Genome-wide association study and network analysis of in vitro transformation in Populus trichocarpa support key roles of diverse phytohormone pathways and cross talk.

Wide variation in amenability to transformation and regeneration (TR) among many plant species and genotypes presents a challenge to the use of genetic engineering in research and breeding. To help understand the causes of this variation, we performed association mapping and network analysis using a population of 1204 wild trees of Populus trichocarpa (black cottonwood). To enable precise and high-throughput phenotyping of callus and shoot TR, we developed a computer vision system that cross-referenced complementary red, green, and blue (RGB) and fluorescent-hyperspectral images. We performed association mapping using single-marker and combined variant methods, followed by statistical tests for epistasis and integration of published multi-omic datasets to identify likely regulatory hubs. We report 409 candidate genes implicated by associations within 5 kb of coding sequences, and epistasis tests implicated 81 of these candidate genes as regulators of one another. Gene ontology terms related to protein-protein interactions and transcriptional regulation are overrepresented, among others. In addition to auxin and cytokinin pathways long established as critical to TR, our results highlight the importance of stress and wounding pathways. Potential regulatory hubs of signaling within and across these pathways include GROWTH REGULATORY FACTOR 1 (GRF1), PHOSPHATIDYLINOSITOL 4-KINASE ß1 (PI-4Kß1), and OBF-BINDING PROTEIN 1 (OBP1).

GWAS supported by computer vision identifies large numbers of candidate regulators of in planta regeneration in Populus trichocarpa.

Plant regeneration is an important dimension of plant propagation and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. Association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover the genetic basis of trait variation in plants; however, the performance of these methods depends on the accuracy and scale of phenotyping. To enable a large-scale GWAS of in planta callus and shoot regeneration in the model tree Populus, we developed a phenomics workflow involving semantic segmentation to quantify regenerating plant tissues over time. We found that the resulting statistics were of highly non-normal distributions, and thus employed transformations or permutations to avoid violating assumptions of linear models used in GWAS. We report over 200 statistically supported quantitative trait loci (QTLs), with genes encompassing or near to top QTLs including regulators of cell adhesion, stress signaling, and hormone signaling pathways, as well as other diverse functions. Our results encourage models of hormonal signaling during plant regeneration to consider keystone roles of stress-related signaling (e.g. involving jasmonates and salicylic acid), in addition to the auxin and cytokinin pathways commonly considered. The putative regulatory genes and biological processes we identified provide new insights into the biological complexity of plant regeneration, and may serve as new reagents for improving regeneration and transformation of recalcitrant genotypes and species.

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa.

Adventitious rooting (AR) is critical to the propagation, breeding, and genetic engineering of trees. The capacity for plants to undergo this process is highly heritable and of a polygenic nature; however, the basis of its genetic variation is largely uncharacterized. To identify genetic regulators of AR, we performed a genome-wide association study (GWAS) using 1148 genotypes of Populus trichocarpa. GWASs are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale; to help overcome this limitation, we developed a computer vision system to measure an array of traits related to adventitious root development in poplar, including temporal measures of lateral and basal root length and area. GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical power. These analyses yielded a total of 277 unique associations, suggesting that genes that control rooting include regulators of hormone signaling, cell division and structure, reactive oxygen species signaling, and other processes with known roles in root development. Numerous genes with uncharacterized functions and/or cryptic roles were also identified. These candidates provide targets for functional analysis, including physiological and epistatic analyses, to better characterize the complex polygenic regulation of AR.

Clinical study of Tongluo-Qubai Decoction combined with routine western medicine therapy in the treatment of proteinuria in chronic glomerulonephritis with renal collaterals unsmooth / 国际中医中药杂志

Objective:To evaluate the clinical effect of Tongluo-Qubai Decoction combined with conventional western medicine on proteinuria of chronic glomerulonephritis (CGN) with renal collaterals unsmooth. Methods:124 patients with CGN proteinuria who met the inclusion criteria from January 2016 to December 2018 were randomly divided into two groups, 62 in each group. The control group took irbesartan tablets and dipyridamole tablets on the basis of conventional western medicine treatment; the observation group took Tongluo-Qubai Decoction on the basis of the control group. Both groups were treated for 3 months. The level of 24 h urinary protein quantification (24 h-Upro) was detected by immunoturbidimetry; plasma viscosity (PV) and TG were detected by automatic biochemical analyzer; to evaluate clinical therapeutic effect and TCM syndrome effect. Results:The total effective rate was 96.5% (60/62) in the observation group and 83.9% (52/62) in the control group. The total effective rate of TCM syndromes in the observation group was 90.3% (56/62) and that of the control group was 79.0% (49/62). The difference between the two groups was statistically significant ( χ2=10.301, P=0.040). After the treatment, 24 h-Upro (1.00 ± 0.65 g vs. 1.48 ± 0.71 g, t=4.998), PV (1.46 ± 0.30 mPa?s vs. 2.27 ± 0.28 mPa?s, t=6.292), TG (2.18 ± 0.68 mmol/L vs. 2.57 ± 0.73 mmol/L, t=7.025) in the observation group were lower than those of the control group ( P<0.01). Conclusions:Tongluo-Qubai Decoction combined with conventional western medicine can effectively improve the clinical symptoms of CGN proteinuria patients.

Clinical diagnosis and treatment of primary thyroid lymphoma: 19 cases / 中华内分泌外科杂志

Primary thyroid lymphoma is rare in the population, and with the improvement of the diagnostic efficiency of the needle biopsy technique, the effect of surgical treatment of primary thyroid lymphoma is reduced, but the surgical biopsy is still irreplaceable when the pathological subtype is not clear. The prognosis of primary thyroid lymphoma is mainly related to the pathological type and the stage of the disease.

Manufacture and comparison of chronic rejection model of orthotopic and heterotopic intestinal ;transplantation in rats / 器官移植

Objective To compare the modeling effect of chronic rejection following orthotopic and heterotopic intestinal transplantation in rats.Methods F344 (RT1 1 vr )rats were used as the donors and Lewis (RT1 1 )rats were used as the recipients.Models of allogeneic heterotopic and orthotopic intestinal transplantation in rats (8 rats in each model) were established,and subcutaneous injection of ciclosporin was given at 0 ~1 4 d after operation.Changes in body weight and survival time of the recipients were observed after operation.In addition,pathological changes in intestinal tissue were observed by hematoxylin-eosin (HE)staining.Changes in collagenous fibers and elastic fibers in intestinal tissue were observed after alcohol and hematoxylin staining.Finally,success rate of modeling of recipients in two groups was calculated.Results Rats in heterotopic and orthotopic intestinal transplantation groups were able to survive for a long time,most of which were more than 90 d.For the rats in orthotopic intestinal transplantation group,normal diet could be recovered at the 3 rd d after operation.Their body weight could recover preoperative level at about the 1 4th d after operation,and then grew slowly.However,most of the rats in orthotopic intestinal transplantation group continued weight loss from the 1 50th d after operation,which could not be reversed with ciclosporin.For the rats in heterotopic intestinal transplantation group,normal diet could be recovered at the 1 st d after operation,and their body weight could recover preoperative level within 25-30 d after operation and gradually rose and remained at a high level within 30-90 d after operation.No pathological changes of chronic rejection and obvious mesangial fibrosis in intestinal tissue were observed at the 90th d after operation,but intestinal tissue developed chronic rejection and obvious mesangial fibrosis at the 1 63 rd d and 200th d after operation in orthotopic intestinal transplantation group.Typical pathological changes of chronic rejection and mesangial fibrosis in intestinal tissue were observed at the 90th d and 200th d after operation for rats in heterotopic intestinal transplantation group.All the rats in heterotopic intestinal transplantation group showed characteristic pathological changes.The success rate of modeling was 1 00% in heterotopic intestinal transplantation group,which was not of statistical significance,compared with the success rate of modeling of 75% in the orthotopic intestinal transplantation group (P >0.05).Conclusions Chronic rejection will occur at different time points with small dose of ciclosporin after operation if models of orthotopic and heterotopic intestinal transplantation are established in combination of F344 → Lewis rats.Compared with orthotopic intestinal transplantation,the rat model of heterotopic intestinal transplantation holds the advantages of simple modeling,shorter chronic rejection and relatively consistent degree of pathological changes,which is more suitable for experimental study.

Disease burden of colorectal cancer in Jinchang cohort / 中华流行病学杂志

<p><b>OBJECTIVE</b>To evaluate the disease burden of colorectal cancer in Jinchang cohort, and provide evidence for preventing colorectal cancer and reducing the disease burden of colorectal cancer in the cohort.</p><p><b>METHODS</b>The colorectal cancer mortality data from 2001 to 2013 and the medical records of colorectal cancer patients from 2001 to 2010 were collected for this retrospective cohort study. The colorectal cancer disease burden was described by using mortality rate, standardized mortality rate, medical expenditure, potential years of life lost (PYLL), average potential years of life lost (APYLL), working potential years of life lost (WPYLL), and average working potential years of life lost (AWPYLL). The development trend in disease burden of colorectal cancer was analyzed by using Spearman correlation and the average growth rate.</p><p><b>RESULTS</b>The crude mortality rate of colorectal cancer from 2001 to 2013 was 9.53/100,000 with the average annual growth rate of 12.89%. The PYLL, APYLL, WPYLL and AWPYLL of colorectal cancer were 485.00 person-years, 9.15 years, 253.00 person-years, and 4.77 years, respectively. The direct medical expenditure due to colorectal cancer was 7064.38 Yuan per case and 408.43 Yuan per day. There was no increasing trend in the direct medical expenditure due to colorectal cancer.</p><p><b>CONCLUSION</b>Colorectal cancer mortolity rate was on the rise and it caused heavy disease burden in Jinchang cohort.</p>

Location of bone marrow mesenchymal stem cells in rats after small intestinal transplantation / 中华胃肠外科杂志

<p><b>OBJECTIVE</b>To study the bone marrow mesenchymal stem cells (MSC) settled in rats after small intestinal transplantation.</p><p><b>METHODS</b>Bone marrow MSCs were taken from 1-month male Lewis rats, isolated and cultured by density gradient centrifugation and differential adherent culture. The surface antigens (CD29, CD90, CD34 and CD45) of MSC were identified by flow cytometry. Final concentration of 5 μg/L CFSE was used to mark the third generation of MSCs. Adult male inbred line F344 rats were used as donor and adult male Lewis rats as acceptor. A heterotopic intestinal transplant rat model was established by F344 to Lewis. Labeled MSCs were injected into model rats through vena dorsalis penis after operation. Tissues at postoperative 7-day were collected for frozen pathology to reveal the location of transplanted MSCs under fluorescence microscope.</p><p><b>RESULTS</b>MSCs were successfully isolated from rat bone marrow. The average positive expression rates of surface antigens CD29, CD90, CD34 and CD45 were 96.48%, 99.77%, 2.41% and 1.39% respectively. MSCs were successfully and effectively marked with CFSE. Seven days after operation, a large number of green fluorescence could be observed in transplanted intestine, spleen and thymus. Autograft intestinal tissues only showed trace fluorescence, and the heart, liver and lung tissue basically did not present the green fluorescence.</p><p><b>CONCLUSION</b>Bone marrow MSCs can settle in transplanted small intestine of rat.</p>