Search

An in-depth study of the phylogenetic relationships of Xylaria species associated with nutshells of fruits and seeds within the genus Xylaria and related genera of Xylaceaecea was conducted in China. The multi-gene phylogenetic analyses were carried out based on ITS, RPB2, and TUB sequences of 100 species of 16 known genera in Xylariaceae around the world. Based on molecular phylogenetic analyses, morphological observations, and ecological habitats, a new genus, Heteroxylaria , is established to accommodate four new species, viz. H. cordiicola , H. juglandicola , H. meliicola , and H. terminaliicola , and four new combinations, viz. H. oxyacanthae , H. palmicola , H. reevesiae , and H. rohrensis . The genus is characterized by cylindrical stromata with conspicuous to inconspicuous perithecial mounds, surface black, having brown to dark brown ascospores with a germ slit, and it grows on nutshell of fruits. The combined ITS+RPB2+TUB sequence dataset of representative taxa in the Xylariaceae demonstrate that Heteroxylaria is grouped with Hypocreodendron but forms a monophyletic lineage. All novelties described herein are morphologically illustrated and compared to similar species and phylogeny is investigated to establish new genera and species.

Morphological and phylogenetic analyses on samples of Xylaria species associated with fallen fruits from China were carried out, and two new species were described, namely X.aleuriticola and X.microcarpa . Xylariaaleuriticola is found on fallen fruits of Aleuritesmoluccana , and characterized by stromata dichotomously branched several times with long acute sterile apices, fertile parts roughened with perithecia and tomentose, and ellipsoid to fusiform ascospores. Xylariamicrocarpa differs in its very small stromata with dark brown tomentum, light brown ascospores with an inconspicuous straight germ slit, and grows on leguminous pods. The differences between the new species and morphologically similar species are discussed. Phylogenetic analyses on ITS-RPB2-TUB sequences confirmed that the two species are clearly separated from other species of the genus Xylaria . Xylarialiquidambaris is reported as a new record from China. A key to the Xylaria species associated with fallen fruits and seeds reported from China is provided to facilitate future studies of the genus., Competing Interests: The authors have declared that no competing interests exist., (An-Hong Zhu, Zi-Kun Song, Jun-Fang Wang, Hao-Wen Guan, Zhi Qu, Hai-Xia Ma.)

Hypoxylaceous fungi are abundant in China, but their discovery and report are uneven in various provinces, with more fungi in Yunnan and Hainan and fewer fungi in Tibet. During the investigation of macro-fungi in Motuo county, Tibet Autonomous Region, we collected a number of xylarialean specimens. Six hypoxylaceous specimens growing on dead angiosperm were collected from the forests of Motuo county, and they were described and illustrated as two new species in Hypoxylon based on a combination of morphological characters and molecular evidence. Hypoxylon diperithecium was characterized by its bistratal perithecia, purple-brown stromatal granules, citrine to rust KOH-extractable pigments, and light brown to brown ascospores ellipsoid-inequilateral with conspicuous coil-like ornamentation. Hypoxylon tibeticum was distinct from other species by having pulvinate and applanate stromata, surface vinaceous, with orange granules, orange KOH-extractable pigments, and brown ascospores with inconspicuous ornamentation. The multi-gene phylogenetic analyses (ITS-LSU-RPB2-TUB) supported the two new taxa as separate lineages in the genus Hypoxylon . A key to all known Hypoxylon taxa from China is provided.

We describe new container host molecules - deep cavitands with benzimidazole walls and ionic feet - to recognize highly hydrophilic guest molecules in water. The aromatic surfaces of the cavity recognize hydrophobic portions of the guest while bound water molecules mediate hydrogen bonding in the complex. Spectroscopic (NMR) evidence indicates slow in/out exchange on the chemical shift timescale and thermodynamic (ITC) methods show large association constants (Ka up to 6 × 10 4 M -1 ) for complexation of small, water-soluble molecules such as THF and dioxane. Quantum chemical calculations are employed to optimize the host-guest geometries and elucidate the hydrogen bonding patterns responsible for the binding.

Morphology plays an important role in fungal fermentation and secondary metabolites biosynthesis. One novel technique, microparticle-enhanced cultivation was successfully utilized to control the morphology of Monascus purpureus precisely and enhance the yield of yellow pigments. The production of yellow pigments increased to 554.2 U/ml when 4 g/L 5000 mesh talc added at 24 h. Field emission scanning electron microscope observation indicated that the actual effect depends on the properties of microparticle. Sharp-edged microparticles showed better stimulatory effects than smooth, round-shaped ones. Particle size analysis, scanning electron microscope, and cell integrity evaluation proved obvious morphological changes were induced by talc addition, including smaller mycelial size, rougher hyphae, and decreased cell integrity. Furthermore, the expression levels of MrpigG, MrpigD, MrpigE, and MrpigH were significantly upregulated by the addition of talc. It indicated that the microparticle could not only affect the mycelial morphology, but also influence the expression levels of key genes in biosynthetic pathway of Monascus yellow pigments., (© 2021 Wiley Periodicals LLC.)

Background and Aims: Microvascular invasion (MVI) is a key pathological factor that severely affects the postoperative prognosis of patients with hepatocellular carcinoma (HCC). However, no MVI classification schemes based on standardized gross sampling protocols of HCC are available at present., Methods: 119 HCC specimens were sampled at multiple sites (3-, 7-, and 13 points) for the optimum MVI detection rate. 16,144 resected HCCs were graded as M0, M1 or M2 by adopting three-tiered MVI grading (MVI-TTG) scheme based on the seven-point sampling protocol (SPSP). Survival analyses were performed on 2573 patients to explore the advantages of MVI-TTG., Results: The MVI detection rate determined by SPSP was significantly higher than that determined by the 3-point sampling method (34.5% vs. 47.1%, p = 0.048), but was similar to that determined by the 13-point sampling method (47.1% vs. 51.3%, p = 0.517). Among 16,144 resected HCCs, the proportions of M0, M1 and M2 specimens according to SPSP were 53.4%, 26.2% and 20.4%, respectively. Postoperative survival analysis in 2573 HCC patients showed that the 3-year recurrence rates in M0, M1 and M2 MVI groups were 62.5%, 71.6% and 86.1%, respectively (p < 0.001), and the corresponding 3-year overall survival (OS) rates were 94.1%, 87.5% and 67.0%, respectively (p < 0.001). M1 grade was associated with early recurrence, while M2 grade was associated with both early and late recurrence. MVI-TTG had a larger area under the curve and net benefit rate than the two-tiered MVI grading scheme for predicting time to recurrence and OS., Conclusions: SPSP is a practical method to balance the efficacy of sampling numbers and MVI detection rates. MVI-TTG based on SPSP is a better prognostic predictor than the two-tiered MVI scheme. The combined use of SPSP and MVI-TTG is recommended for the routine pathological diagnosis of HCC.

Objective: To examine the expression of programmed cell death 1 (PD-1) and its ligand (PD-L1) in epithelial ovarian cancer (EOC) tissues, and investigate the correlation among their expression, clinicopathological features and prognosis. Methods: The specimens of 180 patients with EOC treated in the First Affiliated Hospital of Dalian Medical University from October 2002 to December 2013 were confirmed by pathological examination. The pathological tissue specimens of subtypes ，included 120 cases of serous carcinoma, 30 cases of mucinous carcinoma, 20 cases of endometrioid carcinoma, and 20 cases of clear cell carcinoma. The normal paracancerous tissues of 50 cases randomly selected from the 180 patients as control group. Immunohistochemical SP method was used to detect the expressions of both PD-1 and PD-L1 in epithelial ovarian cancer tissues, and the relationships among their expressions,the clinicopathological parameters and prognosis were respectively analyzed. Results: （1） PD-1 was expressed in lymphocytes infiltrated in EOC tissues, and PD-L1 was expressed in the cell membranes of cancer tissues. In all EOC cases, 33 cases (18.3%, 33/180) of both PD-1 and PD-L1 were highly expressed, and only 1 (2.0%, 1/50) of control group showed high expression. There was statistically significant difference between two groups ( P <0.01). (2) Among the four subtypes tissue specimens of EOC, the high expression rate of PD-1 was 25.0% (30/120) for serous carcinoma, 3/15 for endometrioid carcinoma, 0 (0/30) for mucinous carcinoma, and 0 (0/15) for clear cell carcinoma. The high expression rate of PD-L1 was 23.3% (28/120) for serous carcinoma, 3.3% (1/30) for mucinous carcinoma, 2/15 for endometrioid carcinoma, and 2/15 for clear cell carcinoma. Both PD-1 and PD-L1 expressions in the four sub-types of tissue specimens were significantly different ( P <0.05). The high expression rate of both PD-1 and PD-L1 was 9.2% (8/87) in the early stage and 26.9% (25/93) in the late stage. There was a statistically significant difference between the two groups ( P <0.01). Similarly, the expression of both PD-1 and PD-L1 were significantly higher in the cases of high-grade EOC （type Ⅱ） than those of low-grade （type Ⅰ） and in the cases of EOC distributed bilaterally than that distributed unilaterally, and there were statistically significant differences ( P <0.05). (3) The Kaplan-Meier survival analysis showed that the survival time were respectively 35 and 36 months in the cases with high expressions of both PD-1 and PD-L1, and the survival time were the same as 61 months in the cases with low expression of both PD-1 and PD-L1, and the comparison was statistically significant ( P <0.05). Conclusions: The expression levels of PD-1 and PD-L1 in EOC tissues are higher than those in adjacent tissues, especially in serous carcinomas. The expression of both PD-1 and PD-L1 is higher in specimens of the patients with advanced stages. The results showed that the high expression of both PD-1 and PD-L1 is an indicator of poor prognosis of patients suffering from EOC.

Objective: To detect phosphorylated-extracellular signal-regulated kinase (p-ERK1/2) protein expression in epithelial ovarian cancer and cell lines, and to examine the effects of mitogen-activated protein kinase (MAPK) kinase (MEK) inhibitor AZD6244 on cell proliferation, apoptosis as well as cell cycle of ovarian cancer cells. To explore the function and significance of MAPK/extracellular signal-regulated kinase (ERK) signaling pathway in the development of ovarian cancer. Methods: (1) A total of 104 cases of patients with ovarian cancer who accepted the treatment of gynecological surgery and being confirmed by pathological examination in First Affiliated Hospital, Dalian Medical University from January 2004 to December 2013 were selected. The expressions of p-ERK1/2 protein were detected by immunohistochemistry in ovarian cancer specimens, and the relationship between the expressions of p-ERK1/2 and the clinical features of patients was analyzed. (2) p-ERK1/2 and other related proteins were determined by western blot in various ovarian cancer cells, including SKOV3, OV2008, C13, A2780S, A2780CP, OVCAR4, OVCAR5, OVCAR8 and CAOV3 treated with or without MEK inhibitor. The cellular proliferation, apoptosis and cell cycle of ovarian cancer cells after treatment with MEK inhibitor were analyzed by methyl thiazolyl tetrazolium (MTT) assay and flow cytometry, respectively. Results: (1) The immunohistochemical method showed that p-ERK1/2 between low grade serous carcinoma and clear cell carcinoma were not significantly higher expressed ( P >0.05) . However, a lower level of the p-ERK1/2 expression were observed among high grade serous carcinoma, mucinous carcinoma and endometrioid carcinoma (all P <0.05) . There was no significant correlation between the protein expression of p-ERK1/2 and patients' age, pathological stage of surgery, and preoperative serum CA(125) level ( P >0.05). (2) Western blot showed that the protein p-ERK1/2 was widely expressed in various ovarian cancer cell lines such as SKOV3, OV2008, C13, A2780S, A2780CP, OVCAR4, OVCAR5, OVCAR8 and CAOV3. After treatment with AZD6244 (5, 10 μmol/L), the level of p-ERK1/2 in OVCAR5 and OVCAR8 decreased significantly in dose-dependent manner. Additionally, we found a reduction of the expression level of cyclin D1, caspase-3 and appeared cleaved poly adenosine diphosphate ribose polymerase (PARP) in OVCAR5 and OVCAR8, compared with control groups. MTT assays showed that OVCAR5, OVCAR8 and A2780S were differently inhibited in the dose-dependent manner after being treated with different concentrations of AZD6244 (0, 2.5, 5, 10, 25, 50 and 100 μmol/L, all P <0.05). Further tested by flow cytometry, the results showed that AZD6244 (5, 10 μmol/L) was able to induce the apoptosis of OVCAR5, OVCAR8 and A2780S, as well as G(0)/G(1) phase arrest, both in a dose-dependent manner ( P <0.05). Conclusions: As the main active and functional unit of MAPK/ERK signaling pathway, p-ERK1/2 protein is expressed in both the tissues and various ovarian cancer cell lines. AZD6244 could down-regulated the expression of p-ERK1/2 in ovarian cancer cells, accompanied by the decreased proliferation and increased cell apoptosis of ovarian cancer cells. In conclusion, MAPK/ERK signaling pathway might play a role in the development and progression of ovarian cancer, and may be provide a novel option for molecular targeted therapies of the disease.

Doxorubicin is a widely used anthracycline-based anti-tumor agent for both solid and liquid tumors. Mounting evidence has demonstrated that microRNAs (miRNAs) are involved in chemoresistance and tumorigenesis. However, the roles of microRNA-501-5p (miR-501) in doxorubicin resistance and gastric cancer cell proliferation and invasion are still not fully understood. In this study, we identified that BLID (BH3-like motif-containing protein, cell death inducer) was directly regulated by miR-501 at the post-transcriptional level in multiple gastric cancer cell lines. Endogenous miR-501 was higher, whereas BLID was lower, in doxorubicin-resistant gastric cancer SGC7901/ADR cells compared with their parental SGC7901 cells. miR-501 suppressed gastric cancer cell apoptosis, induced resistance to doxorubicin, and enhanced cell proliferation, migration, and invasion. Subcutaneous injection of miR-501 lentivirus-infected SGC7901 cells resulted in rapid growth of xenograft tumors and resistance to doxorubicin treatment, unlike injection of negative miRNA lentivirus-infected SGC7901 cells. This is achieved at least partially by directly targeting BLID and subsequent inactivation of caspase-9 and caspase-3 and phosphorylation of Akt. Taken together, miR-501 induces doxorubicin resistance and enhances the tumorigenesis of gastric cancer cells by suppressing BLID. miR-501 might be a potential target for doxorubicin resistance and gastric cancer therapy., (Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.)

A lab-scale, completely anaerobic ammonium oxidation (ANAMMOX) process was operated in a municipal wastewater treatment plant (WWTP). Sewage effluent treated by an A/O process and nitrification process was input as the substance to start up the up-flow ANAMMOX filter reactor. After the 109 th day, the ammonia removal rate and nitrite removal rate were greater than 90% for 15 successive days and the nitrogen removal rate was higher than 70%. The ANAMMOX filter reactor successfully started up. From days 245 to 333, the reactor was running during the winter. The weight of biomass reached 12.24 mg·g -1 , and the average nitrogen removal rate was 54.3%. Backwash was adopted at day 461, and the weight of biomass decreased to 8.01 mg·g -1 . From days 605 to 693, the reactor was running in the winter again. The weight of biomass was 10.41 mg·g -1 , and the average nitrogen removal rate was sustained at 69.7%. Compared with the previous winter, the weight of biomass was lighter but the total nitrogen removal loading was 23% greater. For the entire operation, the ANAMMOX rate at high temperature was stable but that at low temperature increased from 1.5 kg·(kg·d) -1 to 3.6 kg·(kg·d) -1 . The results show:Long-term domestication at low temperature was in favor of improving treatment efficiency of ANAMMOX process in cold environment and realized ANAMMOX process operated efficiently in winter.

Lab-scale anaerobic ammonia oxidation and denitrification (SAD) processes were operated simultaneously in a municipal waste water treatment plant (WWTP). Sewage treated by the A/O and nitrification process was used as the substance to start up an anaerobic ammonia oxidation filter reactor. Adding glucose and sodium propionate to influent was used as the substance to start up the SAD filter reactor after the successful start-up of the ANAMMOX reactor. The SAD process performed well with an average total nitrogen concentration in the effluent of 6.41 mg·L -1 when 30 mg·L -1 glucose was added to the effluent sewage at ambient temperature. Compared with the ANAMMOX process, the total nitrogen concentration in the effluent from the SAD process decreased 42%. The stability of the SAD process was destroyed and the SAD process turned into a denitrification process when 30 mg·L -1 glucose was added in the influent sewage in a low temperature environment. In normal and low temperature environments, the SAD process functioned well, and the average total nitrogen concentration of the effluent was 6.54 mg·L -1 when 30 mg·L -1 sodium propionate was added in the influent sewage. Compared with glucose, sodium propionate had little influence on the SAD process.

Traditional Chinese medicine(TCM) modernization has gradually become a worldwide trend. Reverse docking technology has also gradually become a useful tool for TCM modernization. It involves docking a small-molecule drug in the potential binding cavities of a set of clinically relevant macromolecular targets. Detailed analysis of the binding characteristics was used for the ranking of the targets according to the tightness of binding. This process can be used to potentially identify the novel molecular targets for the drug which may be relevant to its mechanism of action or side effect. In order to explore the action mechanism, screen the active ingredients and seek the treating target of TCM, reverse molecular docking technology has been widely used and has achieved remarkable results in recent years. In this review, we summarized the application of reverse molecular docking technology in the target seeking, active ingredients screening and potential mechanism exploration of TCM, which may provide more scientific basis for the clinical research and development of new herbal drugs., Competing Interests: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose., (Copyright© by the Chinese Pharmaceutical Association.)

A laboratory-scale completely autotrophic nitrogen removal over nitrite (CANON) process was operated in a municipal wastewater treatment plant (WWTP). Sewage effluent treated by the anaerobic/oxic (A/O) process and was used to operate a WWTP to obtain the initial substance for the start-up of a CANON filter reactor. On the 48th day, the ammonia removal rate was measured at greater than 90% in successive 10 d samples and the nitrogen removal rate was greater than 70%. The CANON filter was successful at start up. From the 49 th to the 129 th day, the dissolved oxygen in the reactor was maintained at fairly low concentration of 0.2-0.5 mg·L -1 . The effluent contained nearly no ammonia and the maximum total nitrogen (TN) concentration was 15.6 mg·L -1 , which exceeded the national Class 1A Discharge Standards for pollutants from municipal wastewater treatment plants. Nitrite oxidizing bacteria (NOB) proliferated excessively in the reactor. Backwash was implemented on 129th, 169th and 213th days. The nitrogen removal rate was more than 70% for a long time and TN concentration in effluent was below 12 mg·L -1 . The nitrogen concentration in effluent fitted the national Class 1A Discharge Standards and the NOB were effectively inhibited. These results show that backwash has negligible on the structure of filter and its impact on the thickness of the bio-membrane and its functional bacteria was small, however, it is capable of effectively inhibiting the activity of the NOB. Periodically backwashing can be utilized as an engineering application to maintain stable operation of the CANON process.

Objective: To examine the expressions of IKKε protein in the specimens and cells of epithelial ovarian cancer and investigate the effect of IKKε inhibitor on cell proliferation and apoptosis. Methods: (1) A total of 118 cases of patients with the median age of 59 who have accepted surgical treatment due to ovarian cancer in the First Affiliated Hospital of Dalian Medical University from January 2006 to April 2013 were selected. Twenty cases of patients with the median age of 55 who have accepted hysterectomy and salpingo-oophorectomy due to uterine leiomyoma during the same period were selected as the control. The expressions of IKKε protein were detected by immunohistochemistry in normal ovarian tissues and epithelial ovarian cancer specimens, and the relationship between the expressions of IKKε and the clinical features of patients was analyzed. IKKε protein was determined by western blot in various ovarian cancer cells, including SKOV3, OV2008, C13, A2780S, A2780CP, OV4, OV5, OV8, and CAOV3 treated with or without IKKε inhibitor. The cellular proliferation and apoptosis of ovarian cancer cells after 48 hours treatment of IKKε inhibitor were analyzed by methyl thiazolyl tetrazolium (MTT) assay and flow cytometry, respectively. Results: (1) The immunohistochemical results showed that IKKε was highly expressed in epithelial ovarian cancer specimens with the expression rate 66.1% (78/118), compared with normal ovarian tissue with the expression rate 35.0% (7/20), which exhibited statistically significant difference (χ(2)=6.993, P= 0.008). The expression of IKKε protein was correlated with International Federation of Gynecology and Obstetrics (FIGO) stage, histological grade, the level of CA(125) in preoperative serum and distribution of the tumor ( P< 0.05), but no correlation with age, histological type, the incidence pattern, and tumor size (all P> 0.05). (2) IKKε was widely overexpressed in different levels in SKOV3, OV2008, C13, A2780S, A2780CP, OV4, OV5, OV8, and CAOV3 cells, and the expression of IKKε decreased as the increase of the concentration of IKKε inhibitor (0.1 and 0.5 μmol/L) in OV2008, C13, A2780S, and A2780CP cells after 48 hours treatment. Different concentrations of IKKε inhibitor (0.05, 0.1, 0.5, 1, 5, 10, and 25 μmol/L) significantly inhibited the proliferation of OV2008, C13, A2780S, A2780CP, and SKOV3 cells in a concentration-dependent manner ( P< 0.05), and the half maximal inhibitory concentration (IC(50)) was 0.43, 0.86, 0.10, 0.19, and 0.24 μmol/L, respectively. The cell apoptotic rate of OV2008, C13, A2780S, A2780CP, and SKOV3 cells was significantly increased after 48 hours treatment of IKKε inhibitor with the concentration of 0.1 and 0.5 μmol/L ( P< 0.05). Conclusions: The IKKε protein in epithelial ovarian cancer specimens and cells is overexpressed. IKKε inhibitor could inhibit cellular proliferation and induce apoptosis in a concentration-dependent manner. Together, the result indicated that IKKε may be a candidate target for the treatment of ovarian cancer in future.

The present study aimed to review the multidetector computed tomography (MDCT) imaging features of eight mucosa-associated lymphoid tissue (MALT)-lymphoma cases of the parotid gland and to explore the diagnostic value of MDCT. A total of eight patients with pathologically confirmed MALT-lymphomas of the parotid gland underwent pre-operative MDCT plain and dual-phase scans. The changes in the CT values and enhancement patterns of the tumors were assessed. Quantitative analysis was performed to determine the CT value changes of the tumors in the various enhanced phases compared with the plain scan. The MALT-lymphomas of the parotid gland exhibited even density isodense or hyperdense nodules, with occasional calcification and necrosis. The dual-phase scan of the MALT-lymphomas revealed a pattern of lower or moderate enhancement, circumambient enhancement or delayed enhancement. The MALT-lymphomas were closely associated with Sjögre's syndrome and demonstrated malignant features and isodense or hyperdense nodules and lower or moderate enhancement on the CT scans.

Anti-scrapie breeding programs have been initiated to screen for scrapie-resistant sheep based on ovine prion protein gene (PRNP) genotypes at codons 136, 154 and 171 in many countries, especially European Union member states. However, investigation of sheep PRNP genotypes is limited in China, despite the large number of sheep breeds. We analyzed 432 sheep of five different breeds from farms in northwestern China, using PCR-single-strand conformational polymorphism analysis (PCR-SSCP); the corresponding haplotypes of different PRNP alleles were cloned. PRNP allele genotyping was done by amplification refractory mutation system-PCR (ARMS-PCR), according to the haplotype clones of each PRNP allele. The validity of ARMS-PCR was checked by PCR-SSCP. Another 325 unknown PRNP genotypes of other sheep breeds were analyzed according to the established ARMS-PCR. Genotype frequencies of 757 sheep were analyzed with these two methods to evaluate susceptibility to scrapie in northwestern China. Relevant mutations were also detected at other sites. Both methods were effective for ovine PRNP allele genotyping, and the results of the analysis completely coincided. Scrapie-resistant genotypes were found to be uncommon, indicating a high risk for ovine scrapie in northwest China. In addition to codons 136, 154 and 171, we found numerous new mutations; nearly half of them were previously unreported. These sheep populations have a high degree of polymorphism at the PRNP locus.

Due to advances in structural biology, an increasing number of protein structures of unknown function have been deposited in Protein Data Bank (PDB). These proteins are usually characterized by novel structures and sequences. Conventional comparative methodology (such as sequence alignment, structure comparison, or template search) is unable to determine their function. Thus, it is important to identify protein's function directly from its structure, but this is not an easy task. One of the strategies used is to analyze whether there are distinctive structure-derived features associated with functional residues. If so, one may be able to identify the functional residues directly from a single structure. Recently, we have shown that protein weighted contact number is related to atomic thermal fluctuations and can be used to derive motional correlations in proteins. In this report, we analyze the weighted contact-number profiles of both catalytic residues and non-catalytic residues for a dataset of 760 structures. We found that catalytic residues have distinct distributions of weighted contact numbers from those of non-catalytic residues. Using this feature, we are able to effectively differentiate catalytic residues from other residues with a single optimized threshold value. Our method is simple to implement and compares favourably with other more sophisticated methods. In addition, we discuss the physics behind the relationship between catalytic residues and their contact numbers as well as other features (such as residue centrality or B-factors) associated with catalytic residues.

Determination of the transcription level of cellular prion protein (PrP(C)) is essential for understanding its role in organisms and revealing mechanism of susceptibility and resistance to scrapie. However, the expression of prion protein (PrP) mRNA in sheep has not been quantified in great detail in digestive tract which is important during scrapie spread through oral route. Herein, we report on measurement of sheep PrP mRNA using absolute quantitative real-time RT-PCR. Total RNA was isolated from five different regions of the central nervous system (CNS), four regions of lymphoid system, eleven regions of digestive tract, and two reproductive organ tissues of eight sheep of two different genotypes (ARR/ARQ and ARH/ARQ) and PrP mRNA was quantified by real-time RT-PCR using molecular beacon. The results showed that highest levels of PrP mRNA were expressed in thalamus and cerebrum (P < 0.01) of CNS examined, followed by cerebellum, spinal cord, and brain stem. In peripheral organs examined, lymph tissue showed moderate level of PrP expression similar to that in digestive tract and reproduction organs. PrP expression levels in the same tissue of different genotype sheep had significant variation. Our study provided the first detail, tissue-specific and genotype-specific data of PrP mRNA expression in sheep for further studies of pathogenesis of prion diseases.

Background: Current surgical practice for nephron sparing surgery allows at least 1 cm margin of normal tissue around the tumour. However, recent studies show that the width of the margin is not important, even simple enucleation is as effective as partial nephrectomy. We explored whether margin size has significant impacts on clinical outcomes in nephron sparing surgery for renal cell carcinoma of 4 cm or less., Methods: Between 1998 and 2006, 115 patients with sporadic, pathologically confirmed, renal cell carcinoma 4 cm or less (T1a) and normal contralateral kidney were treated by nephron sparing surgery using a margin less than 5 mm. The surgical margin status was evaluated from frozen and permanent paraffin sections., Results: Mean and median tumour diameter were 3.3 cm and 3.5 cm (range 1.0-4.0). The mean margin width was 2.2 mm (median 2.0, range 0-6). In addition, 114 cases had margins 5 mm or less (99.1%), 97 cases (84.3%) had margin 3 mm or less, and 26 cases had margin zero (22.6%). None of the patients had positive surgical margins. No patients died during follow-up (mean 65 months). There were no any major surgical complications and no distant metastasis was detected. Local recurrence was detected in one case (0.9%) at a different site of the kidney., Conclusions: For early localized renal cell carcinoma of 4 cm or less, as long as tumour is completely excised, the size of margin in nephron sparing surgery is not important. Nephron sparing surgery with 5 mm margin is enough for tumour control. It provides excellent renal function preservation, favourable long term progression free survival and is not associated with an increased risk of local recurrence.

Objective: To study the safety and effects of mini-margin nephron sparing surgery (NSS) for renal cell carcinoma (RCC)., Methods: From January 1998 to December 2006, 115 cases of RCC with diameter of 4 cm or less and stage of T1aN0M0 were treated with NSS using a margin of 5 mm or more. The mean diameter of the tumors was 3.3 cm (range 1.0-4.0 cm). Of the cases, 3 were with synchronous bilateral cancer while 112 cases were with normal opposite kidneys. The clinical results were followed and analyzed., Results: All of the operations were technically successful. The mean duration of surgical procedures was 90 min (ranged 80-120 min). The blood loss was 50 -200 ml. No patient needed blood transfusion. Renal arteries were occluded in 98 cases under hypothermic technique for a mean duration of 22 min (20-25 min). While in 17 cases, renal parenchyma squeezing was used for bleeding control. All of the 115 cases were of negative margin by weather frozen or routine pathologic study. The mean follow-up was 62 months (6-96 months). Local recurrence was found in 1 case during follow-up, with a local recurrence rate of 0.9%, while no distant metastasis was detected. All the patients were alive with no evidence of tumor bearing until last evaluation. Secondary gross hematuria occurred in 3 cases during hospital stay and cured by bed limitation. There were no major complications such as bleeding and urinary leakage or urinoma requiring re-operation., Conclusions: Mini-margin nephron sparing surgery is likewise safe and effective in treating early localized renal cell carcinoma 4 cm or less. It provides excellent renal function preservation, favorable long-term progression-free survival, and is not associated with an increased risk of local recurrence.

A total of 22 individuals participated in this benchmark study to characterize the thermodynamics of small-molecule inhibitor-enzyme interactions using Biacore instruments. Participants were provided with reagents (the enzyme carbonic anhydrase II, which was immobilized onto the sensor surface, and four sulfonamide-based inhibitors) and were instructed to collect response data from 6 to 36 degrees C. van't Hoff enthalpies and entropies were calculated from the temperature dependence of the binding constants. The equilibrium dissociation and thermodynamic constants determined from the Biacore analysis matched the values determined using isothermal titration calorimetry. These results demonstrate that immobilization of the enzyme onto the sensor surface did not alter the thermodynamics of these interactions. This benchmark study also provides insights into the opportunities and challenges in carrying out thermodynamic studies using optical biosensors.

Cyclooxygenase-2 (COX-2) has been shown to play oncogenic roles during stepwise gastrocarcinogenesis, and its expression is correlated with Helicobacter pylori infection, tumor necrosis factor alpha-mediated nuclear factor (NF)-kappaB activation, and Wnt signaling. To examine COX-2 expression and the status of its regulatory factors, we examined 49 gastric cancers (GCs), 21 premalignant tissues, and 10 noncancerous gastric mucosa from residents of Dalian, China. Unexpectedly, it was found that COX-2 expression was infrequent in the gastric samples (18.8%, 15/80) regardless of the type of lesion or morphological phenotype. H pylori infection was detected in 19 of 35 tested GC cases. Tumor necrosis factor alpha expression, NF-kappaB nuclear translocation, or Wnt2 overexpression was observed in 56 (82.3%) of 68, 40 (50.0%) of 80, and 62 (77.5%) of 80 of the gastric tissue samples, respectively. Methylation-sensitive restriction enzyme digestion followed by polymerase chain reaction of COX-2 promoter regions revealed a remarkably high hypermethylation rate (100%, 20/20) among the COX-2-negative GCs, which was associated with the overexpression of DNA methyltransferase (DNMT) 1 (r = 0.587, P < .01). These results indicate that (1) in contrast to previous findings using other GC sources, our results show that COX-2 activity may not be a critical molecular event during GC formation, (2) the tumor-promoting effects of H pylori infection and Wnt and NF-kappaB activities may be mediated by COX-2-independent pathways, and (3) promoter hypermethylation is the major cause of COX-2 silencing in Dalian GCs, apparently because of increased expression of DNMTs (especially DNMT1). Consequently, a COX-2-oriented preventive or therapeutic strategy is not practical for Dalian GCs. The frequent COX-2 hypermethylation observed in Dalian GCs could have insightful epigenetic and epidemiologic implications.

The potential correlation of E-cadherin reduction and Wnt2 up-regulation in determining the intracellular distribution of beta-catenin in gastric cancers was investigated by the methods of frozen tissue array-based immunohistochemistry, Western blot and RT-PCR analysis. It was revealed that membranous E-cadherin was reduced frequently in the two major subtypes of gastric cancer (intestinal gastric cancer, i-GC and diffuse gastric cancer, d-GC) and closely correlated with the risk of lymphoid node metastasis (P < 0.05). The reduction of membranous E-cadherin was paralleled with cytosolic and nuclear accumulation of beta-catenin and the increased Wnt2 expression. These results indicate that the reduced E-cadherin is a common genetic phenotype of GCs and plays beneficial roles in tumor metastasis. Altered beta-catenin distribution may result from the imbalance of E-cadherin production and Wnt expression, which confers on gastric cancer cells more aggressive behaviors.

Objective: Renal cell carcinoma (RCC) of 4 cm or less is with a low incidence of multicentricity and metastasis and is usually considered suitable for nephron-sparing surgery (NSS). This study was designed to investigate the distance between extra-pseudocapsule cancer lesions and primary tumors, and to suggest the optimal margin of normal parenchyma in NSS for RCC 4 cm or less., Methods: We prospectively studied 82 kidneys in which RCCs of 4 cm or less were resected by radical nephrectomy. According to UICC TNM classification (1997), all tumors were staged as T1 and classified as conventional RCC in 76 cases and papillary RCC in 6 cases. The kidney samples were first step sectioned at 3mm intervals and examined for multicentricity. Then, on each layer of tissue sectioned, parenchyma margins of 15 mm beyond pseudocapsule were continuously sectioned and examined microscopically to investigate completeness of pseudocapsule and possible presence of extra-pseudocapsule cancer lesions. The greatest distance between extra-pseudocapsule lesions and primary tumors was measured., Results: The diameter of 82 primary tumors was 3.4+/-0.7 mm (range 1.5-4.0 cm). Of them, 31.7% (26/82) were found without intact pseudocapsule. Of the 82 cases, 19.5% (16/82) were with positive cancer lesions beyond pseudocapsule, with invasion into normal parenchyma in 12.2% (10/82), into venule in 2.4% (2/82) and satellite tumors in 4.9%(4/82). The average distance between extra-pseudocapsule cancer lesions and primary tumors was 0.5+/-1.3mm (range 0-5.0mm), with a 95% confidential interval (CI) (0.11, 0.94). No significant difference was found in the incidence of extra-pseudocapsule cancer lesions between the tumors 2.5 cm or less and that greater than 2.5 cm., Conclusions: These data suggest that when partial nephrectomy is performed in RCC 4 cm or less, a 10mm margin may be too large and go against renal function maintaining. Enucleation alone was associated with a significant risk of incomplete excision, and therefore liable for local recurrence. Thorough inspection of the whole kidney before and during operation may help to avoid leaving over large and distant multifocal lesions.

Objective: To investigate the optimal margin in nephron-sparing surgery (NSS) for renal cell carcinoma (RCC) 4 cm or less in diameter., Methods: Eighty-two kidneys with RCC 4 cm or less in diameter resected by radical nephrectomy were prospectively studied. The kidney samples were sectioned at 3 mm interval and examined for multicentricity. On each layer of tissue sectioned, parenchyma margin of 15 mm beyond pseudocapsule was continuously sectioned and examined for completeness of pseudocapsule and extra-pseudocapsule cancer lesion. The farthest distance between extra-pseudocapsule lesion and primary tumor was measured. PCNA expression was detected in 41 patients by using standard SP immunohistochemistry technique., Results: The diameter of 82 primary tumors was 3.4 +/- 0.8 cm (range 1.5 - 4.0 cm). Of these, 31.7% (26/82) were found without intact pseudocapsule and 17.1% (14/82) with positive cancer lesions beyond pseudocapsule. The average distance between extra-pseudocapsule cancer lesion and primary tumor was 0.5 +/- 1.3 mm (range 0 - 5.0 mm), with a confidential interval (CI) of 95% (0.11, 0.94). Statistically, the one side percentile P(95) was 4.9 mm, P(97.5) was 5.0 mm and P(100) was 5.0 mm. The mean PCNA index in the 41 patients with RCC was (29.5 +/- 17.6)%, which was (49.6 +/- 21.5)% in the group with extra-pseudocapsule cancer lesions and (24.6 +/- 12.7)% in the group without (t = 3.162, P = 0.013). The ratio of strong expression was 5/8 in the group with extra-pseudocapsule cancer lesions, and 18.2% (6/33) in the group without the lesions (chi(2) = 6.442, P = 0.011). Logistic regression analysis showed that completeness of pseudocapsule and PCNA index were significant predictors of extra-pseudocapsule cancer lesions (P = 0.019)., Conclusions: These data suggest that when NSS is performed in RCC 4 cm or less in diameter, a margin of more than 5 mm of adjacent parenchyma should be excised with the tumor. Enucleation alone was associated with a significant risk of incomplete excision, and therefore liable for local recurrence. Tumors with incomplete pseudocapsule and(or) high PCNA indices are more likely to have extra-pseudocapsule cancer lesions, so intensive follow-up is necessary after NSS.

To investigate the role of Helicobacter Pylori (HP) infection and other factors in the development of stomach carcinoma, a matched case-control study was conducted in Dalian, China. A total number of 95 paired cases and controls were involved in the study. The cases were divided into two histological types: diffuse- and intestinal-type. IgG antibody of HP in the subjects was tested with ELISA method. The results revealed that the prevalences of HP infection in cases and in controls were 77.5% and 50.0%, respectively, and that the matched OR was 5.0 (2.08-12.01). The stratified analysis showed that the risk effect of HP in intestinal-type was more significant (OR = 5.75, 1.99-16.63) than it in defuse-type (OR = 3.5, 0.73-16.89). Cancer history within family and blood group A were associated with diffuse-type while the environmental factors such as low economic status, irregular eating and fast-eating habits were mainly associated with intestinal-type. We conclude from our findings that HP infection may play a role in the development of stomach cancer, especially for intestinal-type gastric cancer. The two Lauren's histological types of stomach cancer might be different in terms of pathogenesis and characteristics.

Six cases of primary malignant lymphoma in the stomach are reported with a review of 586 cases reported from 1950 through 1987 in our country. The disease is rare. The first case was reported abroad in 1829 and in our country in 1951. Abdominal pain, anorexia and hemorrhage in the gastrointestinal tract were the main symptoms. Surgery was the treatment of choice. The 5-year survival rate was 57.0% abroad and 44.6 at home. Adjuvant postoperative radiotherapy or chemotherapy can improve the 5-year survival. In the review, 5-year survival rate was increased by 6.8% in the group where surgery was combined with radiotherapy and by 5.7% in the group of operation plus chemotherapy. The increase in 10-year survival rate was more obvious. Of these 6 cases, 3 treated by surgical treatment alone died, while 3 treated by operation and postoperative chemotherapy are still alive and tumor-free.