Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae

Cornaceae is a core representative family in Cornales, the earliest branching lineage in the Asterids on the life tree of angiosperms. This family includes the only genus Cornus, a group of ~55 species. These species occur widely in Northern Hemisphere and have been used as resources for horticultural ornaments, medicinal and industrial manufacturing. However, no any genome sequences are available for this family. Here, we reported a chromosome­level genome for Cornus controversa. This was generated using high-fidelity plus Hi–C sequencing, and totally ~771.80 Mb assembled sequences and 39,886 protein-coding genes were obtained. We provided evidence for a whole-genome duplication event (WGD) unique to C. controversa. The evolutionary features of this genome indicated that the expanded and unique genes might have contributed to response to stress, stimulus and defense. By using chromosome-level syntenic blocks shared between eight living genomes, we found high degrees of genomic diversification from the ancestral core-eudicot genome to the present-day genomes, suggesting an important role of WGD in genomic plasticity that leads to speciation and diversification. These results provide foundational insights on the evolutionary history of Cornaceae, as well as on the Asterids diversification.     

Pan‐Cancer analyses of Necroptosis‐Related genes as a potential target to predict immunotherapeutic outcome

Necroptosis is a unique programmed death mechanism of necrotic cells. However, its role and specific mechanism in cancer remain unclear, and a systematic pan‐cancer analysis of necroptosis is yet to be conducted. Thus, we performed a specific pan‐cancer analysis using The Cancer Genome Atlas and Genotype‐Tissue Expression databases to analyse necroptosis expression in terms of cancer prognosis, DNA methylation status, tumour mutative burden, microsatellite instability, immune cell infiltration in different types of cancer and molecular mechanisms. For the first time, we explored the correlation between necroptosis and immunotherapy prognosis. Thus, our study provides a relatively comprehensive understanding of the carcinogenicity of necroptosis in different types of cancer. It is suggested that necroptosis can be used to evaluate the sensitivity of different patients to immunotherapy and may become a potential target for tumour immunotherapy.     

Direct adenylation from 5′-OH-terminated oligonucleotides by a fusion enzyme containing Pfu RNA ligase and T4 polynucleotide kinase

5′-Adenylated oligonucleotides (AppOligos) are widely used for single-stranded DNA/RNA ligation in next-generation sequencing (NGS) applications such as microRNA (miRNA) profiling. The ligation between an AppOligo adapter and target molecules (such as miRNA) no longer requires ATP, thereby minimizing potential self-ligations and simplifying library preparation procedures. AppOligos can be produced by chemical synthesis or enzymatic modification. However, adenylation via chemical synthesis is inefficient and expensive, while enzymatic modification requires pre-phosphorylated substrate and additional purification. Here we cloned and characterized the Pfu RNA ligase encoded by the PF0353 gene in the hyperthermophilic archaea Pyrococcus furiosus. We further engineered fusion enzymes containing both Pfu RNA ligase and T4 polynucleotide kinase. One fusion enzyme, 8H-AP, was thermostable and can directly catalyze 5′-OH-terminated DNA substrates to adenylated products. The newly discovered Pfu RNA ligase and the engineered fusion enzyme may be useful tools for applications using AppOligos.     

Exosomal miR-146a-5p and miR-155-5p promote CXCL12/CXCR7-induced metastasis of colorectal cancer by crosstalk with cancer-associated fibroblasts

C-X-C motif chemokine receptor 7 (CXCR7) is a newly discovered atypical chemokine receptor that binds to C-X-C motif chemokine ligand 12 (CXCL12) with higher affinity than CXCR4 and is associated with the metastasis of colorectal cancer (CRC). Cancer-associated fibroblasts (CAFs) have been known to promote tumor progression. However, whether CAFs are involved in CXCR7-mediated metastasis of CRC remains elusive. We found a significant positive correlation between CXCR7 expression and CAF activation markers in colonic tissues from clinical specimens and in villin-CXCR7 transgenic mice. RNA sequencing revealed a coordinated increase in the levels of miR-146a-5p and miR-155-5p in CXCR7-overexpressing CRC cells and their exosomes. Importantly, these CRC cell-derived miR-146a-5p and miR-155-5p could be uptaken by CAFs via exosomes and promote the activation of CAFs through JAK2–STAT3/NF-κB signaling by targeting suppressor of cytokine signaling 1 (SOCS1) and zinc finger and BTB domain containing 2 (ZBTB2). Reciprocally, activated CAFs further potently enhanced the invasive capacity of CRC cells. Mechanistically, CAFs transfected with miR-146a-5p and miR-155-5p exhibited a robust increase in the levels of inflammatory cytokines interleukin-6, tumor necrosis factor-α, transforming growth factor-β, and CXCL12, which trigger the epithelial–mesenchymal transition and pro-metastatic switch of CRC cells. More importantly, the activation of CAFs by miR-146a-5p and miR-155-5p facilitated tumor formation and lung metastasis of CRC in vivo using tumor xenograft models. Our work provides novel insights into CXCR7-mediated CRC metastasis from tumor–stroma interaction and serum exosomal miR-146a-5p and miR-155-5p could serve as potential biomarkers and therapeutic targets for inhibiting CRC metastasis.Subject terms: Cancer microenvironment, Colon cancer     

黑线仓鼠种群数量动态预测研究

１９８４－１９９１年３－１０月,每月中旬在中国农科院草原研究所试验场的不同牧草和作物地进行调查,１９８４－１９９１年共捕获鼠４０９３只,其中黑线仓鼠２９２０只占７１．３４％。黑线仓鼠种群数量季节和年度变化明显,利用电子计算机对黑线仓鼠种数量进行分析,提出种群数量繁殖指数和动态模型以及短、中、长期预测公式、预测准确率为９０．０％。并对影响种群数量的因素进行了初步分析。     

洈水水库鳡鱼(Elopichthys bambusa)生长规律的研究

本文对洈水水库鳡鱼的生长及其利用进行了分析研究,结果表明:1.该种鱼生长快,高速生长时间长,可连续5年每年生长6kg以上;2.雌、雄鱼体长与体重生长分别适合Von.Bertalanffy的生长公式:L=L_∞(1-e-k(t-t·))和W=W_∞(1-e-k(t-t·))~3;3.雌鱼体重生长速度快于雄鱼,体长生长无明显差别;4.建议大中型水体中的鳡鱼与其它鱼类群落体重之比控制在3—5％为宜。     

Plant ERD2-like proteins function as endoplasmic reticulum luminal protein receptors and participate in programmed cell death during innate immunity

Plant secondary metabolites, such as those derived from the phenylpropanoid pathway, have a beneficial effect on human health. Manipulation of metabolic flux in the phenylpropanoid pathway is important for achieving enhanced production of compounds such as anthocyanins, flavonoids and isoflavonoids. Here, we describe the development of a high-throughput molecular evolution approach that can be used for catalytic improvement of at least four key phenylpropanoid pathway enzymes, within the context of the metabolic pathway. This method uses yeast cells that express plant phenylpropanoid pathway enzymes, leading to formation of a colored intermediate that can be used as a readout in high-throughput screening. Here we report the identification of improved tomato peel 4-coumarate:CoA ligase variants using this approach. We found that the wild-type enzyme is strongly allosterically inhibited by naringenin, a downstream product of the pathway. Surprisingly, at least two of the improved variants are completely insensitive to feedback inhibition by naringenin. We suggest that this inhibition is exerted through a unique and previously unrecognized allosteric domain.     

Effects of fish oil on lymphocyte proliferation,cytokine production and intracellular signalling in weanling pigs

It has been widely documented that fish oil attenuates inflammatory responses partially via down-regulation of T-lymphocyte function. To determine the anti-inflammatory role of fish oil in weanling pigs, we investigated the effects of fish oil and its functional constituents on peripheral blood lymphocyte proliferation, cytokine production and subsequent intracellular signalling in inflammatory-challenged weanling pigs and in in vitro cultured lymphocytes. Fish oil (7%) or corn oil (7%) was supplemented to 72 crossbred pigs (7.6 ± 0.3 kg BW and 28 ± 3 days of age) in a 2 × 2 factorial experiment that included an Escherichia coli lipopolysaccharide (LPS) challenge (challenged or not challenged). On day 14 and 28 of the experiment, 200 μg/kg BW of LPS or an equivalent amount of sterile saline was administered to the pigs by intraperitoneal injection. Blood samples were collected on days 15 and 29 to determine peripheral blood lymphocyte proliferation, interleukin-1β (IL-1β) and interleukin-2 (IL-2) production. The results showed that inflammatory challenge decreased average daily gain (P < 0.05) and average daily feed intake (P < 0.05) during days 15 - 28. Fish oil supplementation had no effect on growth performance. Inflammatory challenge increased lymphocyte proliferative response to concanavalin A (Con A) (P < 0.05) following each challenge. Fish oil tended to suppress (P < 0.1) the proliferation following the first challenge. Similarly, fish oil tended to reduce IL-1β production (P < 0.1) following the second challenge and IL-2 (P < 0.1) production following the first challenge in both challenged and unchallenged pigs compared with corn oil. In parallel in vitro experiments, peripheral blood lymphocytes of weanling pigs were incubated with various concentrations of eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) or linoleic acid (LA) (0, 20, 40, 60, 80, 100 μg/ml). EPA, DHA and high levels of LA predominantly suppressed IL-1β (P < 0.05), IL-2 (P < 0.05) production and subsequent lymphocyte proliferation (P < 0.05). Low levels of LA increased (P < 0.05) IL-2 production. Compared with LA, EPA resulted in a stronger inhibition of lymphocyte proliferation (P < 0.05) and IL-2 (P < 0.01), and DHA resulted in a stronger inhibition of IL-1β (P < 0.05) and IL-2 (P < 0.01). To elucidate the mechanism(s) by which fish oil and its functional constituents suppressed lymphocyte function, the kinetics of intracellular [Ca^{2 +}]_i and protein kinase C activity were determined in in vitro experiments. EPA, DHA and LA exerted very similar dose-dependent stimulatory effects on intracellular Ca^{2 +}. EPA and DHA inhibited protein kinase C activity (P < 0.05), while LA had no significant effect (P > 0.05). These results suggest that fish oil and its functional constituents (EPA and DHA) exerted an anti-inflammatory effect by down-regulation of lymphocyte activation in weanling pigs, possibly by manipulation of intracellular signalling.