Copper doping enhanced the oxidative stress-mediated cytotoxicity of TiO2 nanoparticles in A549 cells

Physicochemical properties of titanium dioxide nanoparticles (TiO₂ NPs) can be tuned by doping with metals or nonmetals. Copper (Cu) doping improved the photocatalytic behavior of TiO₂ NPs that can be applied in various fields such as environmental remediation and nanomedicine. However, interaction of Cu-doped TiO₂ NPs with human cells is scarce. This study was designed to explore the role of Cu doping in cytotoxic response of TiO₂ NPs in human lung epithelial (A549) cells. Characterization data demonstrated the presence of both TiO₂ and Cu in Cu-doped TiO₂ NPs with high-quality lattice fringes without any distortion. The size of Cu-doped TiO₂ NPs (24 nm) was lower than pure TiO₂ NPs (30 nm). Biological results showed that both pure and Cu-doped TiO₂ NPs induced cytotoxicity and oxidative stress in a dose-dependent manner. Low mitochondrial membrane potential and higher caspase-3 enzyme (apoptotic markers) activity were also observed in A549 cells exposed to pure and Cu-doped TiO₂ NPs. We further observed that cytotoxicity caused by Cu-doped TiO₂ NPs was higher than pure TiO₂ NPs. Moreover, antioxidant N-acetyl cysteine effectively prevented the reactive oxygen species generation, glutathione depletion, and cell viability reduction caused by Cu-doped TiO₂ NPs. This is the first report showing that Cu-doped TiO₂ NPs induced cytotoxicity and oxidative stress in A549 cells. This study warranted further research to explore the role of Cu doping in toxicity mechanisms of TiO₂ NPs.

Formal Modeling of mTOR Associated Biological Regulatory Network Reveals Novel Therapeutic Strategy for the Treatment of Cancer

Cellular homeostasis is a continuous phenomenon that if compromised can lead to several disorders including cancer. There is a need to understand the dynamics of cellular proliferation to get deeper insights into the prevalence of cancer. Mechanistic Target of Rapamycin (mTOR) is implicated as the central regulator of the metabolic pathway involved in growth whereas its two distinct complexes mTORC1 and mTORC2 perform particular functions in cellular propagation. To date, mTORC1 is a well defined therapeutic target to inhibit uncontrolled cell division, while the role of mTORC2 is not well characterized. Therefore, the current study is designed to understand the signaling dynamics of mTOR and its partner proteins such as PI3K, PTEN, mTORC2, PKB (Akt), mTORC1, and FOXO. For this purpose, a qualitative model of mTOR-associated Biological Regulatory Network (BRN) is constructed to predict its regulatory behaviors which may not be predictable otherwise. The depleted expression of PTEN and FOXO along with the overexpression of PI3K, mTORC2, mTORC1 and Akt is predicted as a stable steady state which is in accordance with their observed expression levels in the progression of various cancers. The qualitative model also predicts the homeostasis of all the entities in the form of qualitative cycles. The significant qualitative (discrete) cycle is identified by analyzing betweenness centralities of the qualitative (discrete) states. This cycle is further refined as a linear hybrid automaton model with the production (activation) and degradation (inhibition) time delays in order to analyze the real-time constraints for its existence. The analysis of the hybrid model provides a formal proof that during homeostasis the inhibition time delay of Akt is less than the inhibition time delay of mTORC2. In conclusion, our observations characterize that in homeostasis Akt is degraded with a faster rate than mTORC2 which suggests that the inhibition of Akt along with the activation of mTORC2 may be a better therapeutic strategy for the treatment of cancer.

Drainless Abdominoplasty Using Barbed Progressive Tension Sutures

We describe our current technique of drainless abdominoplasty using barbed progressive tension sutures. The perioperative management and detailed steps of procedure are outlined, including indications for concomitantly performing liposuction and repair of diastasis of the rectus abdominis muscles. This approach reliably improves abdominal contour, minimizes complications, and is straightforward to learn and perform.

The pattern of invasive lobular carcinoma in the patients diagnosed with breast cancer from Balochistan

INTRODUCTION

Invasive lobular carcinoma (ILC) is the second most common type of breast cancer accounting for 5%-15% of all the breast cancer cases. The present study was performed on 171 breast cancer patients from Balochistan registered in CENAR (Center for Nuclear Medicine and Radiotherapy), Quetta.

MATERIALS AND METHODS

Written consent was obtained from the patients. The history of the disease was taken from the patients, and the patients' enrollment files were retrieved.

RESULTS

Of the 171 patients, 5 (2.96%) were diagnosed with ILC with tumor Grade II, and stage of the cancer reported was Grade III in all the 5 patients affected with ILC.

CONCLUSION

ILC is the second most common type of breast cancer diagnosed with comparatively lower grade but almost reported infiltrating.

ANTIOXIDANTS AND ANTIFUNGAL ACTIVITIES OF SUBSTITUTED GUANIDINES AND THEIR COPPER COMPLEXES

A series of guanidines and their copper (II) complexes were investigated for their radical scavenging activity including peroxyl radicals (ROO), superoxide anion (O₂), hydroxyl ('OH), and reactive hydrogen per- oxide (H₂0₂) species. Among the Cu(II) complexes, Cu-MR-9-2 shows the highest, Cu-MR-9-3, Cu-MR-9-6 less and Cu-MR-9-1 least antioxidant potential. The Cu(II) complexes show better Fea'-chelating activity than that of ligands. Among the Cu(II) complexes Cu-MR-9-2 was found to have the highest, Cu-MR-9-6 moderate, MR-9-3 less and Cu-MR-9-1 least ferric reducing capacity. The IC50 values for ligands (MR-9-1, MR-9-2, MR- 9-3, MR-9-6) were determined to be 197.53 ± 7.13, 189.07 ± 7.34, 207.98 ± 6.78 and 233.38 ±6.37 pM, which showed lower antioxidant activity than their Cu(II) complexes. The IC,o values for ascorbic acid were found to be 51.60 ± 13.18 pM. The Cu(I) metal compounds (Cu-MR-9-1,Cu-MR-9-2, Cu-MR-9-3 and Cu-MR-9-6) were detected to be the most powerful scavengers of the hydroxyl radical with IC50 up to 108.03 ± 11.34 pM, 101.41 ±12.10 pM, 90.59 ± 11.53 pM and 88.86 ± 13.16 pM, respectively.

VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology

Background

With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides a mean to propose target identification in reduced time and labour. In this regard, high throughput genomic sequencing technologies and supporting bioinformatics tools have greatly facilitated the prompt analysis of pathogens, where various predicted candidates have been found effective against certain infections and diseases. A pipeline, VacSol, is designed here based on a similar approach to predict putative vaccine candidates both rapidly and efficiently.

Results

VacSol, a new pipeline introduced here, is a highly scalable, multi-mode, and configurable software designed to automate the high throughput in silico vaccine candidate prediction process for the identification of putative vaccine candidates against the proteome of bacterial pathogens. Vaccine candidates are screened using integrated, well-known and robust algorithms/tools for proteome analysis, and the results from the VacSol software are presented in five different formats by taking proteome sequence as input in FASTA file format. The utility of VacSol is tested and compared with published data and using the Helicobacter pylori 26695 reference strain as a benchmark.

Conclusion

VacSol rapidly and efficiently screens the whole bacterial pathogen proteome to identify a few predicted putative vaccine candidate proteins. This pipeline has the potential to save computational costs and time by efficiently reducing false positive candidate hits. VacSol results do not depend on any universal set of rules and may vary based on the provided input. It is freely available to download from: https://sourceforge.net/projects/vacsol/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1540-0) contains supplementary material, which is available to authorized users.

Novel Nonsense Variants c.58C>T (p.Q20X) and c.256G>T (p.E85X) in the CHEK2 Gene Identified dentified in Breast Cancer Patients from Balochistan

Breast cancer is the most commonly occurring and leading cause of cancer deaths among women globally. Hereditary cases account 5-10% of all the cases and CHEK2 is considered as a moderate penetrance breast cancer risk gene. CHEK2 plays a crucial role in response to DNA damage to promote cell cycle arrest and repair DNA damage or induce apoptosis. Our objective in the current study was to analyze mutations in the CHEK2 gene related to breast cancer in Balochistan. A total of 271 individuals including breast cancer patients and normal subjects were enrolled. All 14 exons of CHEK2 were amplified and sequenced. The majority of the patients (>95%) had invasive ductal carcinomas (IDCs), 52.1% were diagnosed with tumor grade III and 56.1% and 27.5% were diagnosed with advance stages III and IV. Two novel nonsense variants i.e. c.58C>T (P.Q20X) and c.256G>T (p.E85X) at exon 1 and 2 in two breast cancer patients were identified in the current study. Both the variants identified were novel and have not been reported elsewhere.

Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer

BACKGROUND

Breast cancer (BC) is one of the leading cause of death among females worldwide. The increasing incidence of BC is due to various genetic and environmental changes which lead to the disruption of cellular signaling network(s). It is a complex disease in which several interlinking signaling cascades play a crucial role in establishing a complex regulatory network. The logical modeling approach of René Thomas has been applied to analyze the behavior of estrogen receptor-alpha (ER-α) associated Biological Regulatory Network (BRN) for a small part of complex events that leads to BC metastasis.

METHODS

A discrete model was constructed using the kinetic logic formalism and its set of logical parameters were obtained using the model checking technique implemented in the SMBioNet software which is consistent with biological observations. The discrete model was further enriched with continuous dynamics by converting it into an equivalent Petri Net (PN) to analyze the logical parameters of the involved entities.

RESULTS

In-silico based discrete and continuous modeling of ER-α associated signaling network involved in BC provides information about behaviors and gene-gene interaction in detail. The dynamics of discrete model revealed, imperative behaviors represented as cyclic paths and trajectories leading to pathogenic states such as metastasis. Results suggest that the increased expressions of receptors ER-α, IGF-1R and EGFR slow down the activity of tumor suppressor genes (TSGs) such as BRCA1, p53 and Mdm2 which can lead to metastasis. Therefore, IGF-1R and EGFR are considered as important inhibitory targets to control the metastasis in BC.

CONCLUSION

The in-silico approaches allow us to increase our understanding of the functional properties of living organisms. It opens new avenues of investigations of multiple inhibitory targets (ER-α, IGF-1R and EGFR) for wet lab experiments as well as provided valuable insights in the treatment of cancers such as BC.

Formal modeling and analysis of the hexosamine biosynthetic pathway: role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression

The alteration of glucose metabolism, through increased uptake of glucose and glutamine addiction, is essential to cancer cell growth and invasion. Increased flux of glucose through the Hexosamine Biosynthetic Pathway (HBP) drives increased cellular O-GlcNAcylation (hyper-O-GlcNAcylation) and contributes to cancer progression by regulating key oncogenes. However, the association between hyper-O-GlcNAcylation and activation of these oncogenes remains poorly characterized. Here, we implement a qualitative modeling framework to analyze the role of the Biological Regulatory Network in HBP activation and its potential effects on key oncogenes. Experimental observations are encoded in a temporal language format and model checking is applied to infer the model parameters and qualitative model construction. Using this model, we discover step-wise genetic alterations that promote cancer development and invasion due to an increase in glycolytic flux, and reveal critical trajectories involved in cancer progression. We compute delay constraints to reveal important associations between the production and degradation rates of proteins. O-linked N-acetylglucosamine transferase (OGT), an enzyme used for addition of O-GlcNAc during O-GlcNAcylation, is identified as a key regulator to promote oncogenesis in a feedback mechanism through the stabilization of c-Myc. Silencing of the OGT and c-Myc loop decreases glycolytic flux and leads to programmed cell death. Results of network analyses also identify a significant cycle that highlights the role of p53-Mdm2 circuit oscillations in cancer recovery and homeostasis. Together, our findings suggest that the OGT and c-Myc feedback loop is critical in tumor progression, and targeting these mediators may provide a mechanism-based therapeutic approach to regulate hyper-O-GlcNAcylation in human cancer.

Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets

BACKGROUND

Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets.

RESULTS

The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control.

CONCLUSION

The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.

Visual saliency models for summarization of diagnostic hysteroscopy videos in healthcare systems

In clinical practice, diagnostic hysteroscopy (DH) videos are recorded in full which are stored in long-term video libraries for later inspection of previous diagnosis, research and training, and as an evidence for patients' complaints. However, a limited number of frames are required for actual diagnosis, which can be extracted using video summarization (VS). Unfortunately, the general-purpose VS methods are not much effective for DH videos due to their significant level of similarity in terms of color and texture, unedited contents, and lack of shot boundaries. Therefore, in this paper, we investigate visual saliency models for effective abstraction of DH videos by extracting the diagnostically important frames. The objective of this study is to analyze the performance of various visual saliency models with consideration of domain knowledge and nominate the best saliency model for DH video summarization in healthcare systems. Our experimental results indicate that a hybrid saliency model, comprising of motion, contrast, texture, and curvature saliency, is the more suitable saliency model for summarization of DH videos in terms of extracted keyframes and accuracy.

No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing

BACKGROUND

BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction.

METHODS

We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia.

RESULTS

The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75).

CONCLUSIONS

These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.

Rheumatoid arthritis: What have we learned about the causing factors?

Rheumatoid Arthritis (RA) is a common inflammatory autoimmune disease characterized by the synovitis of both small and large joints, which may lead to the destruction of cartilage and bones causing significant disabilities due to erosion of bones surfaces, if left untreated. It is a multifactorial and heterogeneous disease having contribution of both genetic (50-60%) and environmental factors. The unawareness of general public might be a contributing factor in the high prevalence rate of RA world-wide. This review article focuses on the causing factors (genetics and environmental) involved in this devastating disease. We also gave brief overview of the treatment options and animal models of RA. The literature was reviewed using mesh terms in PubMed search ''etiology of RA, genetics of RA, environmental factors in RA, Genome Wide Association Studies (GWAS) in RA''. The data was thoroughly reviewed and comprehensive information was extracted to help the readers in improving understanding towards the mechanisms, which trigger the outcomes of RA. The more we increase awareness about RA, the better we manage this disease and hence can improve life style and socio-economic status.

Chronic infection of a Brindley sacral nerve root stimulator

The Finetech-Brindley sacral anterior root stimulator (SARS) is implanted for the treatment of bladder dysfunction following spinal cord injury (SCI) and has been successful in improving micturition in many patients with SCI. This case describes a 62-year-old man who presented with a chronic Staphylococcus aureus infection of a Brindley SARS 26 years after implantation following a T5 American Spinal Injury Association A spinal cord injury (T5 ASIA A SCI). He presented with chronic sacral osteomyelitis with a history of periodic implant erosion through the skin. Following a series of interventions, definitive management involved removal of the intradural electrodes and epidural and intradural phlegmon, ligation of the thecal sac and flap reconstruction. In the case of delayed infection of a Brindley SARS, removal of the entire system should be considered, especially if extension of the infection to the intradural compartment is suspected.

The Impact of Protein Nutritional Supplementation for Massive Weight Loss Patients Undergoing Abdominoplasty

BACKGROUND

As more patients undergo bariatric surgery to assist with weight loss, the demand for post-bariatric body contouring surgery, to address both functional and aesthetic concerns, is increasing. However, high wound healing complication rates remain a significant problem for these patients. One theory is that chronic malnourishment and hypoproteinemia may contribute significantly to these wound healing complications.

OBJECTIVE

The purpose of this study was to determine the effect of pretreatment protein nutritional supplementation on wound healing in post-bariatric surgery massive weight loss patients undergoing abdominoplasty. Our hypothesis was that protein supplementation would decrease wound healing complications.

METHODS

A retrospective review was performed of 23 post-bariatric surgery patients undergoing abdominoplasty who received pretreatment protein nutritional supplementation. This group was compared with a historical control group of 23 post-bariatric surgery patients who underwent abdominoplasty in the period immediately before the implementation of the protein supplementation protocol. Patient demographics and procedural characteristics were similar for the two groups.

RESULTS

Forty-six patients were identified who had undergone abdominoplasty, half of whom were prescribed the protein supplementation protocol. Overall wound healing complication rates were significantly lower in the protein-supplemented group (0.0% vs. 21.8%, p = 0.04). There was no significant difference between the protein supplementation and historical control groups in regards to total complication rate.

CONCLUSIONS

Pretreatment protein supplementation is a simple intervention that can significantly decrease wound healing complications in post-bariatric surgery massive weight loss patients undergoing abdominoplasty. LEVEL OF EVIDENCE 4: Therapeutic.

Identification of two novel ALS2 mutations in infantile-onset ascending hereditary spastic paraplegia

Biallelic mutations of ALS2 cause a clinical spectrum of overlapping autosomal recessive neurodegenerative disorders: infantile-onset ascending hereditary spastic paralysis (IAHSP), juvenile primary lateral sclerosis (JPLS), and juvenile amyotrophic lateral sclerosis (ALS2). We report on eleven individuals affected with IAHSP from two consanguineous Pakistani families. A combination of linkage analysis with homozygosity mapping and targeted sequencing identified two novel ALS2 mutations, a c.194T > C (p.Phe65Ser) missense substitution located in the first RCC-like domain of ALS2/alsin and a c.2998delA (p.Ile1000*) nonsense mutation. This study of extended families including a total of eleven affected individuals suggests that a given ALS2 mutation may lead to a phenotype with remarkable intrafamilial clinical homogeneity.

Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice

The CRISPR/Cas technology enables targeted genome editing and the rapid generation of transgenic animal models for the study of human genetic disorders. Here we describe an autosomal recessive human disease in two unrelated families characterized by a split-foot defect, nail abnormalities of the hands, and hearing loss, due to mutations disrupting the SAM domain of the protein kinase ZAK. ZAK is a member of the MAPKKK family with no known role in limb development. We show that Zak is expressed in the developing limbs and that a CRISPR/Cas-mediated knockout of the two Zak isoforms is embryonically lethal in mice. In contrast, a deletion of the SAM domain induces a complex hindlimb defect associated with down-regulation of Trp63, a known split-hand/split-foot malformation disease gene. Our results identify ZAK as a key player in mammalian limb patterning and demonstrate the rapid utility of CRISPR/Cas genome editing to assign causality to human mutations in the mouse in <10 wk.

On the modeling and analysis of the biological regulatory network of NF-$${\kappa }$$B activation in HIV-1 infection

Purpose

The complex interactions between genetic machinery of HIV-1 and host immune cells mediate dynamic adaptive responses leading to Autoimmune Deficiency Syndrome. These interactions are captured as Biological Regulatory Network (BRN) which acts to maintain the viability of host cell machinery through feedback control mechanism which is a characteristic of complex adaptive systems. In this study, the BRN of immune response against HIV-1 infection is modeled to investigate the role of NF-κB and TNF-α in disease transmission using qualitative (discrete) and hybrid modeling formalisms.

Methods

Qualitative and Hybrid modeling approaches are used to model the BRN for the dynamic analysis. The qualitative model is based on the logical parameters while the hybrid model is based on the time delay parameters.

Results

The qualitative model gives useful insights about the physiological condition observed as the homeostasis of all the entities of the BRN as well as pathophysiological behaviors representing high expression levels of NF-κB, TNF-α and HIV. Since the qualitative model is time abstracted, so a hybrid model is developed to analyze the behavior of the BRN by associating activation and inhibition time delays with each entity. HyTech tool synthesizes time delay constraints for the existence of homeostasis.

Conclusion

Hybrid model reveals various viability constraints that characterize the conditional existence of cyclic states (homeostasis). The resultant relations suggest larger cycle period of HIV-1 than the cycle periods of the other two entities (NF-κB and TNF-α) to maintain a homeostatic expressions of these entities.