Jiaxin Chen

In this study we report on the clinical and autoimmune characteristics of severe and critical novel coronavirus pneumonia caused by severe acute respiratory syndrome-associated coronavirus 2 (SARS-CoV-2). The clinical, autoimmune, and laboratory characteristics of 21 patients who had laboratory-confirmed severe and critical cases of coronavirus disease 2019 (COVID-19) from the intensive care unit of the Huangshi Central Hospital, Hubei Province, China, were investigated. A total of 21 patients (13 men and 8 women), including 8 (38.1%) severe cases and 13 (61.9%) critical cases, were enrolled. Cough (90.5%) and fever (81.0%) were the dominant symptoms, and most patients (76.2%) had at least one coexisting disorder on admission. The most common characteristics on chest computed tomography were ground-glass opacity (100%) and bilateral patchy shadowing (76.2%). The most common findings on laboratory measurement were lymphocytopenia (85.7%) and elevated levels of C-reactive protein (94.7%) and interleukin-6 (89.5%). The prevalence of anti-52 kDa SSA/Ro antibody, anti-60 kDa SSA/Ro antibody, and antinuclear antibody was 20%, 25%, and 50%, respectively. We also retrospectively analyzed the clinical and laboratory data from 21 severe and critical cases of COVID-19. Autoimmune phenomena exist in COVID-19 subjects, and the present results provide the rationale for a strategy of preventing immune dysfunction and optimal immunosuppressive therapy.

Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining target genes of TFs and exploring TF functions. Human gene expression profile datasets with TF knockdown and knockout are accumulating rapidly. Based on the urgent need to comprehensively and effectively collect and process these data, we developed KnockTF (http://www.licpathway.net/KnockTF/index.html), a comprehensive human gene expression profile database of TF knockdown and knockout. KnockTF provides a number of resources for human gene expression profile datasets associated with TF knockdown and knockout and annotates TFs and their target genes in a tissue/cell type-specific manner. The current version of KnockTF has 570 manually curated RNA-seq and microarray datasets associated with 308 TFs disrupted by different knockdown and knockout techniques and across multiple tissue/cell types. KnockTF collects upstream pathway information of TFs and functional annotation results of downstream target genes. It provides details about TFs binding to promoters, super-enhancers and typical enhancers of target genes. KnockTF constructs a TF-differentially expressed gene network and performs network analyses for genes of interest. KnockTF will help elucidate TF-related functions and potential biological effects.

The common walnut Juglans regia and its related species in the genus Juglans are important economic trees, which have been widely grown for nut and wood productions in many counties. In the Juglans genus, there are ~ 21 diploid species all with 2n = 32 chromosomes, which can be divided into four major sections based on phylogenetic analyses and fruit morphology – Cardiocaryon (e.g. J. cathayensis and J. mandshurica), Juglans (e.g. J. sigillata and the most popular one J. regia), Trachycaryon (e.g. J. cinerea) and Rhysocaryon (e.g. J. hindsii, J. nigra and J. microcarpa) (Aradhya et al., 2007). For walnuts, the draft genome sequences of several Juglans species had been generated from second-generation sequencing platform (J. regia Chandler N50: 465Kb, Martınez-Garcıa et al., 2016; J. regia Chandler N50: 640Kb, Stevens et al., 2018). Very recently, the J. microcarpa × J. regia hybrid was sequenced using single molecule sequencing technology, and the new methods for haplotype phasing facilitated the genome assembling of the two species (J. regia Serr N50: 2.90 Mb, Zhu et al., 2019). In this study, we aimed to generate a high-quality reference-level de novo assembly and gene annotations of J. regia for genetic and genomic studies in walnut. To search for J. regia with low heterozygous rate, we selected 7 diverse J. regia accessions for Illumina sequencing to estimate the whole-genome-level heterozygosity. The accession Zhongmucha-1 (an ancient tree from Tibet, China; N29°04.889’ E92°44.432’; 3277 ASL) with the lowest (0.385%) heterozygosity was used to generate high-quality genome sequences. The resulting genome assemblies of Zhongmucha-1 contain a total of 353 contigs, with the contig N50 size of 3.34 Mb. Combined with Hi-C data generated in this work and the linkage and physical maps reported previously (Luo et al., 2015; Zhu et al., 2019), the contigs were anchored and ordered, generating chromosome-level sequences of 540 Mb. We found ~ 95% of the RNA-seq reads and 97.25% of the Illumina sequencing reads could be aligned onto the final assembly. The completeness of the genome assembly was then evaluated using BUSCO data sets (Simão et al., 2016), and ~ 94% of the core eukaryotic genes were able to be retrieved. To annotate the walnut genome for protein-coding genes, we used a hybrid gene prediction protocol with combinations of ab initio gene predictions and homologs sequence searching, which was further integrated with RNA-seq data from 9 representative tissues in J. regia (Figure 1a). Based on the collinear relationship with our J. regia genome, the scaffolds from other five Juglans species (J. cathayensis, J. mandshurica, J. sigillata, J. hindsii and J. nigra) were anchored onto chromosomes followed with ordering and orientation, generating 16 pseudochromosomes for each Juglans species. Taken together, coupled with the high-quality assembly of J. microcarpa (Zhu et al., 2019), the chromosome-level sequences are now available for totally seven species from the three major sections in Juglans. Through aligning the assemblies of the six related species with that of J. regia, we identified highly confident variants within coding regions, including 2 270 791 single nucleotide polymorphisms (SNPs), 235 764 small indels of ≤ 20 bp and 52 363 structural variants (SVs). The genome assemblies of all Juglans and the variation data have been deposited at http://xhhuanglab.cn/data/juglans.html, and the assembly of Juglans regia can also be downloaded from BIGD under Bioproject number PRJCA002070. Using single-copy genes, we constructed a phylogenetic tree for the seven Juglans species, their close relatives with reported genome sequences and the core eudicots genomes, along with Oryza sativa from monocots as outgroup (Figure 1b). Self-alignment of the walnut genome sequences based on the 39 432 gene models identified 11 446 paralogous gene groups with 555 synteny blocks, which indicated that the gene pairs were actually due to one-to-one chromosome pairs on the walnut genome (dividing into two sub-genomes – subA and subB in this work; Figure 1c). A total of 11 938 (between red bayberry and walnut subA) and 7978 (between red bayberry and walnut subB) one-to-one orthologous gene pair blocks were found and used to visualize the detailed orthologous chromosome-to-chromosome relationships (Figure 1d). There were 9457 cases with both copies retained in J. regia, 7530 cases with singletons retained in subA and 3204 retained in subB, meaning more than half of the duplicated gene pairs had lost one copy in J. regia after the WGD (Figure 1e). According to the estimation of the WGD time (~24.48 million years ago), coding genes were lost at a rate range from 0.56% to 1.62% per million years for each chromosome. We further focused on 6981 one-to-one collinear gene pairs between sub-genomes to compare the expression patterns in each pair. The correlation coefficient of the expression levels of the two copies in nine tissues was calculated for each gene pair (Figure 1g), and ~22% pairs showed significant correlations (850 pairs with P < 0.05). The other ~78% pairs showed weak or no expression pattern correlations between copies in subA and subB, suggesting the duplicates of each other begin to diverge in expression levels and patterns. As a typical example for co-expressed gene pairs (Figure 1h), the two copies JreCHSsubA and JreCHSsubB (a key enzyme involved in the biosynthesis of flavonoids) showed closely correlated gene expressions, which may indicate that both copies were responsible for the biosynthesis of the flavonoids with less functional divergence. Another contrasting example is JreSRG1 (a gene involved in plant senescence; Figure 1h), of which the subA copy were normally expressed in immature fruit and somatic embryo while the subB copy had no transcripts in these tissues, with numerous changes in promoter regions between the two copies (sequence identity = 45%). The abundant gene copies exhibiting diverse expression patterns were probably due to the sequence divergence in the promoter and other regulation regions (e.g. UTRs and enhancers) between sub-genomes. We then performed hierarchical clustering for these gene pairs based on their expression patterns in each tissue. For the tissue ‘immature fruit’ (Figure 1i), gene pairs could be classified into four distinctive clusters. Frequency distributions of the Ka/Ks ratio in the four clusters showed the clusterD (high expressions in both copies) had the lowest Ka/Ks ratio peak value (ClusterA: 0.2582; ClusterB: 0.2257; ClusterC: 0.2243; ClusterD: 0.1736), which suggested genes in this cluster tended to be conserved (Figure 1j). Along with J. microcarpa (Zhu et al., 2019), now we totally have 7 well-assembled Juglans genomes. Through the estimation of the peak Ks value of whole-genome orthologous genes between J. regia and each of the related species, J. regia speciated with J. sigillata roughly 0.84 million years ago and with other related species ~2.64 million years ago, much later than the WGD event (24.48 million years). Moreover, based on the Ks values, we can estimate the divergence time between M. rubra and J. regia was about 31 million years ago close to previous estimation (Jia et al., 2019), and the ancestry of the J. regia and J. sigillata genome and the origin of J. regia and J. sigillata was dated to ~0.82 Mya. Recently, Zhang et al, 2019 discovered that J. regia (and its landrace J. sigillata) arose as a hybrid between the American and the Asian lineages around 3.45 million year ago. Based on these clues, now we proposed a summarized model for the phylogeny of Juglans, as displayed in Figure 1k. This work is supported by the State Key Laboratory of Tree Genetics and Breeding support programme (Grant No. CAFYBB2019ZY001). We were grateful to Professor Zhong-Shan Gao for providing annotation file of Morella rubra, and Professor Ming-chen Luo for providing marker sequence in linkage map. D.P. conceived and designed the experiments. J.Z, F.J., X.S., G.P., Q.M. and Y.C performed the experiments. W.Z., F.J., J.Q., D.B., R.H. and J.C. analysed the genome data. W.Z. and D.P. wrote the manuscript. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

BACKGROUND: Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored. RESULTS: We report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese J. regia diverged from J. sigillata with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which JrFAD2 and JrANR are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively. CONCLUSIONS: The largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.

Inflammatory responses of nucleus pulposus (NP) can induce imbalanced anabolism and catabolism of extracellular matrix, and the cytosolic dsDNA accumulation and STING–NF–κB pathway activation found in NP inflammation are considered as fairly important cause of intervertebral disc (IVD) degeneration. Herein, we constructed a siSTING delivery hydrogel of aldehyde hyaluronic acid (HA-CHO) and poly(amidoamine) PAMAM/siRNA complex to intervene the abnormal STING signal for IVD degeneration treatment, where the formation of dynamic Schiff base bonds in the system ([email protected]gel) was able to overcome the shortcomings such as low cellular uptake, short half-life, and rapid degradation of siRNA-based strategy. PAMAM not only formed complexes with siRNA to promote siRNA transfection, but also served as dynamic crosslinker to construct hydrogel, and the injectable and self-healing hydrogel efficiently and steadily silenced STING expression in NP cells. Finally, the [email protected]gel significantly eased IVD inflammation and slowed IVD degeneration by prolonging STING knockdown in puncture-induced IVD degeneration rat model, revealing that STING pathway was a therapeutic target for IVD degeneration and such novel hydrogel had great potential for being applied to many other diseases for gene delivery.