Memory leak detection in Plumbr

Platforms with automatic memory management, such as the JVM, are usually considered free of memory leaks. However, memory leaks can happen in such environments, as the garbage collector cannot free objects, which are not used by the application anymore, but are still referenced. Such unused objects can eventually fill up the heap and crash the application. Although this problem has been studied extensively, nevertheless, there are still many rooms for improvement in this area. This paper describes the statistical approach for memory leak detection, as an alternative, along with a commercial tool, Plumbr, which is based on the method. The tool is later analyzed with three case studies of real applications and in the process also analyzes strengths and weaknesses of the statistical approach for memory leak detection. Copyright © 2014 John Wiley & Sons, Ltd.     

Biosynthesis of zinc oxide nanoparticles by petals extract of Rosa indica L., its formulation as nail paint and evaluation of antifungal activity against fungi causing onychomycosis

Aim: The authors report the biological synthesis of zinc oxide nanoparticles (ZnO‐NPs) from the petals extract of Rosa indica L. (rose). Its efficacy was evaluated against two dermatophytes: namely: Trichophyton mentagrophytes and Microsporum canis which cause onychomycosis. The activity of antibiotics against the tested dermatophytes was enhanced, when evaluated in combination with ZnO‐NPs. Methods and results: The synthesised ZnO‐NPs were preliminary detected by using ultraviolet UV visible spectroscopy, which showed specific absorbance. The ZnO‐NPs were further characterised by nanoparticle tracking analysis (NTA), Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), X‐ray diffraction and Zetasizer. Moreover, nanoparticles containing nail paint (nanopaint) was formulated and its antifungal activity was also assessed against T. mentagrophytes and M. canis. ZnO‐NPs and formulated nanopaint containing ZnO‐NPs, both showed significant antifungal activity. The maximum activity was noted against M. canis and lesser against T. mentagrophytes. Minimum inhibitory concentration of ZnO‐NPs was also determined against the dermatophytes causing onychomycosis infection. Conclusion: ZnO‐NPs can be utilised as a potential antifungal agent for the treatment of onychomycosis after more experimental trials.Inspec keywords: diseases, zinc compounds, nanoparticles, nanofabrication, antibacterial activity, microorganisms, nanomedicine, ultraviolet spectra, visible spectra, Fourier transform infrared spectra, transmission electron microscopy, X‐ray diffraction, biomedical materials, patient treatmentOther keywords: zinc oxide nanoparticle biosynthesis, Rosa indica L petals extract, nail paint, antifungal activity evaluation, dermatophyte, Trichophyton mentagrophytes, Microsporum canis, antibiotics activity, ultraviolet‐visible spectroscopy, nanoparticle tracking analysis, Fourier transform infrared spectroscopy, transmission electron microscopy, X‐ray diffraction, zetasizer, antifungal agent, onychomycosis treatment     

Inactivation of PTEN and ZFHX3 in Mammary Epithelial Cells Alters Patterns of Collective Cell Migration

Whole exome sequencing of invasive mammary carcinomas revealed the association of mutations in PTEN and ZFHX3 tumor suppressor genes (TSGs). We generated single and combined PTEN and ZFHX3 knock-outs (KOs) in the immortalized mammary epithelial cell line MCF10A to study the role of these genes and their potential synergy in migration regulation. Inactivation of PTEN, but not ZFHX3, induced the formation of large colonies in soft agar. ZFHX3 inactivation in PTEN KO, however, increased colony numbers and normalized their size. Cell migration was affected in different ways upon PTEN and ZFHX3 KO. Inactivation of PTEN enhanced coordinated cell motility and thus, the collective migration of epithelial islets and wound healing. In contrast, ZFHX3 knockout resulted in the acquisition of uncoordinated cell movement associated with the appearance of immature adhesive junctions (AJs) and the increased expression of the mesenchymal marker vimentin. Inactivation of the two TSGs thus induces different stages of partial epithelial-to-mesenchymal transitions (EMT). Upon double KO (DKO), cells displayed still another motile state, characterized by a decreased coordination in collective migration and high levels of vimentin but a restoration of mature linear AJs. This study illustrates the plasticity of migration modes of mammary cells transformed by a combination of cancer-associated genes.     

Metformin Influence on the Intestinal Microbiota and Organism of Rats with Metabolic Syndrome

Metformin is a first-line drug for DM2 treatment and prevention, but its complex effect on impaired glucose tolerance (IGT), including its influence on myocardial resistance to ischemia-reperfusion injury, is not completely studied. We aimed to evaluate the influence of metformin on the intestinal microbiota (IM), metabolism, and functional and morphological characteristics of myocardium in rats with IGT. IGT was modelled in SPF Wistar rats with a high-fat diet and streptozotocin and nicotinamide injection. Rats were divided into three groups: IGT (without treatment), IGT MET (metformin therapy), and CRL (without IGT induction and treatment). IGT group was characterized by: higher body weight, increased serum glucose and total cholesterol levels, atherogenic coefficient, impairment in the functional parameters of the isolated heart during perfusion, and larger myocardium infarction (MI) size in comparison with the CRL group. IM of IGT rats differed from that of CRL: an increase of Bacteroides, Acinetobacter, Akkermansia, Roseburia, and a decrease of Lactobacillus genera representation. Metformin therapy led to the diminishing of metabolic syndrome (MS) symptoms, which correlated with IM restoration, especially with the growth of Akkermansia spp. and decline of Roseburia populations and their influence on other members of IM. The obtained results allow us to consider from a new point of view the expediency of probiotic A. muciniphila use for MS treatment.     

Structural and Molecular Kinetic Features of Activities of DNA Polymerases

DNA polymerases catalyze DNA synthesis during the replication, repair, and recombination of DNA. Based on phylogenetic analysis and primary protein sequences, DNA polymerases have been categorized into seven families: A, B, C, D, X, Y, and RT. This review presents generalized data on the catalytic mechanism of action of DNA polymerases. The structural features of different DNA polymerase families are described in detail. The discussion highlights the kinetics and conformational dynamics of DNA polymerases from all known polymerase families during DNA synthesis.     

The Role of Natural Polymorphic Variants of DNA Polymerase β in DNA Repair

DNA polymerase β (Polβ) is considered the main repair DNA polymerase involved in the base excision repair (BER) pathway, which plays an important part in the repair of damaged DNA bases usually resulting from alkylation or oxidation. In general, BER involves consecutive actions of DNA glycosylases, AP endonucleases, DNA polymerases, and DNA ligases. It is known that protein–protein interactions of Polβ with enzymes from the BER pathway increase the efficiency of damaged base repair in DNA. However natural single-nucleotide polymorphisms can lead to a substitution of functionally significant amino acid residues and therefore affect the catalytic activity of the enzyme and the accuracy of Polβ action. Up-to-date databases contain information about more than 8000 SNPs in the gene of Polβ. This review summarizes data on the in silico prediction of the effects of Polβ SNPs on DNA repair efficacy; available data on cancers associated with SNPs of Polβ; and experimentally tested variants of Polβ. Analysis of the literature indicates that amino acid substitutions could be important for the maintenance of the native structure of Polβ and contacts with DNA; others affect the catalytic activity of the enzyme or play a part in the precise and correct attachment of the required nucleotide triphosphate. Moreover, the amino acid substitutions in Polβ can disturb interactions with enzymes involved in BER, while the enzymatic activity of the polymorphic variant may not differ significantly from that of the wild-type enzyme. Therefore, investigation regarding the effect of Polβ natural variants occurring in the human population on enzymatic activity and protein–protein interactions is an urgent scientific task.     

The Role of Altered Mitochondrial Metabolism in Thyroid Cancer Development and Mitochondria-Targeted Thyroid Cancer Treatment

Thyroid cancer (TC) is the most common type of endocrine malignancy. Tumour formation, progression, and metastasis greatly depend on the efficacy of mitochondria—primarily, the regulation of mitochondria-mediated apoptosis, Ca²⁺ homeostasis, dynamics, energy production, and associated reactive oxygen species generation. Recent studies have successfully confirmed the mitochondrial aetiology of thyroid carcinogenesis. In this review, we focus on the recent progress in understanding the molecular mechanisms of thyroid cancer relating to altered mitochondrial metabolism. We also discuss the repurposing of known drugs and the induction of mitochondria-mediated apoptosis as a new trend in the development of anti-TC therapy.     

AICAR Protects Vascular Endothelial Cells from Oxidative Injury Induced by the Long-Term Palmitate Excess

Hyperlipidemia manifested by high blood levels of free fatty acids (FFA) and lipoprotein triglycerides is critical for the progression of type 2 diabetes (T2D) and its cardiovascular complications via vascular endothelial dysfunction. However, attempts to assess high FFA effects in endothelial culture often result in early cell apoptosis that poorly recapitulates a much slower pace of vascular deterioration in vivo and does not provide for the longer-term studies of endothelial lipotoxicity in vitro. Here, we report that palmitate (PA), a typical FFA, does not impair, by itself, endothelial barrier and insulin signaling in human umbilical vein endothelial cells (HUVEC), but increases NO release, reactive oxygen species (ROS) generation, and protein labeling by malondialdehyde (MDA) hallmarking oxidative stress and increased lipid peroxidation. This PA-induced stress eventually resulted in the loss of cell viability coincident with loss of insulin signaling. Supplementation with 5-aminoimidazole-4-carboxamide-riboside (AICAR) increased endothelial AMP-activated protein kinase (AMPK) activity, supported insulin signaling, and prevented the PA-induced increases in NO, ROS, and MDA, thus allowing to maintain HUVEC viability and barrier, and providing the means to study the long-term effects of high FFA levels in endothelial cultures. An upgraded cell-based model reproduces FFA-induced insulin resistance by demonstrating decreased NO production by vascular endothelium.