[Construction of a prediction model for predicting rebleeding in patients with obscure gastrointestinal bleeding after capsule endoscopy]

Objective: To explore the risk factors of rebleeding in patients with obscure gastrointestinal bleeding (OGIB) after capsule endoscopy (CE), and construct a model to predict rebleeding. Methods: The data of patients with OGIB who underwent CE in Zhongda Hospital Affiliated to Southeast University from July 2018 to September 2021 were retrospectively analyzed. Follow-up data were obtained via electronic medical records or telephone interviews. Univariate and multivariate Cox regression models were performed to figure out the risk factors of rebleeding in OGIB patients. Then the optimal prediction model was determined and presented as a nomogram. The model was evaluated by C statistic, calibration curve and decision curve analysis. Results: One hundred and thirty patients with OGIB were included, including 64 females and 66 males, aged (55.8±17.2) years (18-87 years), and 39 (30.0%) cases developed rebleeding during follow-up. Univariate and multivariate Cox regression model analysis showed the duration of more than 2 weeks OGIB (HR=3.70, 95%CI: 1.85-7.42, P<0.001), a history of previous gastrointestinal bleeding (HR=5.25, 95%CI: 2.00-13.81, P<0.001), positive CE findings (HR=3.72, 95%CI: 1.66-8.33, P=0.001), and the lowest hemoglobin level before CE<80 g/L (HR=2.00, 95%CI: 1.02-3.84, P=0.044) were risk factors for rebleeding, while specific treatment (HR=0.25, 95%CI: 0.11-0.54, P<0.001) was a protective factor. The corresponding scores of the above five predictive factors were: OGIB duration>2 weeks: 79 points; Previous history of gastrointestinal bleeding: 100 points; The result of CE was positive: 79 points; Specific treatment:-85 points; Minimum hemoglobin before CE<80 g/L: 41 points. The prediction model constructed from the above five variables had good discriminative capability (concordance index=0.798, 95%CI: 0.732-0.865). The calibration curves showed high consistency between nomogram-predicted probabilities and actual observations. The decision curves showed that when the threshold probability was above 0.04, the use of the nomogram to predict rebleeding provided a greater net benefit than the assumption of "all patients rebleeding or no patients rebleeding". Conclusion: The prediction model established in this study has a good ability to predic rebleeding in patients with OGIB after CE examination.

Efficacy of percutaneous cement-augmented screw fixation plus percutaneous kyphoplasty in the management of unstable osteoporotic vertebral compression fractures

OBJECTIVE

The present study was performed to compare the efficacy of percutaneous kyphoplasty (PKP) vs. percutaneous cement-augmented screw fixation plus PKP in the management of unstable osteoporotic vertebral compression fractures (OVCF).

PATIENTS AND METHODS

A total of 197 patients with unstable OVCF treated in the Department of Spine Surgery, Lianyungang First People's Hospital from September 2019 to September 2021 were recruited and assigned via random number table method 1:1 to receive either PKP (group A, n=106) or PKP plus percutaneous cement-augmented screw fixation (group B, n=91). The outcome measures for the evaluation of different surgical methods included visual analogue scale (VAS), the height of the anterior-posterior border of the injured spine, Cobb angle of the posterior convexity, Oswestry disability index (ODI) scores, and Japanese Orthopaedic Association (JOA) scores.

RESULTS

PKP exhibited shorter operative time and length of hospital stay and less intraoperative blood loss vs. PKP plus percutaneous cement-augmented screw fixation (p<0.05). Patients with PKP plus percutaneous cement-augmented screw fixation experienced milder postoperative pain vs. those with PKP alone at 7 days postoperatively, as evidenced by the lower VAS scores (p<0.05). PKP plus percutaneous cement-augmented screw fixation provided more restoration of anterior margin height and posterior convexity Cobb angle vs. PKP alone (p<0.05). Patients with PKP only showed slightly higher Japanese Orthopaedic Association (JOA) scores than those with combined surgery, while the postoperative clinical signs between the two arms were similar (p>0.05).

CONCLUSIONS

Single PKP features the benefits of minimal trauma, simple operation, and rapid postoperative recovery in the treatment of OVCF. PKP plus percutaneous cement-augmented screw fixation for severe OVCF provided distinctly better performance than PKP alone in terms of early pain relief, restoration of vertebral body height, correction of posterior convexity deformity, and firm spinal stability.

Efficacy of minimally invasive transforaminal lumbar interbody fusion plus cement-augmented pedicle screw fixation in the treatment of degenerative lumbar spine disease with osteoporosis in the elderly

OBJECTIVE

The aim of this study was to evaluate the efficacy of minimally invasive transforaminal lumbar interbody fusion (MIS-TLIF) plus cement-augmented pedicle screw fixation in the treatment of degenerative lumbar spine disease with osteoporosis in the elderly.

PATIENTS AND METHODS

From February 2020 to January 2021, 40 elderly patients with degenerative lumbar spine disease with osteoporosis admitted to our hospital were randomly assigned (1:1) to receive either MIS-TLIF plus cement-augmented pedicle screw fixation (group A) or TLIF plus cement augmentation (group B), with 19 cases in group A and 21 cases in group B. Outcome measures included visual analogue scale (VAS), Oswestry Dysfunction Index (ODI) and Japanese Orthopedic Association Scores (JOA), operative duration, intraoperative bleeding, postoperative drainage volume, and the incidence of complications. Frontal and lateral radiographs of the lumbar spine and computed tomography (CT) were performed 3 days after surgery to observe the distribution of bone cement. At 12 months postoperatively, the fusion of the bone graft was evaluated according to the Bridwell intervertebral fusion criteria based on the lumbar frontal and lateral radiographs.

RESULTS

All 40 cases completed the surgery successfully and were followed up for 12 months. The two groups did not differ significantly in terms of operative duration (p>0.05). MIS-TLIF plus cement-augmented pedicle screw fixation was associated with significantly less intraoperative bleeding volume (142.25±40.93 mL) and (76.25±17.54 mL) vs. TLIF plus cement augmentation (322.00±93.45 mL, 159.75±54.74 mL) (p<0.05). The difference in the VAS scores, ODI, and JOA scores between the two groups preoperatively and at the final follow-up showed no statistical significance (p>0.05). Patients receiving MIS-TLIF plus cement-augmented pedicle screw fixation had significantly lower VAS scores and ODI and higher JOA scores vs. TLIF plus cement augmentation (p<0.05). The lumbar frontal and lateral radiographs and CT of the two groups 3 days after surgery showed good cement distribution and no cement leakage. At the final follow-up, no complications were seen in group A, and there was one case of intervertebral cement leakage in group B. The intervertebral graft fusion was grade I in both groups.

CONCLUSIONS

MIS-TLIF plus cement-augmented pedicle screw fixation shortens the operative time, alleviates postoperative pain, facilitates operative lumbar spine function restoration, and provides favorable intervertebral implant fusion.

Fast ion shuttling which is robust versus oscillatory perturbations

Shuttling protocols designed by shortcut-to-adiabaticity techniques may suffer from perturbations and imperfect implementations. We study the motional excitation of a single ion shuttled in harmonic traps with time-dependent, 'systematic' oscillatory perturbations around the nominal parameters. These elementary perturbations could form any other by superposition. Robust shuttling strategies are proposed and compared, and optimizations are performed. This article is part of the theme issue 'Shortcuts to adiabaticity: theoretical, experimental and interdisciplinary perspectives'.

[MiR-4484 regulates the expression of integrin α 6 in gastric cancer tissues and its significance]

Objective: To investigate the relationship between the expression of integrin α 6 (ITGA6), miR-4484 and the pathologic stage of gastric cancer. Methods: Gastric cancer tissues and normal gastric mucosa tissues adjacent to cancer (>5 cm from tumor margin) of 30 patients with primary gastric cancer who underwent direct surgical resection without adjuvant therapy from June to September 2017 in West China Hospital of Sichuan University were selected. Real-time quantitative polymerase chain reaction (PCR) was used to detect the expression levels of miR-4484 and ITGA6, western blot was used to detect the expression level of ITGA6 protein, dual luciferase reporter gene was used to verify the relationship between ITGA6 and miR-4484. Spearman's correlation analysis was used to determine the relationship between miR-4484 and ITGA6 expression levels in gastric cancer tissues. Results: The expression level of ITGΑ6 in gastric cancer (32.30±13.47) was higher than that in matched normal gastric tissues (24.55±10.25, P=0.015), the area under the receiver operating characteristic (ROC) curve was 0.660 and the diagnostic sensitivity and specificity were 43.3% and 96.7%, respectively. The expression level of miR-4484 in gastric cancer (4.11±2.87) was lower than that of matched normal gastric tissues (5.75±2.80, P=0.029), the area under the ROC curve was 0.690 and the diagnostic sensitivity and specificity were 30.0% and 86.7%, respectively. The expression level of miR-4484 was negatively correlated with ITGA6 in gastric cancer tissues (r=-0.621, P<0.001). The expression level of ITGA6 protein in gastric cancer tissues (0.65±0.19) was higher than that in normal adjacent tissues (0.26±0.12, P<0.001). Compared with ITGA6 3'UTR wild-type+ miR-NC group, ITGA6 3'UTR wild-type+ miRNA mimics group had lower luciferase activity (50.69±5.10, 34.00±1.19, P<0.001), while the luciferase activity of ITGA6 3'UTR wild-type+ ASO miR-4484 group was higher than that of ITGA6 3'UTR wild-type+ miR-NC group (82.44±6.37, 50.69±5.10, P<0.001), indicated that ITGA6 was the direct target gene of miR-4484. The expression levels of miR-4484 in T1, T2, T3 and T4 (4a and 4b) gastric cancer tissues were 9.98±2.24, 5.28±2.03, 2.92±2.04 and 4.11±2.87, respectively, with statistical significance (P<0.001). The expression levels of ITGA6 in N0, N1, N2 and N3 gastric cancer tissues were 29.55±8.32, 21.71±3.75, 24.60±8.79 and 40.69±15.83, respectively, with statistical significance (P=0.022). The expression levels of miR-4484 in N0, N1, N2 and N3 gastric cancer tissues were 5.01±3.52, 5.48±2.76, 5.88±1.83 and 2.30±1.56, respectively, with statistical significance (P=0.032). The expression levels of ITGA6 in M0 and M1 gastric cancer tissues were 26.28±7.66 and 52.08±8.12, respectively, with statistical significance (P<0.001). The expression levels of miR-4484 in M0 and M1 gastric cancer tissues were 4.95±2.74 and 1.34±0.80, respectively, with statistical significance (P<0.001). Conclusions: ITGA6 is upregulated in gastric cancer tissues, while miR-4484 is downregulated in the gastric cancer group, and its expression level is related to the clinicopathological features of gastric cancer. ITGA6 is the direct target gene of miR-4484, implicates that miR-4484 may inhibit the invasion and metastasis of gastric cancer by regulating the expression of ITGA6. Both miR-4484 and ITGA6 may be the new prognostic markers and potential therapeutic targets of gastric cancer.

[Efficacy and safety of intraoperative ultrasound-assisted neuroendoscopy in the treatment of hypertensive intracerebral hemorrhage via transsylvian approach]

Objective: To explore the efficacy and safety of intraoperative ultrasound-assisted neuroendoscopy for treating hypertensive intracerebral hemorrhage (HICH) via lateral fissure and insula approach. Methods: The clinical data of 66 patients with HICH in basal ganglia who underwent intraoperative ultrasound-assisted neuroendoscopy via lateral fissure and insula approach for hematoma evacuation were retrospectively analyzed, including operative data and follow-up results. All patients had no brain hernia before operation. The hematoma was located by the ultrasound and then the path into the hematoma cavity was determined. Meanwhile, the residual hematoma was also detected by using the ultrasound. The clearance rate of hematoma was observed by CT. Barthel index was used to evaluate the activity of daily living. Results: The amount of residual hematoma was less than 10% in 63 ases and 10%-20% in 3 cases. There were 11 cases of postoperative pneumonia, of whom 9 cases underwent percutaneous tracheotomy. Rebleeding occurred in 2 cases, but the amount was small, and there was no need for reoperation. Meanwhile, there was 1 case of secondary intracranial infection and 1 case of secondary hydrocephalus. No case of cerebral contusion was reported. Half a year after the operation, Barthel Index grading showed that there were 3 cases of grade I, 25 cases of grade Ⅱ, 34 cases of grade Ⅲ, 3 cases of grade Ⅳ and 1 case of death, respectively. Conclusions: Intraoperative ultrasound-assisted neuroendoscopy via lateral fissure and insula approach can improve the efficacy and safety of treatment for HICH.

[Estimating Postmortem Interval by Protein Chip Detection Technology Combined with Multidimensional Statistics]

Abstract

Objective To obtain the protein expression profile of rat liver tissue after death by the 2100 bioanalyzer combined with protein chip, and infer the relationship between protein expression profile and postmortem interval. Methods Rats were killed by abdominal anesthesia and placed at 16 ℃. Water-soluble proteins in liver tissues were extracted at 14 time points after death. The expression profile data of proteins with relative molecular weight of 14 000-230 000 were obtained using protein chip, and principal component analysis （PCA）, partial least squares-discriminant analysis （PLS-DA） and Fisher discriminant were used to analyze the data. Results According to the changes of protein expression profile, the postmortem interval was divided into group A （0 d）, group B （1-9 d）, group C （12-30 d） according to the result of PLS-DA. The prediction accuracy of the training set and test set of the model were all 100.0%, and the internal cross-validation of the training set was 100.0% according to Fisher discriminant. The Fisher discriminant model at each time point of group B and C was established to narrow the time window of postmortem interval estimation. The prediction accuracy of the training set and test set were all 100.0%, and the internal cross-validation accuracy of the training set was 100.0% in group B. The prediction accuracy of the training set and test set were respectively 95.2% and 78.6% in group C, and the internal cross-validation of the training set was 88.1%. Conclusion Protein chip detection technology can quickly and easily obtain the expression profile of water-soluble proteins of rat liver tissue with a relative molecular weight of 14 000-230 000 at different time points after death. PLS-DA and Fisher discriminant models are established to classify and predict the postmortem interval, in order to provide new ideas and methods for postmortem interval estimation.

[Preliminary application of postoperative fast track transfer to intensive care unit for the geriatric hip fractures under enhanced recovery after surgery]

Objective: To develop a fast track transfer to intensive care unit (ICU) for the perioperative high-risk elderly patients after hip fracture surgery and analyze the preliminary clinical effect of the application. Methods: From January 2014 to December 2017, before the application of postoperative fast track transfer to ICU, the clinical data of 195 elderly patients with hip fracture were included in a retrospective analysis. Among 195 hip fracture patients, 18 were transferred to ICU post operation (non-fast track group). Multivariate logistic regression analysis was applied to investigate relevant risk factors for transferring to ICU after hip fracture surgery. Based on risk factors acquired from the analysis and clinical experience, the fast track transfer to ICU for the perioperative high-risk elderly patients after hip fracture surgery was constructed according to the preliminary and experiential criteria. From January 2018 to December 2019, the clinical data of 70 patients (fast track group) who were transferred to ICU after hip fracture surgery through the fast track were collected and compared with non-fast track group. Results: Multivariate regression analysis revealed that American Society of Anesthesiologists classification(≥Ⅲ) (OR=4.260, 95%CI:1.157-15.683, P=0.029), pre-hospital stage (≥48 h) (OR=4.301, 95%CI:1.212-15.266, P=0.024), hemoglobin concentration at admission(<90 g/L) (OR=7.979, 95%CI:1.936-32.889, P=0.004), coronary heart disease as one comorbidity(OR=6.063, 95%CI:1.695-21.693, P=0.006) were independent risk factors for transferring to ICU after hip fracture surgery. There were no significant difference in gender, age, fracture type, hemoglobin concentration at admission and time of pre-hospital stage between the non-fast track group and fast track group(all P>0.05). However, the number of comorbidities in the fast track group was significantly higher than that in the non-fast track group (Z=-1.995, P=0.046). The time to surgery, postoperative hospital stay, and length of hospital stay in fast track group were all significantly less than those in non-fast track group (Z=-2.121, -2.726, -3.130, all P<0.05). Also, there were fewer medical consultations needed and fewer patients who stayed in ICU more than or equal to 2 nights in fast track group than that in non-fast track group(all P<0.05). There were no significant difference in the rate of patients who transferred from the general ward to ICU after transferring from ICU to the general ward, the proportion of patients who received more than or equal to 4 departments, operation time, hospitalization expense, mortality during hospitalization, 30-day mortality and 90-day mortality after operation between the two groups(all P>0.05). Conclusions: The fast track constructed in this study can reduce time to surgery, postoperative hospitalization stay and length of hospitalization stay for the perioperative high-risk elderly patients with hip fractures and is a specific clinical application of eras concept based on multidisciplinary team.

Determination of Escitalopram in Biological Samples by Dispersive Liquid-Liquid Microextraction Combined with GC-MS/MS

Objective To establish a method for determination of escitalopram in biological samples by ultrasound-assisted ionic liquid-dispersive liquid-liquid microextraction combined with gas chromatography-tandem mass spectrometry （GC-MS/MS） and provide evidences for forensic determination of cases related to escitalopram. Methods The 1-hexyl-3-methylimidazolium hexafluorophosphate （[C₆MIM][PF₆]） was selected as an extract solvent to process biological samples. Ultrasound-assisted extraction was used on the samples. Then the samples were detected by GC-MS/MS. Results The linear range of escitalopram in blood and liver were 5.56-1 111.10 ng/mL and 0.025-5.00 mg/g, respectively. The correlation coefficient （r） were greater than 0.999, limit of detection （LOD） were 4.00 ng/mL and 2.00 μg/g, limit of quantitation （LOQ） were 14.00 ng/mL and 6.00 μg/g, respectively. The extraction recovery rates were all greater than 50%, the interday and intraday precision were less than 20%. Escitalopram was detected in blood and liver samples from the actual poisoning case by this method with a content of 1.26 μg/mL and 0.44 mg/g, respectively. Conclusion The ultrasound-assisted ionic liquid-dispersive liquid-liquid microextraction combined with GC-MS/MS is environment friendly, rapid, has good enriching effect and consumes less organic solvent and can be used for forensic determination of escitalopram related cases.

[Strategies in clinical diagnosis and treatment of steroid-resistant acute rejection after orthotopic liver transplantation]

OBJECTIVE

To explore the diagnostic evidence and treatment strategies for steroid-resistant acute rejection (SRAR) after orthotopic liver transplantation.

METHODS

A retrospective analysis was performed among 1038 patients undergoing orthotopic liver transplantation in our hospital from January 2004 to December 2013. A total of 169 acute rejection (AR) episodes occurred in 153 patients. Sixteen of the patients were diagnosed with SRAR because of no response to large-dose steroid pulse therapy. The diagnosis and treatment of the 16 patients were analyzed retrospectively. Comparison of data was made by χ2 test or t test, and a P value of <0.05 was considered to be significant.

RESULTS

The incidence of AR after liver transplantation was 14.74% (153/1038) in all the patients. The incidence of SRAR was 9.47% (16/169) in patients with AR. In the 16 patients with SRAR, 3 were treated with anti-CD3 monoclonal antibody (OKT3), 9 were treated with monoclonal antibody against IL-2 receptor, and 4 received antithymocyte globulin (ATG) therapy. After treatment, SRAR was reversed in 12 of the 16 patients and caused death of the other 4 patients, yielding a reversal rate of 75% and a mortality rate of 25%.

CONCLUSION

SRAR after liver transplantation has a low incidence rate but poor prognosis. The diagnosis of SRAR is mainly based on the clinical manifestation, laboratory test, liver biopsy, and poor response or rejection to methyl prednisolone pulse therapy. ATG and OKT3 achieve substantial outcomes in most of the patients in the treatment of SRAR. Particularly, compared with OKT3, ATG achieves a higher reversal rate and fewer adverse reactions, which is expected to become the first-line treatment of SRAR.

LECT2 association with macrophage-mediated killing of Helicobacter pylori by activating NF-κB and nitric oxide production

Helicobacter pylori employs unique methods to colonize the stomach, which induces chronic inflammation. It is also able to avoid eradication by macrophages and other immune cells. Leukocyte cell-derived chemotaxin 2 (LECT2), a multi-functional cytokine involved in many pathological conditions, has recently been shown to activate macrophages via the CD209a receptor. Therefore, we aimed to investigate the effects of LECT2 on H. pylori-infected macrophages. Macrophages were treated with recombinant LECT2, and both their ability to kill H. pylori and produce nitric oxide were analyzed. Western blot was performed to determine nuclear translocation and protein phosphorylation of p65, a subunit of nuclear factor (NF)-κB. Transfection experiments were performed to analyze the signaling pathway of LECT2 in macrophages. We found that treatment with LECT2 enhanced H. pylori killing and nitric oxide production in macrophages. In addition, DNA-binding activity and nuclear translocation of p65 were up-regulated by LECT2 treatment. Furthermore, we found that NF-κB activation by LECT2 was mediated by Raf-1 in macrophages, and Raf-1 phosphorylation was specifically altered in response to LECT2. Moreover, LECT2 induced Ser28 phosphorylation in the intracellular domain of CD209a. CD209a Ser28 phosphorylation was required for LECT2-induced Raf-1 and NF-κB activation in RAW264.7 macrophages. Our study showed that the effects of LECT2 on H. pylori killing and nitric oxide production were dependent on CD209a phosphorylation, Raf-1, and NF-κB activation. Together, these results demonstrate for the first time that exposure to LECT2 can modulate specific intracellular mechanisms downstream of CD209a to enhance H. pylori killing and nitric oxide production in macrophages.

Structural and biochemical characteristics of chitin-binding protein SeCBP66 from Spodoptera exigua (Hübner)

Peritrophic membrane proteins are important components of the insect peritrophic membrane. A novel cDNA gene encoding a chitin-binding protein, named secbp66, was identified by immunization screening of the cDNA library of Spodoptera exigua. The full length of secbp66 is 1806 bp, which encodes 602 amino acids. The predicted weight of the protein is 64.2 kDa. Bioinformatic analysis showed that a signal peptide composed of 17 amino acids located at the N-terminal of SeCBP66 contained seven tandem putative Type-II functional chitin-binding domains and five potential N-glycosylation sites, but no O-linked glycosylation sites. To study the properties of SeCBP66, recombinant SeCBP66 was successfully expressed in the insect cell line BTI-Tn-5B1-4 with a Bac-to-Bac expression system. A chitin binding experiment showed that the recombinant SeCBP66 protein could bind to chitin strongly. This study of the novel chitin-binding protein SeCBP66 provides a basis for developing new control targets for S. exigua.

Knockdown of linc-UFC1 suppresses proliferation and induces apoptosis of colorectal cancer

Long intergenic noncoding RNAs (lincRNAs) have important roles in biological functions, molecular mechanisms and prognostic values in colorectal cancer (CRC). In this context, the roles of linc-UFC1 remain to be elucidated. In this study, linc-UFC1 was overexpressed in CRC patient tissues and positively correlated with tumor grade, N stage and M stage. Inhibition of linc-UFC1 resulted in cell proliferation inhibition and G1 cell cycle arrest, which was mediated by cyclin D1, CDK4, Rb and phosphorylated Rb. In addition, inhibition of linc-UFC1 induced cell apoptosis through the intrinsic apoptosis signaling pathway, as evidenced by the activation of caspase-9 and caspase-3. An investigation of the signaling pathway revealed that the effects on proliferation and apoptosis following linc-UFC1 knockdown were mediated by suppression of β-catenin and activation of phosphorylated P38. Furthermore, the P38 inhibitor SB203580 could attenuate the apoptotic effect achieved by linc-UFC1 knockdown, confirming the involvement of P38 signaling in the induced apoptosis. Taken together, linc-UFC1 might have a critical role in pro-proliferation and anti-apoptosis in CRC by regulating the cell cycle, intrinsic apoptosis, and β-catenin and P38 signaling. Thus, linc-UFC1 could be a potential therapeutic target and novel molecular biomarker for CRC.

Multicenter study of autoverification methods of hematology analysis

This study was designed to establish and validate a set of autoverification methods for hematology analysis. One thousand and twenty-four samples were selected from Shanghai Ruijin Hospital and 999 from Beijing Hospital, China. False positive, false negative and autoverification pass rates were verified and the rules were then adjusted and confirmed according to the verification results. After confirmation, at least 10,000 sample cases were selected from Shanghai Ruijin Hospital, Beijing Hospital and China Armed Police General Hospital and checked automatically. The differences in the autoverification pass rate and average report delivery time before and after the application of the autoverification methods were compared between the three hospitals. Preliminary validation results showed that the false negative rates of the Shanghai Ruijin Hospital and Beijing Hospital were less than 2%. The false positive rates of these two hospitals were high, close to 18%. After rule adjustment, the false negative rate was basically the same as before adjustment, but the false positive rate declined obviously while the pass rate of autoverification improved significantly. The autoverification pass rates of the three hospitals were 76.4%, 85.1% and 84.2%, respectively. The turnover time (TAT, time from receipt of sample to report of the result) of the three hospitals decreased by 4.1 min, 8.8 min and 10.2 min, respectively. Autoverification systems using a Mindray BC-6800 auto hematology analyzer and labXpert were confirmed as being effective in reducing TAT and enhancing working efficiency on the premise of ensuring low false negative rate.

Cloning and characterization of the SERK1 gene in triploid Pingyi Tiancha [Malus hupehensis (Pamp.) Rehd. var. pingyiensis Jiang] and a tetraploid hybrid strain

This study aims to explore the roles of somatic embryogenesis receptor-like kinase (SERK) in Malus hupehensis (Pingyi Tiancha). The full-length sequences of SERK1 in triploid Pingyi Tiancha (3n) and a tetraploid hybrid strain 33# (4n) were cloned, sequenced, and designated as MhSERK1 and MhdSERK1, respectively. Multiple alignments of amino acid sequences were conducted to identify similarity between MhSERK1 and MhdSERK1 and SERK sequences in other species, and a neighbor-joining phylogenetic tree was constructed to elucidate their phylogenetic relations. Expression levels of MhSERK1 and MhdSERK1 in different tissues and developmental stages were investigated using quantitative real-time PCR. The coding sequence lengths of MhSERK1 and MhdSERK1 were 1899 bp (encoding 632 amino acids) and 1881 bp (encoding 626 amino acids), respectively. Sequence analysis demonstrated that MhSERK1 and MhdSERK1 display high similarity to SERKs in other species, with a conserved intron/exon structure that is unique to members of the SERK family. Additionally, the phylogenetic tree showed that MhSERK1 and MhdSERK1 clustered with orange CitSERK (93%). Furthermore, MhSERK1 and MhdSERK1 were mainly expressed in the reproductive organs, in particular the ovary. Their expression levels were highest in young flowers and they differed among different tissues and organs. Our results suggest that MhSERK1 and MhdSERK1 are related to plant reproduction, and that MhSERK1 is related to apomixis in triploid Pingyi Tiancha.

The efficacy and safety of zibotentan in the treatment of castration-resistant prostate cancer: a meta-analysis

OBJECTIVE

Recently, novel endothelins like zibotentan and atrasentan and other novel taxanes have been introduced to treat prostate cancer. This study reviews zibotentan in the treatment of castration-resistant prostate cancer (CRPC) and derives a more precise estimate of their effect of treatment.

MATERIALS AND METHODS

Two reviewers searched and extracted data of the published trials and review articles on zibotentan for prostate cancer using the Medline, Embase and Cochrane Controlled Trials Register database. We used hazard ratios (HRs) to assess the effects on overall survival (OS), progression-free survival (PFS), or time to PSA progression (TTP), and relative risk (RR) for the different types of toxicity. Four randomized controlled trials were identified.

RESULTS

The pooled HR showed that zibotentan did not improve OS and PFS (HR = 0.92, 95%CI = 0.82-1.03, p = 0.161, HR = 0.98, 95% CI = 0.89-1.08, p = 0.714). Zibotentan had modest benefits on TTP (HR = 0.94, 95% CI = 0.91-0.97, p = 0.001). In addition, zibotentan led to more peripheral edema, anemia, cardiac failure and pneumonia.

CONCLUSIONS

Our study concludes that zibotentan is not an attractive option for CRPC patients. However, additional studies on other novel therapies are needed to improve patient outcomes.

Suppression of outward K⁺ currents by WIN55212-2 in rat retinal ganglion cells is independent of CB1/CB2 receptors

Cannabinoid CB1 receptor (CB1R) signaling system is extensively distributed in the vertebrate retina. Activation of CB1Rs regulates a variety of functions of retinal neurons through modulating different ion channels. In the present work we studied effects of this receptor signaling on K(+) channels in retinal ganglion cells by patch-clamp techniques. The CB1R agonist WIN55212-2 (WIN) suppressed outward K(+) currents in acutely isolated rat retinal ganglion cells in a dose-dependent manner, with an IC50 of 4.7 μM. We further showed that WIN mainly suppressed the tetraethylammonium (TEA)-sensitive K(+) current component. While CB1Rs were expressed in rat retinal ganglion cells, the WIN effect on K(+) currents was not blocked by either AM251/SR141716, specific CB1R antagonists, or AM630, a selective CB2R antagonist. Consistently, cAMP-protein kinase A (PKA) and mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signaling pathways were unlikely involved in the WIN-induced suppression of the K(+) currents because both PKA inhibitors H-89/Rp-cAMP and MAPK/ERK1/2 inhibitor U0126 failed to block the WIN effects. WIN-induced suppression of the K(+) currents was not observed when WIN was intracellularly applied. Furthermore, an endogenous ligand of the cannabinoid receptor anandamide, the specific CB1R agonist ACEA and the selective CB2R agonist CB65 also suppressed the K(+) currents, and the effects were not blocked by AM251/SR141716 or AM630 respectively. All these results suggest that the WIN-induced suppression of the outward K(+) currents in rat retinal ganglion cells, thereby regulating the cell excitability, were not through CB1R/CB2R signaling pathways.

Sulforaphane enhances the activity of the Nrf2-ARE pathway and attenuates inflammation in OxyHb-induced rat vascular smooth muscle cells

AIM

A growing body of evidence indicates that the nuclear factor erythroid 2-related factor 2-antioxidant response element (Nrf2-ARE) pathway plays a protective role in many physiological stress processes such as inflammatory damage, oxidative stress, and the accumulation of toxic metabolites, which are all involved in the cerebral vasospasm following subarachnoid hemorrhage (SAH). We hypothesized that the Nrf2-ARE pathway might have a protective role in cerebral vasospasm following SAH.

MATERIALS AND METHODS

In our study, we investigate whether the oxyhemoglobin (OxyHb) can induce the activation of the Nrf2-ARE pathway in vascular smooth muscle cells (VSMCs), and evaluate the modulatory effects of sulforaphane (SUL) on OxyHb-induced inflammation in VSMCs.

RESULTS

As a result, both the protein level and the mRNA level of the nuclear Nrf2 were significantly increased, while the mRNA levels of two Nrf2-regulated gene products, both heme oxygenase-1 and NAD(P)H: quinone oxidoreductase-1, were also up-regulated in VSMCs induced with OxyHb. A marked increase of inflammatory cytokines such as IL-1β, IL-6 and TNF-α release was observed at 48 h after cells were treated with OxyHb. SUL enhanced the activity of the Nrf2-ARE pathway and suppressed cytokine release.

CONCLUSIONS

Our results indicate that the Nrf2-ARE pathway was activated in OxyHb-induced VSMCs. SUL suppressed cytokine release via the activation of the Nrf2-ARE pathway in OxyHb-induced VSMCs.

Prokaryotic expression, purification, and refolding of leukocyte cell-derived chemotaxin 2 and its effect on gene expression of head kidney-derived macrophages of a teleost fish, ayu (Plecoglossus altivelis)

Leukocyte cell-derived chemotaxin 2 (LECT2) is reported to be an immunorelevant protein in ayu (Plecoglossus altivelis). In this study, ayu LECT2 mature peptide (aLECT2m) was expressed as insoluble inclusion bodies in Escherichia coli. The denatured recombinant aLECT2m (raLECT2m) was refolded by a size-exclusion chromatography refolding process achieved by using arginine-containing mobile phase and a decreasing urea gradient. The in vitro chemotactic activity assay showed that the refolded raLECT2m had the bioactivity. By using suppression subtractive hybridization (SSH) method, we further identified up-regulated genes in ayu macrophages treated with refolded raLECT2m. These genes were tightly involved in endocytosis, hydrolysis, transcriptional regulation, signal transduction, and so on. Moreover, real-time quantitative PCR (RT-qPCR) results confirmed that selected 10 genes expression was significantly up-regulated in refolded raLECT2m-treated ayu macrophages. This study provides a basis for further studies of the mechanism of cytokine LECT2 in fish immune responses.

Identification and characterization of a novel cathelicidin from ayu, Plecoglossus altivelis

Cathelicidins, one family of antimicrobial peptides, play important roles against infections in animals. In this study, a cDNA sequence coding for cathelicidin was cloned from constructed liver cDNA library of ayu, Plecoglossus altivelis. The deduced ayu cathelicidin (aCATH) has a 20 amino acid residue signal peptide, a conserved cathelin domain of 110 amino acid residues and a mature antimicrobial peptide of 61 amino acid residues. Sequence comparison and phylogenetic tree analysis confirmed aCATH as a distinct member of fish cathelicidins. Real-time quantitative PCR revealed that the aCATH transcripts dramatically increased in various tissues after bacterial infection. Subsequently, aCATH was prokaryotic expressed and purified. Western blot and mass spectrometry revealed that aCATH was cleaved at residue Ile130-Arg131 by human neutrophil elastase to release the mature antimicrobial peptide. The mature peptide of aCATH was chemically synthesized and exhibited potent antimicrobial activity. Thus, aCATH may play an important role in the innate immunity of ayu, and this work enriches our knowledge in fish antimicrobial peptides.

The establishment of a library screening method based on yeast two-hybrid system and its use to determine the potential interactions of liver proteins in ayu, Plecoglossus altivelis

Knowledge of specific protein-protein interaction (PPI) is an important component in understanding biological processes and regulatory mechanisms. A library to library screening method (LLS) was established based on yeast two-hybrid (YTH) system in this research, and applied to study the PPIs in ayu liver. In total, 23 out of 55 interaction pairs were found positive through phenotypic identification, with a positive rate of 41.8%. Of the 11 unique PPIs, 9 interactions including FGB/FGG, CaM/Spna2, C9/Apo-AI-1, α₂M/Ft, RPL10/RPL5, C8α/C9, FGG/Apo-AI-1, LECT2/Tf, and Apo-AI-2/C9 were previously reported. The other two PPIs including FGG/CLR and Wap65/C3 are novel, and in vitro co-immunoprecipitation (co-IP) experiments further confirmed these interactions. FGG/CLR interaction might play a role in regulating the inflammatory response. The interaction between Wap65 and C3 hints that Wap65 might function through the complement activation pathways when microbial infection occurs.

Hierarchically structured carbon-based composites: Design, synthesis and their application in electrochemical capacitors

This feature article provides an overview of the recent research progress on the hierarchically structured carbon-based composites for electrochemical capacitors. The basic principles of electrochemical capacitors, and the design, construction and performance of hierarchically structured carbon-based composites electrode materials with good ions and electron transportation and large specific surface area are discussed. The trend of future development of high-power and large-energy electrochemical capacitors is proposed.

Prevalence of hepatitis B virus genotypes and their relationship to clinical laboratory outcomes in Tibetan and Han Chinese

This study was designed to investigate the prevalence of hepatitis B virus (HBV) genotypes in Tibetan and Han nationalities in Sichuan Province, China, and their clinical significance. Sera from 376 patients (286 Han nationals, 90 Tibetan nationals) were genotyped by polymerase chain reaction. Of the 286 Han nationals, 127 were HBV asymptomatic carriers, 90 were symptomatic patients and 69 had hepatocellular carcinoma. The distribution of HBV genotypes was related to geography as well as ethnicity. The HBV genotype frequencies were: B, 57.9%; C, 16.0%; and BC, 26.1%. Association studies between genotypes and clinical laboratory outcomes showed HBV genotype C to be more virulent. There was a higher prevalence of mixed genotype BC in Tibetan nationals compared with Han nationals. There was no synergistic effect in terms of virulence in patients coinfected with genotypes B and C.

Rapid and sensitive detection of infectious spleen and kidney necrosis virus by loop-mediated isothermal amplification combined with a lateral flow dipstick

Loop-mediated isothermal amplification (LAMP) allows rapid amplification of nucleic acids under isothermal conditions. In this report, a 20-min LAMP amplification of the DPOL gene of infectious spleen and kidney necrosis virus (ISKNV) using a biotin-labeled primer was combined with lateral flow dipstick (LFD) chromatography for rapid and simple visual detection of ISKNV-specific amplicons. The LFD process involves a 5-min specific hybridization with an FITC-labeled DNA probe to confirm the presence of complement ISKNV amplicons that were biotinated in LAMP. The resulting DNA duplexes, consisting of labeled probes and amplicons, migrate along the LFD strip by chromatography for 5 min and are trapped at the test line and visualized by biotin labeling. The detection limit of ISKNV by LAMP-LFD was 10 copies. The results show that the LAMP-LFD method has the advantages of better sensitivity and speed and less dependence on equipment than the standard PCR for specifically detecting low levels of ISKNV DNA, and this can be useful in the field as a routine diagnostic tool.

Hippocampal spine-associated Rap-specific GTPase-activating protein induces enhancement of learning and memory in postnatally hypoxia-exposed mice

Spine-associated Rap-specific GTPase-activating protein (SPAR) is a postsynaptic protein that forms a complex with postsynaptic density (PSD)-95 and N-methyl-d-aspartate receptors (NMDARs), and morphologically regulates dendritic spines. Mild intermittent hypoxia (IH, 16.0% O(2), 4 h/day for 4 weeks) is known to markedly enhance spatial learning and memory in postnatal developing mice. Here, we report that this effect is correlated with persistent increases in SPAR expression as well as long-term potentiation (LTP) in the hippocampus of IH-exposed mice. Furthermore, an infusion of SPAR antisense oligonucleotides into the dorsal hippocampus disrupted elevation of SPAR expression, preventing enhanced hippocampal LTP in IH-exposed developing mice and also reducing LTP in normoxic mice, without altering basal synaptic transmission. In SPAR antisense-treated mice, acquisition of the Morris water maze spatial learning task was impaired, as was memory retention in probe trails following training. This study provides the first evidence that SPAR is functionally required for synaptic plasticity and contributes to the IH-induced enhancement of spatial learning and memory in postnatal developing mice.

Base sequence effects in bending induced by bulky carcinogen-DNA adducts: experimental and computational analysis

The covalent binding of bulky mutagenic or carcinogenic compounds to DNA can lead to bending, which could significantly alter the interactions of DNA with critical replication and transcription proteins. The impact of adducts derived from the highly reactive bay region enantiomeric (+)- and (-)-anti-7,8-diol-9,10-epoxide derivatives of benzo[a]pyrene (BPDE) are of interest because the (+)-7R,8S,9S,10R-anti-BPDE enantiomer is highly tumorigenic in rodents, while the (-)-7S,8R,9R,10S-anti-BPDE enantiomer is not. Both (+)- and (-)-anti-BPDE bind covalently with DNA predominantly by trans addition at the exocyclic amino group of guanine to yield 10S (+)- and 10R (-)-trans-anti-[BP]-N(2)-dG adducts. We have synthesized a number of different oligonucleotides with single (+)- and (-)-trans-anti-[BP]-N(2)-dG adducts (G) in the base sequence context XG*Y, where X and Y are different DNA bases. The G* residues were positioned at or close to the center of 11 base pair ( approximately 1 helical turn) or 16 base pair ( approximately 1.5 turns) duplexes. All bases, except for X and Y and their partners, were identical. These sequences were self-ligated with T4 ligase to form multimers that yield a ladder of bands upon electrophoresis in native polyacrylamide gels. The extent of bending in each oligonucleotide was assessed by monitoring the decrease in gel mobilities of these linear, self-ligated oligomers, relative to unmodified oligonucleotides of the same base sequence. The extent of global bending was then estimated using a sequence-specific three-dimensional model from which the values of the base-pair step parameter roll adjacent to the lesion site could be extracted. We find that (+)-trans-anti-[BP]-N(2)-dG adducts are considerably more bent than the (-) isomers regardless of sequence and that A-T base pairs flanking the [BP]-N(2)-dG lesion site allow for local flexibility consistent with adduct conformational heterogeneity. Interestingly, the fit of computed versus observed gel mobilities using classical reptation treatments requires enhancement of unmodified DNA flexibility in gels, compared to aqueous salt solution. The differences in bending between the two stereoisomeric adduct duplexes and the observed base sequence context effects may play a significant role in the differential processing of these lesions by cellular replication, transcription, and repair enzymes.

A-form conformational motifs in ligand-bound DNA structures

Recognition and biochemical processing of DNA requires that proteins and other ligands are able to distinguish their DNA binding sites from other parts of the molecule. In addition to the direct recognition elements embedded in the linear sequence of bases (i.e. hydrogen bonding sites), these molecular agents seemingly sense and/or induce an "indirect" conformational response in the DNA base-pairs that facilitates close intermolecular fitting. As part of an effort to decipher this sequence-dependent structural code, we have analyzed the extent of B-->A conformational conversion at individual base-pair steps in protein and drug-bound DNA crystal complexes. We take advantage of a novel structural parameter, the position of the phosphorus atom in the dimer reference frame, as well as other documented measures of local helical structure, e.g. torsion angles, base-pair step parameters. Our analysis pinpoints ligand-induced conformational changes that are difficult to detect from the global perspective used in other studies of DNA structure. The collective data provide new structural details on the conformational pathway connecting A and B-form DNA and illustrate how both proteins and drugs take advantage of the intrinsic conformational mechanics of the double helix. Significantly, the base-pair steps which exhibit pure A-DNA conformations in the crystal complexes follow the scale of A-forming tendencies exhibited by synthetic oligonucleotides in solution and the known polymorphism of synthetic DNA fibers. Moreover, most crystallographic examples of complete B-to-A deformations occur in complexes of DNA with enzymes that perform cutting or sealing operations at the (O3'-P) phosphodiester linkage. The B-->A transformation selectively exposes sugar-phosphate atoms, such as the 3'-oxygen atom, ordinarily buried within the chain backbone for enzymatic attack. The forced remodeling of DNA to the A-form also provides a mechanism for smoothly bending the double helix, for controlling the widths of the major and minor grooves, and for accessing the minor groove edges of individual base-pairs.

Protein-directed DNA structure. I. Raman spectroscopy of a high-mobility-group box with application to human sex reversal

Protein-directed reorganization of DNA underlies mechanisms of transcription, replication, and recombination. A molecular model for DNA reorganization in the regulation of gene expression is provided by the sequence-specific high-mobility-group (HMG) box. Structures of HMG-box complexes with DNA are characterized by expansion of the minor groove, sharp bending toward the major groove, and local unwinding of the double helix. The Raman vibrational signature of such DNA reorganization has been identified in a study of the SRY HMG box, encoded by the human male-determining region of the Y chromosome. We observe in the human SRY-HMG:DNA complex extraordinarily large perturbations to Raman bands associated with vibrational modes of the DNA backbone and accompanying large increases in intensities of Raman bands attributable to base unstacking. In contrast, DNA major-groove binding, as occurs for the bZIP protein GCN4 [Benevides, J. M., Li, T., Lu, X.-J., Srinivasan, A. R., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochemistry 39, 548-556], perturbs the Raman signature of DNA only marginally. Raman markers of minor-groove recognition in the human SRY-HMG:DNA complex are due primarily to perturbation of specific vibrational modes of deoxyribose moieties and presumably reflect desolvation at the nonpolar interface of protein and DNA. These Raman markers may be diagnostic of protein-induced DNA bending and are proposed as a baseline for comparative analysis of mutations in SRY that cause human sex reversal.

Protein-directed DNA structure II. Raman spectroscopy of a leucine zipper bZIP complex

Mechanisms of transcription may involve protein-directed changes in DNA structure and DNA-directed changes in protein structure. We have employed Raman spectroscopy to characterize vibrational signatures associated with such induced molecular fitting for two classes of transcription factors-the basic leucine-zipper (bZIP) motif and the high-mobility-group (HMG) box-each with a DNA target site. Results for bZIP are described here; findings for the HMG-box are reported in the preceding paper in this issue [Benevides, J. M., Chan, G., Lu, X.-J., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochemistry 39, 537-547]. The yeast activator GCN4 provides a well-studied example of bZIP recognition, wherein B-DNA serves essentially as a template for protein folding. Analysis of Raman spectra of the 57-residue GCN4 bZIP domain, its AP-1 binding site, and their specific complex confirms a DNA-induced increase in alpha-helicity, attributable to folding of GCN4 basic arms with virtually no change in B-DNA structure, consistent with previous X-ray and NMR structure determinations. The absence of DNA perturbations in the bZIP model contrasts sharply with the HMG box, where DNA structure perturbations predominate. The bZIP and HMG-box models represent two opposing extremes in a range of induced fits identifiable by Raman spectroscopy. Previously characterized lambda repressor/operator complexes [Benevides, J. M., Weiss, M. A., and Thomas, G. J. (1994) J. Biol. Chem. 269, 10869-10878] occupy an intermediate position within this range. A comprehensive tabulation of Raman markers proposed as diagnostic of different protein/DNA recognition motifs is presented. The results are analyzed in terms of available DNA crystal structures (Nucleic Acid Database) to identify details of DNA conformation that correlate with specific Raman recognition markers.

Overview of nucleic acid analysis programs

We outline the mathematical distinctions among seven of the most popular computer programs currently used to analyze the spatial arrangements of bases and base pairs in nucleic acid helical structures. The schemes fall into three basic categories on the basis of their definitions of rotational parameters: matrix-based, projection-based, and combined matrix- and projection-based. The approaches also define and construct base and base-pair coordinate frames in a variety of ways. Despite these mathematical distinctions, the computed parameters from some programs are strongly correlated and directly comparable. By contrast, other programs which use identical methodologies sometimes yield very different results. The choice of reference frame rather than the mathematical formulation has the greater effect on calculated parameters. Any factor which influences the reference frame, such as fitting or not fitting standard bases to the experimentally derived coordinates, will have a noticeable effect on both complementary base pair and dimer step parameters.

Resolving the discrepancies among nucleic acid conformational analyses

Growing interest in understanding the relationship between the global folding of nucleic acids and the sequence-dependent structure of individual base-pair steps has stimulated the development of new mathematical methods to define the geometry of the constituent base-pairs. Several approaches, designed to meet guidelines set by the nucleic acid community, permit rigorous comparative analyses of different three-dimensional structures, as well as allow for reconstruction of chain molecules at the base-pair level. The different computer programs, however, yield inconsistent descriptions of chain conformation. Here we report our own implementation of seven algorithms used to determine base-pair and dimer step parameters. Aside from reproducing the results of individual programs, we uncover the reasons why the different algorithms come to conflicting structural interpretations. The choice of mathematics has only a limited effect on the computed parameters, even in highly deformed duplexes. The results are much more sensitive to the choice of reference frame. The disparate schemes yield very similar conformational descriptions if the calculations are based on a common reference frame. The current positioning of reference frames at the inner and outer edges of complementary bases exaggerates the rise at distorted dimer steps, and points to the need for a carefully defined conformational standard.

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

The deformability of double helical DNA is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the fluctuations and correlations of structural parameters in DNA-protein crystal complexes. These elastic functions provide useful stereochemical measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the DNA-protein complexes, apparently acting as flexible "hinges" fitting the duplex to the protein surface. In addition to the angular parameters widely used to describe DNA deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The observed correlations of base pair bending and shearing motions are important for nonplanar folding of DNA in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic three-dimensional models for the study of long DNA polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences.

Structure and conformation of helical nucleic acids: analysis program (SCHNAaP)

We present a new versatile program, SCHNAaP, for the analysis of double-helical nucleic acid structures. The program uses mathematically rigorous and fully reversible procedures for calculating the structural parameters: the Cambridge University Engineering Department Helix computation Scheme (CEHS) is used to determine the local helical parameters and an analogous procedure is used to determine the global helical parameters. These parameters form a complete set that conforms to the "Cambridge Accord" on definitions and nomenclature of nucleic acid structure parameters. In addition to the two standard Watson-Crick base-pairs, the program handles mismatched base-pairs and chemically modified bases. An analysis of the sugar-phosphate backbone conformation is included. Standardized base-stacking diagrams of each dinucleotide step with reference to the mid-step triad are generated. Structures are classified as one of the four polymorphic families, A/B, Z, W or R, although W- and R-DNA (two types of hypothetical structure) have yet to be observed experimentally.

Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP)

We present a program, SCHNArP, for rebuilding double-helical nucleic acid structures from a set of helical parameters. The parameter sets are based on mathematically reversible schemes that allow direct comparison of data from experimental X-ray crystal structures analyzed using the analysis program, SCHNAaP (see accompanying paper), and structures built using the rebuilding program, SCHNArP. The program uses either local CEHS helical parameters or global helical parameters. A number of standard parameter sets from the literature are included that allow comparison of oligomer and polymer structures generated using different models for sequence-dependent DNA bending. Exact atomic models are provided for the bases. Schematic models that trace the path of the backbone and use rectangular blocks for the bases can be generated.

Construction of double-helical DNA structures based on dinucleotide building blocks

We present a new method for building full 3-D structures of DNA sequences. A database of the conformational properties of dinucleotide steps has been compiled using X-ray crystal structures of oligonucleotides. The protocol uses these dinucleotides as building blocks to generate three dimensional structures of any required sequence in any required conformation.

DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures

Experimental data on the conformational properties of dinucleotides taken from high-resolution X-ray crystal structures of oligonucleotides have been compared with theoretical energy calculations on the base-stacking interactions. The conformational properties of the dinucleotides determined by calculation agree well with the experimental data, which shows that the method used for computing the stacking interactions is reliable. In addition, the calculations provide insight into the origins of the major trends that are observed in the experimental data. The values of the step parameters roll, tilt and rise, are determined entirely by the van der Waals interactions, and this reflects the strong requirement that the bases remain stacked in close contact. Slide, shift and twist do not affect the vertical separation of the bases and are therefore less tightly constrained. Electrostatic interactions play an important role in determining the values of shift and slide, but the base-stacking interaction energy is essentially independent of the value of twist. Thus the experimental value of twist is most likely fixed by the constraints of the backbone, which are missing in these calculations.

Recapitulation of the pathway for trophoblast giant cell differentiation in vitro: stage-specific expression of members of the prolactin gene family

The trophoblast giant cell lineage is characterized by endoreduplication and expression of members of the PRL gene family. This report describes the functional consequences following in vitro manipulation of a rat trophoblast cell line, termed Rcho-1. Rcho-1 cells can be cultured under conditions that promote proliferation or differentiation. Proliferation is maintained by culturing the cells in the presence of fetal bovine serum under subconfluent conditions. Differentiation is induced by growing the cells to confluence and removing the mitogenic source. Differentiation is characterized by continued synthesis of DNA in the absence of proliferation (endoreduplication) and the sequential expression of members of the PRL gene family. Western and Northern blot analyses demonstrated that placental lactogen-I (PL-I) was first expressed, followed sequentially by PL-II, PRL-like protein-A, and PRL-like protein-C. The ontogeny of expression of members of the PRL gene family by the Rcho-1 cells recapitulated the pattern of in situ expression by trophoblast giant cells of the junctional zone of the chorioallantoic placenta. A notable difference between in vivo trophoblast giant cell differentiation and in vitro Rcho-1 cell differentiation is the termination of PL-I expression in normal trophoblast giant cells developing in vivo and the continued expression of PL-I in differentiated Rcho-1 cell cultures. The Rcho-1 cell line provides a unique in vitro model for investigating the initiation and maintenance of the trophoblast giant cell differentiation pathway.

Spontaneous differentiation of trophoblast cells along the spongiotrophoblast cell pathway: expression of members of the placental prolactin gene family and modulation by retinoic acid

The purpose of this study was to examine part of the trophoblast cell multilineage pathway and its modulation by retinoic acid. A method for studying trophoblast cell differentiation along the spongiotrophoblast cell pathway in vitro was established and characterized. Cells were isolated from junctional zones of Day 13 rat chorioallantoic placentas via mechanical dissection, enzymatic digestion, and enrichment through a Percoll cushion. The cells were cultured up to 8 days and analyzed for their purity, morphology, and ability to express members of the placental prolactin (PRL) family. Cell preparations contained minimal mesenchymal contamination as estimated by immunocytochemical analysis for vimentin. The cells expressed PRL-like protein-A (PLP-A), PLP-B, PLP-C, and placental lactogen-I variant (PL-Iv) indicative of their differentiated spongiotrophoblast cell phenotype. Expression of members of the PRL family increased markedly during culture. Temporally the increase in PLP-A expression preceded the increased expression of PLP-B (0.9 kb), PLP-C, and PL-Iv. These in vitro observations paralleled the behavior of spongiotrophoblast cells developing in situ. Some differences were evident, including the immediate activation of PLP-B (1.2 kb) following enzymatic isolation of the cells. These cells were also susceptible to experimental manipulation. Exposure to retinoic acid influenced the morphology of the cells and the profile of members of the placental PRL family expressed by in vitro differentiated cells. In summary, a culture system has been devised to examine the control of spongiotrophoblast cell differentiation and the regulation of expression of members of the placental PRL gene family. Spongiotrophoblast cells spontaneously differentiate in vitro through discrete developmental phases that are susceptible to modulation by retinoic acid.

[Scanning electron microscopy of adult Trichuris trichiura]

The paper reports the result of the observation on the ultrastructure of the body surface of adult T. trichiura by scanning electron microscopy. Unique features of T. trichiura are described including the presence of labial-shape structures at the periphery of mouth, eight cephalic pores and a pair of amphids around the mouth pore and vesicle-shaped cuticular protuberances on the abdomen of T. trichiura. Cuticular pores were found scattering on the surface of T. trichiura. Detailed descriptions of male copulatory sheath and spicule were presented.

[Scanning electron microscopic observations on the copulatory spicules of the male Necator americanus and Ancylostoma duodenale]

Scanning electron microscopic observations were made on the morphological structures of the two copulatory spicules of the male Necator americanus and Ancylostoma duodenale. In both species, one of the two copulatory spicules was in the shape of a concave groove and the other, in the shape of an oblate tube. Owing to the difference in the concavity of the groove shaped copulatory spicule between the two species as shown by the cross sections, Necator americanus usually appear to have only one copulatory spicule whereas Ancylostoma duodenale usually show two separate copulatory spicules in appearance (Figs 1-10).

Joint transform correlator that uses wavelet transforms

A joint transform correlation system based on wavelet transforms is introduced. The selection of wavelets and the optical wavelet transform of images enables this optical correlator to identify the specific features and distinguish similar characters. Preliminary experimental results are given.

Isopentenyl-diphosphate isomerase: irreversible inhibition by 3-methyl-3,4-epoxybutyl diphosphate

Isopentenyl-diphosphate:dimethylallyl-diphosphate isomerase (EC 5.3.3.2) catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl diphosphate (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP). Incubation of yeast IPP isomerase with 3-methyl-3,4-epoxybutyl diphosphate (EIPP) resulted in a time-dependent first-order loss of activity characteristic of an active-site-directed irreversible process, where k2 = 0.63 +/- 0.10 min-1 and KI = 0.37 +/- 0.11 microM. A 1:1 covalent E-I complex was formed upon incubation with [1-14C]EIPP. The inhibited enzyme was treated with trypsin to give two radioactive fragments, which were purified by reversed-phase HPLC on a C18 column. The modified amino acid in each fragment was identified as C139 by sequencing the radiolabeled peptides. Incubation of IPP isomerase with [2,4,5-13C3]EIPP gave a 13C-labeled E-I complex. A 1H-13C heteronuclear multiquantum correlation spectrum had strong cross-peaks at 1.2/28 and 2.9/48 ppm, which we assigned to the labeled methyl group and C(4) methylene, respectively, of the inhibitor. In addition, a weak signal at 2.17/42 ppm may be from the C(2) methylene. Comparison of these chemical shifts with those of a synthetic adduct isolated from treatment of EIPP with cysteine indicates C139 attacks C(4) of EIPP to generate a thioether linkage between the enzyme and the inhibitor.

Ring-array processor distribution topology for optical interconnects

The existing linear and rectangular processor distribution topologies for optical interconnects, although promising in many respects, cannot solve problems such as clock skews, the lack of supporting elements for efficient optical implementation, etc. The use of a ring-array processor distribution topology, however, can overcome these problems. Here, a study of the ring-array topology is conducted with an aim of implementing various fast clock rate, high-performance, compact optical networks for digital electronic multiprocessor computers. Practical design issues are addressed. Some proof-of-principle experimental results are included.