Modulation of specific cell cycle phases in human embryonic stem cells by lncRNA RNA decoys

Recent studies have shown that long noncoding RNAs (lncRNAs) are crucial regulators of human embryonic stem cells (hESCs). However, modes of actions of lncRNAs in hESCs are not well illustrated. Here, we predicted a regulatory network in hESCs in which lncRNAs interact with TFs and thereby control the expressions of downstream targets of TFs. The predicted network is comprised of 2289 3‐motif subgraphs which are characterized by 3 nodes: (i) a lncRNA which is predicted to interact with (ii) a TF and (iii) a gene which is a target of TF and coexpressing with lncRNA. We performed functional annotation of the network by identifying hub nodes followed by pathway enrichment study, which unveiled an active G1‐S cell cycle phase transition‐specific subnetwork that encompasses 2 lncRNAs, MALAT1 and DANCR. Our analysis revealed that MALAT1 and DANCR might be playing key roles in G1‐S phase transition by acting as RNA decoy via interacting with crucial stemness maintaining TFs. We predicted that MALAT1 possibly compete with DNMT1 and CDCA7 genes to bind to E2F1 thereby interrupting repression of DNMT1 and activation of CDCA7 by E2F1 in hESCs, whereas DANCR possibly competes with IPO7 gene to bind to MYC thereby interrupting MYC‐mediated activation of IPO7 in hESCs. Both of these are conjectured to contribute to rapid G1‐S phase transition aiding in stemness maintenance of hESCs. This study presents a crucial TF target cross talks mediated by lncRNAs in hESCs regulating its properties which needs further investigation.     

NPY5R antagonism does not augment the weight loss efficacy of orlistat or sibutramine

Objective: Central counter‐regulatory mechanisms, including those related to the orexigenic hormone neuropeptide Y (NPY), may limit the weight loss observed with conventional pharmacological monotherapy. This study evaluated whether blockade of the NPY Y5 receptor (NPY5R) with the selective antagonist MK‐0557 potentiates sibutramine and orlistat weight loss effects. Research Methods and Procedures: Obese patients (497, BMI 30 to 43 kg/m²) were randomized to 1 of 5 treatment arms [placebo, n = 101; sibutramine 10 mg/d, n = 100; MK‐0557 1 mg/d plus sibutramine 10 mg/d, n = 98; orlistat 120 mg TID, n = 99; MK‐0557 1 mg/d plus orlistat 120 mg TID, n = 99] in conjunction with a hypocaloric diet for 24 weeks. The all‐patients‐treated population, imputing missing data using last observation carried forward, was used to assess weight loss from baseline. Results: The study was completed by 71% of patients in placebo, 76% in sibutramine alone, 79% in MK‐0557 + sibutramine, 69% in orlistat alone, and 76% in MK‐0557 + orlistat groups. Least squares (LS) mean difference [95% confidence interval (CI)] in weight change from baseline between MK‐0557 + sibutramine and sibutramine alone was ?0.1 (?1.6, 1.4) kg (p = 0.892) and between MK‐0557 + orlistat and orlistat alone was ?0.9 (?2.4, 0.6) kg (p = 0.250). Sibutramine alone induced a LS mean weight loss of ?5.9 (?6.9, ?4.9) kg vs. ?4.6 (?5.7, ?3.6) kg for orlistat (p = 0.097). There were no serious drug‐related adverse events and MK‐0557 was well tolerated. Discussion: Blockade of the NPY5R with the potent antagonist MK‐0557 did not significantly increase the weight loss efficacy of either orlistat or sibutramine monotherapy.     

Studies on poly-beta-hydroxybutyrate synthase activity of Nostoc muscorum

This study compares the PHB synthase activity of Nostoc muscorum, a N(2)-fixing cyanobacterium under control (grown in usual BG-11 medium), nitrogen (N) and phosphorus (P) deprivation and chemoheterotrophic conditions. Specific activity of PHB synthase did not depict significant variations in the latter three types of cultures, except for the control one, where a significantly lower activity was recorded. PHB synthase activity was detected only in the soluble fractions of both the control as well as cells incubated under chemoheterotrophic conditions. A K(m) of 80.2 microM DL-beta-hydroxybutyryl-CoA and V(max) of 197.5 nmol thiobenzoate (TNB) mg protein(-1)min(-1) were observed for the enzyme. PHB synthase remained insensitive to acetyl-CoA, ATP, NADP, NADPH supplementation under in vitro condition. Addition of acetyl phosphate was found to activate the enzyme and the level of activation was dependent on the concentration of acetyl phosphate supplementation. Inhibition of PHB synthase in 2,3-butanedione supplemented cultures and reactivation following acetyl phosphate addition proved the post-translational control of acetyl phosphate over PHB synthase.     

Optimization of cultural and nutritional conditions for accumulation of poly-beta-hydroxybutyrate in Synechocystis sp. PCC 6803

Poly-beta-hydroxybutyrate (PHB) accumulation in the unicellular cyanobacterium, Synechocystis sp. PCC 6803, was studied under various cultural and nutritional conditions. Under controlled condition, cells harvested at the stationary phase of growth depicted maximum accumulation of PHB, i.e., 4.5% (w/w of dry cells) as compared to lag (1.8%) or logarithmic (2.9%) phases of cultures. A temperature range of 28-32 degrees C and pH between 7.5 and 8.5 were preferred for PHB accumulation. Cells cultivated under regular light-dark cycles accumulated more PHB (4.5%) than those grown under continuous illumination (2.4%). Nitrogen and phosphorus starvation stimulated PHB accumulation up to the tune of 9.5 and 11% (w/w of dry cells), respectively. Synechocystis cells pre-grown in glucose (0.1%)-supplemented BG-11 medium when subjected to P-deficiency in presence of acetate (0.4%), PHB accumulation was boosted up to 29% (w/w of dry cells), the value almost 6-fold higher with respect to photoautotrophic condition. Fishpond discharges were found as suitable media for PHB accumulation in the test cyanobacterium.     

Semiparametric Bayesian Analysis of Nutritional Epidemiology Data in the Presence of Measurement Error

Summary : We propose a semiparametric Bayesian method for handling measurement error in nutritional epidemiological data. Our goal is to estimate nonparametrically the form of association between a disease and exposure variable while the true values of the exposure are never observed. Motivated by nutritional epidemiological data, we consider the setting where a surrogate covariate is recorded in the primary data, and a calibration data set contains information on the surrogate variable and repeated measurements of an unbiased instrumental variable of the true exposure. We develop a flexible Bayesian method where not only is the relationship between the disease and exposure variable treated semiparametrically, but also the relationship between the surrogate and the true exposure is modeled semiparametrically. The two nonparametric functions are modeled simultaneously via B‐splines. In addition, we model the distribution of the exposure variable as a Dirichlet process mixture of normal distributions, thus making its modeling essentially nonparametric and placing this work into the context of functional measurement error modeling. We apply our method to the NIH‐AARP Diet and Health Study and examine its performance in a simulation study.     

Young patients with colorectal cancer have poor survival in the first twenty months after operation and predictable survival in the medium and long-term: Analysis of survival and prognostic markers

Introduction

Male breast cancer (MBC) is a rare, yet potentially aggressive disease. Although literature regarding female breast cancer (FBC) is extensive, little is known about the etiopathogenesis of male breast cancer. Studies from our laboratory show that MBCs have a distinct immunophenotypic profile, suggesting that the etiopathogenesis of MBC is different from FBCs. The aim of this study was to evaluate and correlate the immunohistochemical expression of cell cycle proteins in male breast carcinoma to significant clinico-biological endpoints.

Methods

75 cases of MBC were identified using the records of the Saskatchewan Cancer Agency over 26 years (1970-1996). Cases were reviewed and analyzed for the immunohistochemical expression of PCNA, Ki67, p27, p16, p57, p21, cyclin-D1 and c-myc and correlated to clinico-biological endpoints of tumor size, node status, stage of the disease, and disease free survival (DFS).

Results

Decreased DFS was observed in the majority of tumors that overexpressed PCNA (98%, p = 0.004). The overexpression of PCNA was inversely correlated to the expression of Ki67 which was predominantly negative (78.3%). Cyclin D1 was overexpressed in 83.7% of cases. Cyclin D1 positive tumors were smaller than 2 cm (55.6%, p = 0.005), had a low incidence of lymph node metastasis (38.2%, p = 0.04) and were associated with increased DFS of >150 months (p = 0.04). Overexpression of c-myc (90%) was linked with a higher incidence of node negativity (58.3%, p = 0.006) and increased DFS (p = 0.04). p27 over expression was associated with decreased lymph node metastasis (p = 0.04). P21 and p57 positive tumors were related to decreased DFS (p = 0.04). Though p16 was overexpressed in 76.6%, this did not reach statistical significance with DFS (p = 0.06) or nodal status (p = 0.07).

Conclusion

Aberrant cell cycle protein expression supports our view that these are important pathways involved in the etiopathogenesis of MBC. Tumors with overexpression of Cyclin D1 and c-myc had better outcomes, in contrast to tumors with overexpression of p21, p57, and PCNA with significantly worse outcomes. P27 appears to be a predictive marker for lymph nodal status. Such observation strongly suggests that dysregulation of cell cycle proteins may play a unique role in the initiation and progression of disease in male breast cancer. Such findings open up new avenues for the treatment of MBC as a suitable candidate for novel CDK-based anticancer therapies in the future.     

A Bayesian semiparametric accelerated failure time model

A Bayesian semiparametric approach is described for an accelerated failure time model. The error distribution is assigned a Pólya tree prior and the regression parameters a noninformative hierarchical prior. Two cases are considered: the first assumes error terms are exchangeable; the second assumes that error terms are partially exchangeable. A Markov chain Monte Carlo algorithm is described to obtain a predictive distribution for a future observation given both uncensored and censored data.     

Ameliorative role of nitric oxide on H2O2 toxicity to a chlorophycean alga Scenedesmus obliquus

A concentration-dependent toxicity of hydrogen peroxide (H(2)O(2)) was observed on growth yield, chlorophyll a content and chlorophyll fluorescence characteristics of the green microalga Scenedesmus obliquus under laboratory batch culture conditions. The addition of sodium nitroprusside, a nitric oxide (NO) donor, in combination with H(2)O(2) prevented chlorophyll losses, and the inhibition level of growth yield, maximum quantum yield of photosystem II (PSII) and the light-adapted quantum yield of PSII were significantly reduced. The antioxidant compounds, penicillamine and thiourea also reduced the damage caused by H(2)O(2) exposure. The protective actions of sodium nitroprusside were, however, arrested in cultures where sodium nitroprusside was supplemented in combination with 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (c-PTIO), a specific scavenger of NO. The NO(3)(-)-grown Scenedesmus depicted less sensitivity to H(2)O(2) toxicity with respect to the quantum yields of PSII as compared to its NH(4)(1)-grown counterpart. The role of NO in providing protection against H(2)O(2) toxicity to the processes under study was discussed.