A bi-Poisson model for clustering gene expression profiles by RNA-seq

With the availability of gene expression data by RNA-seq, powerful statistical approaches for grouping similar gene expression profiles across different environments have become increasingly important. We describe and assess a computational model for clustering genes into distinct groups based on the pattern of gene expression in response to changing environment. The model capitalizes on the Poisson distribution to capture the count property of RNA-seq data. A two-stage hierarchical expectation–maximization (EM) algorithm is implemented to estimate an optimal number of groups and mean expression amounts of each group across two environments. A procedure is formulated to test whether and how a given group shows a plastic response to environmental changes. The impact of gene–environment interactions on the phenotypic plasticity of the organism can also be visualized and characterized. The model was used to analyse an RNA-seq dataset measured from two cell lines of breast cancer that respond differently to an anti-cancer drug, from which genes associated with the resistance and sensitivity of the cell lines are identified. We performed simulation studies to validate the statistical behaviour of the model. The model provides a useful tool for clustering gene expression data by RNA-seq, facilitating our understanding of gene functions and networks.

Identification of Campylobacter jejuni and determination of point mutations associated with macrolide resistance using a multiplex TaqMan MGB real-time PCR

AIMS

The aim of the study was to develop a multiplex real-time PCR method to identify Campylobacter jejuni containing mutations commonly associated with macrolide resistance.

METHODS AND RESULTS

A multiplex fluorescence real-time PCR assay was developed based on TaqMan minor groove binder (MGB) probes. The VS1-MGB probe was designed based on the VS1 gene and was used to identify Camp. jejuni. The 23S rDNA-MGB probe was designed to distinguish macrolide resistance mutations in 23S rDNA, while 57D-MGB and 74D-MGB were designed to detect resistance mutations in ribosomal protein L4. The specificity and accuracy of our method were identical to the conventional biochemical tests, mapA PCR, minimum inhibitory concentration (MIC) determination and DNA sequencing. The linear detection limit of the method was 0·03 ng genomic DNA and three colony formation unit (CFU) per reaction. In 6 of 18 cases, the nature of Erythromycin resistance could be correctly determined from natural isolates; absence of the tested mutations was demonstrated in the remaining four resistant isolates.

CONCLUSIONS

A multiplex TaqMan MGB real-time PCR assay with high specificity and accuracy was developed to simultaneously identify Camp. jejuni and detect the gene mutations associated with macrolide resistance.

SIGNIFICANCE AND IMPACT OF THE STUDY

This multiplex method can potentially simplify the identification of Camp. jejuni and determine macrolide resistance due to mutations in 23S rDNA or ribosomal protein L4. This method has a potential for application in different research areas and molecular surveillance.

Prevalence of myasthenia gravis and associated autoantibodies in paraneoplastic pemphigus and their correlations with symptoms and prognosis

BACKGROUND

Paraneoplastic pemphigus (PNP) involves multiple organs, but little is known about its neurological involvement.

OBJECTIVES

To investigate the symptoms, prognosis and profiles of associated autoantibodies in myasthenia gravis (MG), and their correlations in patients with PNP.

METHODS

Fifty-eight patients with PNP were assessed for myasthenic symptoms and laboratory evidence. Serum autoantibodies against acetylcholine receptor (AChR), acetylcholinesterase (AChE), titin, ryanodine receptor (RyR) and muscle-specific kinase (MuSK) were measured by enzyme-linked immunosorbent assay. Patients with pemphigus vulgaris (PV), pemphigus foliaceus (PF), connective tissue disease (CTD) and non-PNP MG (NP-MG), and healthy donors, served as controls. These autoantibodies in PNP were also compared in the presence or absence of dyspnoea or muscle weakness. Cox regression and log-rank tests were used for survival analysis.

RESULTS

Overall 39% of patients with PNP experienced muscle weakness, and 35% were diagnosed with MG. Moreover, 35% had positive anti-AChR and 28% had anti-AChE antibodies, similarly to NP-MG (33% and 17%, respectively, P > 0·05). However, both were negative in all patients with PV, PF and CTD and healthy donors (P < 0·005). No other antibodies showed significant differences among groups. Anti-AChR and anti-AChE antibody levels were significantly increased in patients with PNP with dyspnoea, while anti-AChR, anti-titin and anti-RyR were significantly increased in patients with PNP with muscle weakness (P < 0·05). Nevertheless, levels and positive rates of these autoantibodies showed no significant differences between PNP with Castleman disease and thymoma. Although anti-AChE levels impacted survival duration (P  =  0·027, odds ratio 3·14), MG complications did not affect the overall survival percentage in PNP.

CONCLUSIONS

MG is a complication of PNP. Anti-AChR and anti-AChE antibodies are prominent in patients with PNP, especially those with dyspnoea.

Maternal and paternal diversity in Xinjiang Kazakh population from China

The ancient silk road of China passed through Xinjiang and facilitated gene exchanges from the East and the West which impacted on the genetic variation and structure of the nomadic Kazakh population residing there. In order to understand the nature of this genetic variation; 151 Xinjiang Kazakh samples were obtained from four main Kazakh groups and were analyzed using mtDNA and Y-chromosome markers. The Xinjiang Kazakh population is heterogeneous, showing the coexistence of matrilineal lineages with different origins. No genetic differentiation of mtDNA is observed among the four different regional Xinjiang Kazakh populations in Xinjiang by AMOVA and Networks. The genetic diversity of Y-STR loci is higher in Xinjiang Kazakhs (0.968 ± 0.014) than the Kazakhs from Kazakhstan (0.629 ± 0.071) and Russia (0.835 ± 0.020). East Eurasians make a more than 50% contribution to the maternal and paternal lineages of Xinjiang Kazakhs. There is more gene flow from West Eurasian into the maternal lineages of Xinjiang Kazakh than to the Kazakhs from Russia and Kazakhstan. Moreover, mtDNA and Y-STR displayed high polymorphism in Xinjiang Kazakhs (the haplotype diversity and power of discrimination were 0.990 ± 0.003, 0.9137 for mtDNA HVS and 0.968 ± 0.014, 0.9489 for Y-STR system, respectively), suggesting they would be very useful and important markers for forensic analysis and population genetic studies.

Genomic organization and expression of immunoglobulin genes in the Chinese hamster (Cricetulus griseus)

In science, the hamsters are widely used as a model for studying the human diseases because they display many features like humans. The utility of the Chinese hamster as a biology model can be further enhanced by further characterization of the genes encoding components of the immune system. Here, we report the genomic organization and expression of the Chinese hamster immunoglobulin heavy and light chain genes. The Chinese hamster IgH locus contains 268 VH segments (132 potentially functional genes, 12 ORFs and 124 pseudogenes), 4 DH segments, 6 JH segments, four constant region genes (μ, γ, ε and α) and one reverse δ remnant fragment. The Igκ locus contains only a single Cκ gene, 4 Jκ segments and 48 Vκ segments (15 potentially functional genes and 33 pseudogenes), whereas the Igλ locus contains 4 Cλ genes, but only Cλ 3 and Cλ 4 each preceded by a Jλ gene segment. A total of 49 Vλ segments (39 potentially functional genes, 3 ORFs and 7 pseudogenes) were identified. Analysis of junctions of the recombined V(D)J transcripts reveals complex diversity in both expressed H and κ sequences, but the microhomology-directed VJ recombination obviously results in very limited diversity in the Chinese hamster λ gene despite more potential germline-encoded combinatorial diversity. This is the first study to make a comprehensive analysis of the Ig genes in the Chinese hamster, which provides insights into the Ig genes in placental mammals.

Control of somatic membrane potential in nociceptive neurons and its implications for peripheral nociceptive transmission

Peripheral sensory ganglia contain somata of afferent fibres conveying somatosensory inputs to the central nervous system. Growing evidence suggests that the somatic/perisomatic region of sensory neurons can influence peripheral sensory transmission. Control of resting membrane potential (E_rest) is an important mechanism regulating excitability, but surprisingly little is known about how E_rest is regulated in sensory neuron somata or how changes in somatic/perisomatic E_rest affect peripheral sensory transmission. We first evaluated the influence of several major ion channels on E_rest in cultured small-diameter, mostly capsaicin-sensitive (presumed nociceptive) dorsal root ganglion (DRG) neurons. The strongest and most prevalent effect on E_rest was achieved by modulating M channels, K2P and 4-aminopiridine-sensitive K_V channels, while hyperpolarization-activated cyclic nucleotide-gated, voltage-gated Na⁺, and T-type Ca²⁺ channels to a lesser extent also contributed to E_rest. Second, we investigated how varying somatic/perisomatic membrane potential, by manipulating ion channels of sensory neurons within the DRG, affected peripheral nociceptive transmission in vivo. Acute focal application of M or K_ATP channel enhancers or a hyperpolarization-activated cyclic nucleotide-gated channel blocker to L5 DRG in vivo significantly alleviated pain induced by hind paw injection of bradykinin. Finally, we show with computational modelling how somatic/perisomatic hyperpolarization, in concert with the low-pass filtering properties of the t-junction within the DRG, can interfere with action potential propagation. Our study deciphers a complement of ion channels that sets the somatic E_rest of nociceptive neurons and provides strong evidence for a robust filtering role of the somatic and perisomatic compartments of peripheral nociceptive neuron.

[Characteristics of lymph node metastasis in patients undergoing radical cystectomy for bladder cancer: a retrospective single-center study of 522 cases]

OBJECTIVE

To investigate the characteristics and related influence factors of lymph node metastases in patients undergoing radical cystectomy and lymph node dissection for bladder cancer.

METHODS

The data of 522 patients who underwent radical cystectomy and pelvic lymph node dissection at Department of Urology, Peking University First Hospital from 1998 to 2012, were retrospectively collected, and the lymph node mapping was performed in all the patients to determine the location of metastatic lymph nodes.

RESULTS

For the 522 patients with bladder cancer, lymph node metastasis occurred in 99 patients, and the incidence of lymph node metastasis was 19.0%. The incidence at different tumor stages was: 3.7% in T1 (6/164), 10.5% in T2 (17/160), 36.7% in T3(40/107), and 41.9% in T4 (36/86). The most common involved lymph nodes were hypogastric/obturator lymph nodes (77/99, 77.8%) and external iliac lymph nodes (35/99, 35.4%). The mean number of lymph nodes dissected was 11.6 (1-51). The lymph node density (number of lymph nodes involved/number of lymph nodes removed) was 44.1%. The incidence of lymph node metastasis was statistical related to tumor stage (P < 0.01, OR 2.71,95% CI 2.13-3.44) and tumor grade (P < 0.01, OR 3.81,95% CI 1.66-8.74), while age, gender, smoke history, and weight had no statistical significance.

CONCLUSION

Lymph node metastasis is the most common metastasis route of bladder cancer. The incidence of lymph node tumor involvement is correlated with increasing tumor stage and tumor grade. The most common involved lymph nodes are hypogastric/obturator lymph nodes and external iliac lymph nodes. Radical cystectomy and bilateral pelvic lymph nodes dissection are of great significance in the treatment of bladder cancer.

A novel microbead-based microfluidic device for rapid bacterial identification and antibiotic susceptibility testing

Effective treatment of infectious diseases depends on the ability to rapidly identify the infecting bacteria and the use of sensitive antibiotics. The currently used identification assays usually take more than 72 h to perform and have a low sensitivity. Herein, we present a microbead-based microfluidic platform that is highly sensitive and rapid for bacterial detection and antibiotic sensitivity testing. The platform includes four units, one of which is used for bacterial identification and the other three are used for susceptibility testing. Our results showed that Escherichia coli O157 at a cell density range of 10(1)-10(5) CFU/μL could be detected within 30 min. Additionally, the effects of three antibiotics on E. coli O157 were evaluated within 4-8 h. Overall, this integrated microbead-based microdevice provides a sensitive, rapid, reliable, and highly effective platform for the identification of bacteria, as well as antibiotic sensitivity testing.

A computational algorithm for functional clustering of proteome dynamics during development

Phenotypic traits, such as seed development, are a consequence of complex biochemical interactions among genes, proteins and metabolites, but the underlying mechanisms that operate in a coordinated and sequential manner remain elusive. Here, we address this issue by developing a computational algorithm to monitor proteome changes during the course of trait development. The algorithm is built within the mixture-model framework in which each mixture component is modeled by a specific group of proteins that display a similar temporal pattern of expression in trait development. A nonparametric approach based on Legendre orthogonal polynomials was used to fit dynamic changes of protein expression, increasing the power and flexibility of protein clustering. By analyzing a dataset of proteomic dynamics during early embryogenesis of the Chinese fir, the algorithm has successfully identified several distinct types of proteins that coordinate with each other to determine seed development in this forest tree commercially and environmentally important to China. The algorithm will find its immediate applications for the characterization of mechanistic underpinnings for any other biological processes in which protein abundance plays a key role.

A model framework for identifying genes that guide the evolution of heterochrony

Heterochrony, the phylogenic change in the time of developmental events or rate of development, has been thought to play an important role in producing phenotypic novelty during evolution. Increasing evidence suggests that specific genes are implicated in heterochrony, guiding the process of developmental divergence, but no quantitative models have been instrumented to map such heterochrony genes. Here, we present a computational framework for genetic mapping by which to characterize and locate quantitative trait loci (QTLs) that govern heterochrony described by four parameters, the timing of the inflection point, the timing of maximum acceleration of growth, the timing of maximum deceleration of growth, and the length of linear growth. The framework was developed from functional mapping, a dynamic model derived to map QTLs for the overall process and pattern of development. By integrating an optimality algorithm, the framework allows the so-called heterochrony QTLs (hQTLs) to be tested and quantified. Specific pipelines are given for testing how hQTLs control the onset and offset of developmental events, the rate of development, and duration of a particular developmental stage. Computer simulation was performed to examine the statistical properties of the model and demonstrate its utility to characterize the effect of hQTLs on population diversification due to heterochrony. By analyzing a genetic mapping data in rice, the framework identified an hQTL that controls the timing of maximum growth rate and duration of linear growth stage in plant height growth. The framework provides a tool to study how genetic variation translates into phenotypic innovation, leading a lineage to evolve, through heterochrony.

Preparation and antibacterial properties of titanium-doped ZnO from different zinc salts

To research the relationship of micro-structures and antibacterial properties of the titanium-doped ZnO powders and probe their antibacterial mechanism, titanium-doped ZnO powders with different shapes and sizes were prepared from different zinc salts by alcohothermal method. The ZnO powders were characterized by X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), ultraviolet-visible spectroscopy (UV-vis), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and selected area electron diffraction (SAED), and the antibacterial activities of titanium-doped ZnO powders on Escherichia coli and Staphylococcus aureus were evaluated. Furthermore, the tested strains were characterized by SEM, and the electrical conductance variation trend of the bacterial suspension was characterized. The results indicate that the morphologies of the powders are different due to preparation from different zinc salts. The XRD results manifest that the samples synthesized from zinc acetate, zinc nitrate, and zinc chloride are zincite ZnO, and the sample synthesized from zinc sulfate is the mixture of ZnO, ZnTiO3, and ZnSO4 · 3Zn (OH)2 crystal. UV-vis spectra show that the absorption edges of the titanium-doped ZnO powders are red shifted to more than 400 nm which are prepared from zinc acetate, zinc nitrate, and zinc chloride. The antibacterial activity of titanium-doped ZnO powders synthesized from zinc chloride is optimal, and its minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) are lower than 0.25 g L-1. Likewise, when the bacteria are treated by ZnO powders synthesized from zinc chloride, the bacterial cells are damaged most seriously, and the electrical conductance increment of bacterial suspension is slightly high. It can be inferred that the antibacterial properties of the titanium-doped ZnO powders are relevant to the microstructure, particle size, and the crystal. The powders can damage the cell walls; thus, the electrolyte is leaked from cells.

Systems mapping of genes controlling chemotherapeutic drug efficiency for cancer stem cells

Cancer can be controlled effectively by using chemotherapeutic drugs to inhibit cancer stem cells, but there is considerable inter-patient variability regarding how these cells respond to drug intervention. Here, we describe a statistical framework for mapping genes that control tumor responses to chemotherapeutic drugs as well as the efficacy of treatments in arresting tumor growth. The framework integrates the mathematical aspects of the cancer stem cell hypothesis into genetic association studies, equipped with a capacity to quantify the magnitude and pattern of genetic effects on the kinetic decline of cancer stem cells in response to therapy. By quantifying how specific genes and their interactions govern drug response, the model provides essential information to tailor personalized drugs for individual patients.

Electron transport enhanced by electrode surface reconstruction: a case study of C60-based molecular junctions

At the C₆₀–Cu(111) interface, electrode surface reconstruction (Rec) increases electrical current compared to that for the unreconstructed (Unrec) surface.

Four new metal–organic frameworks based on a rigid linear ligand: synthesis, optical properties and structural investigation

Four coordination polymers have been synthesized based on a rigid linear carboxylate ligand and different lengths of imidazole ligands.

Tuning the electron transport properties of boron-nitride nanoribbons with electron and hole doping

C chain doped BN nanoribbons can be either metallic or semiconducting, depending on how the C chains are located.

Conservation of the extended substrate specificity profiles among homologous granzymes across species

Granzymes are structurally related serine proteases involved in cell death and immunity. To date four out of five human granzymes have assigned orthologs in mice; however for granzyme H, no murine ortholog has been suggested and its role in cytotoxicity remains controversial. Here, we demonstrate that, as is the case for granzyme C, human granzyme H is an inefficient cytotoxin that together with their similar pattern of GrB divergence and functional similarity strongly hint to their orthologous relationship. Besides analyzing the substrate specificity profile of granzyme H by substrate phage display, substrate cleavage susceptibility of human granzyme H and mouse granzyme C was assessed on a proteome-wide level. The extended specificity profiles of granzymes C and H (i.e. beyond cleavage positions P4-P4') match those previously observed for granzyme B. We demonstrate conservation of these extended specificity profiles among various granzymes as granzyme B cleavage susceptibility of an otherwise granzyme H/C specific cleavage site can simply be conferred by altering the P1-residue to aspartate, the preferred P1-residue of granzyme B. Our results thus indicate a conserved, but hitherto underappreciated specificity-determining role of extended protease-substrate contacts in steering cleavage susceptibility.

Nature of weak magnetism in SrTiO3/LaAlO3 multilayers

We report the observation of weak magnetism in superlattices of LaAlO(3)/SrTiO(3) using β-detected nuclear magnetic resonance. The spin lattice relaxation rate of ^{8}Li in superlattices with a spacer layers of 8 and 6 unit cells of LaAlO(3) exhibits a strong peak near ~35 K, whereas no such peak is observed in a superlattice with spacer layer thickness of 3 unit cells. We attribute the observed temperature dependence to slowing down of weakly coupled electronic moments at the LaAlO(3)/SrTiO(3) interface. These results show that the magnetism at the interface depends strongly on the thickness of the spacer layer, and that a minimal thickness of ~4-6 unit cells is required for the appearance of magnetism. A simple model is used to determine that the observed relaxation is due to small fluctuating moments (~0.002μ(B)) in the two samples with a larger LaAlO(3) spacer thickness.

[Management of idiopathic renal subcapsuler fluid collection: 10 cases report]

OBJECTIVE

To discuss the clinical characteristics of idiopathic renal subcapsuler fluid collection and its treatment.

METHODS

From 2009 to 2012, 10 patients with idiopathic renal subcapsuler fluid collection were treated at Urology Department of Peking University First Hospital and retrospective analysis was performed.

RESULTS

These patients' ages were 19-73 years, with an average age of 39.9 years. All the patients were female. Their tumors were excluded by image studies before any treatment. Eight cases were treated by percutaneous drainage, 1 by surgery, and 1 under active surveillance. The patients were followed up for 3-15 months, with a median follow-up of 7 months. Recurrence occurred in 1 patient who took percutaneous drainage, and later she took capsulectomy. All the other patients had satisfied results.

CONCLUSION

Idiopathic renal subcapsular fluid collection is a rare condition, whose cause is still unknown. The aim of therapy is to relieve symptoms and release the compression to the kidney. Percutaneous drainage or capsulectomy are both therapy options with satisfied results.

[Evaluation of novel gene UCA1 as a tumor biomarker for the detection of bladder cancer]

OBJECTIVE

To evaluate the clinical utility of novel gene urothelial carcinoma antigen 1 (UCA1) as a urinary tumor marker for the diagnosis of bladder urothelial carcinoma.

METHODS

A cohort of 180 cases of bladder cancer (including 94 cases in previous study), 144 cases of non-bladder-cancer individuals as control group (including 85 cases in previous study) from 2005 to 2009 were recruited. Reverse transcription PCR (RT-PCR) of urinary sediments was performed to detect the expression of UCA1. RNasin was added to the urinary sediments collected after 2007 from 86 cases of bladder cancer and 59 cases in control group to improve the quantity and quality of RNA isolation. The parameters of sensitivity, specificity, area under curve (AUC) of ROC and its 95%CI were calculated.χ(2) test was used to compare the sensitivity of UCA1 with NMP22 and cytology in 116 cases of bladder cancer with the parallel data of UCA1 and NMP22 and in 108 cases with the parallel data of UCA1 and cytology.

RESULTS

95.4% of RNA was isolated successfully from urinary sediments after the addition of RNasin UCA1 was highly specific (92.4%, 133/144) and quite sensitive (84.4%, 152/180) in the diagnosis of bladder cancer with a favorable AUC-ROC of 0.898 (95%CI: 0.851 - 0.945). It was especially valuable for superficial G(2)-G(3) patients (sensitivity: 86.4%, 92.3%) at a high risk for muscular invasion.

CONCLUSION

With a high level of sensitivity and specificity, UCA1 is a promising urinary marker for the diagnosis of bladder cancer.

[Complete transperitoneal laparoscopic nephroureterectomy for upper urinary tract urothelial carcinoma]

OBJECTIVE

To discuss the surgical skills and clinical value of complete transperitoneal laparoscopic nephroureterectomy.

METHODS

We collected and analyzed the clinical data of 25 patients (14 renal pelvic carcinoma and 11 carcinoma of ulreter, right side 15 and left side 10) who underwent complete transperitoneal laparoscopic nephroureterectomy for the upper urinary tract urothelial carcinoma (UUT-UC) in Peking University First Hospital from May 2010 to April 2011.

RESULTS

All the operations were successfully done by one surgeon with standard 4 or 5 trocars technique. The mean operative time was 150 min (120-180 min), the blood loss about 20-100 mL (mean 40 mL) and no severe complications observed. The postoperative hospital stay was 4-6 days with an average length of 5.5 days. The mean follow-up was 5.5 (1-11) months. One of 19 patients underwent trans urethral resection of bladder tumour (TURBT) for recurrent non-muscle invasive bladder tumor.

CONCLUSION

Complete transperitoneal laparoscopic nephroureterectomy is a minimally invasive, safe and effective way to treat UUT-UC. The patients recover soon and have a shorter length of stay.

The nucleosome binding protein NSBP1 is highly expressed in human bladder cancer and promotes the proliferation and invasion of bladder cancer cells

NSBP1 is a recently identified member of the HMGN protein family which binds to nucleosomes and regulates gene transcription through chromatin remodeling. In this study, we aimed to investigate the potential role of NSBP1 in human bladder cancer. We examined NSBP1 expression in 114 surgically removed bladder cancer specimens as well as 11 human bladder cell lines by immunohistochemistry and Western blot analysis, and found that NSBP1 level was correlated with the increased tumor grade and pathologic stage, and lymph node metastasis. RNAi-mediated knockdown of NSBP1 in EJ cells, a bladder cancer cell line that overexpressed NSBP1, resulted in moderate decrease of cell viability, moderate blockage of cell cycle at G2/M phase, and decreased cyclin B1 expression, but had no effects on apoptosis. Moreover, NSBP1 knockdown led to reduced activity of MMP-9 but not MMP-2. Taken together, these results suggest that NSBP1 promotes the viability of bladder cancer cells through increased cell proliferation but not decreased apoptosis, and increases the invasion ability of metastatic bladder cancer cells through the upregulation of MMP-9 activity. Our findings not only provide a molecular understanding of the role of NSBP1 in bladder cancer, but also suggest NSBP1 RNAi as a novel therapeutic approach for bladder cancer.

Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network

Background

Protein-protein interaction networks and phenotype similarity information have been synthesized together to discover novel disease-causing genes. Genetic or phenotypic similarities are manifested as certain modularity properties in a phenotype-gene heterogeneous network consisting of the phenotype-phenotype similarity network, protein-protein interaction network and gene-disease association network. However, the quantitative analysis of modularity in the heterogeneous network and its influence on disease-gene discovery are still unaddressed. Furthermore, the genetic correspondence of the disease subtypes can be identified by marking the genes and phenotypes in the phenotype-gene network. We present a novel network inference method to measure the network modularity, and in particular to suggest the subtypes of diseases based on the heterogeneous network.

Results

Based on a measure which is introduced to evaluate the closeness between two nodes in the phenotype-gene heterogeneous network, we developed a Hitting-Time-based method, CIPHER-HIT, for assessing the modularity of disease gene predictions and credibly prioritizing disease-causing genes, and then identifying the genetic modules corresponding to potential subtypes of the queried phenotype. The CIPHER-HIT is free to rely on any preset parameters. We found that when taking into account the modularity levels, the CIPHER-HIT method can significantly improve the performance of disease gene predictions, which demonstrates modularity is one of the key features for credible inference of disease genes on the phenotype-gene heterogeneous network. By applying the CIPHER-HIT to the subtype analysis of Breast cancer, we found that the prioritized genes can be divided into two sub-modules, one contains the members of the Fanconi anemia gene family, and the other contains a reported protein complex MRE11/RAD50/NBN.

Conclusions

The phenotype-gene heterogeneous network contains abundant information for not only disease genes discovery but also disease subtypes detection. The CIPHER-HIT method presented here is effective for network inference, particularly on credible prediction of disease genes and the subtype analysis of diseases, for example Breast cancer. This method provides a promising way to analyze heterogeneous biological networks, both globally and locally.

[Treatment of renal colic with double-J stent during pregnancy: a report of 25 cases]

OBJECTIVE

There is no consensus on the treatment of renal colic, a hazardous condition for both pregnant women and their fetus during pregnancy. The present study was to evaluate the therapeutic safety and efficacy of double-J stent.

METHODS

Twenty-five pregnant women were admitted into our hospital for renal colic between January 2008 and June 2009. The mean age was (28.3 ± 4.9) years old. And the mean gestational week was (20.1 ± 6.9) weeks. The diagnostic and therapeutic procedures were as follows: (1) Upon admission, routine urine and blood tests, chemistry panel and ultrasonography were performed. (2) Analgesics or antispasticity drugs were dispended to the patients, such as progesterone. (3) Magnesium sulfate was used for anti-inflammation. (4) If renal colic was not relieved, a double-J stent was inserted into the ureter via cystoscopy. At pre-, intra- and post-operation, an obstetrician monitored the fetal heart and uterine contraction. (5) Ultrasonography was conducted to check the location of double-J stent. (6) After delivery, the women underwent ESWL (extracorporeal shock wave lithotripsy) and then the double-J stent was extracted.

RESULTS

Five (20%, 5/25) patients had a positive previous history: three for renal calculus (n = 3), solitary kidney (n = 1) and reimplantation of ureter (n = 1). Only one patient run a high fever of 40°C. Most patients (84%) had a positive percussion over renal regions. Only 6 patients (24%, 6/25) were found to have a great quantity of red blood cells in urine. Half of the patients showed 10 - 20 white blood cells (WBC) per high power field in urine. Fifteen patients (60%, 15/25) had an elevated count of WBC in routine blood test. Only one patient was with elevated serum creatinine because of her solitary kidney. The calcium level decreased in 8 patients (32%, 8/25). All patients suffered hydronephrosis while 18 patients (72%, 18/25) were not found with calculus in ureters or kidneys. Pain of six patients (24%, 6/25) was relieved after the dosing of analgesics. Eighteen patients (72%, 18/25) underwent double-J stent insertion and 1 patient (4%, 1/25) received percutaneous renal puncture. Then pain was relieved and hydronephrosis vanished. After delivery, calculi were treated properly and then the double-J stent were extracted. Iconography showed no residual calculi.

CONCLUSION

For pregnant women with renal colic, retrograde intra-ureteral cannula of double-J stent is both safe and effective. It should be recommended for all renal colic women during pregnancy with or without calculus after the ineffective dosing of analgesics.

Phospho-ΔNp63α is a key regulator of the cisplatin-induced microRNAome in cancer cells

Head and neck squamous cell carcinoma (HNSCC) cells exposed to cisplatin (CIS) displayed a dramatic ATM-dependent phosphorylation of ΔNp63α that leads to the transcriptional regulation of downstream mRNAs. Here, we report that phospho (p)-ΔNp63α transcriptionally deregulates miRNA expression after CIS treatment. Several p-ΔNp63α-dependent microRNA species (miRNAs) were deregulated in HNSCC cells upon CIS exposure, including miR-181a, miR-519a, and miR-374a (downregulated) and miR-630 (upregulated). Deregulation of miRNA expression led to subsequent modulation of mRNA expression of several targets (TP53-S46, HIPK2, ATM, CDKN1A and 1B, CASP3, PARP1 and 2, DDIT1 and 4, BCL2 and BCL2L2, TP73, YES1, and YAP1) that are involved in the apoptotic process. Our data support the notion that miRNAs are critical downstream targets of p-ΔNp63α and mediate key pathways implicated in the response of cancer cells to chemotherapeutic drugs.

The substrate specificity profile of human granzyme A

The exact biological function of granzyme A, a granule-associated serine protease belonging to the tryptase family of proteases, is still a matter of debate because conflicting roles have been suggested, such as initiation of caspase-independent apoptosis-like cell death and endogenous modulation of inflammatory processes. In contrast to its well-studied family member, granzyme B, far less is known about the physiological targets of granzyme A. Using an N-terminal peptide-centric proteomics technology, the substrate specificity of human granzyme A was extensively characterized at the level of macromolecular protein substrates. Overall, more than 260 cleavage sites, almost exclusively favoring basic residues at the P1 position, in approximately 200 unique protein substrates, including the well-known in vitro substrates APEX-endonuclease 1 and different histones, were identified. Further substrate characterization was used to delineate physical properties in the substrate specificity profiles, which further highlights important aspects in protease/substrate biology.

Salt supplementation blunts the blood pressure response to telmisartan with or without hydrochlorothiazide in hypertensive patients with type 2 diabetes

AIMS/HYPOTHESIS

We assessed the effects of sodium chloride (NaCl) supplementation on the blood pressure response to treatment with telmisartan with or without hydrochlorothiazide in hypertensive patients with type 2 diabetes and habitually high (HDS, sodium excretion >200 mmol/24 h on two out of three consecutive occasions) or low (LDS, sodium excretion <100 mmol/24 h on two out of three consecutive occasions) salt intake.

METHODS

Patients received 4 weeks of telmisartan followed by 4 weeks of telmisartan plus hydrochlorothiazide. In a double-blind randomised fashion, patients received sodium chloride (NaCl, 100 mmol/24 h) or placebo capsules in addition to their habitual salt intake during the last 2 weeks of telmisartan and telmisartan plus hydrochlorothiazide therapy. The protocol was repeated with NaCl and placebo capsules administered in reverse order to allow each participant to act as his or her own control. At 0, 4, 8, 14, 18 and 22 weeks, 24 h ambulatory blood pressure (ABP) and 24 h urine collections were performed.

RESULTS

No statistically significant differences were seen in the ABP response in the LDS vs HDS groups to any of the interventions (p = 0.58). NaCl supplementation reduced the effect of telmisartan with or without hydrochlorothiazide on systolic BP by approximately 50% (-5.8 mmHg during NaCl supplementation vs -11.3 mmHg during placebo, mean difference 5.6 mmHg [95% CI 1.7-9.4 mmHg], p = 0.005), irrespective of habitual salt intake. By contrast, addition of hydrochlorothiazide increased the antihypertensive effect of telmisartan on systolic BP by approximately 35% (p = 0.048) in both groups of patients.

CONCLUSIONS/INTERPRETATION

NaCl supplementation blunts the effectiveness of telmisartan with or without hydrochlorothiazide in hypertensive patients with type 2 diabetes, independently of habitual low or high salt intake.

Osmotic Swelling Pressure Response of Smart Hydrogels Suitable for Chronically-Implantable Glucose Sensors

In the last few years, a new type of glucose-sensitive hydrogel (GSH) has been developed that shrinks with increasing glucose concentration due to the formation of reversible crosslinks The first osmotic swelling pressure results measured for any member of this new class of GSH are reported, so that their suitability for use in sensors combining pressure transducers and smart gels can be evaluated. Comparison is also made with results obtained for an older type of GSH that expands with increasing glucose concentration due to an increase in the concentration of counterions within the gel. The newer type of GSH exhibits both faster kinetics and weaker fructose interference, and therefore is more suitable for in vivo glucose sensing.

A mouse model of a human multiple GIST family with KIT-Asp820Tyr mutation generated by a knock-in strategy

Several families exhibiting multiple gastrointestinal stromal tumours (GISTs) and germline c-kit gene mutations at exons 8, 11, 13, or 17 have been reported. These patients also exhibit diffuse hyperplasia of the interstitial cells of Cajal (ICCs) as a pre-existing lesion of multiple GISTs. We generated a mouse model of a family with germline c-kit gene mutation at exon 17, and compared the phenotypes between the mice and humans. The mouse counterpart (KIT-Asp818Tyr) of the human KIT-Asp820Tyr mutation was transmitted into germline by a knock-in strategy. Mating of male and female heterozygotes (KIT-Asp818Tyr/+) resulted in the generation of homozygotes (KIT-Asp818Tyr/KIT-Asp818Tyr). Histological examination revealed that all heterozygotes had both a small KIT-positive mesenchymal tumour at the caecum, consistent with GIST, and KIT-positive diffuse spindle-shaped cell proliferation in the distal oesophagus, stomach, proximal duodenum, and colon consistent with ICC hyperplasia. All homozygotes exhibited a larger caecal tumour and more prominent spindle-shaped cell proliferation compared with the heterozygous mice, and they usually died within 10 weeks after birth, likely due to ileus. The small intestine of both genotypes showed no apparent morphological abnormality, and autonomous contraction of the ileal segments appeared normal. Western blotting demonstrated that the caecal tumours expressed phosphorylated KIT, MAPK, Stat1, and Stat5. These mutant mice are considered to be useful for further investigation of the mechanism of GIST development as a result of ICC hyperplasia and for assessment of the in vivo effects of drugs against molecular targets.

MAPK/ERK signalling mediates VEGF-induced bone marrow stem cell differentiation into endothelial cell

Multi-potent adult progenitor cells (MAPCs) differentiate into endothelial cells (ECs) in the presence of vascular endothelial growth factor (VEGF). The mechanism(s) of VEGF-induced differentiation of MAPCs to ECs are not yet known. We, therefore, examined the role of mitogen-activated protein kinase/extracellular signal-regulated kinase (p42/44-MAPK/ERK1/2) signalling in endothelial differentiation from bone marrow stem cells. We observed that VEGF stimulation of MAPCs for 14 days results in a significant expression of endothelial-specific gene and/or proteins including von Willebrand factor (vWF), vascular endothelial-cadherin (VE-cadherin), VEGF receptor-2 (VEGFR2), and CD31. Up-regulation of EC-specific markers was accompanied by a cobblestone morphology, expression of endothelial nitric oxide synthase (eNOS), and Dil-Ac-LDL uptake, typical for EC morphology and function. VEGF induced a sustained activation of p42 MAPK/ERK, but not that of p44 MAPK/ERK during the course of MAPCs differentiation in a time-dependent manner up to 14 days. VEGF-induced activation of p42 MAPK/ERK also led to the nuclear translocation of MAPK/ERK1/2. Incubation of MAPCs with MAPK/ERK1/2 phosphorylation inhibitor PD98059 blocked the sustained VEGF-induced MAPK/ERK1/2 phosphorylation as well as its nuclear translocation in the differentiating MAPCs. Inhibition of MAPK/ERK1/2 phosphorylation by PD98059 also blocked the expression of EC-specific genes in these cells and their differentiation to ECs. These data suggest that VEGF induces MAPC differentiation into EC via a. MAPK/ERK1/2 signalling pathway-mediated mechanism in vitro.

Estrogen-induced and TAFII30-mediated gene repression by direct recruitment of the estrogen receptor and co-repressors to the core promoter and its reversal by tamoxifen

Estradiol (E2) acts through the estrogen receptor (ER) to downregulate many genes, and tamoxifen (Tam) largely reverses this repression but the underlying mechanisms are unclear. Repression of the folate receptor (FR)-alpha P4 core promoter by ER is enhanced by E2 and reversed by Tam. This effect was unaffected by inhibition of new protein synthesis and required the E/F and the DNA-binding domains of ER without direct binding of ER to DNA. The repression by E2/ER was not specific for either Sp1 or TATA elements but was loosely selective for the initiator and flanking sequence. Insertion of a response element or a relatively strong Sp1 cluster to recruit ER upstream of the core promoters caused a switch to activation by E2/ER that was inhibited by Tam. In nuclear extracts, association of ER with a biotinylated core promoter fragment was promoted by E2 but Tam blocked this effect. Repression/de-repression of the P4 promoter and endogenous FR-alpha expression by E2/Tam required SMRT and/or NCoR. ER associated with the chromosomal P4 promoter and SMRT and NCoR associated with it in an ER-dependent manner; these associations were favored by E2 but disrupted by Tam, in the short term, without changes in ER expression. TAFII30 was required for optimal P4 promoter activity and for the repressive association of ER. E2 may thus maintain a low transcriptional status of genes by favoring direct TAFII30-dependent association of ER with the core promoter in a co-repressor complex containing SMRT and/or NCoR; this repression is overridden in target genes containing an upstream element that strongly recruits ER. In addition to suppressing the activation of classical E2 target genes, Tam may upregulate genes by passively dissociating the ER co-repressor complex.

Short-interfering RNA-mediated silencing of proliferating cell nuclear antigen inhibit proliferation and induce apoptosis in HeLa cells

Proliferating cell nuclear antigen (PCNA) is an important protein for DNA polymerase delta in the nucleus, and shown to have a fundamental role in cellular proliferation. It is overexpressed to support cell growth in cervical carcinoma. To study its role in stress response, we design and use short hairpin RNA (shRNA) to inhibit PCNA expression in HeLa cells and validate its effect on cell proliferation. In this study, three PCNA-shRNA expression vectors are constructed and introduced into HeLa cells, and the cell cycle is analyzed by flow cytometry. Apoptotic cell is detected by single cell gel electrophoresis assay (comet assay), and caspase cleavage is studied also. Expression of PCNA is assessed by real-time reverse transcription-polymerase chain reaction and Western blot analysis. Upon transient transfection with plasmid encoding shRNA, it is found that expression of PCNA decreased in shRNA-transfected cells, downregulation of PCNA inhibit cell growth and induce apoptosis in HeLa cells. PCNA downregulation also increase cell population in the G0-G1 phase. In conclusion, our findings demonstrate that shRNA can inhibit the DNA replication and induce apoptosis in HeLa cells effectively and, therefore, could be used as a new potential anticancer tool for therapy of human cervical carcinoma.

The recombinant nonstructural polyprotein NS1 of porcine parvovirus (PPV) as diagnostic antigen in ELISA to differentiate infected from vaccinated pigs

To differentiate pigs infected with porcine parvovirus (PPV) from those vaccinated with inactivated whole-virus vaccine, an enzyme-linked immunosorbent assay (ELISA) based on detection of a nonstructural polyprotein 1 (NS1) was developed. A threshold of 0.23 optical density units was established and the assay had high specificity (100), sensitivity (88), accuracy (90) and positive predictive value (100) using haemagglutination inhibition as the standard method. A reproducibility test revealed that the coefficients of variation of sera within-plates and between-run were less than 10%. The assay showed no cross-reactivity with antibodies to porcine reproductive respiratory syndrome virus, pseudorabies virus, foot and mouth disease virus, Actinobacillus pleuropneumoniae, Toxoplasma or Chlamydia. Sera obtained from pigs infected with PPV reacted with recombinant NS1 protein in the ELISA. Sera from pigs vaccinated with inactivated whole virus did not recognize this protein in the ELISA. In contrast, antibodies against PPV whole virus were present in both PPV-infected and vaccinated animals. Serum conversion against NS1 was first detected 10 days after infection and NS1-specific antibodies were detectable up to half a year post infection. In conclusion, the PPV-NS1 ELISA can differentiate PPV-infected versus inactivated PPV-vaccinated pigs and could be applied in disease diagnosis and surveillance.