Expressed pseudogenes in the transcriptional landscape of human cancers.

Pseudogene transcripts can provide a novel tier of gene regulation through generation of endogenous siRNAs or miRNA-binding sites. Characterization of pseudogene expression, however, has remained confined to anecdotal observations due to analytical challenges posed by the extremely close sequence similarity with their counterpart coding genes. Here, we describe a systematic analysis of pseudogene "transcription" from an RNA-Seq resource of 293 samples, representing 13 cancer and normal tissue types, and observe a surprisingly prevalent, genome-wide expression of pseudogenes that could be categorized as ubiquitously expressed or lineage and/or cancer specific. Further, we explore disease subtype specificity and functions of selected expressed pseudogenes. Taken together, we provide evidence that transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression, especially in light of the recently described ceRNA networks. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.

Toxicological assessment of divalent ion-modified ZnO nanomaterials through artificial intelligence and in vivo study.

The nanotechnology-driven industrial revolution widely relies on metal oxide-based nanomaterial (NM). Zinc oxide (ZnO) production has rapidly increased globally due to its outstanding physical and chemical properties and versatile applications in industries including cement, rubber, paints, cosmetics, and more. Nevertheless, releasing Zn2+ ions into the environment can profoundly impact living systems and affect water-based ecosystems, including biological ones. In aquatic environments, Zn2+ ions can change water properties, directly influencing underwater ecosystems, especially fish populations. These ions can accumulate in fish tissues when fish are exposed to contaminated water and pose health risks to humans who consume them, leading to symptoms such as nausea, vomiting, and even organ damage. To address this issue, safety of ZnO NMs should be enhanced without altering their nanoscale properties, thus preventing toxic-related problems. In this study, an eco-friendly precipitation method was employed to prepare ZnO NMs. These NMs were found to reduce ZnO toxicity levels by incorporating elements such as Mg, Ca, Sr, and Ba. Structural, morphological, and optical properties of synthesized NMs were thoroughly investigated. In vitro tests demonstrated potential antioxidative properties of NMs with significant effects on free radical scavenging activities. In vivo, toxicity tests were conducted using Oreochromis mossambicus fish and male Swiss Albino mice to compare toxicities of different ZnO NMs. Fish and mice exposed to these NMs exhibited biochemical changes and histological abnormalities. Notably, ZnCaO NMs demonstrated lower toxicity to fish and mice than other ZnO NMs. This was attributed to its Ca2+ ions, which could enhance body growth metabolism compared to other metals, thus improving material safety. Furthermore, whether nanomaterials' surface roughness might contribute to their increased toxicity in biological systems was investigated utilizing computer vision (CV)-based AI tools to obtain SEM images of NMs, providing valuable image-based surface morphology data that could be correlated with relevant toxicology studies.

Gene Fusion Markup Language: a prototype for exchanging gene fusion data.

BACKGROUND: An avalanche of next generation sequencing (NGS) studies has generated an unprecedented amount of genomic structural variation data. These studies have also identified many novel gene fusion candidates with more detailed resolution than previously achieved. However, in the excitement and necessity of publishing the observations from this recently developed cutting-edge technology, no community standardization approach has arisen to organize and represent the data with the essential attributes in an interchangeable manner. As transcriptome studies have been widely used for gene fusion discoveries, the current non-standard mode of data representation could potentially impede data accessibility, critical analyses, and further discoveries in the near future. RESULTS: Here we propose a prototype, Gene Fusion Markup Language (GFML) as an initiative to provide a standard format for organizing and representing the significant features of gene fusion data. GFML will offer the advantage of representing the data in a machine-readable format to enable data exchange, automated analysis interpretation, and independent verification. As this database-independent exchange initiative evolves it will further facilitate the formation of related databases, repositories, and analysis tools. The GFML prototype is made available at http://code.google.com/p/gfml-prototype/. CONCLUSION: The Gene Fusion Markup Language (GFML) presented here could facilitate the development of a standard format for organizing, integrating and representing the significant features of gene fusion data in an inter-operable and query-able fashion that will enable biologically intuitive access to gene fusion findings and expedite functional characterization. A similar model is envisaged for other NGS data analyses.

Hepatoprotective effect of silver nanoparticles synthesized using aqueous leaf extract of Rhizophora apiculata.

Background: Liver plays a vital role in the elimination of xenobiotics that can induce hepatotoxicity in living organisms.Silver nanoparticles have evolved recently as an alternative in various industries and are used for their biomedical applications.Rhizophora apiculata is a least studied mangrove-based plant that has been used in the traditional medicine of Southeast Asia for its healing properties. It is a well-known fact that the generation of free radicals has been associated with oxidative stress.  Methods: Hence, in this study we used carbon tetrachloride as a hepatotoxin to induce liver damage. The protective effects of silver nanoparticles synthesized using Rhizophora apiculata on hepatotoxin-induced liver damage in experimental mice were assessed.  Results: The results of the assessment indicate that silver nanoparticles were effective in protecting the liver from damages induced by carbon tetrachloride.  Conclusion: Among existing literature, this is the first ever approach for hepatoprotective effect of nanoparticles derived using plant extract from mangrove ecosystem.

Localization of α 2u-globulin in the acinar cells of preputial gland, and confirmation of its binding with farnesol, a putative pheromone, in field rat (Millardia meltada).

Pheromones, low molecular weight chemical entities that bind to pheromone carrier proteins, are chemical signals that play an important role in the communication system in animals. This has been rather fairly well-studied in the rodents. The preputial gland, a rich source of pheromones in many rodents, contains a low molecular mass protein (18-20 kDa) that acts as one such pheromone carrier. However, the presence of this protein in the notorious rodent pest Millardia meltada has not yet been proven. Therefore, we aimed at identifying this protein, and the pheromones that are bound to it, in this rodent so as to utilize the information in the control of this pest. Twenty volatile compounds were identified in the preputial gland using GC-MS. Total protein of the gland was fractioned by both one and two-dimensional electrophoresis when we identified a low molecular mass protein (19 kDa, pI-4.7). Adopting MALDI-TOF MS and LC-MS analyses, the protein was confirmed as α 2u-globulin. To identify the volatiles bound to this protein, we used column chromatography and GC-MS. We found that farnesol and 6-methyl-1-heptanol are the volatiles that would bind to the protein, which we propose to be putative pheromones. Immunohistochemical analysis confirmed localization of α 2u-globulin in the acinar cells of the preputial gland. Thus, we show that α 2u-globulin, a pheromone-carrier protein, is present in the preputial gland acinar cells of M. meltada and suggest farnesol and 6-methyl-1-heptanol to be the volatiles which would bind to it. The α 2u-globulin together with farnesol and 6-methyl-1-heptanol contribute to pheromonal communication of M. meltada.

Silver nanoparticles provoke apoptosis of Dalton's ascites lymphoma in vivo by mitochondria dependent and independent pathways.

The aim of this report was to investigate the antitumor and apoptotic effects of silver nanoparticles (AgNPs) on the Dalton's ascites lymphoma cells in vivo. Thirty Swiss albino male mice were assigned into five groups of six each. Group I were intact animals. Group II animals served as tumor control injected with DAL cells intraperitonially. Group III induced animals received plant extract (17 mg/kg BW) and Group IV induced animals received AgNPs (35 µg/kg BW). Group V induced animals received standard anticancer drug 5-Fluorouracil (5-FU, 20 µg/kg BW). The treatment period was 10 days excluding the day of tumor injection. Tumor cells were collected after euthanizing the animals and real-time PCR was used to analyze p53, caspase-3, 8, 9, 12 and cytochrome C expressions. Results indicate that the AgNPs were efficient in prolongation of life span, reduction of tumor volume and body weight in tumor animals. All the apoptotic genes were upregulated by treatment with AgNPs. To conclude, the present study elicits that AgNPs are potent in antitumor activity and the molecular mechanism is by the induction of apoptosis through the mitochondrial dependent and independent pathways.