoked heat and tactile BOLD signals were somatotopically appropriate. The magnitude and temporal profiles of the BOLD signals to noxious heat stimuli differed across cortical areas. Comparatively late-peaking but stronger signals were observed in areas 3b and 2, whereas earlier-peaking but weaker signals were observed in areas 3a, 1, and M1. In sum, this study not only confirmed the involvement of somatosensory areas of 3a, 3b, and 1, but also identified the engagements of area 2 and M1 in the processing of heat nociceptive inputs. Differential BOLD response profiles of the individual cortical areas along the central sulcus suggest that these areas play different roles in the encoding of nociceptive inputs. Thermal nociceptive and tactile inputs may be processed by different clusters of neurons in different areas. To critically bridge animal and human pain studies, human fMRI was related to primate fMRI and electrophysiology of nociceptive processing, examining the functional role of the primary somatosensory cortex in heat nociception and demonstrating that subregion areas 3a, 3b, 1, 2, and M1 are responsive to noxious heat stimuli.

High-resolution fMRI maps of cortical activation in nonhuman primates: correlation with intrinsic signal optical images.

One of the most widely used functional brain mapping tools is blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI). This method has contributed to new understandings of the functional roles of different areas in the human brain. However, its ability to map cerebral cortex at high spatial (submillimeter) resolution is still unknown. Other methods such as single- and multiunit electrophysiology and intrinsic signal optical imaging have revealed submillimeter resolution of sensory topography and cortical columnar activations. However, they are limited either by spatial scale (electrophysiology characterizes only local groups of neurons) or by the inability to monitor deep structures in the brain (i.e., cortical regions buried in sulci or subcortical structures). A method that could monitor all regions of the brain at high spatial resolution would be ideal. This capacity would open the doors to investigating, for example, how networks of cerebral cortical columns relate to or produce behavior. In this article we demonstrate that, without benefit of contrast agents, at a magnetic field strength of 9.4 tesla, BOLD fMRI can reveal millimeter-sized topographic maps of digit representation in the somatosensory cortex of the anesthetized squirrel monkey. Furthermore, by mapping the "funneling illusion," it is possible to detect even submillimeter shifts in activation in the cortex. Our data suggest that at high magnetic field strength, the positive BOLD signal can be used to reveal high spatial resolution maps of brain activity, a finding that weakens previous notions about the ultimate spatial specificity of the positive BOLD signal.

High-resolution maps of real and illusory tactile activation in primary somatosensory cortex in individual monkeys with functional magnetic resonance imaging and optical imaging.

Although blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) has been widely used to explore human brain function, questions remain regarding the ultimate spatial resolution of positive BOLD fMRI, and indeed the extent to which functional maps revealed by positive BOLD correlate spatially with maps obtained with other high-spatial-resolution mapping techniques commonly used in animals, such as optical imaging of intrinsic signal (OIS) and single-unit electrophysiology. Here, we demonstrate that the positive BOLD signal at 9.4T can reveal the fine topography of individual fingerpads in single-condition activation maps in nonhuman primates. These digit maps are similar to maps obtained from the same animal using intrinsic optical imaging. Furthermore, BOLD fMRI reliably resolved submillimeter spatial shifts in activation in area 3b previously identified with OIS (Chen et al., 2003) as neural correlates of the "funneling illusion." These data demonstrate that at high field, high-spatial-resolution topographic maps can be achieved using the positive BOLD signal, weakening previous notions regarding the spatial specificity of the positive BOLD signal.

Dependence of BOLD signal change on tactile stimulus intensity in SI of primates.

Recently, we have demonstrated that the fine-digit topography (millimeter sized) previously identified in the primary somatosensory cortex (SI), using electrophysiology and intrinsic signal optical imaging, can also be mapped with submillimeter resolution using blood-oxygenation-level-dependent (BOLD) functional magnetic resonance imaging at high field. In the present study, we have examined the dependence of BOLD signal response on stimulus intensity in two subregions of SI, Areas 3b and 1. In a region(s)-of-interest (ROI) analysis of Area 3b, BOLD signal amplitude increased linearly with increasing amplitude of an 8-Hz vibrotactile stimulus, and BOLD signal was sustained throughout the stimulation period. In contrast, in Area 1, a significant BOLD signal response was only observed with more intense stimuli, and ROI analysis of the dependence of BOLD response showed no significant dependence on stimulus intensity. In addition, activation was not sustained throughout the period of stimulation. Differing responses of Areas 3b and 1 suggest potentially divergent roles for subregions of SI cortices in vibrotactile intensity encoding. Moreover, this study underscores the importance of imaging at small spatial scales. In this case, such high-resolution imaging allows differentiation between area-specific roles in intensity encoding and identifies anatomic targets for detailed electrophysiological studies of somatosensory neuronal populations with different coding properties. These experiments illustrate the value of nonhuman primates for characterizing the dependence of the BOLD signal response on stimulus parameters and on underlying neural response properties.

Optical imaging of a tactile illusion in area 3b of the primary somatosensory cortex.

In the tactile funneling illusion, the simultaneous presentation of brief stimuli at multiple points on the skin produces a single focal sensation at the center of the stimulus pattern even when no physical stimulus occurs at that site. Consistent with the funneling percept, we show with optical imaging in area 3b of the primary somatosensory cortex (SI) that simultaneous stimulation of two fingertips produces a single focal cortical activation between the single fingertip activation regions. Thus, in contrast to traditional views of the body map, topographic representation in the SI reflects the perceived rather than the physical location of peripheral stimulation.