PLEX.I: a tool to discover features in multiplex networks that reflect clinical variation.

Molecular profiling technologies, such as RNA sequencing, offer new opportunities to better discover and understand the molecular networks involved in complex biological processes. Clinically important variations of diseases, or responses to treatment, are often reflected, or even caused, by the dysregulation of molecular interaction networks specific to particular network regions. In this work, we propose the R package PLEX.I, that allows quantifying and testing variation in the direct neighborhood of a given node between networks corresponding to different conditions or states. We illustrate PLEX.I in two applications in which we discover variation that is associated with different responses to tamoxifen treatment and to sex-specific responses to bacterial stimuli. In the first case, PLEX.I analysis identifies two known pathways i) that have already been implicated in the same context as the tamoxifen mechanism of action, and ii) that would have not have been identified using classical differential gene expression analysis.

Capturing the dynamics of microbial interactions through individual-specific networks.

Longitudinal analysis of multivariate individual-specific microbiome profiles over time or across conditions remains dauntin. Most statistical tools and methods that are available to study microbiomes are based on cross-sectional data. Over the past few years, several attempts have been made to model the dynamics of bacterial species over time or across conditions. However, the field needs novel views on handling microbial interactions in temporal analyses. This study proposes a novel data analysis framework, MNDA, that combines representation learning and individual-specific microbial co-occurrence networks to uncover taxon neighborhood dynamics. As a use case, we consider a cohort of newborns with microbiomes available at 6 and 9 months after birth, and extraneous data available on the mode of delivery and diet changes between the considered time points. Our results show that prediction models for these extraneous outcomes based on an MNDA measure of local neighborhood dynamics for each taxon outperform traditional prediction models solely based on individual-specific microbial abundances. Furthermore, our results show that unsupervised similarity analysis of newborns in the study, again using the notion of a taxon's dynamic neighborhood derived from time-matched individual-specific microbial networks, can reveal different subpopulations of individuals, compared to standard microbiome-based clustering, with potential relevance to clinical practice. This study highlights the complementarity of microbial interactions and abundances in downstream analyses and opens new avenues to personalized prediction or stratified medicine with temporal microbiome data.

An overview of machine learning methods for monotherapy drug response prediction.

For an increasing number of preclinical samples, both detailed molecular profiles and their responses to various drugs are becoming available. Efforts to understand, and predict, drug responses in a data-driven manner have led to a proliferation of machine learning (ML) methods, with the longer term ambition of predicting clinical drug responses. Here, we provide a uniquely wide and deep systematic review of the rapidly evolving literature on monotherapy drug response prediction, with a systematic characterization and classification that comprises more than 70 ML methods in 13 subclasses, their input and output data types, modes of evaluation, and code and software availability. ML experts are provided with a fundamental understanding of the biological problem, and how ML methods are configured for it. Biologists and biomedical researchers are introduced to the basic principles of applicable ML methods, and their application to the problem of drug response prediction. We also provide systematic overviews of commonly used data sources used for training and evaluation methods.

Differentiation potential of human CD133 positive hematopoietic stem cells into motor neuron- like cells, in vitro.

Spinal cord injuries and motor neuron-related disorders impact on life of many patients around the world. Since pharmacotherapy and surgical approaches were not efficient to regenerate these types of defects; stem cell therapy as a good strategy to restore the lost cells has become the focus of interest among the scientists. Umbilical cord blood CD133+ hematopoietic stem cells (UCB- CD133+ HSCs) with self- renewal property and neural lineage differentiation capacity are ethically approved cell candidate for use in regenerative medicine. In this regard the aim of this study was to quantitatively evaluate the capability of these cells to differentiate into motor neuron-like cells (MNL), in vitro. CD133+ HSCs were isolated from human UCB using MACS system. After cell characterization using flow cytometry, the cells were treated with a combination of Retinoic acid, Sonic hedgehog, Brain derived neurotrophic factor, and B27 through a 2- step procedure for two weeks. The expression of MN-specific markers was examined using qRT- PCR, flow cytometry and immunocytochemistry. By the end of the two-week differentiation protocol, CD133+ cells acquired unipolar MNL morphology with thin and long neurites. The expression of Isl-1(62.15%), AChE (41.83%), SMI-32 (21.55%) and Nestin (17.46%) was detected using flow cytometry and immunocytochemistry. The analysis of the expression of PAX6, ISL-1, ACHE, CHAT and SMI-32 revealed that MNLs present these neural markers at levels comparable with undifferentiated cells. In Conclusion Human UCB- CD133+ HSCs are remarkably potent cell candidates to transdifferentiate into motor neuron-like cells, in vitro.

Evaluation of motor neuron differentiation potential of human umbilical cord blood- derived mesenchymal stem cells, in vitro.

Many people suffer from spinal cord injuries annually. These deficits usually threaten the quality of life of patients. As a postpartum medically waste product, human Umbilical Cord Blood (UCB) is a rich source of stem cells with self- renewal properties and neural differentiation capacity which made it useful in regenerative medicine. Since there is no report on potential of human umbilical cord blood-derived mesenchymal stem cells into motor neurons, we set out to evaluate the differentiation properties of these cells into motor neuron-like cells through administration of Retinoic Acid(RA), Sonic Hedgehog(Shh) and BDNF using a three- step in vitro procedure. The results were evaluated using Real-time PCR, Flowcytometry and Immunocytochemistry for two weeks. Our data showed that the cells changed into bipolar morphology and could express markers related to motor neuron; including Hb-9, Pax-6, Islet-1, NF-H, ChAT at the level of mRNA and protein. We could also quantitatively evaluate the expression of Islet-1, ChAT and NF-H at 7 and 14days post- induction using flowcytometry. It is concluded that human UCB-MSCs is potent to express motor neuron- related markers in the presence of RA, Shh and BDNF through a three- step protocol; thus it could be a suitable cell candidate for regeneration of motor neurons in spinal cord injuries.

Urease inhibitory activities of ß-boswellic acid derivatives.

BACKGROUND AND THE PURPOSE OF THE STUDY: Boswellia carterii have been used in traditional medicine for many years for management different gastrointestinal disorders. In this study, we wish to report urease inhibitory activity of four isolated compound of boswellic acid derivative. METHODS: 4 pentacyclic triterpenoid acids were isolated from Boswellia carterii and identified by NMR and Mass spectroscopic analysis (compounds 1, 3-O-acetyl-9,11-dehydro-ß-boswellic acid; 2, 3-O-acetyl-11-hydroxy-ß-boswellic acid; 3. 3-O- acetyl-11-keto-ß-boswellic acid and 4, 11-keto-ß-boswellic acid. Their inhibitory activity on Jack bean urease were evaluated. Docking and pharmacophore analysis using AutoDock 4.2 and Ligandscout 3.03 programs were also performed to explain possible mechanism of interaction between isolated compounds and urease enzyme. RESULTS: It was found that compound 1 has the strongest inhibitory activity against Jack bean urease (IC50 = 6.27 ± 0.03 µM), compared with thiourea as a standard inhibitor (IC50 = 21.1 ± 0.3 µM). CONCLUSION: The inhibition potency is probably due to the formation of appropriate hydrogen bonds and hydrophobic interactions between the investigated compounds and urease enzyme active site and confirms its traditional usage.

Involvement of the CA1 GABAA receptors in ACPA-induced impairment of spatial and non-spatial novelty detection in mice.

RATIONALE: Cannabinoids are shown to modulate the hippocampal memory processing through different neuronal systems such as GABAergic and glutamatergic. This study investigates the effects of dorsal hippocampal (CA1) GABA(A) receptors on spatial and non-spatial novelty detection deficit, induced by a selective CB1 receptor agonist (ACPA), during a non-associative task. METHODS: Male mice weighing 30-35 g were used. Open field paradigm was employed to assess the spatial and non-spatial memory retention. RESULTS: Our data showed that intraperitoneal injection of the higher doses of ACPA (0.005, 0.01 and 0.02 mg/kg) decreases spatial change detection as well as the reaction to non-spatial novelty. Moreover, isolated intra-CA1 injection of bicuculline (GABA(A) receptor antagonist) at 0.0625, 0.125 and 0.25 µg/mouse did not alter the spatial change detection and non-spatial novelty in saline treated mice. On the other hand, intra-CA1 injection of the higher doses of muscimol (GABA(A) receptor agonist) at 0.25, 0.5 and 1 µg/mouse, not only impaired the spatial change detection on its own, but also affected the reaction to non-spatial novelty. In addition, the subthreshold dose of bicuculline reversed the impaired spatial and non-spatial memory in mice which received post-training injection of ACPA effective dose (0.02 mg/kg). Meanwhile, co-administration of the subthreshold and effective doses of muscimol and ACPA (0.005 mg/kg) could only impair the spatial change detection ability but not the reaction to non-spatial novelty. CONCLUSION: Our results suggested that the ACPA induced impairment of memory retention, may occur through dorsal hippocampal (CA1) GABA(A) receptors thus, blockade of these receptors can possibly reverse this phenomenon.

Possible interaction of cholinergic and GABAergic systems between MS and CA1 upon memory acquisition in rats.

The present study explored the possibility that cholinergic and GABAergic systems of medial septum (MS) might influence acquisition of memory by regulation of acetylcholine (Ach) and γ-aminobutyric acid (GABA) receptors function in hippocampus and vice versa. The step-through passive avoidance (PA) task was used. The results showed that pre-training intra-MS/CA1 administration of nonselective muscarinic Ach antagonist, scopolamine (0.5, 1 and 2 µg/rat) and GABA(A) receptor agonist, muscimol (0.01 and 0.02 µg/rat) impaired, while acetylcholinesterase inhibitor, physostigmine (0.5 and 1 µg/rat) and GABA(A) receptor antagonist, bicuculline (0.25 µg/rat) improved memory acquisition. Moreover, intra-CA1/MS administration of a subthreshold dose of muscimol or bicuculline increased and reversed the impairment induced by scopolamine in MS/CA1 respectively (cross injection). Also, the result revealed that, intra-CA1/MS administration subthreshold dose of muscimol reduced improvement of memory induced by physostigmine in the MS/CA1, respectively (cross injection). On the other hand, subthreshold dose of bicuculline in CA1/MS did not alter memory improvement induced by physostigmine in the other site (MS/CA1). In conclusion, both cholinergic and GABAergic systems not only seem to play a role in the modulation of memory in the MS and CA1 but also to have a complex interaction.

Hydroxy decenoic acid down regulates gtfB and gtfC expression and prevents Streptococcus mutans adherence to the cell surfaces.

BACKGROUND: 10-Hydroxy-2-decenoic acid, an unsaturated fatty acid is the most active and unique component to the royal jelly that has antimicrobial properties. Streptococcus mutans is associated with pathogenesis of oral cavity, gingivoperiodontal diseases and bacteremia following dental manipulations. In the oral cavity, S. mutans colonize the soft tissues including tongue, palate, and buccal mucosa. When considering the role of supragingival dental plaque in caries, the proportion of acid producing bacteria (particularly S. mutans), has direct relevance to the pathogenicity of the plaque. The genes that encode glucosyltransferases (gtfs) especially gtfB and gtfC are important in S. mutans colonization and pathogenesis. This study investigated the hydroxy-decenoic acid (HDA) effects on gtfB and gtfC expression and S. mutans adherence to cells surfaces. METHODS: Streptococcus mutans was treated by different concentrations of HPLC purified HDA supplied by Iran Beekeeping and Veterinary Association. Real time RT-PCR and western blot assays were conducted to evaluate gtfB and gtfC genes transcription and translation before and after HDA treatment. The bacterial attachment to the cell surfaces was evaluated microscopically. RESULTS: 500 µg ml-1 of HDA inhibited gtfB and gtfC mRNA transcription and its expression. The same concentration of HDA decreased 60% the adherence of S. mutans to the surface of P19 cells. CONCLUSION: Hydroxy-decenoic acid prevents gtfB and gtfC expression efficiently in the bactericide sub-concentrations and it could effectively reduce S. mutans adherence to the cell surfaces. In the future, therapeutic approaches to affecting S. mutans could be selective and it's not necessary to put down the oral flora completely.

Large scale screening of commonly used Iranian traditional medicinal plants against urease activity.

BACKGROUND AND PURPOSE OF THE STUDY: H. pylori infection is an important etiologic impetus usually leading to gastric disease and urease enzyme is the most crucial role is to protect the bacteria in the acidic environment of the stomach. Then urease inhibitors would increase sensitivity of the bacteria in acidic medium. METHODS: 137 Iranian traditional medicinal plants were examined against Jack bean urease activity by Berthelot reaction. Each herb was extracted using 50% aqueous methanol. The more effective extracts were further tested and their IC50 values were determined. RESULTS: 37 plants out of the 137 crude extracts revealed strong urease inhibitory activity (more than 70% inhibition against urease activity at 10 mg/ml concentration). Nine of the whole studied plants crude extracts were found as the most effective with IC50 values less than 500 µg/ml including; Rheum ribes, Sambucus ebulus, Pistachia lentiscus, Myrtus communis, Areca catechu, Citrus aurantifolia, Myristica fragrans, Cinnamomum zeylanicum and Nicotiana tabacum. CONCLUSIONS: The most potent urease inhibitory was observed for Sambucus ebulus and Rheum ribes extracts with IC50 values of 57 and 92 µg/ml, respectively.