Imaging findings for intravascular large B-cell lymphoma of the liver

Intravascular large B-cell lymphoma (IVLBCL) is a rare subtype of extranodal diffuse large B-cell lymphoma that most commonly involves the central nervous system and skin. To our knowledge, no state-of-the art imaging findings have been reported for hepatic IVLBCL in the English literature. We report the first case of hepatic involvement of IVLBCL along with a literature review

Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection

Background The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for the reliability of seed market and stable yield as well as for quarantine procedure. However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment. Main body Here, we developed a web-application, Soybean-VCF2Genomes, http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. Based on principal component analysis (PCA), we simplified genotype matrix for lowering computational burden while maintaining accurate clustering. With our web-application, users can simply upload single sample VCF file created by more than 10x resequencing strategy to find the closest samples along with linkage dendrogram of the reference genotype matrix. Conclusion The information of the closest soybean cultivar will allow breeders to estimate relative germplasmic position of their query sample to determine soybean breeding strategies. Moreover, our VCF2Genomes scheme can be extended to other plant species where the whole genome sequences of core collection are publicly available.Publication of this article has been funded by Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ01333901) Rural Development Administration, Republic of Korea and the fund of research promotion program, Gyeongsang National University, 2017

The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression data for Kalanchoë fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identify signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock, and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops

A Facile Method Using a Flux to Improve Quantum Efficiency of Submicron Particle Sized Phosphors for Solid-State Lighting Applications

This work successfully verified that the addition of a flux (NH4F, NH4Cl, and H3BO3) during synthesis has an impact on the crystallite size and quantum efficiency of submicron-sized particles of CaMgSi2O6:Eu2+ phosphors. The addition of NH4F or NH4Cl increased the crystallite size in the submicron-sized particles, yielding an increase in emission intensity and quantum efficiency. On the other hand, the use of the H3BO3 flux crystallized a secondary phase, SiO2, and changed the lattice parameters, which degraded the luminescent properties. In addition, an excessive amount of NH4Cl was examined, resulting in nucleation of a secondary phase, CaSiO3, which changed the lattice parameters with no improvement in luminescent properties. These results demonstrate that the addition of a flux could be a method to improve the quantum efficiency of submicron-sized particles composed of nanocrystallites; however, a judicious choice of the flux composition and amount has to be carefully considered

Design and synthesis of phosphors to improve efficiency for solid state lighting application

White-emitting light sources based on light-emitting diodes (white-emitting LEDs) are considered to be the next generation in lighting. A common approach to create a white-emitting LED is to combine a blue-emitting InGaN LED with a yellow-emitting phosphor, but it has a low color rendering index (CRI) value due to the rack of red emission. An alternative approach is to combine a near UV-LED (nUV-LED) with blue-, green-, and red-emitting phosphors. However, the development of phosphors for the white-emitting LEDs is still challenging due to the numerous factors that influence on the luminescent properties. In this research, five approaches have been investigated to design and synthesize phosphors for solid state lighting: First, the Debye temperature (DT) was used as a descriptor for phosphors with high quantum efficiency (QE) (> 80%). Compositions with DT > 500K were considered. CaMgSi2O6:Eu2+ and Ca7Mg(SiO4)4:Eu2+ were synthesized through a co-precipitation and a sol-gel reactions, respectively, due to the high DT. However, a correlation between high DT and high QE was not found. Second, a flux (NH4F, NH4Cl, or H3BO3) was introduced during co-precipitation synthesis of CaMgSi2O6:Eu2+ to increase the QE. The flux affected both the crystallite size and the QE of the submicron sized phosphors. It was found that the QE increased 3X compared to no flux. Third, newly identified phosphors, green-emitting Sr2LiAlO4:Eu2+ and blue-emitting Sr2LiAlO4:Ce3+ were discovered by data mining unexplored chemistries for potentially high QE. The new, Sr2LiAlO4:Eu2+ and Sr2LiAlO4:Ce3+ were successfully predicted and synthesized.Fourth, color tunable single phase phosphors were developed using the Eu2+ and Ce3+ co-activated Sr2LiAlO4 for improvement of QE. The QE increased by 40% with Eu2+ and Ce3+ co-activation compared to the singly activated phosphors.Fifth, the synthesis of Na2SiF6 was demonstrated through a green synthetic method without toxic HF that is typically used for fluorides synthesis. The red-emitting phosphor, Na2SiF6:Mn4+ was prepared in a low concentration HF solution using the synthesized Na2SiF6 as a host. This study provides strategies to design and synthesize phosphors with improved quantum efficiency and thermal stability for white-emitting near-UV LEDs for potential applications in solid state lighting

Genome structure variation in glycine species

The genus Glycine includes Glycine max, soybean, which is one of the most important crops due in part to its nitrogen fixation capacity through symbiosis with soil-borne microorganisms. However, the narrow genetic diversity of elite cultivars poses a potential threat due to constantly evolving threats such as disease and other biotic and abiotic stresses. Therefore, the development of genomic tools for wild Glycine species has been undertaken to provide an infrastructure in order to find useful genetic variation and move it into cultivated soybean. This genomic infrastructure includes genetic maps from the crosses between G. max and G. soja (the undomesticated ancestor of soybean), whole genome sequence and BAC-based physical maps. Current sequencing technology limits our ability to use sequence information to describe and understand structural variation between genomes in that sequence reads are short and long-range mate pairs sequencing is difficult. However, once a genome is sequenced as a reference genome, the genomes of relatives can be relatively easily assembled with low sequence coverage. The length of reads determined by current sequencing technology are often not long enough to distinguish large-scale structural variation inresequencing as compared to a reference genome. BAC-based FingerPrinted Contig (FPC) physical maps were constructed and integrated with the draft sequence of G. max as a framework to begin to explore structural variation within and between G. max and G. soja. The G. max FPC map covers up to 95% of the soybean draft genome sequence (Gmax1.01) incorporating 4,628 genetic markers that were used to align the physical maps with genetic linkage maps. A minimum set of BAC clones covering as much as possible of the draft sequence was selected to provide a minimum tiling path of clones that can be used for further investigations and gene cloning. A BAC-based FPC map of Glycine soja was also constructed and aligned to G. max genome sequence map using BES (BAC end sequence) information. In order to detect chromosomal variation between G. max and G. soja, the FPC contigs of G. soja that aligned to 2 or more chromosomes of G. max were chosen as candidate contigs spanning potential chromosomal rearrangements such as reciprocal translocations. Other molecular techniques, such as BAC sequencing and fluorescent in situ Hybridization (FISH), will be used to confirm these computationally predicted rearrangements. Two to four BAC clones covering candidate breakpoints will be sequenced per contig to test our pipeline to identify chromosomal rearrangement between two species. Since more than 50% of soybean genome consists of repetitive sequences, the candidate BAC clones will be sequences with enough coverage to be assembled de novo then the BAC sequences will be aligned to the draft sequence of G. max to identify chromosomal variation. Centromeres play an evolutionarily conserved role in chromosome movement at meiosis and mitosis. Paradoxically, even though they play an essential role, the DNA sequences that underlie centromeric loci are not conserved even in a single genus. Since in most high eukaryotic organisms centromeres consist of the most frequent tandem repeats in the genomes, tandem repetitive sequences common in genomes have been identified in wild Glycine species using a combination of computation approaches, including Glycine canescens, Glycine cyrtoloba, Glycine falcata, Glycine stenophita, Glycine syndetika, Glycine tomentella D3 and Glycine tomentella T2. Centromeric repeats was identified and tested cytogenetically in G. falcata and G. canescens. We built and verified the pipeline to identify candidate centromeric repeats and evolutionary processes of centromeres in seven wild perennial Glycines were characterized. This study sheds light on chromosome structural variation within the Glycine species and provides a framework for comparative genomics, gene cloning and evolutionary analyses of legume genomes

The complete mitochondrial genome of the biodiesel plant Jatropha curcas L.

Jatropha curcas (Linnaeus, 1753) is a plant species in the order Malpighiales and the family Euphorbiaceae and is native to the tropical regions of America, such as Mexico and Argentina. Currently, this plant species inhabits tropical and subtropical regions of the world. Jatropha has been widely used as a biofuel plant to produce high-quality diesel engine fuel. In this study, the complete mitochondrial genome sequence of J. curcas was assembled into 561,839 bp circular nucleotides with a GC content of 44.6%. The mitochondrial genome of J. curcas comprises 33 known protein-coding genes, 22 tRNA genes, three rRNA genes, one ncRNA gene, and 85 open reading frame genes. Phylogenetic analysis showed this species is closely related to the castor bean (Ricinus communis)

Biosynthetic Pathway of Proanthocyanidins in Major Cash Crops

Proanthocyanidins (PAs) are a group of oligomers or polymers composed of monomeric flavanols. They offer many benefits for human fitness, such as antioxidant, anticancer, and anti-inflammatory activities. To date, three types of PA have been observed in nature: procyanidins, propelargonidins, and prodelphinidins. These are synthesized as some of the end-products of the flavonoid pathway by different consecutive enzymatic activities, from the same precursor—naringenin. Although the general biosynthetic pathways of PAs have been reported in a few model plant species, little is known about the species-specific pathways in major crops containing different types of PA. In the present study, we identified the species-specific pathways in 10 major crops, based on the presence/absence of flavanol-based intermediates in the metabolic pathway, and found 202 orthologous genes in the reference genomic database of each species, which may encode for key enzymes involved in the biosynthetic pathways of PAs. Parallel enzymatic reactions in the pathway are responsible for the ratio between PAs and anthocyanins, as well as among the three types of PAs. Our study suggests a promising strategy for molecular breeding, to regulate the content of PAs and anthocyanins and improve the nutritional quality of food sources globally

The complete mitochondrial genome of the biodiesel plant <i>Jatropha curcas</i> L.

Jatropha curcas (Linnaeus, 1753) is a plant species in the order Malpighiales and the family Euphorbiaceae and is native to the tropical regions of America, such as Mexico and Argentina. Currently, this plant species inhabits tropical and subtropical regions of the world. Jatropha has been widely used as a biofuel plant to produce high-quality diesel engine fuel. In this study, the complete mitochondrial genome sequence of J. curcas was assembled into 561,839 bp circular nucleotides with a GC content of 44.6%. The mitochondrial genome of J. curcas comprises 33 known protein-coding genes, 22 tRNA genes, three rRNA genes, one ncRNA gene, and 85 open reading frame genes. Phylogenetic analysis showed this species is closely related to the castor bean (Ricinus communis).</p