Genome-Wide Analyses of the NAC Transcription Factor Gene Family in Pepper (Capsicum annuum L.): Chromosome Location, Phylogeny, Structure, Expression Patterns, Cis-Elements in the Promoter, and Interaction Network.

The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family, which is involved in the regulation of tissue development in response to biotic and abiotic stress. To date, there have been no comprehensive studies investigating chromosomal location, gene structure, gene phylogeny, conserved motifs, or gene expression of NAC in pepper (Capsicum annuum L.). The recent release of the complete genome sequence of pepper allowed us to perform a genome-wide investigation of Capsicum annuum L. NAC (CaNAC) proteins. In the present study, a comprehensive analysis of the CaNAC gene family in pepper was performed, and a total of 104 CaNAC genes were identified. Genome mapping analysis revealed that CaNAC genes were enriched on four chromosomes (chromosomes 1, 2, 3, and 6). In addition, phylogenetic analysis of the NAC domains from pepper, potato, Arabidopsis, and rice showed that CaNAC genes could be clustered into three groups (I, II, and III). Group III, which contained 24 CaNAC genes, was exclusive to the Solanaceae plant family. Gene structure and protein motif analyses showed that these genes were relatively conserved within each subgroup. The number of introns in CaNAC genes varied from 0 to 8, with 83 (78.9%) of CaNAC genes containing two or less introns. Promoter analysis confirmed that CaNAC genes are involved in pepper growth, development, and biotic or abiotic stress responses. Further, the expression of 22 selected CaNAC genes in response to seven different biotic and abiotic stresses [salt, heat shock, drought, Phytophthora capsici, abscisic acid, salicylic acid (SA), and methyl jasmonate (MeJA)] was evaluated by quantitative RT-PCR to determine their stress-related expression patterns. Several putative stress-responsive CaNAC genes, including CaNAC72 and CaNAC27, which are orthologs of the known stress-responsive Arabidopsis gene ANAC055 and potato gene StNAC30, respectively, were highly regulated by treatment with different types of stress. Our results also showed that CaNAC36 plays an important role in the interaction network, interacting with 48 genes. Most of these genes are in the mitogen-activated protein kinase (MAPK) family. Taken together, our results provide a platform for further studies to identify the biological functions of CaNAC genes.

Detection of respiratory tumour motion using intrinsic list mode-driven gating in positron emission tomography.

PURPOSE: Respiratory motion of organs during PET scans is known to degrade PET image quality, potentially resulting in blurred images, attenuation artefacts and erroneous tracer quantification. List mode-based gating has been shown to reduce these pitfalls in cardiac PET. This study evaluates these intrinsic gating methods for tumour PET scans. METHODS: A total of 34 patients with liver or lung tumours (14 liver tumours and 27 lung tumours in all) underwent a 15-min single-bed list mode PET scan of the tumour region. Of these, 15 patients (8 liver and 11 lung tumours in total) were monitored by a video camera registering a marker on the patient's abdomen, thus capturing the respiratory motion for PET gating (video method). Further gating information was deduced by dividing the list mode stream into 200-ms frames, determining the number of coincidences (sensitivity method) and computing the axial centre of mass of the measured count rates in the same frames (centre of mass method). Additionally, these list mode-based methods were evaluated using only coincidences originating from the tumour region by segmenting the tumour in sinogram space (segmented sensitivity/centre of mass method). Measured displacement of the tumours between end-expiration and end-inspiration and the increase in apparent uptake in the gated images served as a measure for the exactness of gating. To estimate the accuracy, a thorax phantom study with moved activity sources simulating small tumours was also performed. RESULTS: All methods resolved the respiratory motion with varying success. The best results were seen in the segmented centre of mass method, on average leading to larger displacements and uptake values than the other methods. The simple centre of mass method performed worse in terms of displacements due to activities moving into the field of view during the respiratory cycle. Both sensitivity- and video-based methods lead to similar results. CONCLUSION: List mode-driven PET gating, especially the segmented centre of mass method, is feasible and accurate in PET scans of liver and lung tumours.

The Alcohol and Epoxy Alcohol of Zingiberene, Produced in Trichomes of Wild Tomato, Are More Repellent to Spider Mites Than Zingiberene.

Allelochemicals that are present in trichome secretions of wild tomato species play a major role in mediating interactions with arthropods, often conferring a high level of resistance via antibiosis and antixenosis. Many accessions of the wild tomato relative, Solanum habrochaites (S.h), possess high levels of resistance to arthropods. The monocyclic sesquiterpene hydrocarbon, 7-epi-zingiberene, is a major defensive component found in trichome secretions of certain accessions of S.h. We have used LA2329, an S.h. accession, as a donor in a breeding program designed to introgress zingiberene into cultivated tomato. However, the composition of trichome secretions in our population of LA2329 is segregating, with some individuals producing mainly 7-epi-zingiberene in their secretions while others producing two additional, unidentified compounds in their trichome secretions. To investigate if these other compounds may also contribute to arthropod resistance, trichome secretions were collected from plants of S.h LA2329 grown under greenhouse conditions and then major compounds were isolated by silica gel column chromatography and tested for their ability to repel two spotted-spider mite (TSSM), Tetranychus urticae. Isolation and identification of allelochemicals were aided by use of gas chromatography/mass spectroscopy. The results revealed the presence of three predominate chromatographic peaks: 7-epi-zingiberene, 9-hydroxy zingiberene, and 9-hydroxy,10,11-epoxy-zingiberene. Results of testing isolated compounds for repellency to TSSM using bridge bioassays revealed that the repellent activities of 9-hydroxy zingiberene and 9-hydroxy,10,11-epoxy-zingiberene were each significantly higher than that for 7-epi-zingiberene. These results support the idea that the degree of repellency may differ among plant allelochemicals and also emphasize the potential value of introgressing the presence of 9-hydroxy zingiberene and 9-hydroxy,10,11-epoxy-zingiberene into cultivated tomato to enhance its arthropod resistance.

List mode-driven cardiac and respiratory gating in PET.

UNLABELLED: Gating methods acquiring biosignals (such as electrocardiography [ECG] and respiration) during PET enable one to reduce motion effects that potentially lead to image blurring and artifacts. This study evaluated different cardiac and respiratory gating methods: one based on ECG signals for cardiac gating and video signals for respiratory gating; 2 others based on measured inherent list mode events. METHODS: Twenty-nine patients with coronary artery disease underwent a 20-min ECG-gated single-bed list mode PET scan of the heart. Of these, 17 were monitored by a video camera registering a marker on the patient's abdomen, thus capturing the respiratory motion for PET gating (video method). Additionally, respiratory and cardiac gating information was deduced without auxiliary measurements by dividing the list mode stream in 50-ms frames and then either determining the number of coincidences (sensitivity method) or computing the axial center of mass and SD of the measured counting rates in the same frames (center-of-mass method). The gated datasets (respiratory and cardiac gating) were reconstructed without attenuation correction. Measured wall thicknesses, maximum displacement of the left ventricular wall, and ejection fraction served as measures of the exactness of gating. RESULTS: All methods successfully captured respiratory motion and significantly decreased motion-induced blurring in the gated images. The center-of-mass method resulted in significantly larger left ventricular wall displacements than did the sensitivity method (P < 0.02); other differences were nonsignificant. List mode-based cardiac gating was found to work well for patients with high (18)F-FDG uptake when the center-of-mass method was used, leading to an ejection fraction correlation coefficient of r = 0.95 as compared with ECG-based gating. However, the sensitivity method did not always result in valid cardiac gating information, even in patients with high (18)F-FDG uptake. CONCLUSION: Our study demonstrated that valid gating signals during PET scans cannot be obtained only by tracking the external motion or applying an ECG but also by simply analyzing the PET list mode stream on a frame-by-frame basis.

Optimal number of respiratory gates in positron emission tomography: a cardiac patient study.

Respiratory gating is the method of dividing the data from a tomographic scan with respect to the respiratory phase of the patient. It enables more accurate images by reducing the effects of motion blur and attenuation artifacts due to motion. However, it induces image degradation due to higher noise levels as the number of events per gate is reduced. Due to lack of systematic studies in this regard, different numbers of gates are being used in the scientific and clinical practice. The present study aims at examining the relationship between the respiratory signal, the number of gates required for accurate motion detection, and the level of noise with two different methods of gating: (1) Amplitude-based gating and (2) time-based gating. Patient data with a wide range of motion are used for the study. The results show that time-based gating underestimates the real respiratory displacement by up to 50%. The optimal number of gates is 8 for amplitude- and 6 for time-based gatings. The noise properties remain the same with either method but noise increases with increasing number of gates.

Effective methods to correct contrast agent-induced errors in PET quantification in cardiac PET/CT.

UNLABELLED: In combined PET/CT studies, x-ray attenuation information from the CT scan is generally used for PET attenuation correction. Iodine-containing contrast agents may induce artifacts in the CT-generated attenuation map and lead to an erroneous radioactivity distribution on the corrected PET images. This study evaluated 2 methods of thresholding the CT data to correct these contrast agent-related artifacts. METHODS: PET emission and attenuation data (acquired with and without a contrast agent) were simulated using a cardiac torso software phantom and were obtained from patients. Seven patients with known coronary artery disease underwent 2 electrocardiography-gated CT scans of the heart, the first without a contrast agent and the second with intravenous injection of an iodine-containing contrast agent. A 20-min PET scan (single bed position) covering the same axial range as the CT scans was then obtained 1 h after intravenous injection of (18)F-FDG. For both the simulated data and the patient data, the unenhanced and contrast-enhanced attenuation datasets were used for attenuation correction of the PET data. Additionally, 2 threshold methods (one requiring user interaction) aimed at compensating for the effect of the contrast agent were applied to the contrast-enhanced attenuation data before PET attenuation correction. All PET images were compared by quantitative analysis. RESULTS: Regional radioactivity values in the heart were overestimated when the contrast-enhanced data were used for attenuation correction. For patients, the mean decrease in the left ventricular wall was 23%. Use of either of the proposed compensation methods reduced the quantification error to less than 5%. The required time for postprocessing was minimal for the user-independent method. CONCLUSION: The use of contrast-enhanced CT images for attenuation correction in cardiac PET/CT significantly impairs PET quantification of tracer uptake. The proposed CT correction methods markedly reduced these artifacts; additionally, the user-independent method was time-efficient.

Respiratory gating in positron emission tomography: a quantitative comparison of different gating schemes.

Respiratory gating is used for reducing the effects of breathing motion in a wide range of applications from radiotherapy treatment to diagnostical imaging. Different methods are feasible for respiratory gating. In this study seven gating methods were developed and tested on positron emission tomography (PET) listmode data. The results of seven patient studies were compared quantitatively with respect to motion and noise. (1) Equal and (2) variable time-based gating methods use only the time information of the breathing cycle to define respiratory gates. (3) Equal and (4) variable amplitude-based gating approaches utilize the amplitude of the respiratory signal. (5) Cycle-based amplitude gating is a combination of time and amplitude-based techniques. A baseline correction was applied to methods (3) and (4) resulting in two new approaches: Baseline corrected (6) equal and (7) variable amplitude-based gating. Listmode PET data from seven patients were acquired together with a respiratory signal. Images were reconstructed applying the seven gating methods. Two parameters were used to quantify the results: Motion was measured as the displacement of the heart due to respiration and noise was defined as the standard deviation of pixel intensities in a background region. The amplitude-based approaches (3) and (4) were superior to the time-based methods (1) and (2). The improvement in capturing the motion was more than 30% (up to 130%) in all subjects. The variable time (2) and amplitude (4) methods had a more uniform noise distribution among all respiratory gates compared to equal time (1) and amplitude (3) methods. Baseline correction did not improve the results. Out of seven different respiratory gating approaches, the variable amplitude method (4) captures the respiratory motion best while keeping a constant noise level among all respiratory phases.

Lung motion correction on respiratory gated 3-D PET/CT images.

Motion is a source of degradation in positron emission tomography (PET)/computed tomography (CT) images. As the PET images represent the sum of information over the whole respiratory cycle, attenuation correction with the help of CT images may lead to false staging or quantification of the radioactive uptake especially in the case of small tumors. We present an approach avoiding these difficulties by respiratory-gating the PET data and correcting it for motion with optical flow algorithms. The resulting dataset contains all the PET information and minimal motion and, thus, allows more accurate attenuation correction and quantification.

Organ movement reduction in PET/CT using dual-gated list-mode acquisition.

PURPOSE: Imaging of moving organs using the PET leads to blurred images due to long acquisition times. Simultaneous cardiac and respiratory gating of list-mode PET/CT is evaluated with the aim to improve image quality and assess the organ movement. METHODS: We performed a N-13 ammonia PET/CT scan with a human volunteer, using the Siemens Biograph Sensation 16 scanner with list-mode acquisition. For ECG gating we used the scanner's integrated ECG device. Respiratory gating was done with the BioVet pneumatic sensor system. RESULTS: The sorting of the list-mode data post acquisition produced the desired matrix of eight cardiac times eight respiratory images. Organ movement could be measured in the series of gated PET images. The quantitation of tracer uptake in the myocardium showed artifacts due to the CT-based attenuation correction. CONCLUSION: Double gating is feasible in human PET/CT scans using a list-mode-based scan protocol. The image quality can be enhanced using double gated list-mode acquisition in PET/CT Attenuation correction protocols in PET using a single not gated fast CT introduces artifacts in moving organs.

A dual-Kinect approach to determine torso surface motion for respiratory motion correction in PET.

PURPOSE: Respiratory gating is commonly used to reduce blurring effects and attenuation correction artifacts in positron emission tomography (PET). Established clinically available methods that employ body-attached hardware for acquiring respiration signals rely on the assumption that external surface motion and internal organ motion are well correlated. In this paper, the authors present a markerless method comprising two Microsoft Kinects for determining the motion on the whole torso surface and aim to demonstrate its validity and usefulness-including the potential to study the external/internal correlation and to provide useful information for more advanced correction approaches. METHODS: The data of two Kinects are used to calculate 3D representations of a patient's torso surface with high spatial coverage. Motion signals can be obtained for any position by tracking the mean distance to a virtual camera with a view perpendicular to the surrounding surface. The authors have conducted validation experiments including volunteers and a moving high-precision platform to verify the method's suitability for providing meaningful data. In addition, the authors employed it during clinical (18)F-FDG-PET scans and exemplarily analyzed the acquired data of ten cancer patients. External signals of abdominal and thoracic regions as well as data-driven signals were used for gating and compared with respect to detected displacement of present lesions. Additionally, the authors quantified signal similarities and time shifts by analyzing cross-correlation sequences. RESULTS: The authors' results suggest a Kinect depth resolution of approximately 1 mm at 75 cm distance. Accordingly, valid signals could be obtained for surface movements with small amplitudes in the range of only few millimeters. In this small sample of ten patients, the abdominal signals were better suited for gating the PET data than the thoracic signals and the correlation of data-driven signals was found to be stronger with abdominal signals than with thoracic signals (average Pearson correlation coefficients of 0.74 ± 0.17 and 0.45 ± 0.23, respectively). In all cases, except one, the abdominal respiratory motion preceded the thoracic motion-a maximum delay of approximately 600 ms was detected. CONCLUSIONS: The method provides motion information with sufficiently high spatial and temporal resolution. Thus, it enables meaningful analysis in the form of comparisons between amplitudes and phase shifts of signals from different regions. In combination with a large field-of-view, as given by combining the data of two Kinect cameras, it yields surface representations that might be useful in the context of motion correction and motion modeling.

A mass conservation-based optical flow method for cardiac motion correction in 3D-PET.

PURPOSE: Cardiac positron emission tomography (PET) images usually show two kinds of artifacts: the limited resolution of PET leads to partial volume effects and the motion of the heart induces blurring. These phenomena degrade the PET images and induce errors in the quantification. One method of reducing this problem is to use gated PET data. However, the reduction of information per phase leads to an increase in noise on the reconstructed images. Alternatively, the PET data have to be corrected for motion and partial volume effects. METHODS: Optical flow methods have been shown to accurately estimate the motion between PET image frames. These methods assume that the brightness of the objects remains constant between the frames. This condition is not fulfilled in cardiac PET data because the brightness of the cardiac muscle tissue (myocardium) is not accurately resolved due to the partial volume effect. Therefore, the use of a newly developed optical flow method based upon the conservation of mass condition is proposed to correct the cardiac PET data. Mass conservation is applicable to PET images as the total activity in the field of view may be assumed to remain almost constant, if the data are precorrected for radioactive decay. Two variants of the method using the quadratic and the nonquadratic penalization are presented. The methods were evaluated with respect to correlation coefficient, myocardial thickness and the blood pool activity in the left ventricle on phantom data and on 14 patient image volumes. RESULTS: The proposed methods showed that the cardiac motion can be efficiently corrected despite partial volume effects. The correlation coefficient between the image volumes increased from 0.87 to 0.98 on average. The change in myocardial thickness was reduced from 28% to 3%. The variation in blood pool activity was reduced from 80% to 8%. The algorithm needed only about 4 s for execution. CONCLUSIONS: A mass preserving optical flow method of cardiac motion correction in 3D PET data has been presented and tested on phantom as well as patient data. The results show that the motion was corrected for all datasets effectively.

Respiratory motion correction in 3-D PET data with advanced optical flow algorithms.

The problem of motion is well known in positron emission tomography (PET) studies. The PET images are formed over an elongated period of time. As the patients cannot hold breath during the PET acquisition, spatial blurring and motion artifacts are the natural result. These may lead to wrong quantification of the radioactive uptake. We present a solution to this problem by respiratory-gating the PET data and correcting the PET images for motion with optical flow algorithms. The algorithm is based on the combined local and global optical flow algorithm with modifications to allow for discontinuity preservation across organ boundaries and for application to 3-D volume sets. The superiority of the algorithm over previous work is demonstrated on software phantom and real patient data.

Motion correction in respiratory gated cardiac PET/CT using multi-scale optical flow.

Respiratory motion is a source of degradation in positron emission tomography. As the patients cannot hold breath during the PET acquisition, spatial blurring and motion artifacts are unavoidable which may lead to wrong quantification of the data. A solution based on respiratory-gating and optical flow based correction of the PET data is proposed. This includes deformation of the CT data for accurate attenuation and listmode based reconstruction. All methods are applied to real patient data and are evaluated with respect to three criteria.