A phantom for the quantitative determination and improvement of the spatial resolution in slice-selective 2D-FT magnetic resonance micro-imaging and -microscopy based on Deep X-ray Lithography (DXRL)

Introduction: The most important assessed quality-control (QC) criteria for improvements in high-resolution imaging are represented by the contrast-to-noise-ratio and spatial resolution. Ultra-High-Field (UHF) Magnetic-Resonance-scanners (B ≥ 7 T) for medical research allowed for the improvement in spatial resolution up to the microimaging and nominal microscopy range [pixel-size: ps < (100 μm)2], even in-vivo on humans just recently. Preclinical MRI- and dedicated MR-microscopy (MRM) scanners already allow for microimaging and MRM (1-256 μm) but lack a sensible spatial resolution phantom for QC and performance improvements in hardware, pulse-sequencing and MRprotocols. In most scientific MRI articles, the spatial resolution is characterized by the ps, though this measurement parameter only limits the actual resolution. Methods: Here the Modulation-Transfer-Function (MTF) is used as evaluation concept for the determination of the spatial resolution in MRM using simple intensity profiles. The resolution limit is defined using a critical modulation-level. In approaching visual impressions on spatial resolution an additional criterion derived from the Modulation-depth-to-Noise-Ratio (MNR) is proposed. A practical method for assessment based on a concrete phantom design and its realization is shown. Results: The phantom design consists of several sets of fine grids, specifically featuring high structural anisotropy for optimum SNR and CNR, with different spatial periods ranging from a1 = 256 μm down to a8 = 2 μm, not only for a quick visual qualitative check, but also for quantification of resolution using the MTF for two different spatial encodings in two orthogonal in-plane directions. The challenging demands on the manufacturing technology especially with regard to the aspect-ratio are approached using Deep-X-Ray-Lithography (DXRL) relying on the high brilliance of Synchroton-radiation. Smallest grid plates with width of 4 μm corresponding to 125 line pairs/mm at a plate depth of 100 μm were achieved. Discussion: MR-microscopic images, originating from a microscopy insert on a human UHF-MR-scanner, were used for demonstration of the evaluation process with two independent resolution-criteria. The developed prototype offers unique possibilities for quantitative resolution QC on UHF human and preclinical MR-scanners. Such a resolution-phantom might be very important for the improvement of MR-pulse-sequences, MR-protocols and even hardware. In principle the phantom can also be used for other microscopic imaging-modalities as for instance μCT and Optical-Coherence-Tomography (OCT)

Multiple promoters are a common feature of mitochondrial genes in Arabidopsis

Mitochondrial genes in the plant Arabidopsis thaliana are transcribed by two phage-type RNA polymerases encoded in the nucleus. Little is known about cis-elements that are recognized by these enzymes and mediate the transcription of the Arabidopsis mitochondrial genome. Here, 30 transcription initiation sites of 12 mitochondrial genes and gene clusters have been determined using 5′-RACE and ribonuclease protection analysis of primary transcripts labelled in vitro by guanylyltransferase. A total of 9 out of 12 genes were found to possess multiple promoters, revealing for the first time that multiple promoters are a common feature of mitochondrial genes in a dicotyledonous plant. No differences in promoter utilization were observed between leaves and flowers, suggesting that promoter multiplicity reflects a relaxed promoter specificity rather than a regulatory role of promoter selection. Nearly half the identified transcription initiation sites displayed immediately upstream a CRTA core sequence, which was mostly seen within the previously described CRTAAGAGA promoter motif or a novel CGTATATAA promoter element. About as many promoters possessed an ATTA or RGTA core. Our data indicate that the majority of mitochondrial promoters in Arabidopsis deviate significantly from the nonanucleotide consensus derived earlier for dicot mitochondrial promoters

Intraspecific taxonomy of plant genetic resources – Important for differentiation of medicinal and aromatic plants?

Taxonomy of plant genetic resources is an important input in characterising and evaluating cultivated plants and essential for identification and documentation of the diversity of genebank collections. In former times taxonomical determination was based only on morphological characters. Nowadays, new molecular and chemical methods and techniques are available for providing additional information. As examples, investigations of parsley (Petroselinum crispum [Mill.] Nyman, Apiaceae) and opium poppy (Papaver somniferum L., Papaveraceae) collections of the German genebank are demonstrated. In addition to morphological description, the molecular distance and the phylogenetic relationship of the accessions were performed with molecular marker analysis. Essential oil compound and content for parsley and the content of the five main alkaloids (morphine, codeine, thebaine, noscapine, papaverine) for opium poppy were measured with GC (gas chromatography) and HPLC (high pressure liquid chromatography), respectively. For parsley the results of the three methods support the existing taxonomy partly, a separation of root and leaf parsley was confirmed. However, the taxonomy of opium poppy should be revised because molecular and chemical data do not verify the morphological results. But nevertheless taxonomy of cultivated plants is an important tool to describe the variability of plant genetic resources

Insight into the genetic contribution of maximum yield potential, spikelet development and abortion in barley

Societal Impact Statement To feed the world's ever‐increasing population, new genetic approaches are required. Increasing the number of living spikelets is one promising way to improve grain yield. This, in turn, increases the number of spikelets per plant, thereby increasing the total yield. We present the first evidence for genetic control of alive spikelets in barley. Discovering natural variation as well as genomic regions associated with these traits will serve as a benchmark in future breeding for improving grain yield. Summary The primary goal of most breeding programmes is to increase grain yield. However, one of the many methods for raising yield that is yet to be fully investigated is increasing the number of spikelets by minimising spikelet abortion. Spikelet abortion dramatically increases during the late reproductive phase, but the molecular and genetic mechanisms remain unknown. Here, we employed a phenotyping approach in which developed and undeveloped spikelets were detected and counted during spike development and their maximum yield potential (MYP) was investigated. We studied 20 agronomic and spikelet‐related traits using a set of 184 diverse spring barley accessions under field conditions. By employing a set of >125K  SNPs, GWAS was conducted. Our analysis revealed 26 genetic clusters associated with MYP and the number of developed and undeveloped spikelets. Most of the significant associated genomic regions were co‐located near the candidate genes of phytohormones such as ABA, auxin, and cytokinin suggesting the importance of phytohormones in keeping spikelets alive, their development, and MYP. Our findings point to a potential link between jasmonic acid and the MYP, development and abortion of spikelets. We further provide genetic evidence that sugar‐related genes and sucrose have the potential to regulate MYP, spikelet development and spikelet survival. Our findings can be used for marker‐assisted breeding and as a resource for future molecular and genetic validation. Collectively, we propose a new genetic network linking spikelet‐related traits to grain yield determinants

A phantom for the quantitative determination and improvement of the spatial resolution in slice-selective 2D-FT magnetic resonance micro-imaging and -microscopy based on Deep X-ray Lithography (DXRL)

Introduction: The most important assessed quality-control (QC) criteria for improvements in high-resolution imaging are represented by the contrast-to-noise-ratio and spatial resolution. Ultra-High-Field (UHF) Magnetic-Resonance-scanners (B ≥ 7 T) for medical research allowed for the improvement in spatial resolution up to the microimaging and nominal microscopy range [pixel-size: ps &lt; (100 μm)2], even in-vivo on humans just recently. Preclinical MRI- and dedicated MR-microscopy (MRM) scanners already allow for microimaging and MRM (1-256 μm) but lack a sensible spatial resolution phantom for QC and performance improvements in hardware, pulse-sequencing and MRprotocols. In most scientific MRI articles, the spatial resolution is characterized by the ps, though this measurement parameter only limits the actual resolution.Methods: Here the Modulation-Transfer-Function (MTF) is used as evaluation concept for the determination of the spatial resolution in MRM using simple intensity profiles. The resolution limit is defined using a critical modulation-level. In approaching visual impressions on spatial resolution an additional criterion derived from the Modulation-depth-to-Noise-Ratio (MNR) is proposed. A practical method for assessment based on a concrete phantom design and its realization is shown.Results: The phantom design consists of several sets of fine grids, specifically featuring high structural anisotropy for optimum SNR and CNR, with different spatial periods ranging from a1 = 256 μm down to a8 = 2 μm, not only for a quick visual qualitative check, but also for quantification of resolution using the MTF for two different spatial encodings in two orthogonal in-plane directions. The challenging demands on the manufacturing technology especially with regard to the aspect-ratio are approached using Deep-X-Ray-Lithography (DXRL) relying on the high brilliance of Synchroton-radiation. Smallest grid plates with width of 4 μm corresponding to 125 line pairs/mm at a plate depth of 100 μm were achieved.Discussion: MR-microscopic images, originating from a microscopy insert on a human UHF-MR-scanner, were used for demonstration of the evaluation process with two independent resolution-criteria. The developed prototype offers unique possibilities for quantitative resolution QC on UHF human and preclinical MR-scanners. Such a resolution-phantom might be very important for the improvement of MR-pulse-sequences, MR-protocols and even hardware. In principle the phantom can also be used for other microscopic imaging-modalities as for instance μCT and Optical-Coherence-Tomography (OCT)

A third mitochondrial RNA polymerase in the moss Physcomitrella patens

In most organisms, the mitochondrial genes are transcribed by RNA polymerases related to the single-subunit RNA polymerases of bacteriophages like T3 and T7. In flowering plants, duplication(s) of the RpoTm gene coding for the mitochondrial RNA polymerase (RPOTm) led to the evolution of additional RNA polymerases transcribing genes in plastids (RPOTp) or in both mitochondria and plastids (RPOTmp). Two putative RPOTmp enzymes were previously described to be encoded by the nuclear genes RpoTmp1 and RpoTmp2 in the moss Physcomitrella patens. Here, we report on a third PhyscomitrellaRpoT gene. We determined the sequence of the cDNA. Comparison of the deduced amino acid sequence with sequences of plant organellar RNA polymerases suggests that this gene encodes a functional phage-type RNA polymerase. The 78 N-terminal amino acids of the putative RNA polymerase were fused to GFP and found to target the fusion protein exclusively to mitochondria in Arabidopsis protoplasts. P. patens is the only known organism to possess three mitochondrial RNA polymerases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00294-013-0405-y) contains supplementary material, which is available to authorized users

Overstated carbon emission reductions from voluntary REDD+ projects in the Brazilian Amazon

Reduced Emissions from Deforestation and forest Degradation (REDD+) has gained international attention over the past decade, as manifested in both United Nations policy discussions and hundreds of voluntary projects launched to earn carbon-offset credits. There are on-going discussions about whether and how projects should be integrated into national efforts under the Paris Agreement. One consideration is whether these projects have generated additional impacts over and above national policies and other conservation measures. To help inform these discussions, we compare the crediting baselines established ex-ante by voluntary REDD+ projects in the Brazilian Amazon to counterfactuals constructed ex-post based on the quasi-experimental synthetic control method. We find that the crediting baselines assume consistently higher deforestation than counterfactual forest loss in synthetic control sites. This gap is partially due to decreased deforestation in the Brazilian Amazon during the early implementation phase of the REDD+ projects considered here. This suggests that forest carbon finance must strike a balance between controlling conservation investment risk and ensuring the environmental integrity of carbon emission offsets. Relatedly, our results point to the need to better align project- and national-level carbon accounting.German Federal Ministry of Education and Researc

The Maintenance and Exploitation of ex situ Genebank Collections – Association Mapping for Flowering Time in Wheat

It is estimated that world-wide existing germplasm collections contain about 7.4 million accessions of plant genetic resources. Wheat (Triticum and Aegilops) represents the biggest group with about 900,000 accessions. One of the largest ex situ genebanks worldwide is located at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. This collection comprises wild and primitive forms, landraces as well as old and more recent cultivars of mainly cereals but also other crops. As on the global scale wheat is the largest group having almost 30,000 accessions. Beside the long term storage and frequent regeneration of the material phenotypic characterisation and evaluation data are collected as a prerequisite for gene identification and mapping. We report the outcome of an association-based mapping study to elucidate the genetic basis of flowering time in winter wheat. A core collection of 96 cultivars was subjected to a genome-wide scan using diversity array technology markers. The same set of accessions had been earlier evaluated for flowering time over six consecutive seasons. Some of the resulting marker-trait associations (MTAs) mapped to chromosomal locations in which known major genes affecting flowering time are known to reside. However, most of the MTAs identified genomic locations where no such genes are known to map, so providing new opportunities to exploit genetic variation for flowering time in wheat breeding programmes

Fingerprinting of wheat protein profiles for improved distinction between wheat cultivars and species

Background and objectives Wheat protein composition is commonly characterized by reversed‐phase (RP)‐HPLC‐UV after extraction of albumins/globulins, gliadins (ω5‐, ω1,2‐, α‐, and γ‐gliadins), and glutenins (high‐ and low‐molecular‐weight glutenin subunits). However, this traditional classification does not consider the individual distribution of peaks, resulting in loss of information on protein fingerprints. We developed a new approach to peak integration and evaluated its suitability to differentiate between wheat cultivars and species. Findings Integration events were performed every 20 s, and the relative proportions of the peaks were calculated. We compared the traditional and new integration methods on two sample sets, the first comprising 60 common wheat cultivars from 1891 to 2010 and the second comprising 40 common wheat, spelt, durum wheat, emmer, and einkorn cultivars. The new integration method performed better in differentiating old and modern common wheat cultivars and was also applicable to different wheat species. Conclusions Unique cultivars were identified that stood out because of their protein composition. Four samples warrant further research to identify the specific proteins that are responsible for the differences. Significance and novelty The new integration allowed us to map the cultivar‐ and species‐specific fingerprints, identify cultivars with exceptional protein composition, and group similar cultivars