Integrating massive RNA-seq data to elucidate transcriptome dynamics in Drosophila melanogaster.

The volume of ribonucleic acid (RNA)-seq data has increased exponentially, providing numerous new insights into various biological processes. However, due to significant practical challenges, such as data heterogeneity, it is still difficult to ensure the quality of these data when integrated. Although some quality control methods have been developed, sample consistency is rarely considered and these methods are susceptible to artificial factors. Here, we developed MassiveQC, an unsupervised machine learning-based approach, to automatically download and filter large-scale high-throughput data. In addition to the read quality used in other tools, MassiveQC also uses the alignment and expression quality as model features. Meanwhile, it is user-friendly since the cutoff is generated from self-reporting and is applicable to multimodal data. To explore its value, we applied MassiveQC to Drosophila RNA-seq data and generated a comprehensive transcriptome atlas across 28 tissues from embryogenesis to adulthood. We systematically characterized fly gene expression dynamics and found that genes with high expression dynamics were likely to be evolutionarily young and expressed at late developmental stages, exhibiting high nonsynonymous substitution rates and low phenotypic severity, and they were involved in simple regulatory programs. We also discovered that human and Drosophila had strong positive correlations in gene expression in orthologous organs, revealing the great potential of the Drosophila system for studying human development and disease.

Mannose and phosphomannose isomerase regulate energy metabolism under glucose starvation in leukemia.

Diverse metabolic changes are induced by various driver oncogenes during the onset and progression of leukemia. By upregulating glycolysis, cancer cells acquire a proliferative advantage over normal hematopoietic cells; in addition, these changes in energy metabolism contribute to anticancer drug resistance. Because leukemia cells proliferate by consuming glucose as an energy source, an alternative nutrient source is essential when glucose levels in bone marrow are insufficient. We profiled sugar metabolism in leukemia cells and found that mannose is an energy source for glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Leukemia cells express high levels of phosphomannose isomerase (PMI), which mobilizes mannose to glycolysis; consequently, even mannose in the blood can be used as an energy source for glycolysis. Conversely, suppression of PMI expression or a mannose load exceeding the processing capacity of PMI inhibited transcription of genes related to mitochondrial metabolism and the TCA cycle, therefore suppressing the growth of leukemia cells. High PMI expression was also a poor prognostic factor for acute myeloid leukemia. Our findings reveal a new mechanism for glucose starvation resistance in leukemia. Furthermore, the combination of PMI suppression and mannose loading has potential as a novel treatment for driver oncogene-independent leukemia.

Hybrid-type and two-tetrad antiparallel telomere DNA G-quadruplex structures in living human cells.

Although the telomeric sequence has been reported to form various G-quadruplex topologies in vitro and in Xenopus laevis oocytes, in living human cells, the topology of telomeric DNA G-quadruplex remains a challenge. To investigate the human telomeric DNA G-quadruplex in a more realistic human cell environment, in the present study, we demonstrated that the telomeric DNA sequence can form two hybrid-type and two-tetrad antiparallel G-quadruplex structures by in-cell 19F NMR in living human cells (HELA CELLS). This result provides valuable information for understanding the structures of human telomeric DNA in living human cells and for the design of new drugs that target telomeric DNA.

A Nucleoside Derivative 5-Vinyluridine (VrU) for Imaging RNA in Cells and Animals.

In the present study, we used a nucleoside derivative 5-vinyluridine (VrU) for labeling during cell division and for tumor imaging in living mice. We demonstrated that the functional nucleoside bearing a 5-vinyl group is metabolically incorporated into cellular RNA and can be used to image RNA using a Diels-Alder reaction. The reagent allows for simultaneous and clear imaging of DNA and RNA in mammalian cells at single-cell resolution. We extended this approach to observe DNA and RNA behaviors in several basic stages of cell division. We further demonstrated that the derivative can be used for fluorescence imaging of tumor in live mice.

Epitaxial Growth of GaN Films on Chemical-Vapor-Deposited 2D MoS2 Layers by Plasma-Assisted Molecular Beam Epitaxy.

The van der Waals epitaxy of wafer-scale GaN on 2D MoS2 and the integration of GaN/MoS2 heterostructures were investigated in this report. GaN films have been successfully grown on 2D MoS2 layers using three different Ga fluxes via a plasma-assisted molecular beam epitaxy (PA-MBE) system. The substrate for the growth was a few-layer 2D MoS2 deposited on sapphire using chemical vapor deposition (CVD). Three different Ga fluxes were provided by the gallium source of the K-cell at temperatures of 825, 875, and 925 °C, respectively. After the growth, RHEED, HR-XRD, and TEM were conducted to study the crystal structure of GaN films. The surface morphology was obtained using FE-SEM and AFM. Chemical composition was confirmed by XPS and EDS. Raman and PL spectra were carried out to investigate the optical properties of GaN films. According to the characterizations of GaN films, the van der Waals epitaxial growth mechanism of GaN films changed from 3D to 2D with the increase in Ga flux, provided by higher temperatures of the K-cell. GaN films grown at 750 °C for 3 h with a K-cell temperature of 925 °C demonstrated the greatest crystal quality, chemical composition, and optical properties. The heterostructure of 3D GaN on 2D MoS2 was integrated successfully using the low-temperature PA-MBE technique, which could be applied to novel electronics and optoelectronics.

Anti-AIDS agents 87. New bio-isosteric dicamphanoyl-dihydropyranochromone (DCP) and dicamphanoyl-khellactone (DCK) analogues with potent anti-HIV activity.

Six 3'R,4'R-di-O-(S)-camphanoyl-2',2'-dimethyldihydropyrano[2,3-f]chromone (DCP) and two 3'R,4'R-di-O-(S)-camphanoyl-(+)-cis-khellactone (DCK) derivatives were designed, synthesized, and evaluated for inhibition of HIV-1(NL4-3) replication in TZM-bl cells. 2-Ethyl-2'-monomethyl-1'-oxa- and -1'-thia-DCP (5a, 6a), as well as 2-ethyl-1'-thia-DCP (7a) exhibited potent anti-HIV activity with EC(50) values of 30, 38 and 54 nM and therapeutic indexes of 152.6, 48.0 and 100.0, respectively, which were better than or comparable to those of the lead compound 2-ethyl-DCP in the same assay. 4-Methyl-1'-thia-DCK (8a) also showed significant inhibitory activity with an EC(50) of 128 nM and TI of 237.9.

[Detection of lymph node micrometastasis for patients with extrahepatic cholangiocarcinoma and its prognostic significance].

OBJECTIVE: To observe the expression of antibodies of cytokeratin 19 and 20 in lymph node micrometastasis in patients with extrahepatic cholangiocarcinoma (EHCC), evaluate the prognostic significance of lymph node (LN) micrometastasis and study the correlation between lymph node micrometastasis and clinicopathological features, CA19-9 and CEA. METHODS: A total of 279 lymph nodes was intra-operatively collected from 59 EHCC patients and routine histological examination performed. Immunohistochemical staining was performed on all samples by the murine antibodies of anti-CK19 and anti-CK20 respectively. Then the micrometastasis was identified microscopically according to the color of cells. The results were analyzed according to clinical, pathological and follow-up data. And the relation of micrometastasis with clinical pathological factors and its impact upon survival rate were analyzed. RESULTS: Among 59 EHCC patients, 14 (23.72%) LN metastasis were found with HE staining and 21 micrometastases with CK staining. The incidence of nodal involvement in 59 EHCC patients increased from 5.37% (15/279) by HE staining to 13.98% (39/279) by CK staining. Among 45 patients not positive for LN metastases with HE staining, CK staining was positive in 7 patients and the incidence of micrometastasis was 15.56%. The preoperative serum CA19-9 levels in patients with LN micrometastasis was higher than that those without LN metastasis (P < 0.05). And there was a positive correlation between occult nodal micrometastasis and serum concentrations of CA19-9 (r(s) = 0.371, P < 0.05). The histological type and lymphatic vessel infiltration of tumor were the most importance factors for LN micrometastasis through Logistic regression analysis (P < 0.05). CONCLUSION: The CK immunohistochemical staining can detect the micrometastases in HE negative LN. And LN micrometastasis can more accurately predict the prognosis of EHCC patients.

[Expression of Survivin protein in extrahepatic cholangiocarcinoma and its relationship with the prognosis].

OBJECTIVES: To investigate the expression of Survivin in patients with extrahepatic cholangiocarcinoma (EHCC) and its relationship with clinicopathological features of EHCC, and the correlation between the expression of Survivin and lymph node micrometastasis, tumor markers, and the prognosis of EHCC. METHODS: The expression of Survivin protein in paraffin-embedded specimens of 59 patients with EHCC and their 20 para-carcinoma tissues were evaluated by S-P method of immunohistochemical staining. The correlation between the expression of Survivin and the lymph node micrometastasis, clinicopathological features of EHCC and the prognosis of EHCC were analyzed. RESULTS: The positive expression rate of Survivin protein was 67.8% (40/59) in paraffin-embedded specimens of 59 patients with EHCC and was 20.0% (4/20) in para-carcinoma tissues, and difference between carcinoma tissues and para-carcinoma tissues was significant (P<0.01). Histological differentiation in EHCC had a negative correlation with the expression of Survivin protein, while the expression of Survivin protein in EHCC had a positive correlation with TNM of EHCC, lymphatic vessel infiltration, lymph node metastasis and perineural invasion (P<0.05). The serum CA19-9 levels in the positive group with expression of Survivin protein was (290,300+/-55 500) U/L and was obviously higher than that in the negative group [(113,300+/-31,400) U/L, P<0.05]. The mean survival time of the patients with negative expression of Survivin protein was higher than that of the patients with positive expression (43.5 vs. 21.1 months, P<0.01). Screened to significance univariate, the multivariate analysis through Cox proportional hazard model analysis showed that lymph node metastasis, residual tumor margins, and expression of Survivin protein were independent prognosis factors of the patients with EHCC (P<0.05, P<0.01, P<0.01). CONCLUSIONS: The expression of Survivin protein in EHCC has a negative correlation with histological differentiation, while has a positive correlation with lymphatic vessel infiltration and serum CA19-9 concentrations. The expression of Survivin protein maybe an independent prognosis factor of the patients with EHCC.

Fluorescence imaging of chromosomal DNA using click chemistry.

Chromosome visualization is essential for chromosome analysis and genetic diagnostics. Here, we developed a click chemistry approach for multicolor imaging of chromosomal DNA instead of the traditional dye method. We first demonstrated that the commercially available reagents allow for the multicolor staining of chromosomes. We then prepared two pro-fluorophore moieties that served as light-up reporters to stain chromosomal DNA based on click reaction and visualized the clear chromosomes in multicolor. We applied this strategy in fluorescence in situ hybridization (FISH) and identified, with high sensitivity and specificity, telomere DNA at the end of the chromosome. We further extended this approach to observe several basic stages of cell division. We found that the click reaction enables direct visualization of the chromosome behavior in cell division. These results suggest that the technique can be broadly used for imaging chromosomes and may serve as a new approach for chromosome analysis and genetic diagnostics.

Antitumor and immunomodulatory activity of resveratrol on experimentally implanted tumor of H22 in Balb/c mice.

AIM: To study the antitumor and immunomodulatory activity of resveratrol on experimentally implanted tumor of H22 in Balb/c mice. METHODS: The cytotoxicity of peritoneal macrophages (Mphi) against H22 cells was measured by the radioactivity of ((3)H)TdR assay, mice with H22 tumor were injected with different concentrations of resveratrol, and the inhibitory rates were calculated and IgG contents were determined by single immunodiffusion method. the plaque forming cell (PFC) was measured by improved Cunningham method, the levels of serum tumor necrosis factor-alpha (TNF-alpha) were measured by cytotoxic assay against L929 cells. RESULTS: Resveratrol 2.5 mg x L(-1), 5.0 mg x L(-1), 10.0 mg x L(-1), 20.0 mg x L(-1) (E:T=10:1, 20:1) promoted the cytotoxicity of Mphi against H22 cells. Resveratrol ip 500 mg x kg(-1), 1 000 mg x kg(-1) and 1,500 mg x kg(-1) could curb the growth of the implanted tumor of H22 in mice. The inhibitory rates were 31.5 %, 45.6 % and 48.7 %, respectively (P<0.05), which could raise the level of serum IgG and PFC response to sheep red blood cell. Resveratrol 1,000 mg x kg(-1) and 1,500 mg x kg(-1) and BCG 200 mg x kg(-1) ip could increase the production of serum TNF-alpha in mice H22 tumor. However, the effect of resveratrol was insignificant (P>0.05). CONCLUSION: Resveratrol could inhibit the growth of H22 tumor in Balb/c mice. The antitumor effect of resveratrol might be related to directly inhibiting the growth of H22 cells and indirectly inhibiting its potential effect on nonspecific host immunomodulatory activity.

Anti-hepatoma activity of resveratrol in vitro.

AIM: To study the anti-tumor effect of resveratrol alone and the synergistic effects of resveratrol with 5-FU on the growth of H22 cells line in vitro. METHODS: The number of cells was measured by MTT method the morphological changes of H22 cells were investigated under microscopy and electron microscopy examination. RESULTS: Resveratrol inhibited the growth of hepatoma cells line H22 in a dose- and time-dependent manner, IC50 of the resveratrol on H22 cells was 6.57mg x L(-1),The synergistic anti-tumor effects of resveratrol with 5-FU increased to a greater extent than for H22 cells treated with 5-FU alone (70.2% vs 28.4%) P<0.05 .Under microscope and electron microscope, characteristics of apoptosis such as typical apoptotic bodies were commonly found in tumor cells in the drug-treated groups. CONCLUSION: Resveratrol can suppresses the growth of H22 cells in vitro,its anti-tumor activity may occur through the induction of apoptosis.

Effect of NF-kappaB and p38 MAPK in activated monocytes/macrophages on pro-inflammatory cytokines of rats with acute pancreatitis.

AIM: Proinflammatory cytokines TNF-alpha and IL-6 play a main role in acute pancreatitis (AP). Cytokine biosynthesis runs through two major signaling pathways at the level of proteins: nuclear transcription factor-kappaB (NF-kappaB) and p38 mitogen-activated protein kinase (p38 MAPK). The aim of the study was to investigate the effect of NF-kappaB and p38 MAPK in activated monocytes/macrophages on cytokines of rats with acute pancreastitis. METHODS: Taurocholate (3% and 5%) at doses of 1 mL/kg was administered into the biliopancreatic duct of male Sprague-Dawley (SD) rats to reduce acute edematous pancreariris (AEP) and acute necrotizing pancreatitis (ANP). Pancreatic tissues were prepared immediately after death. At this point, blood was obtained for determination of serum amylase and pro-inflammatory TNF-alpha and IL-6. Activated monocytes/macrophages were captured from blood and so were ascites. NF-kappaB and p38 MAPK in activated monocytes/macrophages were measured by immunohistochemistry method. Pancreatic tissue samples were prepared for routine light microscopy, using hematoxylin and eosin (HE) staining. RESULTS: The serum levels of amylase were 3,056.00+/-1,232.35 IU/L and 4,865.12+/-890.34 IU/L at 3 and 6 hours in ANP group, which were significantly higher than those (3,056.00+/-1,232.35 IU/L and 3,187.17+/-821.16 IU/L) (P<0.05, respectively) in AEP group. In ascites the levels were 3.32+/-1.01 g and 3.76+/-1.12 g at 3 and 6 hours in ANP group, which were significantly higher than those (1.43+/-1.02 g and 2.56+/-1.21 g) (P<0.05, respectively) in AEP group. The serum levels of TNF-alpha were 54.27+/-23.48 pg/ml and 67.83+/-22.02 pg/ml in AEP group and 64.28+/-20.79 pg/ml and 106.59+/-43.71 pg/ml in ANP group, and the serum levels of IL-6 were 428.12+/-140.30 pg/ml and 420.13+/-139.40 pg/ml in AEP group and 1,600.32+/-309.78 pg/ml and 2,203.76+/-640.85 pg/ml in ANP group, which were far significantly higher than those in sham group (P<0.001, respectively). The serum level of TNF-alpha 6 hours after establishment of the studied model and that of IL-6 at 3 and 6 hours in ANP group were significantly higher than those in AEP (P<0.05, P<0.001, P<0.05). In ANP group, the levels of serum TNF-alpha and IL-6 6 hours after establishment of the studied model were significantly higher than those 3 hours after establishment of studied model (P<0.05, P<0.05, respectively). Three and 6 hours after establishment of the model, typical pathological changes of AEP and ANP were found, such as large numbers of inflammatory cells, edema, hemorrhage, necrosis, large amount of ascites. In AEP, NF-kappaB and p38 MAPK in activated monocytes/macrophages were moderately found at 3 and 6 hours after introduction of the model. However, in ANP, the expression of NF-kappaB and p38 MAPK in activated monocytes/macrophages was upregulated evidently at 3 and 6 hours after introduction of the model, reaching their highest levels at 6 hours after introduction of the model, which were consistent with the levels of TNF-alpha and IL-6. CONCLUSION: Cytokine TNF-alpha and IL-6 play a main role in acute pancreatitis, expression of NF-kappaB and p38 MAPK in activated monocytes/macrophages might play a major role in cytokine transcription and biosynthesis.

Antitumor agents 292. Design, synthesis and pharmacological study of S- and O-substituted 7-mercapto- or hydroxy-coumarins and chromones as potent cytotoxic agents.

Thirty-five S- and O-substituted 7-mercaptocoumarin (9-23) and 7-hydroxy- or 7-mercapto-chromone (24-43) analogs were designed, synthesized and evaluated in vitro against four human tumor cell lines [KB (nasopharyngeal), KB-vin (vincristine-resistant subline), A549 (lung) and DU145 (prostate)] with paclitaxel as the positive control. Many of the synthesized compounds exhibited potent cytotoxic activity. Among them, compounds 10 and 18 showed broad spectrum activity with GI(50) values ranging from 0.92 to 2.11 µM and 2.06-14.07 µM, respectively. However, 33, a 3-brominated compound, displayed significant and selective inhibition against MDR KB-vin with a GI(50) of 5.84 µM. Regardless of the size of the 7-alkoxy group, 2-α-bromoethyl-8-bromomethyl compounds (40-43) exhibited increased cytotoxicity compared with 2-ethyl-8-bromomethyl compounds (36-39). Moreover, in a preliminary pharmacological study, 10 not only remarkably increased cellular apoptosis in a concentration-dependent manner, but also clearly induced A549 cell cycle arrest at the G2/M phase. Thus, these coumarin derivatives merit investigation as novel potential antitumor agents with further structural modification to produce an optimal lead compound and elucidate the detailed pharmacological mechanism(s).