Kelp (Saccharina japonica) has been intensively cultured in China for almost a century. Its genetic improvement is comparable with that of rice. However, the development of its molecular tools is extremely limited, thus its genes, genetics and genomics. Kelp performs an alternative life cycle during which sporophyte generation alternates with gametophyte generation. The gametophytes of kelp can be cloned and crossed. Due to these characteristics, kelp may serve as a reference for the biological and genetic studies of Volvox, mosses and ferns. We constructed a high density single nucleotide polymorphism (SNP) linkage map for kelp by restriction site associated DNA (RAD) sequencing. In total, 4,994 SNP-containing physical (tag-defined) RAD loci were mapped on 31 linkage groups. The map expanded a total genetic distance of 1,782.75 cM, covering 98.66% of the expected (1,806.94 cM). The length of RAD tags (85 bp) was extended to 400–500 bp with Miseq method, offering us an easiness of developing SNP chips and shifting SNP genotyping to a high throughput track. The number of linkage groups was in accordance with the documented with cytological methods. In addition, we identified a set of microsatellites (99 in total) from the extended RAD tags. A gametophyte sex determining locus was mapped on linkage group 2 in a window about 9.0 cM in width, which was 2.66 cM up to marker_40567 and 6.42 cM down to marker_23595. A high density SNP linkage map was constructed for kelp, an intensively cultured brown alga in China. The RAD tags were also extended so that a SNP chip could be developed. In addition, a set of microsatellites were identified among mapped loci, and a gametophyte sex determining locus was mapped. This map will facilitate the genetic studies of kelp including for example the evaluation of germplasm and the decipherment of the genetic bases of economic traits.
In recent years, with the continuous development of deep learning, the scope of neural networks that can be expressed is becoming wider and their expressive ability stronger. Traditional deep learning methods based on extracting latent representations have achieved satisfactory results. However, in the field of hyperspectral image compression, the high computational cost and the degradation of their generalization ability reduce their application. We analyze the objective formulation of traditional learning-based methods and draw the conclusion that rather than treating the hyperspectral image as an entire tensor to extract the latent representation, it is preferred to view it as a stream of video data, where each spectral band represents a frame of information and variances between spectral bands represent transformations between frames. Moreover, in order to compress the hyperspectral image of this video representation, neural video representation that decouples the spectral and spatial dimensions from each other for representation learning is employed so that the information about the data is preserved in the neural network parameters. Specifically, the network utilizes the spectral band index and the spatial coordinate index encoded with positional encoding as its input to perform network overfitting, which can output the image information of the corresponding spectral band based on the index of that spectral band. The experimental results indicate that the proposed method achieves approximately a 5 dB higher PSNR compared with traditional deep learning-based compression methods and outperforms another neural video representation method by 0.5 dB when using only the spectral band index as input.
Zostera marina is the only seagrass species whose seeds have been successfully used in large‐scale restoration. Although progress has been made in refining Z. marina restoration protocols, additional information on Z . marina seed physiology is necessary as the science of seagrass restoration evolves. We tested the germination rates of Z. marina seeds under different relative humidities and temperatures for different periods of time. Z. marina seed moisture content (MC) and germination rates were also tested when seeds were exposed to a temperature of 25°C and relative humidity of 50%. Z. marina seeds suffered higher mortality when exposed to lower relative humidity and higher temperature for longer period of exposure time. A significant negative correlation was detected between seed germination rate and MC. Z. marina seeds are sensitive to desiccation exposure and long periods of exposure to air should be prevented to minimize seed mortality when seeds are used in restoration projects.
s results.They have since determined that results reported in Tables 3 and4 are unreliable due to methodological errors, and that YL-0919 is not a selective SERT/5-HT 1A receptor agonist as reported in the article.Specifically, the collected membrane protein used to evaluate the affinity of the compound YL-0919 for 5-HT transporter (SERT) and 5-HT 1A receptor was extracted from rat brain tissue over a period of 7-9 hours and the membrane proteins are not expected to maintain their naive biological activity under the experimental conditions used.In experiments conducted after the publication of [1], the homogeneous membrane protein showed time-dependent degradation, leading to a continuous decrease in total binding per loading sample.The negative control also showed a high affinity binding curve characteristic resulting in false positive results in the SERT and 5-HT 1A binding assay.An expert member of the Editorial Board confirmed that the experimental conditions described in [1] are likely to result in significant degradation.They further noted that the buffer used in the experiments affects high affinity binding by known ligands and therefore the results obtained using the buffer should be considered inconsistent and not reliable.In light of the above issues, the authors retract this article.
Abstract The coast of the Yellow Sea in China, like many other temperate coastal zones, has been experiencing a dramatic decline in the abundance of seagrass. Intensive efforts have been made to restore seagrass communities along the coast to restore the function of the coastal ecosystem. Transplanting adult Zostera marina shoots is labor‐intensive, time‐consuming, expensive, and detrimental to donor beds; thus, restoring seagrass communities through the use of seeds is highly valued in current, large‐scale restoration trials. In this study, an effective method for collecting, processing, and storing Z. marina seeds was developed. From 2009 to 2013, respectively, 122,000, 421,000, 364,000, 1,041,000, and 1,091,000 seeds were successfully collected. Two‐way analysis of variance ( ANOVA ) showed the interaction between salinity and temperature significantly affected the cumulative germination rate (CGR) ( p < 0.01) during the storage period and the viability ( p < 0.01) of seeds after storage. The germination rate after storage was significantly affected by salinity and temperature ( p < 0.01). The highest viability (89.8 ± 1.0%) and germination rate (75.6 ± 4.5%) were found among seeds stored at 4°C and a salinity of 44.5 psu for 7 months. The cost for planting 1 ha of sea bottom with Z. marina seeds ranged from $2,613 to $80,900 depending on the seeding density and seed loss during storage. The average cost per Z. marina seed in this study was $0.00586.
Biological organisms are complex systems that are composed of functional networks of interacting molecules and macro-molecules. Complex phenotypes are the result of orchestrated, hierarchical, heterogeneous collections of expressed genomic variants. However, the effects of these variants are the result of historic selective pressure and current environmental and epigenetic signals, and, as such, their co-occurrence can be seen as genome-wide correlations in a number of different manners. Biomass recalcitrance (i.e., the resistance of plants to degradation or deconstruction, which ultimately enables access to a plant's sugars) is a complex polygenic phenotype of high importance to biofuels initiatives. This study makes use of data derived from the re-sequenced genomes from over 800 different Populus trichocarpa genotypes in combination with metabolomic and pyMBMS data across this population, as well as co-expression and co-methylation networks in order to better understand the molecular interactions involved in recalcitrance, and identify target genes involved in lignin biosynthesis/degradation. A Lines Of Evidence (LOE) scoring system is developed to integrate the information in the different layers and quantify the number of lines of evidence linking genes to target functions. This new scoring system was applied to quantify the lines of evidence linking genes to lignin-related genes and phenotypes across the network layers, and allowed for the generation of new hypotheses surrounding potential new candidate genes involved in lignin biosynthesis in P. trichocarpa, including various AGAMOUS-LIKE genes. The resulting Genome Wide Association Study networks, integrated with Single Nucleotide Polymorphism (SNP) correlation, co-methylation and co-expression networks through the LOE scores are proving to be a powerful approach to determine the pleiotropic and epistatic relationships underlying cellular functions and, as such, the molecular basis for complex phenotypes, such as recalcitrance.
Abstract Dongfang no.7 ( Saccharina japonica ) was bred and maintained by hybridizing gametophytes, self-crossing the best individuals, selecting the best self-crossing line and seedling-raising from yearly reconstructed sporophytes. It increased the air dry yield by 43.2% in average over 2 widely farmed controls. Dongfang no.7 was seedling-raised from bulked sporophytes reconstructed from its representative gametophyte clones. Such strategy ensured it against variety contamination due to possible cross fertilization and occasional mixing and inbred depletion due to self-crossing number-limited sporophytes year after year. It derived from an intraspecific hybrid through 4 rounds of self-crossing and selection and retained a certain degree of genetic heterozygosity, thus being immune to inbred depletion due to purification of unknown detrimental alleles. Most importantly, it can be farmed in currently available system as the seedlings for large scale culture can be raised from reconstructed Dongfang no.7 sporophytes. Breeding and maintaining Dongfang no.7 provided a model that other varieties of kelp ( S. japonica ) and brown algae may follow during their domestication.
Unwinding DNA and unleasing inflammation Fighting infections often comes with collateral damage, which sometimes can be deadly. For instance, in septic shock, the overwhelming release of inflammatory mediators drives multi-organ failure. Rialdi et al. now report a potential new therapeutic target for controlling excessive inflammation: the DNA unwinding enzyme topoisomerase I (Top1) (see the Perspective by Pope and Medzhitov). Upon infection, Top1 specifically localizes to the promoters of pathogen-induced genes and promotes their transcription by helping to recruit RNA polymerase II. Pharmacological inhibition of Top1 in a therapeutic setting increased survival in several mouse models of severe microbially induced inflammation. Science , this issue p. 10.1126/science.aad7993 ; see also p. 1058
The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes (rbcL, matK, ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests.
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