Presentation of microstructural diffusion components by color schemes in abdominal organs.

PURPOSE: Development of a color scheme representation to facilitate the interpretation of tri-exponential DWI data from abdominal organs, where multi-exponential behavior is more pronounced. METHODS: Multi-exponential analysis of DWI data provides information about the microstructure of the tissue under study. The tri-exponential signal analysis generates numerous parameter images that are difficult to analyze individually. Summarized color images can simplify at-a-glance analysis. A color scheme was developed in which the slow, intermediate, and fast diffusion components were each assigned to a different red, green, and blue color channel. To improve the appearance of the image, histogram equalization, gamma correction, and white balance were used, and the processing parameters were adjusted. Examples of the resulting color maps of the diffusion fractions of healthy and pathological kidney and prostate are shown. RESULTS: The color maps obtained by the presented method show the merged information of the slow, intermediate, and fast diffusion components in a single view. A differentiation of the different fractions becomes clearly visible. Fast diffusion regimes, such as in the renal hilus, can be clearly distinguished from slow fractions, such as in dense tumor tissue. CONCLUSION: Combining the diffusion information from tri-exponential DWI analysis into a single color image allows for simplified interpretation of the diffusion fractions. In the future, such color images may provide additional information about the microstructural nature of the tissue under study.

Traumatized German soldiers with moral injury - value-based cognitive-behavioral group therapy to treat war-related shame.

Introduction: During deployment, soldiers are confronted with potentially morally injurious events. In many cases, these events violate their personal values and belief systems, resulting in feelings of anger, alienation, guilt, and shame. The psychological distress caused by such transgressions is defined as moral injury. It remains unclear to date, which therapeutic interventions are most appropriate for addressing this specific psychological condition. This study examines the effectiveness of value-based cognitive-behavioral group therapy combining elements of cognitive-behavioral therapy, acceptance and commitment therapy, spiritual care, and adaptive disclosure therapy. Materials and methods: This controlled study uses the Compass of Shame Scale to assess symptom severity among participants both before and after a three-week inpatient group therapy regimen for moral injury. An intervention group (n = 45) was compared to a waiting-list control group (n = 40). A one-way between subjects ANOVA was conducted to determine the differences between the two measurement points in the intervention group compared to the control group. A positive ethics vote from the Humboldt University Berlin (Charité) was available (No.EA1/092/15). Results: A significant difference was found on the shame-associated maladaptive strategies subscales of attack self (F (1, 83) = 5.942, p = 0.017, Cohen's f = 0,27), withdrawal (F (1, 83) = 8.263, p = 0.005, Cohen's f = 0,32), and attack others (F (1, 83) = 10.552, p = 0.002, Cohen's f = 0,36) of the Compass of Shame Scale between the intervention group and the control group at the p < 0.05 level in the pre- and post-treatment (t1-t2) comparison. Conclusion: This study suggests that the special therapeutic focus in cognitive-behavioral group therapy can alter shame-based maladaptive coping behaviors in response to war-related moral injury. This study provides further evidence that therapeutic approaches - through fostering a reconciliatory, compassionate, and forgiving approach toward oneself and others - target the underlying mechanisms of moral injury. Therefore, value-based cognitive-behavioral interventions should be considered as a standard element of trauma care in a military setting. Future studies should further examine such interventions in randomized control trials. It would also be particularly valuable for future studies to include a follow-up time point.

Interrelated dataset of rebound numbers, ultrasonic pulse velocities and compressive strengths of drilled concrete cores from an existing structure and new fabricated concrete cubes.

Two test series were examined using nondestructive measuring methods by six independent laboratories before determining their compressive strength. The nondestructive test methods used were the rebound hammer and ultrasonic pulse velocity measurement. Two types of geometries were investigated: drilled cores and cubes. The measurement procedure for each of these datasets is conditioned to the geometry and is therefore different. The first series consists of 20 drilled cores (approximately diameter/height = 10 cm/20 cm) from the 55-year-old Lahntal Viaduct near Limburg, Germany. After preparation in the first laboratory, the lateral surface of the drilled cores was tested with the rebound hammer using a given pattern. Every laboratory tested every drilled core at different locations. Ultrasonic measurements in transmission were performed repeatedly at predefined points on the flat surfaces of the specimen. The second series consisted of 25 newly manufactured concrete cubes of a mix with a target concrete strength class of C30/37. The edge length was 15 cm. Each laboratory received five specimens of this test series. Thus, contrary to the first series, each specimen was tested by only one laboratory. Two side faces of each cube were tested with the rebound hammer. In addition, ultrasonic measurements were performed by one laboratory. The time of flight was measured between the tested side faces of the rebound hammer at different positions. For both series, rebound hammers were used to determine the R-value as well as the Q-value. The rebound hammer models within the laboratories were always the same, while they differed between the laboratories. The ultrasonic measurements took place with different measurement systems and couplants. Finally, both specimen series were tested destructively for compressive strength. The dataset contains the raw data summarized in tabular form. In addition, relevant calculated data are included in some cases. For the ultrasonic measurements, the time of flight has already been converted into the ultrasonic velocity. Besides, in addition to the raw data of the compressive strength test (force, weight, and geometry values), the calculated compressive strengths and densities are also provided.

J-difference GABA-edited MRS reveals altered cerebello-thalamo-cortical metabolism in patients with hepatic encephalopathy.

Hepatic encephalopathy (HE) is a common neurological manifestation of liver cirrhosis and is characterized by an increase of ammonia in the brain accompanied by a disrupted neurotransmitter balance, including the GABAergic and glutamatergic systems. The aim of this study is to investigate metabolic abnormalities in the cerebello-thalamo-cortical system of HE patients using GABA-edited MRS and links between metabolite levels, disease severity, critical flicker frequency (CFF), motor performance scores, and blood ammonia levels. GABA-edited MRS was performed in 35 participants (16 controls, 19 HE patients) on a clinical 3 T MRI system. MRS voxels were placed in the right cerebellum, left thalamus, and left motor cortex. Levels of GABA+ and of other metabolites of interest (glutamine, glutamate, myo-inositol, glutathione, total choline, total NAA, and total creatine) were assessed. Group differences in metabolite levels and associations with clinical metrics were tested. GABA+ levels were significantly increased in the cerebellum of patients with HE. GABA+ levels in the motor cortex were significantly decreased in HE patients, and correlated with the CFF (r = 0.73; p < .05) and motor performance scores (r = -0.65; p < .05). Well-established HE-typical metabolite patterns (increased glutamine, decreased myo-inositol and total choline) were confirmed in all three regions and were closely linked to clinical metrics. In summary, our findings provide further evidence for alterations in the GABAergic system in the cerebellum and motor cortex in HE. These changes were accompanied by characteristic patterns of osmolytes and oxidative stress markers in the cerebello-thalamo-cortical system. These metabolic disturbances are a likely contributor to HE motor symptoms in HE. In patients with hepatic encephalopathy, GABA+ levels in the cerebello-thalamo-cortical loop are significantly increased in the cerebellum and significantly decreased in the motor cortex. GABA+ levels in the motor cortex strongly correlate with critical flicker frequency (CFF) and motor performance score (pegboard test tPEG), but not blood ammonia levels (NH3).

Image downsampling expedited adaptive least-squares (IDEAL) fitting improves intravoxel incoherent motion (IVIM) analysis in the human kidney.

PURPOSE: To improve the reliability of intravoxel incoherent motion (IVIM) model parameter estimation for the DWI in the kidney using a novel image downsampling expedited adaptive least-squares (IDEAL) approach. METHODS: The robustness of IDEAL was investigated using simulated DW-MRI data corrupted with different levels of Rician noise. Subsequently, the performance of the proposed method was tested by fitting bi- and triexponential IVIM model to in vivo renal DWI data acquired on a clinical 3 Tesla MRI scanner and compared to conventional approaches (fixed D* and segmented fitting). RESULTS: The numerical simulations demonstrated that the IDEAL algorithm provides robust estimates of the IVIM parameters in the presence of noise (SNR of 20) as indicated by relatively low absolute percentage bias (maximal sMdPB <20%) and normalized RMSE (maximal RMSE <28%). The analysis of the in vivo data showed that the IDEAL-based IVIM parameter maps were less noisy and more visually appealing than those obtained using the fixed D* and segmented methods. Further, coefficients of variation for nearly all IVIM parameters were significantly reduced in cortex and medulla for IDEAL-based biexponential (coefficients of variation: 4%-50%) and triexponential (coefficients of variation: 7.5%-75%) IVIM modelling compared to the segmented (coefficients of variation: 4%-120%) and fixed D* (coefficients of variation: 17%-174%) methods, reflecting greater accuracy of this method. CONCLUSION: The proposed fitting algorithm yields more robust IVIM parameter estimates and is less susceptible to poor SNR than the conventional fitting approaches. Thus, the IDEAL approach has the potential to improve the reliability of renal DW-MRI analysis for clinical applications.

UTE-T2* versus conventional T2* mapping to assess posterior cruciate ligament ultrastructure and integrity-an in-situ study.

Background: Clinical-standard morphologic magnetic resonance imaging (MRI) is limited in the refined diagnosis of posterior cruciate ligament (PCL) injuries. Quantitative MRI sequences such as ultrashort echo-time (UTE)-T2* mapping or conventional T2* mapping have been theorized to quantify ligament (ultra-) structure and integrity beyond morphology. This study evaluates their diagnostic potential in identifying and differentiating partial and complete PCL injuries in a standardized graded injury model. Methods: Ten human cadaveric knee joint specimens were imaged on a clinical 3.0 T MRI scanner using morphologic, conventional T2* mapping, and UTE-T2* mapping sequences before and after standardized arthroscopic partial and complete PCL transection. Following manual segmentation, quantitative T2* and underlying texture features (i.e., energy, homogeneity, and variance) were analyzed for each specimen and PCL condition, both for the entire PCL and its subregions. For statistical analysis, Friedman's test followed by Dunn's multiple comparison test was used against the level of significance of P≤0.01. Results: For the entire PCL, T2* was significantly increased as a function of injury when acquired with the UTE-T2* sequence [entire PCL: 11.1±3.1 ms (intact); 10.9±4.6 ms (partial); 14.3±4.9 ms (complete); P<0.001], but not when acquired with the conventional T2* sequence [entire PCL: 10.0±3.2 ms (intact); 11.4±6.2 ms (partial); 15.5±7.8 ms (complete); P=0.046]. The PCL subregions and texture variables showed variable changes indicative of injury-associated disorganization. Conclusions: In contrast to the conventional T2* mapping, UTE-T2* mapping is more receptive in the detection of structural damage of the PCL and allows quantitative assessment of ligament (ultra-)structure and integrity that may help to improve diagnostic differentiation of distinct injury states. Once further substantiated beyond the in-situ setting, UTE-T2* mapping may refine diagnostic evaluation of PCL injuries and -possibly- monitor ligament healing, ageing, degeneration, and inflammation.

Lorentzian-Corrected Apparent Exchange-Dependent Relaxation (LAREX) Ω-Plot Analysis-An Adaptation for qCEST in a Multi-Pool System: Comprehensive In Silico, In Situ, and In Vivo Studies.

Based on in silico, in situ, and in vivo studies, this study aims to develop a new method for the quantitative chemical exchange saturation transfer (qCEST) technique considering multi-pool systems. To this end, we extended the state-of-the-art apparent exchange-dependent relaxation (AREX) method with a Lorentzian correction (LAREX). We then validated this new method with in situ and in vivo experiments on human intervertebral discs (IVDs) using the Kendall-Tau correlation coefficient. In the in silico experiments, we observed significant deviations of the AREX method as a function of the underlying exchange rate (kba) and fractional concentration (fb) compared to the ground truth due to the influence of other exchange pools. In comparison to AREX, the LAREX-based Ω-plot approach yielded a substantial improvement. In the subsequent in situ and in vivo experiments on human IVDs, no correlation to the histological reference standard or Pfirrmann classification could be found for the fb (in situ: τ = −0.17 p = 0.51; in vivo: τ = 0.13 p = 0.30) and kba (in situ: τ = 0.042 p = 0.87; in vivo: τ = −0.26 p = 0.04) of Glycosaminoglycan (GAG) with AREX. In contrast, the influence of interfering pools could be corrected by LAREX, and a moderate to strong correlation was observed for the fractional concentration of GAG for both in situ (τ = −0.71 p = 0.005) and in vivo (τ = −0.49 p < 0.001) experiments. The study presented here is the first to introduce a new qCEST method that enables qCEST imaging in systems with multiple proton pools.

Evaluation of Radiographic Contrast-Induced Nephropathy by Functional Diffusion Weighted Imaging.

Contrast-induced nephropathy (CIN) resembles an important complication of radiographic contrast medium (XCM) displayed by a rise in creatinine levels 48-72 h after XCM administration. The purpose of the current study was to evaluate microstructural renal changes due to CIN in high-risk patients by diffusion weighted (DWI) and diffusion tensor imaging (DTI). Fifteen patients (five CIN and ten non-CIN) scheduled for cardiological intervention were included in the study. All patients were investigated pre- and post-intervention on a clinical 3T scanner. After anatomical imaging, renal DWI was performed by a paracoronal echo-planar-imaging sequence. Renal clinical routine serum parameters and advanced urinary injury markers were determined to monitor renal function. We observed a drop in cortical and medullar apparent diffusion coefficient (ADC) and fractional anisotropy (FA) before and after XCM administration in the CIN group. In contrast, the non-CIN group differed only in medullary ADC. The decrease of ADC and FA was apparent even before serum parameters of the kidney changed. In conclusion, DWI/DTI may be a useful tool for monitoring high-risk CIN patients as part of multi-modality based clinical protocol. Further studies, including advanced analysis of the diffusion signal, may improve the identification of patients at risk for CIN.

Feasibility of quantitative susceptibility mapping (QSM) of the human kidney.

OBJECTIVE: To evaluate the feasibility of in-vivo quantitative susceptibility mapping (QSM) of the human kidney. METHODS: An axial single-breath-hold 3D multi-echo sequence (acquisition time 33 s) was completed on a 3 T-MRI-scanner (Magnetom Prisma, Siemens Healthineers, Erlangen, Germany) in 19 healthy volunteers. Graph-cut-based unwrapping combined with the T2*-IDEAL approach was performed to remove the chemical shift of fat and to quantify QSM of the upper abdomen. Mean susceptibility values of the entire, renal cortex and medulla in both kidneys and the liver were determined and compared. Five subjects were measured twice to examine the reproducibility. One patient with severe renal fibrosis was included in the study to evaluate the potential clinical relevance of QSM. RESULTS: QSM was successful in 17 volunteers and the patient with renal fibrosis. Anatomical structures in the abdomen were clearly distinguishable by QSM and the susceptibility values obtained in the liver were comparable to those found in the literature. The results showed a good reproducibility. Besides, the mean renal QSM values obtained in healthy volunteers (0.04 ± 0.07 ppm for the right and - 0.06 ± 0.19 ppm for the left kidney) were substantially higher than that measured in the investigated fibrotic kidney (- 0.43 ± - 0.02 ppm). CONCLUSION: QSM of the human kidney could be a promising approach for the assessment of information about microscopic renal tissue structure. Therefore, it might further improve functional renal MR imaging.

First record of characterization, concentration and distribution of microplastics in coastal sediments of an urban fjord in south west Norway using a thermal degradation method.

Plastic waste is of increasing concern in the aquatic environment. A large proportion of plastic waste is generated onshore from where it eventually reaches the marine environment, which is considered the main sink of plastic debris To date there is a substantial lack of knowledge on the composition of these accumulated polymers, their environmental levels and distribution in marine and coastal areas. Current efforts are underway to develop standardized methods to characterize and quantify the occurrence of microplastic in different environmental matrices using microscopy-oriented methods using Fourier Transformed Infra-Red (FTIR) or Raman techniques. However, time-consuming sample preparation, processing and interpretation of complex data limits their use within monitoring programs. As an alternative, a thermal degradation method based on a gas chromatographic mass spectrometer coupled with pyrolysis represents a validated method for qualitative and quantitative polymer analyses. A technique has been developed that combines sample preparation and thermo-analysis for identifying microplastics in samples of marine sediment. Quantification and polymeric composition of plastic particles found in sediment samples taken from ten sites located in Boknafjorden subjected to diverse sources of pollution and anthropogenic pressure were investigated. Plastic microparticles were extracted from 8 kg of wet sediments per site, purified, size-fractionated thorough a set of stainless-steel certified sieves covering the range of 10-250 µm mesh size, pre-concentrated on fiberglass filters and whole filters analyzed by thermal desorption pyrolysis gas chromatography/mass spectrometry. Most of the detected polymers were identified as polypropylene, polyethylene, polyethylene terephthalate, polyvinylchloride, polystyrene or polyamide. In most of the sites, the largest fraction of the extracted micro debris fell in the size range 10-40 µm. Some shifts in size distribution were also observed in some sites and were likely related to the marine sea bottom currents and the influence of specific anthropogenic activities. The adopted thermal degradation method showed good sensitivity, reliability and rapidity and therefore represents a promising technique for microplastic analysis within monitoring activities.

MISA-web: a web server for microsatellite prediction.

MOTIVATION: Microsatellites are a widely-used marker system in plant genetics and forensics. The development of reliable microsatellite markers from resequencing data is challenging. RESULTS: We extended MISA, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application. We improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis. AVAILABILITY AND IMPLEMENTATION: MISA-web can be accessed under http://misaweb.ipk-gatersleben.de/. The website provides tutorials, usage note as well as download links to the source code. CONTACT: scholz@ipk-gatersleben.de.

A conserved apomixis-specific polymorphism is correlated with exclusive exonuclease expression in premeiotic ovules of apomictic boechera species.

Apomixis (asexual seed production) is characterized by meiotically unreduced egg cell production (apomeiosis) followed by its parthenogenetic development into offspring that are genetic clones of the mother plant. Fertilization (i.e. pseudogamy) of the central cell is important for the production of a functional endosperm with a balanced 2:1 maternal:paternal genome ratio. Here, we present the APOLLO (for apomixis-linked locus) gene, an Aspartate Glutamate Aspartate Aspartate histidine exonuclease whose transcripts are down-regulated in sexual ovules entering meiosis while being up-regulated in apomeiotic ovules at the same stage of development in plants of the genus Boechera. APOLLO has both "apoalleles," which are characterized by a set of linked apomixis-specific polymorphisms, and "sexalleles." All apomictic Boechera spp. accessions proved to be heterozygous for the APOLLO gene (having at least one apoallele and one sexallele), while all sexual genotypes were homozygous for sexalleles. Apoalleles contained a 20-nucleotide polymorphism present in the 5' untranslated region that contains specific transcription factor-binding sites for ARABIDOPSIS THALIANA HOMEOBOX PROTEIN5, LIM1 (for LINEAGE ABNORMAL11, INSULIN1, MECHANOSENSORY PROTEIN3), SORLIP1AT (for SEQUENCES OVERREPRESENTED IN LIGHT-INDUCED PROMOTERS IN ARABIDOPSIS THALIANA1), SORLIP2AT, and POLYA SIGNAL1. In the same region, sexalleles contain transcription factor-binding sites for DNA BINDING WITH ONE FINGER2, DNA BINDING WITH ONE FINGER3, and PROLAMIN BOX-BINDING FACTOR. Our results suggest that the expression of a single deregulated allele could induce the cascade of events leading to asexual female gamete formation in an apomictic plant.

Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae.

Numerous CCT domain genes are known to control flowering in plants. They belong to the CONSTANS-like (COL) and PREUDORESPONSE REGULATOR (PRR) gene families, which in addition to a CCT domain possess B-box or response-regulator domains, respectively. Ghd7 is the most recently identified COL gene to have a proven role in the control of flowering time in the Poaceae. However, as it lacks B-box domains, its inclusion within the COL gene family, technically, is incorrect. Here, we show Ghd7 belongs to a larger family of previously uncharacterized Poaceae genes which possess just a single CCT domain, termed here CCT MOTIF FAMILY (CMF) genes. We molecularly describe the CMF (and related COL and PRR) gene families in four sequenced Poaceae species, as well as in the draft genome assembly of barley (Hordeum vulgare). Genetic mapping of the ten barley CMF genes identified, as well as twelve previously unmapped HvCOL and HvPRR genes, finds the majority map to colinear positions relative to their Poaceae orthologues. Combined inter-/intra-species comparative and phylogenetic analysis of CMF, COL and PRR gene families indicates they evolved prior to the monocot/dicot divergence ∼200 mya, with Poaceae CMF evolution described as the interplay between whole genome duplication in the ancestral cereal, and subsequent clade-specific mutation, deletion and duplication events. Given the proven role of CMF genes in the modulation of cereals flowering, the molecular, phylogenetic and comparative analysis of the Poaceae CMF, COL and PRR gene families presented here provides the foundation from which functional investigation can be undertaken.

Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae.

The genomes of cereals such as wheat (Triticum aestivum) and barley (Hordeum vulgare) are large and therefore problematic for the map-based cloning of agronomicaly important traits. However, comparative approaches within the Poaceae permit transfer of molecular knowledge between species, despite their divergence from a common ancestor sixty million years ago. The finding that null variants of the rice gene cytokinin oxidase/dehydrogenase 2 (OsCKX2) result in large yield increases provides an opportunity to explore whether similar gains could be achieved in other Poaceae members. Here, phylogenetic, molecular and comparative analyses of CKX families in the sequenced grass species rice, brachypodium, sorghum, maize and foxtail millet, as well as members identified from the transcriptomes/genomes of wheat and barley, are presented. Phylogenetic analyses define four Poaceae CKX clades. Comparative analyses showed that CKX phylogenetic groupings can largely be explained by a combination of local gene duplication, and the whole-genome duplication event that predates their speciation. Full-length OsCKX2 homologues in barley (HvCKX2.1, HvCKX2.2) and wheat (TaCKX2.3, TaCKX2.4, TaCKX2.5) are characterized, with comparative analysis at the DNA, protein and genetic/physical map levels suggesting that true CKX2 orthologs have been identified. Furthermore, our analysis shows CKX2 genes in barley and wheat have undergone a Triticeae-specific gene-duplication event. Finally, by identifying ten of the eleven CKX genes predicted to be present in barley by comparative analyses, we show that next-generation sequencing approaches can efficiently determine the gene space of large-genome crops. Together, this work provides the foundation for future functional investigation of CKX family members within the Poaceae.

Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice.

BACKGROUND: Well preserved genomic colinearity among agronomically important grass species such as rice, maize, Sorghum, wheat and barley provides access to whole-genome structure information even in species lacking a reference genome sequence. We investigated footprints of whole-genome duplication (WGD) in barley that shaped the cereal ancestor genome by analyzing shared synteny with rice using a approximately 2000 gene-based barley genetic map and the rice genome reference sequence. RESULTS: Based on a recent annotation of the rice genome, we reviewed the WGD in rice and identified 24 pairs of duplicated genomic segments involving 70% of the rice genome. Using 968 putative orthologous gene pairs, synteny covered 89% of the barley genetic map and 63% of the rice genome. We found strong evidence for seven shared segmental genome duplications, corresponding to more than 50% of the segmental genome duplications previously determined in rice. Analysis of synonymous substitution rates (Ks) suggested that shared duplications originated before the divergence of these two species. While major genome rearrangements affected the ancestral genome of both species, small paracentric inversions were found to be species specific. CONCLUSION: We provide a thorough analysis of comparative genome evolution between barley and rice. A barley genetic map of approximately 2000 non-redundant EST sequences provided sufficient density to allow a detailed view of shared synteny with the rice genome. Using an indirect approach that included the localization of WGD-derived duplicated genome segments in the rice genome, we determined the current extent of shared WGD-derived genome duplications that occurred prior to species divergence.

Molecular signatures of apomictic and sexual ovules in the Boechera holboellii complex.

Apomixis, a natural form of asexual seed production in plants, has evolved independently in various taxa, and represents an important potential technology for agriculture. The switch to apomixis is based on de-regulation of developmental pathways originally leading to sexual seed formation. Hybridization and polyploidy, both typical characteristics of asexual plants and animals, are mechanisms that could trigger de-regulation. Here we show that up-regulation of alleles in apomeiotic ovules is mediated by genomic duplication, heterochrony and the residual effects of ancient hybridization in diploid apomicts of the Boechera holboellii complex. Using SuperSAGE, we have identified over 4000 differentially expressed mRNA tags between micro-dissected ovules from two diploid sexual (Boechera stricta and B. holboellii) and two diploid apomictic (Boechera divaricarpa) accessions. Pairwise sequence comparisons between tags enabled identification of allelic variants of the same loci. Up-regulated candidate apomeiosis alleles consistently have more than three related alleles, thus demonstrating transcription from duplicated loci. A further 543 alleles were heterochronically expressed between sexual and apomeiotic ovules at developmental stages 2-II to 2-IV. Intriguingly, 69 B. holboellii specific alleles were preferentially up-regulated in apomeiotic ovules, thus showing a remnant'parent of origin' effect stemming from the Pleistocene origin of the hybrid B. divaricarpa from taxa related to B. holboellii and B. stricta. These data implicate polyploid gene dosage in the expression of asexual seed formation, and support hypotheses of de-regulation of the sexual pathway. The observed 'parent of origin' effect suggests that the genomic memory of hybridization has somehow been maintained after hundreds, if not thousands, of asexual generations.

A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics.

An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (EST)-based markers (total 1,055 loci: 607 RFLP, 190 SSR, and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups. The map covers 1118.3 cM with individual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identification of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information.

Analysis of sequence, map position, and gene expression reveals conserved essential genes for iron uptake in Arabidopsis and tomato.

Arabidopsis (Arabidopsis thaliana) and tomato (Lycopersicon esculentum) show similar physiological responses to iron deficiency, suggesting that homologous genes are involved. Essential gene functions are generally considered to be carried out by orthologs that have remained conserved in sequence and map position in evolutionarily related species. This assumption has not yet been proven for plant genomes that underwent large genome rearrangements. We addressed this question in an attempt to deduce functional gene pairs for iron reduction, iron transport, and iron regulation between Arabidopsis and tomato. Iron uptake processes are essential for plant growth. We investigated iron uptake gene pairs from tomato and Arabidopsis, namely sequence, conserved gene content of the regions containing iron uptake homologs based on conserved orthologous set marker analysis, gene expression patterns, and, in two cases, genetic data. Compared to tomato, the Arabidopsis genome revealed more and larger gene families coding for the iron uptake functions. The number of possible homologous pairs was reduced if functional expression data were taken into account in addition to sequence and map position. We predict novel homologous as well as partially redundant functions of ferric reductase-like and iron-regulated transporter-like genes in Arabidopsis and tomato. Arabidopsis nicotianamine synthase genes encode a partially redundant family. In this study, Arabidopsis gene redundancy generally reflected the presumed genome duplication structure. In some cases, statistical analysis of conserved gene regions between tomato and Arabidopsis suggested a common evolutionary origin. Although involvement of conserved genes in iron uptake was found, these essential genes seem to be of paralogous rather than orthologous origin in tomato and Arabidopsis.