Model-based in silico analysis of the PI3K/Akt pathway: the elucidation of cross-talk between diabetes and breast cancer

BACKGROUND

A positive association between diabetes and breast cancer has been identified by various epidemiological and clinical studies. However, the possible molecular interactions between the two heterogeneous diseases have not been fully determined yet. There are several underlying mechanisms which may increase the risk of breast cancer in diabetic patients.

INTRODUCTION

In this study, we focused on the role of O-GlcNAc transferase (OGT) enzyme in the regulation of phosphatidylinositol-3 kinase (PI3K) pathway through activation/deactivation of Akt protein. The efficiency of insulin signaling in adipocytes is reduced as a result of OGT overexpression which further attenuates Akt signaling; as a result, the efficiency of insulin signaling is reduced by downregulation of insulin-responsive genes. On the other hand, increased expression of OGT results in Akt activation in breast cancer cells, leading to enhanced cell proliferation and inhibition of the apoptosis. However, the interplay amongst these signaling pathways is still under investigation.

METHODS

In this study, we used Petri nets (PNs) to model and investigate the role of PI3K and OGT pathways, acting as key players in crosstalk between diabetes and breast cancer, resulting in progression of these chronic diseases. Moreover, in silico perturbation experiments were applied on the model to analyze the effects of anti-cancer agents (shRNA and BZX) and anti-diabetic drug (Metformin) on the system.

RESULTS

Our PN model reflects the alterations in protein expression and behavior and the correlation between breast cancer and diabetes. The analysis proposed two combination therapies to combat breast cancer progression in diabetic patients including combination of OGTmRNA silencing and OGT inhibitor (BZX) as first combination and BZX and Metformin as the second.

CONCLUSION

The PN model verified that alterations in O-GlcNAc signaling affect both insulin resistance and breast cancer. Moreover, the combination therapy for breast cancer patients consisting of anti-diabetic drugs such as Metformin along with OGT inhibitors, for example BZX, can produce better treatment regimens.

The Canadian Plastic Surgery Workforce Analysis: Forecasting Future Need

BACKGROUND

Projecting the demand for plastic surgeons has become increasingly important in a climate of scarce public resource within a single payer health-care system. The goal of this study is to provide a comprehensive workforce update and describe the perceptions of the workforce among Canadian Plastic Surgery residents and surgeons.

METHODS

Two questionnaires were developed by a national task force under the Canadian Plastic Surgery Research Collaborative. The surveys were distributed to residents and practicing surgeons, respectively.

RESULTS

Two-hundred fifteen (49%) surgeons responded, with a mean age of 51.4 years (standard deviation [SD] = 11.5); 78% were male. Thirty-three percent had been in practice for 25 years or longer. More than half of respondents were practicing in a large urban center. Fifty-nine percent believed their group was going to hire in the next 2 to 3 years; however, only 36% believed their health authority/provincial government had the necessary resources. The mean desired age of retirement was 67 years (SD = 6.4). We predict the surgeons-to-population ratio to be 1.55:100 000 and the graduate-to-retiree ratio to be 2.16:1 within the next 5 to 10 years. Seventy-seven (49%) residents responded. Most were "very satisfied" with their training (61%) and operative experience (90%). Eighty-nine percent of respondents planned to pursue addqitional training after residency, with 70% stating that the current job market was contributing to their decision. Most residents responded that they were concerned with the current job market.

CONCLUSIONS

The results of this study predict an adequate number of plastic surgeons will be trained within the next 10 years to suit the population's requirements; however, there is concern that newly trained surgeons will not have access to the necessary resources to meet growing demands. Furthermore, there is an evident shortage of those practicing in rural areas. Many trainees worry about the availability of jobs, despite evidence of active recruitment. The workforce may benefit from structured career mentorship in residency and improved transparency in hiring practices, particularly to attract young surgeons to smaller communities. It may also benefit from a coordinated national approach to recruitment and succession planning.

Modeling and analysis of the impacts of jet lag on circadian rhythm and its role in tumor growth

Circadian rhythms maintain a 24 h oscillation pattern in metabolic, physiological and behavioral processes in all living organisms. Circadian rhythms are organized as biochemical networks located in hypothalamus and peripheral tissues. Rhythmicity in the expression of circadian clock genes plays a vital role in regulating the process of cell division and DNA damage control. The oncogenic protein, MYC and the tumor suppressor, p53 are directly influenced by the circadian clock. Jet lag and altered sleep/wake schedules prominently affect the expression of molecular clock genes. This study is focused on developing a Petri net model to analyze the impacts of long term jet lag on the circadian clock and its probable role in tumor progression. The results depict that jet lag disrupts the normal rhythmic behavior and expression of the circadian clock proteins. This disruption leads to persistent expression of MYC and suppressed expression of p53. Thus, it is inferred that jet lag altered circadian clock negatively affects the expressions of cell cycle regulatory genes and contribute in uncontrolled proliferation of tumor cells.

Model of the adaptive immune response system against HCV infection reveals potential immunomodulatory agents for combination therapy

A regulated immune system employs multiple cell types, diverse variety of cytokines and interacting signalling networks against infections. Systems biology offers a promising solution to model and simulate such large populations of interacting components of immune systems holistically. This study focuses on the distinct components of the adaptive immune system and analysis, both individually and in association with HCV infection. The effective and failed adaptive immune response models have been developed followed by interventions/perturbations of various treatment strategies to get better assessment of the treatment responses under varying stimuli. Based on the model predictions, the NK cells, T regulatory cells, IL-10, IL-21, IL-12, IL-2 entities are found to be the most critical determinants of treatment response. The proposed potential immunomodulatory therapeutic interventions include IL-21 treatment, blocking of inhibitory receptors on T-cells and exogenous anti-IL-10 antibody treatment. The relative results showed that these interventions have differential effect on the expression levels of cellular and cytokines entities of the immune response. Notably, IL-21 enhances the expression of NK cells, Cytotoxic T lymphocytes and CD4+ T cells and hence restore the host immune potential. The models presented here provide a starting point for cost-effective analysis and more comprehensive modeling of biological phenomenon.

Analyzing the Behavior of Neuronal Pathways in Alzheimer's Disease Using Petri Net Modeling Approach

Alzheimer's Disease (AD) is the most common neuro-degenerative disorder in the elderly that leads to dementia. The hallmark of AD is senile lesions made by abnormal aggregation of amyloid beta in extracellular space of brain. One of the challenges in AD treatment is to better understand the mechanism of action of key proteins and their related pathways involved in neuronal cell death in order to identify adequate therapeutic targets. This study focuses on the phenomenon of aggregation of amyloid beta into plaques by considering the signal transduction pathways of Calpain-Calpastatin (CAST) regulation system and Amyloid Precursor Protein (APP) processing pathways along with Ca2+ channels. These pathways are modeled and analyzed individually as well as collectively through Stochastic Petri Nets for comprehensive analysis and thorough understating of AD. The model predicts that the deregulation of Calpain activity, disruption of Calcium homeostasis, inhibition of CAST and elevation of abnormal APP processing are key cytotoxic events resulting in an early AD onset and progression. Interestingly, the model also reveals that plaques accumulation start early (at the age of 40) in life but symptoms appear late. These results suggest that the process of neuro-degeneration can be slowed down or paused by slowing down the degradation rate of Calpain-CAST Complex. In the light of this study, the suggestive therapeutic strategy might be the prevention of the degradation of Calpain-CAST complexes and the inhibition of Calpain for the treatment of neurodegenerative diseases such as AD.

Expanding the phenotype associated with biallelic WDR60 mutations: Siblings with retinal degeneration and polydactyly lacking other features of short rib thoracic dystrophies

Ciliopathies are disorders of the primary cilium that can affect almost all organs and that are characterized by pleiotropy and extensive intra- and interfamilial phenotypic variability. Accordingly, mutations in the same gene can cause different ciliopathy phenotypes of varying severity. WDR60 encodes a protein thought to play a role in the primary cilium's intraflagellar transport machinery. Mutations in this gene are a rare cause of Jeune asphyxiating thoracic dystrophy (JATD) and short-rib polydactyly syndrome (SRPS). Here we report on a milder and distinct phenotype in a consanguineous Pakistani pedigree with two adolescent sisters affected by retinal degeneration and postaxial polydactyly, but lack of any further skeletal or chondrodysplasia features. By targeted high-throughput sequencing of genes known or suspected to be involved in ciliogenesis, we detected a novel homozygous N-terminal truncating WDR60 mutation (c.44delC/p.Ala15Glufs*90) that co-segregated with the disease in the family. Our finding broadens the spectrum of WDR60-related phenotypes and shows the utility of broad multigene panels during the genetic work-up of patients with ciliopathies.

Using RT-PCR and glutathione level to study the effect of follicular fluid on in vitro maturation and gene expression of sheep oocytes

The aim of this study is to evaluate the effect of sheep follicular fluid (SFF) supplementation of the in vitro maturation (IVM) media of sheep oocytes on the resumption of meiosis, glutathione (GSH) level, and expression of apoptosis (Bax, Bcl-2) as well as heat shock protein beta-1 (HSPB1) genes. Sheep ovaries were collected from the central slaughterhouse of Riyadh city, KSA. Oocytes were aspirated from 3 to 8 mm follicles. Sheep oocytes were cultured in maturation medium with different concentrations of sheep follicular fluid: 0% (control), 10%, 20% and 40% for 24 h. The results indicated that the maturation rate of oocytes was significantly (p ≤ .05) decreased in 40% SFF (36.87%) versus the control (61.3%), 10% SFF (63.95%) and 20% SFF (64.08%). The supplementation of the IVM medium with 10% SFF induced an intra-oocyte GSH concentration that was significantly higher than in sheep oocytes cultured with 20% and 40% SFF and similar to the GSH content in oocytes cultured without SFF. Real-time polymerase chain reaction analysis of gene expression revealed no significant differences in the Bax and HSPB1 genes between the control and 10% SFF, whereas they were significantly higher in 40% FF (p ≤ .05) compared to the control. The expression of Bax:Bcl-2 was significantly higher in 20% and 40% SFF compared to the control group. In conclusion, the addition of SFF to the IVM culture of sheep oocytes is recommended to support nuclear maturation and increase oocyte competence.

Facial expression recognition as a candidate marker for autism spectrum disorder: how frequent and severe are deficits?

Background

Impairments in social communication are a core feature of Autism Spectrum Disorder (ASD). Because the ability to infer other people’s emotions from their facial expressions is critical for many aspects of social communication, deficits in expression recognition are a plausible candidate marker for ASD. However, previous studies on facial expression recognition produced mixed results, which may be due to differences in the sensitivity of the many tests used and/or the heterogeneity among individuals with ASD. To ascertain whether expression recognition may serve as a diagnostic marker (which distinguishes people with ASD from a comparison group) or a stratification marker (which helps to divide ASD into more homogeneous subgroups), a crucial first step is to move beyond identification of mean group differences and to better understand the frequency and severity of impairments.

Methods

This study tested 46 individuals with ASD and 52 age- and IQ-matched typically developing (TD) participants on the Films Expression Task, which combines three key features of real-life expression recognition: naturalistic facial expressions, a broad range of simple and complex emotions, and short presentation time. Test-retest reliability was assessed in 28 individuals who did not participate in the main study and revealed acceptable reliability (ICC r = .74).

Results

Case-control comparisons showed highly significant mean group differences for accuracy (p = 1.1 × 10^− 10), with an effect size (Cohen’s d = 1.6), more than twice as large as the mean effect size reported in a previous meta-analysis (Uljarevic and Hamilton, 2012, J Autism Dev Disord). The ASD group also had significantly increased mean reaction times overall (p = .00015, d = .83) and on correct trials (p = .0002, d = .78). However, whereas 63% of people with ASD showed severe deficits (they performed below two standard deviations of the TD mean, a small subgroup (15.3%) performed normally (within one standard deviation of the mean).

Conclusion

These findings indicate that the majority of people with ASD have severe expression recognition deficits and that the Films Expression Test is a sensitive task for biomarker research in ASD. Future work is needed to establish whether ASD subgroups with and without expression recognition deficits differ from one another in terms of their symptom profile or neurobiological underpinnings.

Electronic supplementary material

The online version of this article (10.1186/s13229-018-0187-7) contains supplementary material, which is available to authorized users.

Effect of Incorporating Stevia and Moringa in Cookies on Postprandial Glycemia, Appetite, Palatability, and Gastrointestinal Well-Being

BACKGROUND

Medicinal plants including stevia and moringa constitute an important source of health-beneficial bioactive components, and hence their intake may beneficially modulate biomarkers of chronic diseases.

OBJECTIVE

The objective of the present study was to investigate the effect of incorporating stevia and moringa leaf powder in cookies on postprandial glycemia, appetite, palatability, and gastrointestinal well-being in humans.

METHOD

In a randomized crossover design, 20 healthy subjects consumed 3 isocaloric test foods (each providing 50 g available carbohydrates) of control cookies (CC) made from 100% wheat flour, cookies containing stevia leaf powder (SC, 3% w/w), and cookies containing moringa leaf powder (MC, 5% w/w) as breakfast. Blood glucose and subjective appetite were measured at fasting and at 15, 30, 45, 60, 90, and 120 min after the consumption of the cookies. Palatability and gastrointestinal well-being were measured using standard questionnaires.

RESULTS

Compared to CC, MC resulted in a significant decrease in postprandial blood glucose concentration at 30 and 45 min (p = 0.002 and p = 0.003, respectively) and showed a tendency (p = 0.077) for lower blood glucose incremental area under the curve (iAUC). Subjects were significantly less hungry after SC and MC intake (p = 0.035 and p = 0.041, respectively) compared to CC. All the cookies were liked by the subjects without any reported gastrointestinal discomfort.

CONCLUSION

The results showed that compared to CC, MC improved postprandial glycemia and reduced hunger, while SC reduced hunger only. Future studies are now warranted to explore the mechanisms responsible for these observed effects.

Medical Image Retrieval with Compact Binary Codes Generated in Frequency Domain Using Highly Reactive Convolutional Features

Efficient retrieval of relevant medical cases using semantically similar medical images from large scale repositories can assist medical experts in timely decision making and diagnosis. However, the ever-increasing volume of images hinder performance of image retrieval systems. Recently, features from deep convolutional neural networks (CNN) have yielded state-of-the-art performance in image retrieval. Further, locality sensitive hashing based approaches have become popular for their ability to allow efficient retrieval in large scale datasets. In this paper, we present a highly efficient method to compress selective convolutional features into sequence of bits using Fast Fourier Transform (FFT). Firstly, highly reactive convolutional feature maps from a pre-trained CNN are identified for medical images based on their neuronal responses using optimal subset selection algorithm. Then, layer-wise global mean activations of the selected feature maps are transformed into compact binary codes using binarization of its Fourier spectrum. The acquired hash codes are highly discriminative and can be obtained efficiently from the original feature vectors without any training. The proposed framework has been evaluated on two large datasets of radiology and endoscopy images. Experimental evaluations reveal that the proposed method significantly outperforms other features extraction and hashing schemes in both effectiveness and efficiency.

MicroRNA pharmacogenomics based integrated model of miR-17-92 cluster in sorafenib resistant HCC cells reveals a strategy to forestall drug resistance

Among solid tumors, hepatocellular carcinoma (HCC) emerges as a prototypical therapy-resistant tumor. Considering the emerging sorafenib resistance crisis in HCC, future studies are urgently required to overcome resistance. Recently noncoding RNAs (ncRNAs) have emerged as significant regulators in signalling pathways involved in cancer drug resistance and pharmacologically targeting these ncRNAs might be a novel stratagem to reverse drug resistance. In the current study, using a hybrid Petri net based computational model, we have investigated the harmonious effect of miR-17-92 cluster inhibitors/mimics and circular RNAs on sorafenib resistant HCC cells in order to explore potential resistance mechanisms and to identify putative targets for sorafenib-resistant HCC cells. An integrated model was developed that incorporates seven miRNAs belonging to miR-17-92 cluster (hsa-miR-17-5p, hsa-miR-17-3p, hsa-miR-19a, hsa-miR-19b, hsa-miR-18a, hsa-miR-20a and hsa-miR-92) and crosstalk of two signaling pathways (EGFR and IL-6) that are differentially regulated by these miRNAs. The mechanistic connection was proposed by the correlation between members belonging to miR-17-92 cluster and corresponding changes in the protein levels of their targets in HCC, specifically those targets that have verified importance in sorafenib resistance. Current findings uncovered potential pathway features, underlining the significance of developing modulators of this cluster to combat drug resistance in HCC.

Petri Net-Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma

Tight junctions help prevent the passage of digestive enzymes and microorganisms through the space between adjacent epithelial cells lining. However, Helicobacter pylori encoded virulence factors negatively regulate these tight junctions and contribute to dysfunction of gastric mucosa. Here, we have predicted the regulation of important tight junction proteins, such as Zonula occludens-1, Claudin-2 and Connexin32 in the presence of pathogenic proteins. Molecular events such as post translational modifications and crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation are explored which may compromise the integrity of these tight junction proteins. Furthermore, the signaling pathways disrupted by dysregulated kinases, proteins and post-translational modifications are reviewed to design an abstracted computational model showing the situation-dependent dynamic behaviors of these biological processes and entities. A qualitative hybrid Petri Net model is therefore constructed showing the altered host pathways in the presence of virulence factor cytotoxin-associated gene A, leading to the disruption of tight junction proteins. The model is qualitative logic-based, which does not depend on any kinetic parameter and quantitative data and depends on knowledge derived from experiments. The designed model provides insights into the tight junction disruption and disease progression. Model is then verified by the available experimental data, nevertheless formal in vitro experimentation is a promising way to ensure its validation. The major findings propose that H. pylori activated kinases are responsible to trigger specific post translational modifications within tight junction proteins, at specific sites. These modifications may favor alterations in gastric barrier and provide a route to bacterial invasion into host cells.

(μ2-Adipato-κ4O,O':O'',O''')bis-[aqua-(benzene-1,2-di-amine-κ2N,N')-chlorido-cadmium]: crystal structure and Hirshfeld surface analysis

The full mol-ecule of the binuclear title compound, [Cd2Cl2(C6H8O4)(C6H8N2)2(H2O)2], is generated by the application of a centre of inversion located at the middle of the central CH2-CH2 bond of the adipate dianion; the latter chelates a CdII atom at each end. Along with two carboxyl-ate-O atoms, the CdII ion is coordinated by the two N atoms of the chelating benzene-1,2-di-amine ligand, a Cl- anion and an aqua ligand to define a distorted octa-hedral CdClN2O3 coordination geometry with the monodentate ligands being mutually cis. The disparity in the Cd-N bond lengths is related to the relative trans effect exerted by the Cd-O bonds formed by the carboxyl-ate-O and aqua-O atoms. The packing features water-O-H⋯O(carboxyl-ate) and benzene-1,2-di-amine-N-H⋯Cl hydrogen bonds, leading to layers that stack along the a-axis direction. The lack of directional inter-actions between the layers is confirmed by a Hirshfeld surface analysis.