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.     

Small molecules inhibit ex vivo tumor growth in bone

Bone is a common site of metastasis for breast, prostate, lung, kidney and other cancers. Bone metastases are incurable, and substantially reduce patient quality of life. To date, there exists no small-molecule therapeutic agent that can reduce tumor burden in bone. This is partly attributed to the lack of suitable in vitro assays that are good models of tumor growth in bone. Here, we take advantage of a novel ex vivo model of bone colonization to report a series of pyrrolopyrazolone small molecules that inhibit cancer cell invasion and ex vivo tumor growth in bone at single-digit micromolar concentration. We find that the compounds modulated the expression levels of genes associated with bone-forming osteoblasts, bone-destroying osteoclasts, cancer cell viability and metastasis. Our compounds provide chemical tools to uncover novel targets and pathways associated with bone metastasis, as well as for the development of compounds to prevent and reverse bone tumor growth in vivo.     

Pseudotyped baculovirus is an effective gene expression tool for studying molecular function during axolotl limb regeneration

Axolotls can regenerate complex structures through recruitment and remodeling of cells within mature tissues. Accessing the underlying mechanisms at a molecular resolution is crucial to understand how injury triggers regeneration and how it proceeds. However, gene transformation in adult tissues can be challenging. Here we characterize the use of pseudotyped baculovirus (BV) as an effective gene transfer method both for cells within mature limb tissue and within the blastema. These cells remain competent to participate in regeneration after transduction. We further characterize the effectiveness of BV for gene overexpression studies by overexpressing Shh in the blastema, which yields a high penetrance of classic polydactyly phenotypes. Overall, our work establishes BV as a powerful tool to access gene function in axolotl limb regeneration.     

Differentially expressed genes: OCT-4, SOX2, STAT3, CDH1 and CDH2, in cultured mesenchymal stem cells challenged with serum of women with endometriosis

Endometriosis is a common chronic gynecological disorder defined as the presence of ectopic functional endometrial tissues, outside uterine cavity, primarily on the pelvic peritoneum and the ovaries. Several studies revealed a correlation between aberrant stem-cell activity in the endometrium and endometriosis. Yet the molecular and cellular behaviors of mesnchymal stem cells in development of endometriosis are hampered by lack of invitro experiments. Our aim was to explore morphological and molecular changes associated with mesenchymal stem cells (MSCs) exposition to serum derived from women with severe endometriosis. Two cell cultures of MSCs isolated from endometrial tissues of two endometriosis-free women. Each cell culture was treated individually with the serum of women with endometriosis (experimental group/n =?7), and serum of women without endometriosis (control group/ n = 4) for 14?days. Quantitative Real-Time PCR was performed later to reveal expression of OCT-4, CDH1 and CDH2, STAT3 and SOX2 genes. Morphologically, cells showed no significant changes. However from molecular point of view, we found increased expression in OCT-4, CDH1 and CDH2. For STAT3 and SOX2 we did not find a significant difference. This study shows that endometriosis serum induced molecular changes in human endometrial MSCs (EnMSCs) that might be related to altered cell behavior which may be a step in differentiation that may be completed invivo by other factors to complete the process of transition. Further researches are needed for optimization to reach differentiation.     

Design,synthesis and biological assessment of N-adamantyl,substituted adamantyl and noradamantyl phthalimidines for nitrite,TNF-α and angiogenesis inhibitory activities

A library of 15 novel and heretofore uncharacterized adamantyl and noradamantyl phthalimidines was synthesized and evaluated for neuroprotective and anti-angiogenic properties. Phthalimidine treatment in LPS-challenged cells effected reductions in levels of secreted TNF-α and nitrite relative to basal amounts. The primary SAR suggests nitration of adamantyl phthalimidines has marginal effect on TNF-α activity but promotes anti-nitrite activity; thioamide congeners retain anti-nitrite activity but are less effective reducing TNF-α. Site-specific nitration and thioamidation provided phthalimidine 24, effecting an 88.5% drop in nitrite concurrent with only a 4% drop in TNF-α. Notable anti-angiogenesis activity was observed for 20, 21 and 22.     

Assessment of surface water quality in Legedadie and Dire catchments,Central Ethiopia,using multivariate statistical analysis

The quality of surface water in an area could be determined both by anthropogenic actions and natural processes. The current study assessed surface water quality in Legedadie and Dire catchments that cover a total area of 285 km2 in Central Ethiopia northeast of the nation’s capital Addis Ababa and within close proximity (20-30 m) from this city.. Accordingly, Addis Ababa is, and will continue to be, the major beneficiary of the the catchments which are in fact the primary sources of potable water supply to the city. Despite its potential ecosystem benefits, the catchment area was seriously affected by the rapid socioeconomic development phenomena that had been taking place in and around the city over the previous six decades. As a result, the catchment water resources are characterized by decades of deterioration because of severe pollution problems directly associated with mismanagement of natural resources coupled with other several factors. Hence, the current study was sought to examine the temporal and spatial determinants of catchment water pollutants. To that end, 14 water quality monitoring stations were selected and set up both in upstream and downstream parts of six rivers and two reservoirs. The water samples collected from different sites were monitored for 30 standard water quality parameters including nutrients, inorganic variable, and trace metals. Seasonal data were then measured for the 30 parameters monitored across two seasons (summer and autumn) over a two-year period (June 2014 – November 2015). The complex two-year seasonal data matrix that comprised of 3,660 observations was treated using multivariate statistical techniques: cluster analysis (CA), factor analysis/principal components (FA/PCA), and discriminant analysis (DA). CA successfully classified both the temporal (summer, autumn, and summer predominant) and spatial (natural, agricultural, urban, and mixed) clusters of water quality monitoring sites. Dimension reduction from FA/PCA was not as substantial as expected since it enabled only30% reduction from the original data matrix. On the other hand, DA procedures demonstrated the best result regarding data reduction and pattern recognition in both temporal and spatial analysis. It extracted data significantly and provided 5 parameters (Temp, pH, DO, salinity, and TN) to afford 96.8% right allocations during temporal analysis and only 7 parameters (pH, Turbidity, TN, Total hardness, Pb, Fe, and Cu) to yield 85.2% right allocations during the spatial analysis.Thus, these water quality parameters were most significant for seasonal and spatial water quality variation in the catchment. Therefore, DA enabled a significant reduction of the dimension of the original data matrix into a few significant parameters that affect water quality. In conclusion, the study demonstrated that multivariate statistical techniques are very useful for analysis and interpretation of complex water quality data sets for efficient assessment of water quality and identification of pollution sources as well as an effective understanding of the space and time effects of water quality.     

Changes in membrane hydrogen and sodium conductances during progesterone-induced maturation of Ambystoma oocytes

A voltage-gated hydrogen ion-selective conductance has been previously described in the immature oocyte of the urodele amphibian Ambystoma. The present study was prompted by reports that changes in membrane voltage and internal pH, as well as in internal sodium ion concentration, occur during the hormone-induced maturation of oocytes from other amphibians. As activation of membrane currents might mediate changes in internal ion concentrations in addition to altering the membrane voltage, microelectrode recording techniques have been employed to examine changes in membrane conductances which occur during maturation of Ambystoma oocytes. It was observed that during the first 5 hr of maturation the magnitude of the hydrogen ion conductance gradually decreased, and that subsequently there was an increase in the amplitude of a voltage-dependent noninactivating sodium conductance. After 6 to 7 hr, after the loss of the hydrogen conductance and at about the time of germinal vesicle breakdown, the resting potential of the oocyte spontaneously shifted from approximately -10 mV to approximately +30 mV, where it remained until at least 24 hr after the initiation of maturation. This voltage transition was due to the appearance of mechanisms generating inward current in the oocyte membrane; part of this inward current was due to the tonic activation of the sodium conductance. Changes in internal pH and internal sodium ion concentration occurred during maturation, as judged from shifts in the reversal potentials of both hydrogen and sodium currents. A gradual decrease in internal hydrogen ion concentration was observed up until the time of disappearance of the hydrogen conductance (change in internal pH from about 7.15 in immature oocytes to about 7.40 by 3 hr after application of progesterone). This was followed, as sodium conductance increased, by an apparent rise in the internal sodium ion concentration (from about 6 mM to about 17 mM by 10 hr postprogesterone).     

Development of a stereoselective and scalable process for the preparation of a methylcyclobutanol-pyridyl ether

The evolution of a scalable process for the preparation of methylcyclobutanol-pyridyl ether 1 is described. Key aspects of this development including careful control of the stereochemistry, elimination of chromatography, and application to kilogram-scale synthesis are addressed.     

State of the Art Technology for Bone Tissue Engineering and Drug Delivery

BackgroundCritical size bone defect and fracture unable to regenerate itself, inspire the origination and technological advancement in the field of bone tissue engineering (BTE). The strategies of bone tissue engineering are often classified into three groups: First, is a direct injection of cells into the tissue of interest; second is grafting of cell-scaffold constructs; and third is scaffold-based signaling molecules, drug delivery or both. Much research was available on the first two categories, still finding the structure and property of scaffold close towards the natural tissue is yet to achieve.Aim of the ReviewThe proposed mini review focus on ceramic biomaterials uses for bone regeneration and drug delivery. It covers the fabrication process of scaffold including conventional and non-conventional i.e. rapid prototyping approach along with it advantage. The use of scaffold for drug delivery and signaling molecules such as growth factor is an emerging field of research in tissue engineering.ConclusionThe biodegradable beads used as a local drug delivery system are ubiquitous in surgery to treat post-operative infections but does not play any role in tissue regeneration. The use of this clinically accepted drug delivery technique in bone regeneration is an alternative way for the treatment on several bone infections (especially osteomyelitis and arthritis associated with tuberculosis). It is predicted to be the future of organ replacement and treatment.     

Synthesis and urease inhibitory potential of benzophenone sulfonamide hybrid in vitro and in silico

This study deals with the synthesis of benzophenone sulfonamides hybrids (1–31) and screening against urease enzyme in vitro. Studies showed that several synthetic compounds were found to have good urease enzyme inhibitory activity. Compounds 1 (N′-((4′-hydroxyphenyl)(phenyl)methylene)-4′′-nitrobenzenesulfonohydrazide), 2 (N′-((4′-hydroxyphenyl)(phenyl)methylene)-3′′-nitrobenzenesulfonohydrazide), 3 (N′-((4′-hydroxyphenyl)(phenyl)methylene)-4′′-methoxybenzenesulfonohydrazide), 4 (3′′,5′′-dichloro-2′′-hydroxy-N′-((4′-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide), 6 (2′′,4′′-dichloro-N′-((4′-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide), 8 (5-(dimethylamino)-N′-((4-hydroxyphenyl)(phenyl)methylene)naphthalene-1-sulfono hydrazide), 10 (2′′-chloro-N′-((4′-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide), 12 (N′-((4′-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide) have found to be potently active having an IC₅₀ value in the range of 3.90–17.99?µM. These compounds showed superior activity than standard acetohydroxamic acid (IC₅₀?=?29.20?±?1.01?µM). Moreover, in silico studies on most active compounds were also performed to understand the binding interaction of most active compounds with active sites of urease enzyme. Structures of all the synthetic compounds were elucidated by ¹H NMR, ¹³C NMR, EI-MS and FAB-MS spectroscopic techniques.     

Development of subcutaneous fat in Spanish and Latin American children and adolescents: Reference values for biceps,triceps, subscapular and suprailiac skinfolds

Subcutaneous fat skinfolds represent a reliable assessment instrument of adiposity status. This study provides current percentile references for four subcutaneous skinfolds (biceps, triceps, subscapular, suprailiac) applicable to children and adolescents in Spain and in Latin American countries where data are scarce.The design consisted of a cross-sectional multicenter study performed with identical methods in 5 countries (Argentina, Cuba, Mexico, Spain and Venezuela). Total sample comprised 9163 children and youths (boys 4615 - girls 4548) aged 6–18 years, healthy and without apparent pathologies. Percentiles 3, 5, 10, 25, 50, 75, 90, 95 and 97 were calculated by the LMS method. Sexual dimorphism was assessed using the t-test and age differences with ANOVA. Normalized growth percentile references were obtained according to sex and age for each skinfold. The mean values of four skinfolds were significantly greater in girls than boys (p < 0.001) and, in both sexes, all skinfolds show statistical differences through age (p < 0.001) with different magnitudes.Except triceps in girls, peaks between 11 and 12 years of age are more noticeable in boys than in girls. Although the general model of growth is known, the skinfold measurements show variability among populations and differences of magnitude are presented according to the analyzed population. Therefore, these age and sex-specific reference percentile values for biceps, triceps, subscapular and suprailiac skinfolds, derived from a large sample of Spanish and Latin American children and adolescents, are a useful tool for adiposity diagnosis in this population for which no reference values were available.     

The cholangiocyte primary cilium in health and disease

Cholangiocytes, like most cells, express primary cilia extending from their membranes. These organelles function as antennae which detect stimuli from bile and transmit the information into cells regulating several signaling pathways involved in secretion, proliferation and apoptosis. The ability of primary cilia to detect different signals is provided by ciliary associated proteins which are expressed in its membrane. Defects in the structure and/or function of these organelles lead to cholangiociliopathies that result in cholangiocyte hyperproliferation, altered fluid secretion and absorption. Since primary cilia dysfunction has been observed in several epithelial tumors, including cholangiocarcinoma (CCA), primary cilia have been proposed as tumor suppressor organelles. In addition, the loss of cilia is associated with dysregulation of several molecular pathways resulting in CCA development and progression. Thus, restoration of the primary cilia may be a potential therapeutic approach for several ciliopathies and CCA.