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The shelterin proteins protect telomeres against activation of the DNA damage checkpoints and recombinational repair. We show here that a dimer of the shelterin subunit TRF2 wraps ∼ 90 bp of DNA through several lysine and arginine residues localized around its homodimerization domain. The expression of a wrapping-deficient TRF2 mutant, named Top-less, alters telomeric DNA topology, decreases the number of terminal loops (t-loops), and triggers the ATM checkpoint, while still protecting telomeres against non-homologous end joining (NHEJ). In Top-less cells, the protection against NHEJ is alleviated if the expression of the TRF2-interacting protein RAP1 is reduced. We conclude that a distinctive topological state of telomeric DNA, controlled by the TRF2-dependent DNA wrapping and linked to t-loop formation, inhibits both ATM activation and NHEJ. The presence of RAP1 at telomeres appears as a backup mechanism to prevent NHEJ when topology-mediated telomere protection is impaired., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Vesicoureteral reflux (VUR) is a common and serious urinary disease in children. It usually causes renal scar, urinary tract infection, and chronic renal failure. Previous studies showed the angiotensin converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism might be associated with VUR; however, the conclusions were inconsistent. Therefore we used the meta-analytic approach to clarify the effect of ACE I/D polymorphism on VUR risk.We systematically searched the PubMed, CNKI, and EMBASE databases to identify all the potentially related studies published up to February 4, 2015. Two reviewers independently selected studies and extracted data. The strength of the association was assessed using odd ratio (OR) with its 95% confidence interval (CI) based on fixed or random effects model. The STATA 12.0 software was used for data analysis.A total of 14 case-control studies involving 1197 VUR patients and 1320 healthy controls met the eligibility criteria. Results of meta-analysis showed significant association between ACE I/D polymorphism and VUR risk (D vs. I: OR = 1.28, 95% CI = 1.06-1.54, P = 0.01; DD vs. II: OR = 1.44, 95% CI = 1.12-1.85, P = 0.01; DD vs. DI + II: OR = 1.49, 95% CI = 1.23-1.79, P < 0.01; DD + DI vs. II: OR = 1.20, 95% CI = 0.84-1.72, P = 0.31). Subgroup analyses revealed varied results. In Turkish people, results of all the genetic models other than DI vs. II showed statistical significance; in Caucasians, DD vs. DI + II showed statistical significance; and in Asians, DI versus II showed statistical significance.Our meta-analysis indicated that the ACE I/D polymorphism might be associated with increased risk of VUR in children. However, due to the limitations, we suggest conducting additional studies with larger sample size and adjustment for various risk factors, in the future for further clarification., Competing Interests: The authors have no conflicts of interest to disclose.

Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis studies.

Autophagy regulates cell differentiation, proliferation, and survival in multiple cell types, including cells of the immune system. In this study, we examined the effects of a disruption of autophagy on the differentiation of invariant NKT (iNKT) cells. Using mice with a T lymphocyte-specific deletion of Atg5 or Atg7, two members of the macroautophagic pathway, we observed a profound decrease in the iNKT cell population. The deficit is cell-autonomous, and it acts predominantly to reduce the number of mature cells, as well as the function of peripheral iNKT cells. In the absence of autophagy, there is reduced progression of iNKT cells in the thymus through the cell cycle, as well as increased apoptosis of these cells. Importantly, the reduction in Th1-biased iNKT cells is most pronounced, leading to a selective reduction in iNKT cell-derived IFN-γ. Our findings highlight the unique metabolic and genetic requirements for the differentiation of iNKT cells., (Copyright © 2015 by The American Association of Immunologists, Inc.)

The sampling-analysis method for CPM of stationary source was established and the sampling device was developed. The determination method was compared with EPA method 202 and applied in real-world test in coal-fired power plants. The result showed the average CPM emission concentration in the coal-fired power plant was (21.2 ± 3.5) mg · m(-3) while the FPM was (20.6 ± 10.0) mg · m(-3) during the same sampling period according to the method in the national standard. The high-efficiency dust removal device could efficiently reduce FPM emission but showed insignificant effect on CPM. The mass contribution of CPM to TPM would rise after high-efficiency dust removal rebuilding project, to which more attention should be paid. The condensate contributed 68% to CPM mass while the filter contributed 32%, and the organic component contributed little to CPM, accounting for only 1%.

Background: Integrated 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) is widely performed for staging solitary pulmonary nodules (SPNs). However, the diagnostic efficacy of SPNs based on PET/CT is not optimal. Here, we propose a method of detection based on PET/CT that can differentiate malignant and benign SPNs with few false-positives., Method: Our proposed method combines the features of positron-emission tomography (PET) and computed tomography (CT). A dynamic threshold segmentation method was used to identify lung parenchyma in CT images and suspicious areas in PET images. Then, an improved watershed method was used to mark suspicious areas on the CT image. Next, the support vector machine (SVM) method was used to classify SPNs based on textural features of CT images and metabolic features of PET images to validate the proposed method., Results: Our proposed method was more efficient than traditional methods and methods based on the CT or PET features alone (sensitivity 95.6%; average of 2.9 false positives per scan).

Background: Tumor-associated macrophages (TAMs) are a major component of leukocyte infiltration in the tumor microenvironment. Osteopontin is related to tumor metastasis and proliferation. Osteopontin is expressed not only by tumor cells but also by TAMs. The purpose of the current study was to assess the prognostic significance of osteopontin expressed by TAMs (TOPN) in patients with non-small cell lung cancer., Methods: Tissue microarray was used to detect the expression of TOPN, TAMs, and microvascular density in 159 patients with non-small cell lung cancer undergoing complete pulmonary resection in our hospital between 2003 and 2006. The correlations between TOPN, TAMs, and clinicopathologic data were analyzed with χ(2) tests. Quantitation of TAMs or TOPN and microvascular density analyses was performed using Bonferroni correction and the Student's t test. The prognostic value of TOPN was evaluated by univariate Kaplan-Meier survival analysis and multivariate Cox proportional hazard model analysis., Results: In the recurrence and metastasis group, microvascular density was higher than that in the control group (14.4 ± 1.06 versus 8.9 ± 1.02; p = 0.0002). In the TOPN-positive group, microvascular density was increased compared with that in the TOPN-negative group (14.3 ± 1.37 versus 10.7 ± 0.91; p = 0.0273). Osteopontin expressed by TAMs was an independent predictor for overall survival (p = 0.017) and disease-free survival (p < 0.001), especially for stage I non-small cell lung cancer. The 6-year overall and disease-free survival rates in TOPN-positive patients were 22.64% and 16.98%, respectively, which were significantly lower than those of TOPN-negative patients (50.00% and 39.62%, respectively)., Conclusions: Osteopontin expressed by TAMs is a valuable independent predictor of tumor recurrence and survival in patients with non-small cell lung cancer., (Copyright © 2015 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.)

Objective: This study aimed to explore the expression of tumor-derived colony-stimulating factor 1 (CSF1), its prognostic significance and underlying related mechanisms in resected lung adenocarcinoma (ADC)., Methods: Immunohistochemistry and tissue microarray were used to detect the expression of CSF1, epidermal growth factor receptor (EGFR), and CD68 in 266 patients with lung adenocarcinoma treated in our department between 2004 and 2008., Results: In the 266 ADC cases, the positive rates of expression of CSF1, EGFR and CD68 proteins were 56.4%, 42.1% and 81.2%, respectively. The expression level of CSF1 was positively correlated with TNM stage, number of involved nodal stations, tumor recurrence and EGFR expression (P<0.05). Univariate analysis indicated that TNM stage, number of involved lymph nodes, number of involved nodal stations, CSF1 expression, the combination of CSF1/EGFR and co-expression of CSF1/CD68/EGFR were statistically significant for prognosis (P<0.05). The results of multivariate analysis showed that TNM stage, co-expression of CSF1/EGFR and CSF1/CD68/EGFR were significant and independent risk factors for survival (P<0.05). Correlational analysis showed that expression of CSF1 and EGFR in the tumors was positively correlated to the degree of infiltration of interstitial tumor-associated macrophages (TAMs) (respectively; P<0.05)., Conclusions: The expression of CSF1 indicates a poor prognosis in postoperative lung adenocarcinoma. Co-expression of CSF1 and EGFR may be a valuable independent prognostic predictor, and its mechanism is probably involved in the interaction of cancer cells and TAMs in the progression of lung adenocarcinoma.

Children in early infancy do not mount effective antibody responses to many vaccines against commons infectious pathogens, which results in a window of increased susceptibility or severity infections. In addition, vaccine-preventable infections are among the leading causes of morbidity in pregnant women. Immunization during pregnancy can generate maternal immune protection as well as elicit the production and transfer of antibodies cross the placenta and via breastfeeding to provide early infant protection. Several successful vaccines are now recommended to all pregnant women worldwide. However, significant gaps exist in our understanding of the efficacy and safety of other vaccines and in women with conditions associated with increased susceptible to high-risk pregnancies. Public acceptance of maternal immunization remained to be improved. Broader success of maternal immunization will rely on the integration of advances in basic science in vaccine design and evaluation and carefully planned clinical trials that are inclusive to pregnant women.

Pseudogenes are degraded fossil copies of genes. Here, we report a comparison of pseudogenes spanning three phyla, leveraging the completed annotations of the human, worm, and fly genomes, which we make available as an online resource. We find that pseudogenes are lineage specific, much more so than protein-coding genes, reflecting the different remodeling processes marking each organism's genome evolution. The majority of human pseudogenes are processed, resulting from a retrotranspositional burst at the dawn of the primate lineage. This burst can be seen in the largely uniform distribution of pseudogenes across the genome, their preservation in areas with low recombination rates, and their preponderance in highly expressed gene families. In contrast, worm and fly pseudogenes tell a story of numerous duplication events. In worm, these duplications have been preserved through selective sweeps, so we see a large number of pseudogenes associated with highly duplicated families such as chemoreceptors. However, in fly, the large effective population size and high deletion rate resulted in a depletion of the pseudogene complement. Despite large variations between these species, we also find notable similarities. Overall, we identify a broad spectrum of biochemical activity for pseudogenes, with the majority in each organism exhibiting varying degrees of partial activity. In particular, we identify a consistent amount of transcription (∼15%) across all species, suggesting a uniform degradation process. Also, we see a uniform decay of pseudogene promoter activity relative to their coding counterparts and identify a number of pseudogenes with conserved upstream sequences and activity, hinting at potential regulatory roles.

Objective: To study the effect of length of cervical anterior fusion on adjacent levels by Biomechanical test., Methods: Six fresh-frozen human cervical specimens were used in this study. The specimens were tested in flexion, extension, bending and rotation on a spine 3D test system. The specimens were tested intact and then underwent a single-level anterior cervical discectomy and fusion (ACDF) at the C4-5 first, a double-level fusion at the C4-6, and finally extended to triple-level at the C4-7, Based on a hybrid test method. Changes in overall range of motion (ROM), segmental motion and facet joints pressure during flexion, extension, bending and rotation were measured and statistically analyzed., Results: The overall ROM of the entire spinal construct decreased progressively as the single-level fixation extending to 2-level and 3-level (P < 0.05). A progressive increase in ROM above (C3-4) the fused motion segment units (MSUs) was found during flexion, extension and bending (P < 0.05). In bending and extension, a same result was recorded on the average pressure and max pressure of C3-4 facet joints (P < 0.05)., Conclusions: This study has demonstrated that the biomechanics at adjacent levels to a cervical spine fusion are altered and that there was progressively increased adjacent segment motion and stress as a single-level ACDF extended to a 3-level fusion, which might lead to the acceleration of adjacent segment degeneration.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

Hemodynamic situation is an important factor of recurrence of postoperative carotid artery aneurysm. In order to investigate the hemodynamic factors of postoperative carotid artery aneurysm affect carotid artery aneurysm recurrence, we established a 3D finite element carotid artery aneurysm for the preoperative and postoperative periods using the three-dimensional reconstruction techniques. And then we measured the hemodynamic factors of carotid artery aneurysm of preoperative and postoperative by the finite element method. The carotid artery aneurysm model has an accurate and realistic shape; the pressure of the recurrence of aneurysm was reduced significantly after surgery,wall shear stress increased significantly at residual neck, and blood flow velocity increased significantly, which will increase the risk of recurrence. The hemodynamic analysis provides a reference for development of aneurysm clinical treatment programs and prevention of recurrence.

Objective: To explore the relationship of the activity of plasma FVII with isolated blunt traumatic brain injury and progressive hemorrhagic injury., Methods: Eight-one isolated traumatic brain patients with moderate-to-severe injury, aged ≥ 16 yrs, were recruited from August 2010 to December 2012. The plasma factor VII activity was measured after admission. On arrival at emergency department, blood samples were collected to analyze the parameters of activated partial thromboplastic time (aPTT), international normalized ratio (INR), platelet count and activity of factor VII. TBI-associated coagulopathy was defined as elevated international normalized ratio >1.2 or prolonged activated partial thromboplastic time >40 seconds or platelet count <120×10(9)/L at admission. Progressive hemorrhagic injury was present when follow-up computed tomography (CT) noted any increase in size or number of hemorrhagic lesions. Logistic regression examined the risks for coagulopathy and progressive hemorrhagic injury after isolated traumatic brain injury., Results: FVII activity in patients with coagulopathy was 86% ± 35%. And it was significantly lower than those without coagulopathy (100 ± 29%, P < 0.05). Isolated traumatic brain injury patients with FVII activity <77.5% had an odds ratio for coagulopathy of 5.52 (95% confidence interval 1.82-16.68, P < 0.05) relative to those with FVII activity ≥ 77.5%. FVII activity in patients with progressive hemorrhagic injury was 71% ± 18%. And it was significantly lower than those without progressive hemorrhagic injury (106% ± 32%, P < 0.001). Stepwise Logistic regression analysis identified FVII < 77.5% as a predisposing risk factor independently associated with the presence of progressive hemorrhagic injury. The overall mortality rate in the surveyed population was 7.4% (6/81). The plasma FVII in deceased patients (91% ± 47%) was slightly lower than that in survivors (92% ± 32%, P > 0.05). No significant difference existed between two groups (P > 0.05)., Conclusions: Decreased activity of FVII is closely correlated with coagulopathy in patients with isolated blunt traumatic brain injury. And coagulopathy and decreased FVII activity are predisposing risk factors independently associated with progressive hemorrhagic injury.

Background: Given the importance of factor VII (FVII) in extrinsic pathway of coagulation cascade, we sought to elucidate the relationship between FVII and traumatic brain injury-induced coagulopathy and progressive hemorrhagic injury (PHI)., Methods: Eighty-one patients with isolated traumatic brain injury, 16 years or older, were recruited between 2010 and 2012. Blood was collected on arrival in the emergency department and analyzed with activated partial thromboplastic time, international normalized ratio, platelet count, and activity of FVII. Coagulopathy was defined as thrombocytopenia (platelet count < 120,000/μL) or elevated international normalized ratio of greater than 1.2 or prolonged activated partial thromboplastin time greater than 40 seconds at admission. PHI was present when the follow-up computed tomographic scan reported any increase in size or number of the hemorrhagic lesions. Logistic regression examined the risks for coagulopathy and PHI., Results: Mean (SD) FVII activity in patients with coagulopathy was 85.69% (34.88%), which was significantly lower than patients without coagulopathy (99.57% [29.37%], p = 0.04). Isolated traumatic brain injury patients with FVII activity less than 77.5% have an odds ratio for coagulopathy of 5.52 (95% confidence interval, 1.82-16.68; p = 0.03) relative to patients with FVII activity of 77.5% or greater. Mean (SD) FVII activity in patients with PHI was 70.76% (18.21%), which was significantly lower than patients without PHI (105.76% [32.27%], p < 0.001). A stepwise logistic regression analysis identified FVII less than 77.5% (odds ratio, 4.53; 95% confidence interval, 1.62-12.67; p = 0.004) as a predisposing risk factors independently associated with the presence of PHI. The overall mortality rate in the study population was 7.4% (n = 6). The plasma FVII in death patients (91.44% [47.19%]) was slightly lower than that in survival patients (92.01% [32.04%]). However, there was no statistical difference between the two groups (p = 0.95)., Conclusion: A decrease of FVII activity significantly contributes to the coagulopathy and PHI in patients with isolated traumatic brain injury., Level of Evidence: Prognostic study, level III.

In primates and other animals, reverse transcription of mRNA followed by genomic integration creates retroduplications. Expressed retroduplications are either "retrogenes" coding for functioning proteins, or expressed "processed pseudogenes," which can function as noncoding RNAs. To date, little is known about the variation in retroduplications in terms of their presence or absence across individuals in the human population. We have developed new methodologies that allow us to identify "novel" retroduplications (i.e., those not present in the reference genome), to find their insertion points, and to genotype them. Using these methods, we catalogued and analyzed 174 retroduplication variants in almost one thousand humans, which were sequenced as part of Phase 1 of The 1000 Genomes Project Consortium. The accuracy of our data set was corroborated by (1) multiple lines of sequencing evidence for retroduplication (e.g., depth of coverage in exons vs. introns), (2) experimental validation, and (3) the fact that we can reconstruct a correct phylogenetic tree of human subpopulations based solely on retroduplications. We also show that parent genes of retroduplication variants tend to be expressed at the M-to-G1 transition in the cell cycle and that M-to-G1 expressed genes have more copies of fixed retroduplications than genes expressed at other times. These findings suggest that cell division is coupled to retrotransposition and, perhaps, is even a requirement for it.

Taking the two-year old potted Prunus sibirica seedlings as test materials, and using CIRAS-2 photosynthetic system, this paper studied the CO2 response process of P. sibirica photosynthesis in semi-arid loess hilly region under eight soil moisture conditions. The CO2 response data of P. sibirica were fitted and analyzed by rectangular hyperbola model, exponential equation, and modified rectangular hyperbola model. Meanwhile, the quantitative relationships between the photosynthesis and the soil moisture were discussed. The results showed that the CO2 response process of P. sibirica photosynthesis had obvious response characteristics to the soil moisture threshold. The relative soil water content (RWC) required to maintain the higher photosynthetic rate (P(n)) and carboxylation efficiency (CE) of P. sibirica was in the range of 46.3%-81.9%. In this RWC range, the photosynthesis did not appear obvious CO2 saturated inhibition phenomenon. When the RWC exceeded this range, the photosynthetic capacity (P(n max)), CE, and CO2 saturation point (CSP) decreased evidently. Under different soil moisture conditions, there existed obvious differences among the three models in simulating the CO2 response data of P. sibirica. When the RWC was in the range of 46.3%-81.9%, the CO2 response process and the characteristic parameters such as CE, CO2 compensation point (see symbol), and photorespiration rate (R(p)) could be well fitted by the three models, and the accuracy was in the order of modified rectangular hyperbola model > exponential equation > rectangular hyperbola model. When the RWC was too high or too low, namely, the RWC was > 81.9% or < 46.3%, only the modified rectangular hyperbola model could well fit the CO2 response process and the characteristic parameters. It was suggested that when the RWC was from 46.3% to 81.9%, the photosynthetic efficiency of P. sibirica was higher, and, as compared with rectangular hyperbola model and exponential equation, modified rectangular hyperbola model had more applicability to fit the CO2 response data of P. sibirica photosynthesis under different soil moisture conditions.

A major issue in telomere research is to understand how the integrity of chromosome ends is controlled. The fact that different types of nucleoprotein complexes have been described at the telomeres of different organisms raises the question of whether they have in common a structural identity that explains their role in chromosome protection. We will review here how telomeric nucleoprotein complexes are structured, comparing different organisms and trying to link these structures to telomere biology. It emerges that telomeres are formed by a complex and specific network of interactions between DNA, RNA, and proteins. The fact that these interactions and associated activities are reinforcing each other might help to guarantee the robustness of telomeric functions across the cell cycle and in the event of cellular perturbations. We will also discuss the recent notion that telomeres have evolved specific systems to overcome the DNA topological stress generated during their replication and transcription. This will lead to revisit the way we envisage the functioning of telomeric complexes since the regulation of topology is central to DNA stability, replication, recombination, and transcription as well as to chromosome higher-order organization.

Vibrio cholerae is the causative agent of the devastating diarrheal disease cholera. A number of regulatory pathways are involved in V. cholerae pathogenesis and antibiotic resistance. For example, there are over 40 LysR-family proteins in the V. cholerae genome, but most of their functions are unknown. In this study, we examine the role of VC2323 (TehAVc) and its divergently transcribed LysR-family regulator VC2324 (TehRVc) in V. cholerae pathogenesis. We found that in V. cholerae C6706, the expression of tehAVc is dependent on TehRVc. VC2323 (TehAVc), homologous to the Escherichia coli tellurite resistance protein (TehAEc), differs from TehAEc in that TehAVc has no noticeable role in tellurite resistance but instead contributes to chloramphenicol resistance. Interestingly, both tehAVc and tehRVc mutants were defective in colonization of infant mice. Though the expression of a key virulence gene tcpA was not affected in either of these mutants, tehAVc mutants failed to attach to mouse intestinal surfaces in the presence of crude bile, suggesting a new role of the TehAVc-TehRVc pair in V. cholerae pathogenesis.

In view of the shortage of medical equipment road transportation simulation platform, we put forward a road transportation simulation method based on 6-DOF parallel robots. A 3D road spectrum model was built by the improvement of the harmonic superposition method. The simulation model was then compared with the standard model to verify its performance. Taking the road spectrum as the excitation, we could get the robot motion data to control the parallel robot through the S-shaped linear interpolation of the absolute position. It can simulate the movement of vehicles with different speed under various road conditions efficiently and accurately.

Bayesian network model is widely used for reverse engineering of biological network structures. An advantage of this model is its capability to integrate prior knowledge into the model learning process, which can lead to improving the quality of the network reconstruction outcome. Some previous works have explored this area with focus on using prior knowledge of the direct molecular links, except for a few recent ones proposing to examine the effects of molecular orderings. In this study, we propose a Bayesian network model that can integrate both direct links and orderings into the model. Random weights are assigned to these two types of prior knowledge to alleviate bias toward certain types of information. We evaluate our model performance using both synthetic data and biological data for the RAF signaling network, and illustrate the significant improvement on network structure reconstruction of the proposing models over the existing methods. We also examine the correlation between the improvement and the abundance of ordering prior knowledge. To address the issue of generating prior knowledge, we propose an approach to automatically extract potential molecular orderings from knowledge resources such as Kyoto Encyclopedia of Genes and Genomes (KEGG) database and Gene Ontology (GO) annotation.

Sulfatide-reactive CD1d-restricted natural killer T (NKT) lymphocytes belong to the type II NKT cell subset with diverse TCRs, and have been found to regulate experimental auto-immune encephalomyelitis, tumor immunity, and experimental hepatitis in murine models. NKT cells can be activated by self-lipids presented by CD1d, manifested as autoreactivity. The identity of most of these self-lipids remains unknown. By isolating lipids from a CD1d-expressing, highly stimulatory antigen presenting cell, we identified isoforms of β-glucosylceramide (GlcCer), with sphingosine and fatty acid chain lengths of C24:0 and C16:0, that activated a sulfatide-reactive type II NKT cell hybridoma. A screen of structurally related glycosphingolipids demonstrated β-galactosylceramide (GalCer) as another ligand, and further, that the lysoforms were the most potent isoform of the glycosphingo-lipid ligands, followed by isoforms with a long fatty acid chain of C24. Thus, the same type II NKT cell was activated by several ligands, namely sulfatide, GlcCer, and GalCer. However, CD1d-dependent reactivity to antigen presenting cells lacking all GlcCer-based glycosphingolipids, or all glycosphingolipids, was maintained. This suggests that other endogenous, nonglycosphingolipid, lipid ligands contribute to steady-state autoreactivity by type II NKT cells., (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Background: Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data., Results: As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large-scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection., Conclusions: At one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes.

The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.

Background: To determine potential social, psychological, and environmental-structural factors that may result in motivating female sex workers (FSWs), who are rural-to-urban migrants, and their paying partners in Shanghai, China to promote consistent condom use (CCU)., Methods: A cross-sectional study was conducted in five districts of Shanghai, including three suburbs and two downtown locales. We adopted a cluster randomized sampling method to obtain 20 geographic sites, which consisted of 1 or more communities/villages proximal to a location where FSWs were accessible. Five hundred four FSWs from 132 Xitou Fang (shampoo wash rooms), massage parlors, and hair salons who explicitly provided sexual services were enrolled in the study. Each participant completed a questionnaire survey and interview aimed to collect information on the perceptions and behaviors of individuals associated with a risk for human immunodeficiency virus/acquired immunodeficiency syndrome(HIV/AIDS),self-efficacy at negotiating safe sex,and the physical, social, and policy environment of the establishments where they worked., Results: The percentage of FSWs who reported consistent condom use with their paying partners was 63.3%. Controlling for socio-demographic characteristics in multivariate analyses, environmental-structural support (OR, 3.96; CI, 2.52-6.22) for condom use was the most significant positive predictor of CCU among FSWs and their regular paying partners. A high perception of susceptibility and risk of HIV/AIDS (OR, 1.96; CI, 1.25-3.01), a high perception of benefits on condom use to protect themselves (OR, 2.06; CI, 1.32-3.22), and high safe sex self-efficacy (OR, 2.52; CI, 1.64-3.85) also play important roles on CCU based on multivariate analyses., Conclusions: Environmental-structural factor support for condom use, in addition to social, psychological, and individual cognitive factors are significant predictors of CCU among FSWs, which should be assessed and addressed in research and interventions related to HIV/AIDS prevention among FSWs in China.

Many statistical methods have been developed to screen for differentially expressed genes associated with specific phenotypes in the microarray data. However, it remains a major challenge to synthesize the observed expression patterns with abundant biological knowledge for more complete understanding of the biological functions among genes. Various methods including clustering analysis on genes, neural network, Bayesian network and pathway analysis have been developed toward this goal. In most of these procedures, the activation and inhibition relationships among genes have hardly been utilized in the modeling steps. We propose two novel Bayesian models to integrate the microarray data with the putative pathway structures obtained from the KEGG database and the directional gene-gene interactions in the medical literature. We define the symmetric Kullback-Leibler divergence of a pathway, and use it to identify the pathway(s) most supported by the microarray data. Monte Carlo Markov Chain sampling algorithm is given for posterior computation in the hierarchical model. The proposed method is shown to select the most supported pathway in an illustrative example. Finally, we apply the methodology to a real microarray data set to understand the gene expression profile of osteoblast lineage at defined stages of differentiation. We observe that our method correctly identifies the pathways that are reported to play essential roles in modulating bone mass.

Natural killer T (NKT) cells are a T cell subpopulation that were named originally based on coexpression of receptors found on natural killer (NK) cells, cells of the innate immune system, and by T lymphocytes. The maturation and activation of NKT cells requires presentation of glycolipid antigens by CD1d, a cell surface protein distantly related to the major histocompatibility complex (MHC)-encoded antigen presenting molecules. This specificity distinguishes NKT cells from most CD4(+) and CD8(+) T cells that recognize peptides presented by MHC class I and class II molecules. The rapid secretion of a large amount of both Th1 and Th2 cytokines by activated NKT cells endows them with the ability to play a vital role in the host immune defense against various microbial infections. In this review, we summarize progress on identifying the sources of microbe-derived glycolipid antigens recognized by NKT cells and the biochemical basis for their recognition., (© 2012 New York Academy of Sciences.)

TRF1 and TRF2 are key proteins in human telomeres, which, despite their similarities, have different behaviors upon DNA binding. Previous work has shown that unlike TRF1, TRF2 condenses telomeric, thus creating consequential negative torsion on the adjacent DNA, a property that is thought to lead to the stimulation of single-strand invasion and was proposed to favor telomeric DNA looping. In this report, we show that these activities, originating from the central TRFH domain of TRF2, are also displayed by the TRFH domain of TRF1 but are repressed in the full-length protein by the presence of an acidic domain at the N-terminus. Strikingly, a similar repression is observed on TRF2 through the binding of a TERRA-like RNA molecule to the N-terminus of TRF2. Phylogenetic and biochemical studies suggest that the N-terminal domains of TRF proteins originate from a gradual extension of the coding sequences of a duplicated ancestral gene with a consequential progressive alteration of the biochemical properties of these proteins. Overall, these data suggest that the N-termini of TRF1 and TRF2 have evolved to finely regulate their ability to condense DNA.

Background: Leprosy is a chronic infectious disease caused by Mycobacterium leprae. Cell-mediated (Th1) immune response and humoral (Th2) immune response play different roles in leprosy infection. Interleukin 4 (IL-4) is a typical Th2 cytokine. It is a critical mediator of the Th1/Th2 balance., Objective: The objective of this study is to investigate the association between IL-4 gene -590T/C polymorphism and the susceptibility to leprosy in a Chinese population., Methods: The IL-4 variant -590T/C was detected by polymerase chain reaction-restriction fragment length polymorphism in 432 leprosy cases and 465 age-matched healthy controls. Data were analyzed using the chi-square test., Results: Frequencies of the IL-4-590TC and CC genotypes and the -590C allele were significantly lower in patients with leprosy than in healthy controls (odds ratio [OR]=0.74, 95% confidence interval [CI] 0.55-0.99, p=0.044; OR=0.46, 95% CI 0.25-0.84, p=0.010; and OR=0.68, 95% CI 0.54-0.86, p=0.001, respectively)., Conclusions: Our data suggest that the -590T/C polymorphism of the IL-4 gene is associated with decreased susceptibility of leprosy.

Invariant natural killer T (iNKT) cells are an evolutionary conserved T cell population characterized by features of both the innate and adaptive immune response. Studies have shown that iNKT cells are required for protective responses to Gram-positive pathogens such as Streptococcus pneumoniae, and that these cells recognize bacterial diacylglycerol antigens presented by CD1d, a non-classical antigen-presenting molecule. The combination of a lipid backbone containing an unusual fatty acid, vaccenic acid, as well as a glucose sugar that is weaker or not stimulatory when linked to other lipids, is required for iNKT cell stimulation by these antigens. Here we have carried out structural and biophysical studies that illuminate the reasons for the stringent requirement for this unique combination. The data indicate that vaccenic acid bound to the CD1d groove orients the protruding glucose sugar for TCR recognition, and it allows for an additional hydrogen bond of the glucose with CD1d when in complex with the TCR. Furthermore, TCR binding causes an induced fit in both the sugar and CD1d, and we have identified the CD1d amino acids important for iNKT TCR recognition and the stability of the ternary complex. The studies show also how hydrogen bonds formed by the glucose sugar can account for the distinct binding kinetics of the TCR for this CD1d-glycolipid complex. Therefore, our studies illuminate the mechanism of glycolipid recognition for antigens from important pathogens., Competing Interests: The authors have declared that no competing interests exist.

We utilized a sulcus-based computational approach to investigate the relationship between the three-dimensional (3D) morphology of the central sulcus (CS) and age. The anterior and posterior walls of the CS were manually outlined using high-resolution magnetic resonance images of 295 right-handed healthy participants (age range: 18~94years). Surface reconstruction and parameterization methods were employed to create anatomical correspondence of surface locations across participants. Four surface metrics, including average sulcal length (SL), surface area, fractal dimension (FD) and sulcal span, were used to represent the 3D morphology of the CS. We found significant age-related decreases in the surface area for all walls of the CS, the SL for posterior walls of the CS and the FD for posterior wall of right CS. Age-related increases were found in the sulcal spans between the anterior and posterior walls. These surface metrics (except FD) exhibited leftward asymmetries. Specifically, age-related changes in surface morphology progressed more rapidly in the posterior than in the anterior walls. Finally, sex differences were found only in the FD of the right anterior wall of the CS. Taken together, our results show age-related changes in the surface morphology of the CS and therefore provide insights into the normal aging process., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Natural killer T cells (NKT cells) recognize glycolipid antigens presented by CD1d. These cells express an evolutionarily conserved, invariant T cell antigen receptor (TCR), but the forces that drive TCR conservation have remained uncertain. Here we show that NKT cells recognized diacylglycerol-containing glycolipids from Streptococcus pneumoniae, the leading cause of community-acquired pneumonia, and group B Streptococcus, which causes neonatal sepsis and meningitis. Furthermore, CD1d-dependent responses by NKT cells were required for activation and host protection. The glycolipid response was dependent on vaccenic acid, which is present in low concentrations in mammalian cells. Our results show how microbial lipids position the sugar for recognition by the invariant TCR and, most notably, extend the range of microbes recognized by this conserved TCR to several clinically important bacteria.

Invariant NKT cells (iNKT cells) are a unique subset of T lymphocytes that rapidly carry out effector functions. In this study, we report that a majority of sterile house dust extracts (HDEs) tested contained antigens capable of activating mouse and human iNKT cells. HDEs had adjuvant-like properties in an ovalbumin (OVA)-induced asthma model, which were dependent on Vα14i NKT cells, as vaccinated animals deficient for iNKT cells displayed significantly attenuated immune responses and airway inflammation. Furthermore, the administration of HDEs together with OVA mutually augmented the synthesis of cytokines by Vα14i NKT cells and by conventional CD4(+) T cells in the lung, demonstrating a profound immune response synergy for both Th2 cytokines and IL-17A. These data demonstrate that iNKT cell antigens are far more widely dispersed in the environment than previously anticipated. Furthermore, as the antigenic activity in different houses varied greatly, they further suggest that iNKT cell responses to ambient antigens, particular to certain environments, might promote sensitization to conventional respiratory allergens.

NKT cells with an invariant Ag receptor (iNKT cells) represent a highly conserved and unique subset of T lymphocytes having properties of innate and adaptive immune cells. They have been reported to regulate a variety of immune responses, including the response to cancers and the development of autoimmunity. The development and activation of iNKT cells is dependent on self-Ags presented by the CD1d Ag-presenting molecule. It is widely believed that these self-Ags are glycosphingolipids (GSLs), molecules that contain ceramide as the lipid backbone. In this study, we used a variety of methods to show that mammalian Ags for mouse iNKT cells need not be GSLs, including the use of cell lines deficient in GSL biosynthesis and an inhibitor of GSL biosynthesis. Presentation of these Ags required the expression of CD1d molecules that could traffic to late endosomes, the site where self-Ag is acquired. Extracts of APCs contain a self-Ag that could stimulate iNKT cells when added to plates coated with soluble, rCD1d molecules. The Ag(s) in these extracts are resistant to sphingolipid-specific hydrolase digestion, consistent with the results using live APCs. Lyosphosphatidylcholine, a potential self-Ag that activated human iNKT cell lines, did not activate mouse iNKT cell hybridomas. Our data indicate that there may be more than one type of self-Ag for iNKT cells, that the self-Ags comparing mouse and human may not be conserved, and that the search to identify these molecules should not be confined to GSLs.

This paper designed a ventilator control system to control proportional valves and motors. It used LabVIEW to control the object mentioned above and design ,validate, evaluate arithmetic, and establish hardware in loop platform. There are two system' s hierarchies. The high layer was used to run non-real time program and the low layer was used to run real time program. The two layers communicated through TCP/IP net. The program can be divided into several modules, which can be expanded and maintained easily. And the harvest in the prototype designing can be seamlessly used to embedded products. From all above, this system was useful in employing OEM products.

The title layered coordination polymer, [Cd(C(14)H(16)N(5)O(3))(2)](n) or [Cd(ppa)(2)](n), where ppa is 8-ethyl-5-oxo-2-(piperazin-1-yl)-5,8-dihydro-pyrido[2,3-d]pyrimidine-6-carboxyl-ate, was syn-thesized under hydro-thermal conditions. The Cd(II) atom (site symmetry 2) exhibits a distorted cis-CdN(2)O(4) octa-hedral geometry defined by two N-monodentate and two O,O'-bidentate ppa monoanions. The extended two-dimensional structure resulting from the bridging ppa species is a grid lying parallel to (001). An N-H⋯O hydrogen bond helps to establish the crystal packing.

Objective: To explore the relationship between expressions of estrogen (ER) and progesterone (PR) receptors and syndromes of traditional Chinese medicine (TCM) in gastric carcinoma and to establish prognostic indicators for gastric carcinoma., Methods: A total of 72 patients with gastric carcinoma were divided into six groups according to TCM syndrome differentiation. Specimens were collected after operation and ER and PR protein expressions were detected by EnVision immunohistochemical method., Results: The common syndromes in female patients with gastric carcinoma were disharmony between liver and stomach, yin impairment due to stomach heat, and insufficiency of both qi and blood; while in males, interior retention of stagnant toxin, interior retention of phlegm and dampness, and deficiency-cold in spleen and stomach were common. Different TCM syndromes were related with gender (P<0.01), pathology (P<0.01), cell differentiation (P<0.05), infiltration depth (P<0.01), lymphaden metastasis (P<0.05), distant metastasis (P<0.05), and TNM stage (P<0.01). Deficiency and excess syndromes were associated with gender (P<0.05), pathology (P<0.05), tumor location (P<0.01) and TNM stage (P<0.05). The deficiency syndromes were common in female patients. The total positive rates of ER and PR expressions were 8.33% and 37.5% respectively. There was a significant difference in PR expression among different TCM syndromes (P<0.01). PR expression was significantly higher in the syndrome of yin deficiency due to stomach heat than in the other syndromes. The PR expressions in deficiency syndromes were significantly higher than those in excess syndromes (P<0.01). No correlation was found between ER expression and different TCM syndromes., Conclusion: There is a correlation between PR expression and different TCM syndromes in gastric carcinoma.

Background: China is currently facing a rapid and widespread increase in human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS). The activities of female sex workers (FSWs) have contributed to the mounting epidemic of HIV/AIDS and other sexually transmitted diseases (STDs). Therefore, this study aimed to assess the HIV/AIDS-related knowledge, attitude and risk behaviors among FSWs operating in Shanghai China., Methods: A cross-sectional study was conducted in five districts of Shanghai, including three suburbs and two downtown locales. We adopted a cluster randomized sampling method to obtain ten geographic sites which consisted of one or more communities/villages proximal to a location where FSWs were accessible. A total of 324 FSWs from 109 Xitou Fang, massage parlors and hair salons who explicitly provided sexual services were enrolled in the study. Each participant completed a questionnaire survey and interview aimed to collect information on the individual's knowledge, attitude, and behaviors associated with risk for HIV/AIDs., Results: The overall correct answer rate of HIV/AIDS-related knowledge was 60.8%, and the knowledge of FSWs from downtown areas was significantly higher than those from suburban areas (P < 0.05). The percentage of FSWs who reported having experiences in commercial sexual services without the use of condoms was 33.6%. Condom slippage or breakage was reported as having occurred at least once by 51.2% of the FSWs. FSWs from suburban areas were found to more often engage in high-risk behaviors, including oral and anal sex, than those from downtown areas (P < 0.001). Many of the FSWs (65.7%) reported having non-client sexual partners (most were identified as boyfriends or husbands); however, condom usage with these partners were lower (34.3%)., Conclusions: Based on the findings from our survey, we advise that promotion of HIV/AIDS-related knowledge be targeted towards FSWs in Shanghai, especially those operating in the suburbs. HIV prevention efforts, such as urging constant condom usage with both clients and steady partners, should be sustained and reinforced among the female sex workers population.

The characteristics of 30 carriers with occult hepatitis B virus (HBV) infection (OBI) were compared with those of 30 individuals diagnosed as being HBV carriers at the time of blood donation, 60 asymptomatic carriers, and 60 chronic hepatitis patients. The prevalence of genotype C was significantly higher in carriers with OBIs than in any other HBsAg-positive (HBsAg(+)) group (P < 0.001). Specific amino acid substitutions in the regions from amino acids 117 to 121 and amino acids 144 to 147 located in the major hydrophilic region of the S gene were associated with carriers with OBIs (P < 0.01 for carriers with OBIs versus HBsAg(+) donors, carriers with OBIs versus HBsAg(+) asymptomatic carriers, and carriers with OBIs versus HBsAg(+) chronic hepatitis patients). G145R was the major variation in the HBV isolates responsible for local occult HBV infections.

A Bayesian network model can be used to study the structures of gene regulatory networks. It has the ability to integrate information from both prior knowledge and experimental data. In this study, we propose an approach to efficiently integrate global ordering information into model learning, where the ordering information specifies the indirect relationships among genes. We demonstrate that, compared with a traditional Bayesian network model that uses only local prior knowledge, utilising additional global ordering knowledge can significantly improve the model's performance. The magnitude of this improvement depends on abundance of global ordering information and data quality.

Microarray experiments produce expression patterns for thousands of genes at once. On the other hand, biomedical literature contains large amounts of gene regulation relationship information accumulated over the years. One obvious requirement is an automated way of comparing microarray data with the collection of known gene regulation relationships. Such an automated comparison is imperative because it can help biologists rapidly understand the context of a given microarray experiment. In addition, the consistency measure can be used to either validate or refute the hypothesis being tested using the microarray experiment. In this paper we present a systematic way of examining the consistency between a given set of microarray data and known gene regulation relationships. We first introduce a simple gene regulation network model with two separate algorithms designed to isolate a maximally consistent network. Subsequently, we extend the model to take into account multiple regulating factors for a single gene while highlighting both consistencies and inconsistencies. We illustrate the effectiveness of our approach with two practical examples, one that picks the peroxisome proliferator-activated receptor (PPAR) pathway as highly consistent from multiple pathways of Kyoto encyclopedia of genes and genomes (KEGG), and another that isolates key regulatory relationships involving nfkb1 and others known for macrophage's counter response to inflammation.

A quantitative real-time PCR assay was developed to measure the proviral load of human T-lymphotropic virus type I (HTLV-I) in peripheral blood. The technology utilizes special primers and Taqman MGB fluorescence probe to measure amplification products from the gag-pro-pol polyprotein gene of HTLV-I. HTLV-I copy number was normalized to the amount of cellular DNA by quantitation of the beta-actin gene, The amplification system was sensitive to detect 5 copy/microL. The standard curve had a good linearity when the quantity for the gene was between 10(3) and 10(7) copy/microL (R2 = 0.999). Good reproducibility was observed in each intra- and inter-assay. We also measured proviral load in peripheral blood in 12 HTLV-I seropositive former blood donors. Proviral load for HTLV-I infected donors ranged from 0.015 to 12.819 copy/cell in WBC with the mean of 3.116 copy/cell.

Occult hepatitis B virus (HBV) infection status of blood donors in a southern city in China was investigated by immunological assays and nucleic acid testing. Overall, 17 (0.19%, 95% CI: 0.11%-0.30%) of the 9023 HBsAg negative samples were found to be positive for the presence of HBV DNA. "A" epitope sequences were obtained from 14 among them. Mutation(s) in aa124-aa147 existed in 6 (42.9%, 6/14) samples and 4 (66.7%, 4/6)were G145R mutation. Ratio of genotype C in occult donors (10/17) was statistically higher than HBs-positive donors (0/15, P<0.01), which implied that HBV genotype C leaded to occult infection more easily.

Radiation-induced bystander effects (RIBE) have been demonstrated to occur widely in various cell lines. However, very little data is available on the genotoxic effects of RIBE combined with other factor(s). We reported previously that with a low dose of alpha-particle irradiation, the fraction of gamma-H2AX foci-positive cells in non-irradiated bystander cells was significantly increased under elevated NaCl culture conditions. In this study, we further investigated the functional role of NaCl in the enhancement of RIBE using a specially designed co-culture system and micronucleus (MN) test. It was shown that the MN frequency was not increased significantly by elevated NaCl (9.0 g/L) alone or by medium exposure. However, with 1.0 cGy alpha-particle irradiation, the induced MN frequency increased significantly in both irradiated and non-irradiated bystander regions. Additional studies showed that elevated NaCl made the non-irradiated bystander cells more vulnerable to bystander factors. Furthermore, it was found that the induced MN frequency in cells both in irradiated and non-irradiated bystander regions was weakened when the hypertonic medium was changed to normotonic medium for 2h before irradiation. Such observations were quite similar to the co-effect of NaCl and hydrogen peroxide (H(2)O(2)), indicating that elevated NaCl might sensitize non-irradiated cells to bystander factors-induced oxidative stress.

Many studies have shown that arsenite is a potent inducer of apoptosis both in cells and tissues. However, there is a lack of appropriate in vivo animal models to study the underlying mechanisms of arsenite-induced apoptosis. Caenorhabditis elegans is an excellent model organism for studying many biological processes. We showed previously that C. elegans could be used as an in vivo system to investigate the genotoxic effects of arsenite. In order to elucidate the underlying mechanisms of arsenite-induced apoptosis in vivo, in the present study, we used the mutated alleles of the C. elegans homologue of known mammalian genes that are involved in the regulation of apoptosis. Our results showed that the loss-of-function mutations of p53/ cep-1 and DNA damage response (DDR) genes hus-1, clk-2, and egl-1 exhibited significant increase in germline apoptosis under arsenite exposure, whereas arsenite-induced germline apoptosis was blocked in loss-of-function alleles of extracellular signal-regulated kinase (ERK) (lin-45 (ku51), mek-2 (n1989), and mpk-1 (ku1)), c-Jun N-terminal kinase (JNK) (jkk-1 (km2), mek-1 (ks54), jnk-1 (gk7), mkk-4 (ju91)), and p38 ( nsy-1 (ag3), sek-1 (ag1), and pmk-1 (km25)) MAPK cascades. These results suggest that arsenite-induced apoptosis occurs independently of p53/ cep-1 and the DNA damage response (DDR) genes hus-1, clk-2, and egl-1 and that the C. elegans caspase gene ced-3, Apaf-1 homologue ced-4, and the MAPK signaling pathways are essential for germline apoptosis. Moreover, our study demonstrates that C. elegans could be a mammalian in vivo substitute model to study the mechanisms of apoptosis.

Mouse natural killer T (NKT) cells expressing an invariant T cell antigen receptor (TCR) recognize glycosphingolipids (GSLs) from Sphingomonas bacteria. The synthetic antigens previously tested, however, were designed to closely resemble the potent synthetic agonist alpha-galactosyl ceramide (alphaGalCer), which contains a monosaccharide and a C18:0 sphingosine lipid. Some Sphingomonas bacteria, however, also have oligosaccharide-containing GSLs, and they normally synthesize several GSLs with different sphingosine chains including one with a cyclopropyl ring-containing C21:0 (C21cycl) sphingosine. Here we studied the stimulation of NKT cells with synthetic GSL antigens containing natural tetrasaccharide sugars, or the C21cycl sphingosine. Our results indicate that there is a great degree of variability in the antigenic potency of different natural Sphingomonas glycolipids, with the C21cycl sphingosine having intermediate potency and the oligosaccharide-containing antigens exhibiting limited or no stimulatory capacity.

The transition metal cadmium (Cd) has been shown to induce apoptosis in a variety of cell lines and tissues. Caspase activation of the tumor suppressor gene p53 and mitogen-activated protein kinase (MAPK) signaling cascades have been reported to be involved in Cd-induced apoptosis. However, the underlying pathways of Cd-induced apoptosis have not been clearly elucidated in the in vivo systems, primarily for the lack of appropriate animal models. The nematode Caenorhabditis elegans has been shown to be a good model to study basic biological processes, including apoptosis. In this study, we used the mutated alleles of C. elegans homologs of known mammalian genes that are involved in regulation of apoptosis. Sublethal doses of Cd exposure increased C. elegans germline apoptosis in a dose- and time-dependent manner. The loss-of-function mutations of DNA damage response (DDR) genes HUS1 and p53 exhibited significant increase in germline apoptosis under Cd exposure, and the depletion of p53 antagonist ABL1 significantly enhanced apoptosis. Cd-induced apoptosis was blocked in the loss-of-function alleles of both c-Jun N-terminal kinase (JNK) and p38 MAPK cascades, which behaved normally under gamma-irradiation. Our findings implicate that both JNK and p38 MAPK cascades participate in Cd-induced apoptosis. Together, the results of this study suggest the nonessential roles of the DDR genes hus1 and p53 in Cd-induced germline apoptosis and that the apoptosis occurs through the ASK1/2-MKK7-JNK and ASK1/2-MKK3/6-p38 signaling pathways in a caspase-dependent manner. Finally, our study demonstrates that C. elegans is a mammalian in vivo substitute model to study the mechanisms of Cd-induced apoptosis.

Background: Several genotyping methods for six clinically relevant human platelet antigens (HPAs) have been reported. A four-color real-time polymerase chain reaction (PCR) method using displacing probes for genotyping of the six HPAs is described., Study Design and Methods: Primers and four differently fluorophor-labeled displacing probes were designed and synthesized to detect single-nucleotide polymorphisms responsible for each of the HPA-1, -2, -3, -4, -5, and -15 genotypes. Two HPA systems were analyzed in a single PCR procedure. After validation with samples of known genotypes, a total of 150 blood samples from healthy donors were genotyped. The results were compared with PCR with sequence-specific primers (SSP), PCR-restriction fragment length polymorphism (RFLP), and/or direct DNA sequencing. The frequencies of each HPA allele were calculated., Results: Unequivocal real-time PCR genotyping results were obtained with minimal manual manipulation and carryover contamination. All 150 blood samples were correctly genotyped as confirmed by PCR-SSP, PCR-RFLP, and/or direct DNA sequencing. The allelic frequencies of HPA-1 through -5 and -15 among the Chinese population in Xiamen were comparable with those previously reported with Chinese living in other territories. For each specimen, genotyping of all six HPA biallelic systems was achieved in three tubes of PCR within 90 minutes and with material cost of no more than $1., Conclusion: Genotyping of HPA with real-time PCR using displacing probes is more rapid and reliable compared with PCR-SSP and PCR-RFLP methods and is more affordable than existing real-time PCR-based HPA genotyping assays. Thus, our approach is more suitable for routine HPA analysis and ideal for both urgent clinical testing and high-throughput screening.

Bystander effects induced by low-dose ionizing radiation have been shown to occur widely in many cell types and may have a significant impact on radiation risk assessment. Although the region of radiation damage is known to be much greater than the initial target volume irradiated, it remains to be seen whether this response is limited to the specific organ irradiated, spans a limited region of the body, or even covers the whole body of the target. To determine whether long-distance bystander/abscopal effects exist in whole organisms and to clarify the problem of intercellular communication, in the present study a specific cell group, the shoot apical meristem in Arabidopsis embryo, was irradiated with a defined number of protons and examined for root development postirradiation. The results showed that after direct damage to the shoot apical meristem from ion traversals, root hair differentiation, primary root elongation and lateral root initiation were all inhibited significantly in postembryonic development, suggesting that radiation-induced long-distance bystander/abscopal responses might exist in the whole organism. To further scrutinize the mechanism(s) underlying these inhibitory effects, a DR5-GUS transgenic Arabidopsis was used. The results showed that accumulation of the reporter GUS gene transcript in irradiated shoot apical meristem embryos decreased in the postembryonic development. Treatment with either 2,4-dichlorophenoxyacetic acid, a synthetic plant auxin, or DMSO, a effective reactive oxygen species (ROS) scavenger, could rescue the reporter GUS enzyme accumulation and the length of primary root in irradiated shoot apical meristem embryos, indicating that ROS or probably the ROS related auxin and auxin-dependent transcription process may be involved in radiation-induced long-distance bystander/abscopal effects.