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Molecular breeding of a novel orange-brown tomato fruit with enhanced beta-carotene and chlorophyll accumulation
No full textAbstract
Background
Tomatoes provide a significant dietary source of the carotenoids, lycopene and \u3b2-carotene. During ripening, carotenoid accumulation determines the fruit colors while chlorophyll degradation. These traits have been, and continue to be, a significant focus for plant breeding efforts. Previous work has found strong evidence for a relationship between CYC-B gene expression and the orange color of fleshy fruit. Other work has identified a point mutation in SGR that impedes chlorophyll degradation and causes brown flesh color to be retained in some tomato varieties.
Methods
We crossed two inbred lines, KNY2 (orange) and KNB1 (brown) and evaluated the relationship between these genes for their effect on fruit color. Phenotypes of F2 generation plants were analyzed and a novel \u2018orange-brown\u2019 fruit color was identified.
Results
We confirm two SNPs, one in CYC-B and another in SGR gene sequence, associated with segregation of \u2018orange-brown\u2019 fruit color in F2 generation. The carotenoid and chlorophyll content of a fleshy fruit was assessed across the different phenotypes and showed a strong correlation with expression pattern of carotenoid biosynthesis genes and SGR function. The orange-brown fruit has high \u3b2-carotene and chlorophyll. Our results provide valuable information for breeders to develop tomato fruit of a novel color using molecular markers
Realization of III\u2013V Semiconductor Periodic Nanostructures by Laser Direct Writing Technique
No full textAbstract
In this paper, we demonstrated the fabrication of one-dimensional (1D) and two-dimensional (2D) periodic nanostructures on III\u2013V GaAs substrates utilizing laser direct writing (LDW) technique. Metal thin films (Ti) and phase change materials (Ge
2
Sb
2
Te
5
(GST) and Ge
2
Sb
1.8
Bi
0.2
Te
5
(GSBT)) were chosen as photoresists to achieve small feature sizes of semiconductor nanostructures. A minimum feature size of about 50\ua0nm about a quarter of the optical diffraction limit was obtained on the photoresists, and 1D III\u2013V semiconductor nanolines with a minimum width of 150\ua0nm were successfully acquired on the GaAs substrate which was smaller than the best results acquired on Si substrate ever reported. 2D nanosquare holes were fabricated as well by using Ti thin film as the photoresist, with a side width of about 200\ua0nm, but the square holes changed to a rectangle shape when GST or GSBT was employed as the photoresist, which mainly resulted from the interaction of two cross-temperature fields induced by two scanning laser beams. The interacting mechanism of different photoresists in preparing periodic nanostructures with the LDW technique was discussed in detail
Achievement of Diverse Domain Structures in Soft Magnetic Thin Film through Adjusting Intrinsic Magnetocrystalline Anisotropy
No full textAbstract
Oriented soft magnetic hcp-Co
1\u2009\u2212\u2009
x
Ir
x
films with a fixed thickness of 120\ua0nm were fabricated. All prepared films exhibit soft magnetic properties but various magnetocrystalline anisotropies with the variation of Ir content. The measured data shows that diverse domain structures including the N\ue9el wall, Bloch wall, and stripe domains present in a fixed film thickness. It is singular for the single-layer soft magnetic film to possess diverse domains in a fixed thickness. This phenomenon was explained by introducing intrinsic magnetocrystalline anisotropy energy into soft magnetic films rather than the structural parameters of the film, inner stress, and microstructure effect
Near- and Far-Field Optical Response of Eccentric Nanoshells
No full textAbstract
We study the optical response of eccentric nanoshells (i.e., spherical nanoparticles with an eccentric spherical inclusion) in the near and the far field through finite-difference time-domain simulations. Plasmon hybridization theory is used to explain the obtained results. The eccentricity generates a far-field optical spectrum with various plasmon peaks. The number, position, and width of the peaks depend on the core offset. Near-field enhancements in the surroundings of these structures are significantly larger than those obtained for equivalent concentric nanoshells and, more importantly, they are almost independent of the illumination conditions. This opens up the door for using eccentric nanoshells in applications requiring intense near-field enhancements
Bi 5 FeTi 3 O 15 nanofibers/graphene nanocomposites as an effective counter electrode for dye-sensitized solar cells
No full textAbstract
The present study reports Bi
5
FeTi
3
O
15
(BFTO) nanofibers/graphene (Gr) nanocomposites (BGr) as counter electrodes (CEs) in dye-sensitized solar cells (DSSCs). BFTO nanofibers with diameters of 40\u2013100\ua0nm were fabricated by sol-gel based electrospinning technique. The microstructure and surface morphology of the BFTO nanofibers and the BGr nanocomposites were characterized by X-ray diffraction, scanning electron microscopy and transmission electron microscopy. The electrochemical performances of BGr CEs were comprehensively characterized and investigated. Compared to pristine BFTO, the nanocomposites have a marked improvement in electrocatalytic performance for the reduction of triiodide because of larger surface area and lower transfer resistance on the electrolyte-electrode interface. The maximum power conversion efficiency has reached 9.56%, which is much larger than that of pure BFTO CEs (0.22%)
GTB \u2013 an online genome tolerance browser
No full textAbstract
Background
Accurate methods capable of predicting the impact of single nucleotide variants (SNVs) are assuming ever increasing importance. There exists a plethora of in silico algorithms designed to help identify and prioritize SNVs across the human genome for further investigation. However, no tool exists to visualize the predicted tolerance of the genome to mutation, or the similarities between these methods.
Results
We present the Genome Tolerance Browser (GTB, http://gtb.biocompute.org.uk ): an online genome browser for visualizing the predicted tolerance of the genome to mutation. The server summarizes several in silico prediction algorithms and conservation scores: including 13 genome-wide prediction algorithms and conservation scores, 12 non-synonymous prediction algorithms and four cancer-specific algorithms.
Conclusion
The GTB enables users to visualize the similarities and differences between several prediction algorithms and to upload their own data as additional tracks; thereby facilitating the rapid identification of potential regions of interest
LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells
No full textAbstract
Background
Lipopolysaccharide (endotoxin, LPS) is a strong inducer of the innate immune response. It is widespread in our environment, e.g. in house dust and contributes to asthma. Compared to humans, horses are even more sensitive to LPS. However, data on LPS effects on the equine transcriptome are very limited. Using RNA-seq we analysed LPS-induced differences in the gene expression in equine peripheral blood mononuclear cells at the gene and gene-network level in two half-sib families and one group of unrelated horses.
Results
24\ua0h-LPS challenge of equine immune cells resulted in substantial changes in the transcriptomic profile (1,265 differentially expressed genes) showing partial overlap with human data. One of the half-sib families showed a specific response different from the other two groups of horses. We also identified co-expressed gene modules that clearly differentiated 24\ua0h-LPS- from non-stimulated samples. These modules consisted of 934 highly interconnected genes and included genes involved in the immune response (e.g. IL6 , CCL22 , CXCL6, CXCL2 ), however, none of the top ten hub genes of the modules have been annotated as responsive to LPS in gene ontology.
Conclusions
Using weighted gene co-expression network analysis we identified ten co-expressed gene modules significantly regulated by in vitro stimulation with LPS. Apart from 47 genes (5%) all other genes highly interconnected within the most up- and down-regulated modules were also significantly differentially expressed (FDR\u2009<\u20090.05). The LPS-regulated module hub genes have not yet been described as having a role in the immune response to LPS (e.g. VAT1 and TTC25 )
Both mechanism and age of duplications contribute to biased gene retention patterns in plants
No full textAbstract
Background
All extant seed plants are successful paleopolyploids, whose genomes carry duplicate genes that have survived repeated episodes of diploidization. However, the survival of gene duplicates is biased with respect to gene function and mechanism of duplication. Transcription factors, in particular, are reported to be preferentially retained following whole-genome duplications (WGDs), but disproportionately lost when duplicated by tandem events. An explanation for this pattern is provided by the Gene Balance Hypothesis (GBH), which posits that duplicates of highly connected genes are retained following WGDs to maintain optimal stoichiometry among gene products; but such connected gene duplicates are disfavored following tandem duplications.
Results
We used genomic data from 25 taxonomically diverse plant species to investigate the roles of duplication mechanism, gene function, and age of duplication in the retention of duplicate genes. Enrichment analyses were conducted to identify Gene Ontology (GO) functional categories that were overrepresented in either WGD or tandem duplications, or across ranges of divergence times. Tandem paralogs were much younger, on average, than WGD paralogs and the most frequently overrepresented GO categories were not shared between tandem and WGD paralogs. Transcription factors were overrepresented among ancient paralogs regardless of mechanism of origin or presence of a WGD. Also, in many cases, there was no bias toward transcription factor retention following recent WGDs.
Conclusions
Both the fixation and the retention of duplicated genes in plant genomes are context-dependent events. The strong bias toward ancient transcription factor duplicates can be reconciled with the GBH if selection for optimal stoichiometry among gene products is strongest following the earliest polyploidization events and becomes increasingly relaxed as gene families expand
Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae
No full textAbstract
Background
The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma , this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined.
Results
The chloroplast genome of Gracilaria firma maps as a circular molecule of 187,001\ua0bp and contains 252 genes, which are distributed on both strands and consist of 35 RNA genes (3 rRNAs, 30 tRNAs, tmRNA and a ribonuclease P RNA component) and 217 protein-coding genes, including the unidentified open reading frames. The chloroplast genome of G. firma is by far the largest reported for Gracilariaceae, featuring a unique intergenic region of about 7000\ua0bp with discontinuous vestiges of red algal plasmid DNA sequences interspersed between the nblA and cpeB genes. This chloroplast genome shows similar gene content and order to other Florideophycean taxa. Phylogenomic analyses based on the concatenated amino acid sequences of 146 protein-coding genes confirmed the monophyly of the classes Bangiophyceae and Florideophyceae with full nodal support. Relationships within the subclass Rhodymeniophycidae in Florideophyceae received moderate to strong nodal support, and the monotypic family of Gracilariales were resolved with maximum support.
Conclusions
Chloroplast genomes hold substantial information that can be tapped for resolving the phylogenetic relationships of difficult regions in the Rhodymeniophycidae, which are perceived to have experienced rapid radiation and thus received low nodal support, as exemplified in this study. The present study shows that chloroplast genome of G. firma could serve as a key link to the full resolution of Gracilaria sensu lato complex and recognition of Hydropuntia as a genus distinct from Gracilaria sensu stricto
CX 3 C chemokine receptor 1 deficiency modulates microglia morphology but does not affect lesion size and short-term deficits after experimental stroke
No full textAbstract
Background
The fractalkine/CX
3
C chemokine receptor 1 (CX
3
CR1) pathway has been identified to play an essential role in the chemotaxis of microglia, leukocyte trafficking and microglia/macrophage recruitment. It has also been shown to be important in the regulation of the inflammatory response in the early phase after experimental stroke. The present study was performed to investigate if CX
3
CR1 deficiency affects microglia during the first 14\ua0days with consequences for tissue damage after experimental stroke.
Results
CX3CR1 deficiency significantly increased the number of intersections of GFP positive microglia in the proximal peri-infarct area at 2, 7 and 14\ua0days following tMCAO compared to heterozygous and wildtype littermates. In addition, the length of microglial branches increased until day 7 in CX
3
CR1 knockout mice while the presence of a functional CX3CR1 allele resulted in a gradual reduction of their length following tMCAO. After stroke, wildtype, heterozygous and CX3CR1 deficient mice did not show differences in the composite neuroscore and assessment of infarct volumes from CX3CR1 wildtype, heterozygous and deficient mice revealed no differences between the genotypes 7 and 14\ua0days after stroke.
Conclusion
Results demonstrate that CX3CR1 deficiency affects the morphology of GFP positive microglia located in the proximal peri-infarct region during the first 14\ua0days after tMCAO. Our data also indicate that CX3CR1 deficiency does not affect definite infarct volumes. Modulation of the CX3CR1 pathway may have implication for microglia function contributing to mechanisms of tissue reorganization in the post-ischemic brain