A novel algorithm for network-based prediction of cancer recurrence

To develop accurate prognostic models is one of the biggest challenges in “omics”-based cancer research. Here, we propose a novel computational method for identifying dysregulated gene subnetworks as biomarkers to predict cancer recurrence. Applying our method to the DNA methylome of endometrial cancer patients, we identified a subnetwork consisting of differentially methylated (DM) genes, and non-differentially methylated genes, termed Epigenetic Connectors (EC), that are topologically important for connecting the DM genes in a protein-protein interaction network. The ECs are statistically significantly enriched in well-known tumorgenesis and metastasis pathways, and include known epigenetic regulators. Importantly, combining the DMs and ECs as features using a novel random walk procedure, we constructed a support vector machine classifier that significantly improved the prediction accuracy of cancer recurrence and outperformed several alternative methods, demonstrating the effectiveness of our network-based approach.     

Expression of Leptospira membrane proteins Signal Peptidase (SP) and Leptospira Endostatin like A (Len A) in BL-21(DE3) is toxic to the host cells

Heterologous expression of Integral Membrane Proteins (IMPs) is reported to be toxic to the host system in many studies. Even though there are reports on various concerns like transformation efficiency, growth properties, protein toxicity, inefficient expression and protein degradation in IMP overexpression, no studies so far addressed these issues in a comprehensive way. In the present study, two transmembrane proteins of the pathogen Leptospira interrogans, namely Signal peptidase (SP), and Leptospira Endostatin like A (Len-A) were taken along with a cytosolic protein Hydrolase (HYD) to assess the differences in transformation efficiency, protein toxicity, and protein stability when over expressed in Escherichia coli (E. coli). Bioinformatics analysis to predict the transmembrane localization indicated that both SP and Len are targeted to the membrane. The three proteins were expressed in full length in the E. coli expression strain, BL 21 (DE3). Significant changes were observed for the strains transformed with IMP genes under the parameters analysed such as, the transformation efficiency, survival of colonies on IPTG-plate, culture growth kinetics and protein expression compared to the strain harbouring the cytosolic protein gene.     

Insights into the RNA quadruplex binding specificity of DDX21

Guanine quadruplexes can form in both DNA and RNA and influence many biological processes through various protein interactions. The DEAD-box RNA helicase protein DDX21 has been shown to bind and remodel RNA quadruplexes but little is known about its specificity for different quadruplex species. Previous reports have suggested DDX21 may interact with telomeric repeat containing RNA quadruplex (TERRA), an integral component of the telomere that contributes to telomeric heterochromatin formation and telomere length regulation. Here we report that the C-terminus of DDX21 directly interacts with TERRA. We use, for the first time, 2D saturation transfer difference NMR to map the protein binding site on a ribonucleic acid species and show that the quadruplex binding domain of DDX21 interacts primarily with the phosphoribose backbone of quadruplexes. Furthermore, by mutating the 2′OH of loop nucleotides we can drastically reduce DDX21's affinity for quadruplex, indicating that the recognition of quadruplex and specificity for TERRA is mediated by interactions with the 2′OH of loop nucleotides.     

Therapeutic potential of the methanolic extract of Lepidium sativum seeds on mice infected with Trypanosoma evansi

The present study aimed to investigate the therapeutic potential of the methanolic extract of Lepidium sativum seeds in mice experimentally infected with Trypanosoma evansi. A total of thirty-two male Swiss albino mice were randomly divided into four groups: the first group was the normal control, while the second, third and fourth groups were infected intraperitoneally with 1 × 10⁴ trypanosomes. The third and fourth groups were treated with 100 μl of Lepidium sativum seed extract (LSSE) at a dose of 200 mg/kg body weight intraperitoneally (infected + LSSEI) and orally (infected + LSSEO) respectively, once a day, for a period of four days.Parasitaemia was found to be significantly raised in the untreated infected group, reaching 2 × 10⁷ at day 4 post-infection, but was significantly reduced by 65.5% and 88% in the mice treated orally and intraperitoneally with LSSE, respectively. The erythrocyte count, HCT, haemoglobin content, leucocyte count and the percentage of lymphocytes was significantly reduced in the untreated infected group, while the treatment with LSSE returned these parameters to their pre-infection values. In addition, our study proved that LSSE provided protection against liver tissue damage and decreased the levels of aspartate aminotransferase (AST) and alanine aminotransferase (ALT). The present study also established that intraperitoneal injection of LSSE is more effective than oral administration in the treatment of trypanosome infection in mice. In conclusion, the infection caused haematological, biochemical and histological changes that were ameliorated following treatment with LSSE.     

Effects of diverse androgens on the sexual behavior and morphology of castrated male quail

Castrated male Japanese quail were injected for 15 days with 1 mg/day of testosterone propionate (TP), testosterone (T), androstenedione (AE), androsterone (AO), 5α-dihydrotestosterone benzoate (5α-DHTB), or 5β-dihydrotestosterone (5β-DHT), or with oil. Copulation was activated to a significant extent only by TP and T. Strutting was activated only by TP, T, and AE. Proctodeal (foam) glands were well-developed in birds injected with TP, T, AE, or 5α-DHTB. Additional data were obtained following implantation of pellets of crystalline T, AE, AO, or 5α-DHT. T pellets activated copulation, but AO and 5α-DHT pellets did not. Effects of AE require further study. These results suggest that conversion of androgen to estrogen is necessary for the activation of copulation in the male quail.     

Parent-offspring conflict and the evolution of infant-directed song

We present a theory of the origin and evolution of infant-directed song, a form of music found in many cultures. After examining the ancestral ecology of parent-infant relations, we propose that infant-directed song arose in an evolutionary arms race between parents and infants, stemming from the dynamics of parent-offspring conflict. We describe testable predictions that follow from this theory, consider some existing evidence for them, and entertain the possibility that infant-directed song could form the basis for the development of other, more complex forms of music.     

Design and synthesis of thiazolylhydrazone derivatives as inhibitors of chitinolytic N-acetyl-β-d-hexosaminidase

N-acetyl-β-d-hexosaminidase (Hex) is potential target for pesticide design. Here, a series of thiazolylhydrazone derivatives were designed, synthesized and evaluated as competitive inhibitors of OfHex1, a Hex from the agricultural pest Ostrinia furnacalis. The derivative 3k, with a (benzyloxy)methyl group at the N3 atom, demonstrated greater potency with a K_i of 10.2?µM. Molecular docking analysis indicated that the (benzyloxy)methyl group of 3k was bound to a previously unexplored pocket formed by Loop478-496. Then further optimization around naphthalene ring led to find the more potency substituent phenyl. The derivative 7, with phenoxyethyl group at R₁ and a phenyl group at R₂, demonstrated an augmented potency with a K_i of 2.1?µM. Molecular docking analysis indicated that 7 was bound to the active pocket of OfHex1 more favorably than 3k. This work suggests a novel scaffold for developing specific Hex inhibitors.     

Isoxazolo[3,4-d]pyridazinones positively modulate the metabotropic glutamate subtypes 2 and 4

Isoxazolo[3,4-d] pyridazinones ([3,4-d]s) are selective positive modulators of the metabotropic glutamate receptors (mGluRs) subtypes 2 and 4, with no functional cross reactivity at mGluR_1a, mGLuR₅ or mGluR₈. Modest binding for two of the [3,4-d]s is observed at the allosteric fenobam mGluR₅ site, but not sufficient to translate into a functional effect. The structure activity relationship (SAR) for mGluR₂ and mGluR₄ are distinct: the compounds which select for mGluR₂ all contain fluorine on the N-6 aryl group. Furthermore, the [3,4-d]s in this study showed no significant binding at inhibitory GABA_A, nor excitatory NMDA receptors, and previously we had disclosed that they lack significant activity at the System Xc-Antiporter. A homology model based on Conn’s mGluR₁ crystal structure was examined, and suggested explanations for a preference for allosteric over orthosteric binding, subtype selectivity, and suggested avenues for optimization of efficacy as a reasonable working hypothesis.     

Dynamically engaged smiling predicts cooperation above and beyond average smiling levels

Smiling has been conceptualized as a signal of cooperative intent, yet smiles are easy to fake. We suggest that contextually appropriate, dynamically engaged smiling imposes an attentional cost, thereby making engaged smiling a plausible “honest signal” of cooperative intent. To test this hypothesis, we analyzed data from 123 pairs of same-sex strangers having “getting-to-know-you” conversations who subsequently played a one-shot prisoner's dilemma together. We calculated the strength of engagement in smiling using a cross-lagged auto-regressive model for dyadic data. We found that when an individual's partner (the signaler) tended to smile in a more responsive way, that individual (the receiver) was more likely to cooperate. Conversely, when a signaler tended to smile in a less responsive way, the receiver was less likely to cooperate. These effects were present over-and-above the effects of average levels of smiling and self-reported liking, which also predicted likelihood of cooperation. However, dynamically engaged smiling did not predict cooperation on the part of the signaler, suggesting that receivers weight the importance of engagement more highly than they should, or even that engaged smiling might be a manipulative display. These results illustrate how conversational dynamics can influence evolutionary signaling.     

Consistency of mate choice in eye and hair colour: Testing possible mechanisms

Partner preferences are formed by several mechanisms, including an imprinting-like effect (parent-similarity) and homogamy (self-similarity). It is still unknown, however, whether these preferences remain stable throughout an individual’s lifetime. We have therefore tested the consistency of mate choice in eye and hair colour both in a shortand long-term context. In other words, we tested whether people systematically choose partners with a particular eye and hair colour. We asked 1,048 respondents to indicate the eye and hair colour of themselves, their opposite-sex and same-sex parent, and all the romantic partners they had in their lives. Our results show that people consistently choose partners of a particular eye and hair colour in both short- and long-term contexts, which suggests that people do have their ‘types’. Nevertheless, the consistency was significantly higher in a long-term context than in a short-term context. Furthermore, the eye colour of one's partner was predicted by the eye colour of one's opposite-sex as well as same-sex parent, but the strongest parental effect was found when both parents had same eye colour. There were no significant results for hair colour. Our results thus suggest that preferences for eye colour are determined by the imprinting-like effect rather than by homogamy, and that they remain stable over time. These findings also indirectly support an assumption of stability of this imprinting-like effect in humans, since people consistently choose partners with their opposite-sex parent's eye-colour.     

Efficiency of excitation energy trapping in the green photosynthetic bacterium Chlorobaculum tepidum

During the millions of years of evolution, photosynthetic organisms have adapted to almost all terrestrial and aquatic habitats, although some environments are obviously more suitable for photosynthesis than others. Photosynthetic organisms living in low-light conditions require on the one hand a large light-harvesting apparatus to absorb as many photons as possible. On the other hand, the excitation trapping time scales with the size of the light-harvesting system, and the longer the distance over which the formed excitations have to be transferred, the larger the probability to lose excitations. Therefore a compromise between photon capture efficiency and excitation trapping efficiency needs to be found. Here we report results on the whole cells of the green sulfur bacterium Chlorobaculum tepidum. Its efficiency of excitation energy transfer and charge separation enables the organism to live in environments with very low illumination. Using fluorescence measurements with picosecond resolution, we estimate that despite a rather large size and complex composition of its light-harvesting apparatus, the quantum efficiency of its photochemistry is around ~87% at 20?°C, ~83% at 45?°C, and about ~81% at 77?K when part of the excitation energy is trapped by low-energy bacteriochlorophyll a molecules. The data are evaluated using target analysis, which provides further insight into the functional organization of the low-light adapted photosynthetic apparatus.     

Prevalence of Escherichia coli strains resistance to antibiotics in wound infections and raw milk

Antibiotic-resistant Escherichia coli strains including extended-spectrum β-lactamase (ESBL) isolates are globally widespread in medical, food, and environmental sources. Some of these strains are considered the most pathogenic bacteria in humans. The present work examined the predominance of antibiotic resistance in E. coli strains in wound infections comparing with E. coli strains isolated from a raw milk as a potential source of those strains. The wound infections included abdomen, anus, arm, back, buttock, chest, foot, hand, head, leg, lung, mouth, neck, penis, thigh, toe, and vagina infections. In total, 161 and 153 isolates identified as E. coli were obtained from wound infections and raw milk, respectively. A Vitek 2 system innovated by bioMérieux, France was applied to perform the identification and susceptibility tests. The E. coli isolates that have ability to produce ESBL were detected by an ESBL panel and NO45 card (bioMérieux). Over half of the E. coli were from abdomen, back, and buttock wound infections. More than 50%of the E. coli isolates obtained from wound infections were resistant to cefazolin, ampicillin, cefuroxime, ciprofloxacin, mezlocillin, moxifloxacin, piperacillin, and tetracycline; 70% of the isolates from wound infections and 0% of the isolates from raw milk were E. coli isolates produced ESBL. The data showed that the strains resistance to multi-antibiotic and produced ESBL are more widespread among wound infections than in raw milk.     

Do men with more masculine voices have better immunocompetence?

The human voice is often considered to be a secondary sexual characteristic that signals underlying information about the immunocompetence of the speaker (i.e. the immunocompetence handicap hypothesis; ICHH). However, no studies have yet shown a relationship between vocal characteristics and biomarkers of immune function or self-reported health. In a sample of 108 men, we examined correlations between masculine vocal characteristics [i.e. relatively low fundamental frequency (F₀), low F₀ variability (F₀-SD), low formant position (P_f), and high vocal tract length (VTL)] in relation to salivary immunoglobulin-A (sIgA; a marker of mucosal immunity), testosterone (T), and well-validated measures of self-reported health status. Results showed that sIgA correlated with masculinized F₀, P_f, and VTL. Self-report health correlated with masculinized P_f and VTL. Anticipated future health correlated negatively with F₀-SD and sick role propensity (less interference of illness in daily life) correlated positively with VTL. Perceived susceptibility to infection correlated with more feminized F₀ and F₀-SD. Our results demonstrated a small relationship between men's vocal characteristics and one putative indicator of mucosal immunity along with self-identified health status. We suggest that more research is warranted to determine whether the masculinity of men's voices may serve as an indicator of their phenotypic quality.     

Advances in thermochemical conversion of woody biomass to energy,fuels and chemicals

Biomass has been recognised as a promising resource for future energy and fuels. The biomass, originated from plants, is renewable and application of its derived energy and fuels is close to carbon-neutral by considering that the growing plants absorb CO₂ for photosynthesis. However, the complex physical structure and chemical composition of the biomass significantly hinder its conversion to gaseous and liquid fuels.This paper reviews recent advances in biomass thermochemical conversion technologies for energy, liquid fuels and chemicals. Combustion process produces heat or heat and power from the biomass through oxidation reactions; however, this is a mature technology and has been successfully applied in industry. Therefore, this review will focus on the remaining three thermochemical processes, namely biomass pyrolysis, biomass thermal liquefaction and biomass gasification. For biomass pyrolysis, biomass pretreatment and application of catalysts can simplify the bio-oil composition and retain high yield. In biomass liquefaction, application of appropriate solvents and catalysts improves the liquid product quality and yield. Gaseous product from biomass gasification is relatively simple and can be further processed for useful products. Dual fluidised bed (DFB) gasification technology using steam as gasification agent provides an opportunity for achieving high hydrogen content and CO₂ capture with application of appropriate catalytic bed materials. In addition, multi-staged gasification technology, and integrated biomass pyrolysis and gasification as well as gasification for poly-generation have attracted increasing attention.     

Comparison of the effects of estradiol-17beta and the synthetic estrogen, RU-2858, on lordosis behavior in adult female rats and guinea pigs

Female sexual behavior (as assessed by lordosis responses) in adult ovariectomized guinea pigs and rats was measured after a single subcutaneous injection of either the synthetic estrogen RU-2858 or estradiol-17β (E) and a subsequent injection of progesterone (P). Thresholds for responsiveness to each estrogen were determined over a range of doses from 1 to 640 μg/kg of body weight. RU-2858 was able to stimulate lordosis at doses several times lower than E in both guinea pigs and rats. In general, guinea pigs were less sensitive to both estrogenic compounds than rats and were particularly insensitive to E. Approximately 40% of guinea pigs given RU-2858 displayed lordosis prior to P injection. Subsequent P injection did not greatly enhance the intensity of lordosis responses in these animals. These guinea pigs were also more sensitive than the remaining 60% of RU-2858-injected guinea pigs on several indexes of lordosis intensity (e.g., lordosis threshold, duration of heat, duration of individual lordosis responses). Rats did not respond behaviorally to RU-2858 without a subsequent P injection nearly as frequently as did guinea pigs. At the doses used in this study, E did not facilitate lordosis behavior in rats or guinea pigs in the absence of a subsequent P injection.