Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China

Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.

Metabolomic profiles of breath odor compounds for prognostic prediction in patients with acute-on-chronic liver failure: A pilot study

AIM

The aim of this study was to use a metabonomics approach to identify potential biomarkers of exhaled breath condensate (EBC) for predicting the prognosis of acute-on-chronic liver failure (ACLF).

METHODS

Using liquid chromatography mass spectrometry, EBC metabolites of ACLF patients surviving without liver transplantation (n = 57) and those with worse outcomes (n = 45), and controls (n = 15) were profiled from a specialized liver disease center in Beijing. The metabolites were used to identify candidate biomarkers, and the predicted performance of potential biomarkers was tested.

RESULTS

Forty-one metabolites, involving glycerophospholipid metabolism, sphingolipid metabolism, arachidonic acid metabolism, and amino acid metabolism, as candidate biomarkers for discriminating the different outcomes of ACLF were selected. A prognostic model was constructed by a panel of four metabolites including phosphatidylinositol [20:4(5Z,8Z,11Z,14Z)/13:0], phosphatidyl ethanolamine (12:0/22:0), L-metanephrine and ethylbenzene, which could predict the worse prognosis in ACLF patients with sensitivity (84.4%) and specificity (89.5%) (area under the receiver operating characteristic curve [AUC] = 0.859, 95% confidence interval [CI] = 0.787-0.931). Compared with Model for End-Stage Liver Disease (MELD) score (AUC = 0.639, 95% CI = 0.526-0.753) and MELD-sodium (MELD-Na) score (AUC = 0.692, 95% CI = 0.582-0.803), EBC-associated metabolite signature model could better predict worse outcomes in patients with ACLF (p < 0.05). Using the MELD-Na score and EBC metabolite signatures, a decision tree model was built for predicting the prognosis of ACLF identified on logistic regression analyses (AUC = 0.906, 95% CI = 0.846-0.965).

CONCLUSION

EBC metabolic signatures show promise as potential biomarkers for predicting worse prognosis of ACLF.

[Investigation of mental workload and related factors among nurses from tertiary hospitals in Shandong]

Objective: To investigate mental workload among nurses from tertiary hospitals in Shandong Province, and analyze various factors related to mental workload. Methods: From May to July 2019, a cluster sampling method was used to select 8255 nurses from 20 third class a general hospitals in 16 cities of Shandong Province as the research objects, and 8159 valid questionnaires were collected. The general information and psychological load of nurses were investigated by general information questionnaire and task load index scale. The measurement data were expressed in percentage (%) ; the nurses' psychological load scores were in accordance with normal distribution, and the differences between groups were compared by t-test or ANOVA; the related influencing factors of nurses' psychological load were analyzed by multiple stepwise regression analysis. Results: The average scores of mental workload among nurses was 77.83 (SD=12.88) . Time demands and physical demands were the two highest rated dimensions of mental workload. the average scores were 90.77 (SD=12.47) and 79.92 (SD=15.23) . Multiple stepwise regression analysis showed that Satisfaction with income, monthly average night shift and professional titles were the significant predictors of mental workload (R(2)=0.08) . Conclusion: Nurses with higher psychological load, lower income satisfaction, higher number of night shifts per month and lower title have higher psychological load.

[Molecular identification of Tricula spp. and the parasitized trematode cercariae in schistosomiasis-endemic areas of Yunnan Province]

OBJECTIVE

To characterize a species of the genus Tricula and parasitized trematodes in schistosomiasis-endemic areas of Yunnan Province using a molecular analysis, so as to understand their taxonomic positions.

METHODS

Tricula spp. and Oncomelania snails were collected from Xiangyun County, Yunnan Province, and cercaria parasitizing snails were observed using crushing followed by microscopy. Cercaria parasitizing Tricula snails at various morphologies were sampled using a shedding method. Genomic DNA was extracted from snail soft tissues and cercariae, and the 16S rRNA, COI, 28S rDNA genes in snails and the ND1 and 28S rDNA genes in cercariae were amplified using a PCR assay and sequenced. The species of Tricula snails and their parasitized trematodes was characterized using sequence alignment and phylogenetic analysis.

RESULTS

Among 382 Tricula snails detected, there were three types of trematode cercariae found, including the non-forked (20.94%, 80/382), double-forked (3.40%, 13/382) and swallow shapes (7.07%, 27/382). Sequence and phylogenetic analyses showed that the 16S rRNA, COI and 28S rDNA gene sequences of this species of Tricula had high homology to those in Delavaya dianchiensis, and were clustered in a branch. Sequencing analysis of the ND1 and 28S rDNA genes revealed that the non-forked cercariae belonged to the family Pleu- rogenidae, the swallow-shaped cercariae belonged to the family Opecoelidae, and the double-forked cercariae belonged to another species of the genus Schistosoma that was different from S. sinensium and S. ovuncatum.

CONCLUSIONS

The species and taxonomy of Triculla spp. and their parasitized trematodes are preliminarily determined in schistosomiasis-endemic areas of Yunnan Province; however, further studies are required to investigate the more definite taxonomy and pathogenicity.

[Comparison of endoscopic features between colorectal sessile serrated adenoma/polyp with or without cytologic dysplasia and hyperplastic polyp]

Objective: To investigate the morphological features of colorectal sessile serrated adenoma/polyp (SSA/P) and hyperplastic polyp (HP) by white light endoscope (WLE) and Image enhancement endoscope (IEE) . Methods: The data of 7 384 patients who underwent colonoscopy at the Center of Digestive Endoscopy, Peking University International Hospital from August 1, 2016 to February 29, 2018 were analyzed retrospectively. WLE and IEE[Fuji intelligent chromo endoscopy (FICE) or Blue Laser Imaging (BLI) ]were used to compare the morphological features of SSA/P with HP, SSA/P-CD(+)with SSA/P-CD(-). The diagnostic values of endoscopic features in SSA/P and SSA/P-CD(+)were analyzed. Results: A total of 3 401 polyps were detected in 7 384 patients, including 164 SSA/Ps (135 patients). During the same period, there were 270 HPs (223 patients) in accordance with the admission criteria. Compared with HP group, SSA/P group was more common in the right colon with a diameter>5 mm and more likely to be manifested as: Ⅱ-O pit pattern, surface mucus, cumulus-like surface, irregular morphology, VMV, redness, and also more likely to be associated with colon adenoma, colon cancer elsewhere in the colorectum. The differences were statistically significant (P<0.01). Compared with SSA/P-CD(-)group, SSA/P-CD(+)group was more common in the right colon with a diameter>5 mm and more likely to be manifested as: Ⅱ-O pit pattern, surface mucus, cumulus-like surface, irregular morphology, VMV. The differences were statistically significant (P<0.001). The differential diagnosis between SSA/P and HP was predicted by combining any two endoscopic morphological features (right colon, Ⅱ-O pit pattern, surface mucus, cumulus surface, irregular morphology, VMV, diameter>5 mm, at least 2 of 7 endoscopic features). The sensitivity, specificity, accuracy, positive likelihood ratio and negative likelihood ratio were 59.15%, 95.56%, 81.80%, 13.32 and 0.43, respectively. Similarly, the differential diagnosis between SSA/P-CD(+) and HP was predicted. The sensitivity, specificity, accuracy, positive likelihood ratio and negative likelihood ratio were 92.16%, 95.56%, 95.02%, 20.76 and 0.08, respectively. Conclusion: Comprehensive analysis of the WLE and FICE/BLI morphological features of the lesions can effectively distinguish SSA/P from HP, especially SSA/P-CD(+) from HP.

[Clinicopathological analysis of aggressive angiomyxoma of soft tissue in abdomino-pelvic cavity]

Aggressive angiomyxoma is a rare mesenchymal tumor. To discuss the clinicopathological characteristics, treatment and prognosis of aggressive angiomyxoma, four cases of aggressive angiomyxoma of soft tissue in abdominopelvic cavity were collected from January 2015 to August 2017 in Peking University International Hospital. The clinical data, imaging examination, histopathological features, immunophenotype, therapy and prognosis were analysed. The related literatures were reviewed. All of the patients were adult females, age range from 27 to 49 years and mean 33 years. The clinical complaint was abdominal distention with no definite predisposing factor, or occasional physical-exam finding with no obvious discomfort. Three cases were primary and one case was recurrent. Typical layered or swirled structural sign was presented by CT and MRI scanning of three cases. All tumors located in the pelvic cavity, and attached to the uterus, vagina, rectum, bladder or ureter. One case was involved in the abdominal cavity simultaneously,adhesive to the spine, inferior vena cava and spleen. The gross appearance of tumors was from 5 to 22 cm in maximum diameter. The sectioned surfaces were soft, solid, white or yellow-gray, focally accompanied by edema, mucoid degeneration or cystic change. Microscopic observation showed that tumor cells were short spindle shaped and little atypical, the stroma was loose like edematous mucus or collagen, and the vessels were rich in thin and thick-wall. Partially the vessel wall expressed hyaline degeneration. Also tumors might infiltrate surrounding tissue, such as fat or nerve. The immunohistochemistry results of all cases were estrogen receptor and progesterone receptor diffusely moderate positive, Desmin and smooth muscle actin mostly positive, whereas CD34 expressed only in vessel and S-100 protein, CD117 and Dog1 all negative. All the tumors were complete surgical excision. During follow-up, one case recurred the second time. Our conclusions are the diagnosis of aggressive angiomyxoma is based on pathological morphology supplemented by immunohistochemistry, and the tumor may relapse after surgical resection.

Role and influence of p75NTR receptor on antioxidative damage of retinal pigment epithelial cells

The study aimed to investigate the role and mechanism of the p75 NTR receptor in the oxidative damage of retinal pigment epithelial cells (RPE). RPE cells transfected with the p75 NTR receptor were used as the experimental group, and the untransfected RPE cells as the control group. BrdU (5-Bromo-2-deoxyUridine) was used to detect cell proliferation activity; PI/Annexin V-FITC (fluorescein isothiocyanate, FITC) double staining was used to detect the apoptosis rate of the cells. The expression of reactive oxygen species (ROS) in cells was observed by laser microscope, and the expression of ROS, mitochondrial markers, and C expression of cytochrome in cells was detected by flow cytometry. Western blot was used to detect the Fas protein, pyrolysis Caspase-3, and expression level of the vascular endothelial growth factor 165 (VEGF165) protein. The results showed that the proliferation activity of RPE cells in the experimental group decreased gradually with the increase of transfection time, and the apoptosis rate of RPE cells in the experimental group increased gradually with the increase of transfection time, and the apoptosis rate of RPE cells at each time point was significantly higher than that of the control group. The fluorescence intensity of ROS in the experimental group was significantly stronger than that in the control group (P less than 0.01). The fluorescence intensity of cytochrome C in the RPE cells in the experimental group was significantly higher than that in the control group, while the number of positive mitochondria markers in the experimental group was less than that of the control group and the fluorescence intensity was weakened. The expression of Fas protein, Caspase-3 and VEGF165 protein in the experimental group was significantly higher than that in the control group (P less than 0.01). In conclusion, p75 NTR receptor may be a cause of oxidative damage in RPE cells. .

[Retroperitoneal dedifferentiated liposarcoma with rhabdomyoblastic differentiation: a clinicopathological analysis]

Objective: To investigate the clinicopathological features, differential diagnosis, treatment and prognosis of dedifferentiated liposarcoma with rhabdomyoblastic differentiation. Methods: Six cases of retroperitoneal dedifferentiated liposarcoma with rhabdomyoblastic features were collected from December 2014 to August 2017 at Peking University International Hospital. The clinical manifestations, histomorphology, immunophenotype, treatment and follow-up data were analyzed, and relevant literature reviewed. Results: The six patients included two males and four females, with age range of 47 to 66 years (mean 56 years). One case was primary and the five cases were recurred; four cases received radiotherapy and/or chemotherapy. The tumor diameters were 10 to 30 cm. Microscopically, the dedifferentiated areas were well demarcated from the well-differentiated areas, and resembled malignant fibrous histiocytoma, fibrosarcoma or solitary fibrous tumor with obvious mitotic figures or necrosis. Rhabdomyoblastic cells made up 10% to 30% of dedifferentiated area, and were scattered or focally distributed, being rounded, band-like or spindled, mostly with abundant eosinophilic cytoplasm. No striated structure was found, and the nucleis were rounded, oval or irregular shape with central or eccentric prominent nucleoli. Rare rhabdomyoblastic cells were lymphocytoid. The tumors encroached the muscular layer of intestinal wall in two cases and perirenal adipose tissue in one case. By immunohistochemical staining, the rhabdomyoblastic cells of all cases were all positive for desmin, myogenin, myoD1 and SMA; S-100 protein was expressed in one case (1/6). Well-differentiated area in two cases and dedifferentiated areas in all six cases were positive for MDM2, CDK4 and p16. After resection of the tumor and adjacent organs, one case recurred three months later, but there was no distant metastasis. Conclusions: Dedifferentiated liposarcoma with rhabdomyoblastic differentiation is a rare dedifferentiated liposarcoma. Pathological diagnosis is based on morphology, with supplementary immunohistochemical or molecular evaluation for further differential diagnosis. Multiple relapses may occur after surgical ablation plus adjuvant therapy.

[Clinicopathologic characteristics of head and neck carcinoma showing thymus-like element]

Objective: To investigate clinicopathological features of carcinoma showing thymus-like elements (CASTLE) in the head and neck regions. Methods: Clinicopathological data of 7 patients with CASTLE in the head and neck regions were retrospectively reviewed.Immunohistochemical staining and in situ hybridization for EBER were performed. BRAF(V600E) mutation was examined by ARMS method in 6 cases. Results: There were 5 females and 2 males with age between 49 and 78 years (average of 65.6 years). All tumors were solitary nodular lesions with an infiltrative border, including 6 intrathyroid tumors and 1 extrathyroid tumor in the laryngeal pharynx.The tumors were 1.7-4.1 cm in diameter (average of 3.0 cm). Four cases demonstrated lymph node metastasis.All patients were alive without metastasis during follow-up, except one consultation case (with FNA sample) developed recurrence at the primary site. The cases showed different immunoreaction to CD5, diffuse immunoreaction with p63, CK5/6 and CD117, but negative staining for TTF1, TG and calcitonin. One case showed positive immunoreaction with Synin less than 30% tumor cells. The Ki-67 labeling index was between 3% and 90%. No BRAF(V600E) mutation and EB virus infection were detected. Conclusions: Extrathyroid CASTLE involving laryngeal pharynx shows the similar morphological and immunohistochemical features with intrathyroid CASTLE.Immunohistochemical markers of CD5 and CD117 are helpful in the diagnosis. Ki-67 labeling index can be high in CASTLE, especially in lymphoepithelioma type. CD5-negative CASTLE may have neuroendocrine differentiation. BRAF(V600E) mutation and EB virus may not be involved in the carcinogenesis of CASTLE.

p28(GANK) associates with p300 to attenuate the acetylation of RelA

Oncoprotein p28(GANK), overexpressed in hepatocellular carcinomas (HCC), binds to RelA and retains NF-κB in the cytoplasm to suppress NF-κB transactivation. However, the mechanism has not yet been elucidated. In this study, we clarified the mechanism of NF-κB regulated by p28(GANK). p28(GANK) reduced TNF-α-induced nuclear translocation of RelA/NF-κB independent of HDAC3. p28(GANK) interacted with p300 to attenuate assembly of RelA with p300, which lessened acetylation of RelA on the lysine 310 sites. Moreover, overexpression of p28(GANK) attenuated the capability of NF-κB binding to the target gene IκBα promoter, but also weakened adriamycin-induced NF-κB pro-apoptotic gene Fas and FasL expression, which subsequently made p53-deficient tumor cells resistance to adriamycin. These results present mechanistic insight into the key role of p28(GANK) in post-translational regulation of RelA/NF-κB.