| 1. |
|
|
| 2. |
- Deng, Min, et al.
(författare)
-
Genome-wide association analyses in Han Chinese identify two new susceptibility loci for amyotrophic lateral sclerosis
- 2013
-
Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 45:6, s. 697-
-
Tidskriftsartikel (refereegranskat)abstract
- To identify susceptibility genes for amyotrophic lateral sclerosis (ALS), we conducted a genome-wide association study (GWAS) in 506 individuals with sporadic ALS and 1,859 controls of Han Chinese ancestry. Ninety top SNPs suggested by the current GWAS and 6 SNPs identified by previous GWAS were analyzed in an independent cohort of 706 individuals with ALS and 1,777 controls of Han Chinese ancestry. We discovered two new susceptibility loci for ALS at 1q32 (CAMK1G, rs6703183, P-combined = 2.92 x 10(-8), odds ratio (OR) = 1.31) and 22p11 (CABIN1 and SUSD2, rs8141797, P-combined = 2.35 x 10(-9), OR = 1.52). These two loci explain 12.48% of the overall variance in disease risk in the Han Chinese population. We found no association evidence for the previously reported loci in the Han Chinese population, suggesting genetic heterogeneity of disease susceptibility for ALS between ancestry groups. Our study identifies two new susceptibility loci and suggests new pathogenic mechanisms of ALS.
|
|
| 3. |
- Liu, Hui, et al.
(författare)
-
Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
|
|
| 4. |
- Xu, Chao-Qun, et al.
(författare)
-
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production
- 2019
-
Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 8:2
-
Tidskriftsartikel (refereegranskat)abstract
- Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. Conclusions Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.
|
|
| 5. |
- Cheng, Shi-Ping, et al.
(författare)
-
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
-
Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
-
Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
|
|
| 6. |
- Wang, Huijiao, et al.
(författare)
-
Oxidation of emerging biocides and antibiotics in wastewater by ozonation and the electro-peroxone process
- 2019
-
Ingår i: Chemosphere. - : Elsevier. - 0045-6535 .- 1879-1298. ; 235, s. 575-585
-
Tidskriftsartikel (refereegranskat)abstract
- This study investigated the abatement of a number of antimicrobials frequently detected in municipal wastewater by conventional ozonation and a recently developed ozone-based advanced oxidation process, the electro-peroxone (E-peroxone) process. A synthetic water and a real secondary wastewater effluent were spiked with fourteen antimicrobials, including antibiotics and biocides, and then treated by the two processes. The results show that most of the antibiotics investigated (e.g., ofloxacin, trimethoprim, norfloxacin, and ciprofloxacin) readily react with ozone (O3) and could therefore be efficiently eliminated from the water matrices by direct O3 oxidation during both processes. In contrast, most of the biocides tested in this study (e.g., clotrimazole, pentamidine, bixafen, propiconazole, and fluconazole) were only moderately reactive, or non-reactive, with O3. Therefore, these biocides were removed at considerably lower rate than the antibiotics during the two ozone-based processes, with hydroxyl radical (OH) oxidation playing an important role in their abatement mechanisms. When compared with conventional ozonation, the E-peroxone process is defined by the in situ electrogeneration of hydrogen peroxide, which considerably enhances the transformation of O3 to OH. As a result, the E-peroxone process significantly accelerated the abatement of biocides and required a considerably shorter treatment time to eliminate all of the tested compounds from the water matrices than conventional ozonation. In addition, the E-peroxone process enhanced the contributions of OH fractions to the abatement of moderately ozone reactive benzotriazoles. These results demonstrate that the E-peroxone process holds promise as an effective tertiary treatment option for enhancing the abatement of ozone-resistant antimicrobials in wastewater.
|
|
| 7. |
- Wang, Sheng-Jun, 1981-, et al.
(författare)
-
Influence of synaptic interaction on firing synchronization and spike death in excitatory neuronal networks
- 2008
-
Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - New York : American Physical Society through the American Institute of Physics. - 1063-651X .- 1095-3787. ; 78:6, s. 061906-
-
Tidskriftsartikel (refereegranskat)abstract
- We investigate the influence of efficacy of synaptic interaction on firing synchronization in excitatoryneuronal networks. We find spike death phenomena: namely, the state of neurons transits from the limit cycleto a fixed point or transient state. The phenomena occur under the perturbation of an excitatory synapticinteraction, which has a high efficacy. We show that the decrease of synaptic current results in spike deaththrough depressing the feedback of the sodium ionic current. In the networks with the spike death property thedegree of synchronization is lower and insensitive to the heterogeneity of neurons. The mechanism of theinfluence is that the transition of the neuron state disrupts the adjustment of the rhythm of the neuronsoscillation and prevents a further increase of the firing synchronization.
|
|
| 8. |
- Yang, Fu-Sheng, et al.
(författare)
-
Chromosome-level genome assembly of a parent species of widely cultivated azaleas
- 2020
-
Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea. Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.
|
|
| 9. |
|
|
| 10. |
- Guan, Jian-Yue, et al.
(författare)
-
Cooperation influenced by the correlation degree of two-layered complex networks in evolutionary prisoner's dilemma games
- 2010
-
Ingår i: Chinese Physics B. - : Institute of Physics (IOP). - 1674-1056. ; 19:2
-
Tidskriftsartikel (refereegranskat)abstract
- An evolutionary prisoner's dilemma game is investigated on two-layered complex networks respectively representing interaction and learning networks in one and two dimensions. A parameter q is introduced to denote the correlation degree between the two-layered networks. Using Monte Carlo simulations we studied the effects of the correlation degree on cooperative behaviour and found that the cooperator density nontrivially changes with q for different payoff parameter values depending on the detailed strategy updating and network dimension. An explanation for the obtained results is provided.
|
|
