A pan-cancer analysis of pituitary tumor-transforming 3, pseudogene.

BACKGROUND: Although evidence regarding pituitary tumor-transforming 3, pseudogene (PTTG3P) involvement in human cancers has been acquired via human and animal model-based molecular studies, there is a lack of pan-cancer analysis of this gene in human tumors. METHODS: Tumor-causing effects of PTTG3P in 24 human tumors were explored using The Cancer Genome Atlas (TCGA) datasets from different bioinformatics databases and applying in silico tools such as The University of ALabama at Birmingham CANcer (UALCAN), Human Protein Atlas (HPA), Kaplan Meier (KM) plotter, cBioPortal, Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Cytoscape, Database for Annotation, Visualization, and Integrated Discovery (DAVID), Tumor IMmune Estimation Resource (TIMER), and Comparative Toxicogenomics Database (CTD). Then, via in vitro experiments, including RNA sequencing (RNA-seq) and targeted bisulfite sequencing (bisulfite-seq), expression and promoter methylation levels of PTTG3P were verified in cell lines. RESULTS: The PTTG3P expression was overexpressed across 23 malignancies and its overexpression was further found significantly effecting the overall survival (OS) durations of the esophageal carcinoma (ESCA) and head and neck cancer (HNSC) patients. This important information helps us to understand that PTTG3P plays a significant role in the development and progression of ESCA and HNSC. As for PTTG3P functional mechanisms, this gene along with its other binding partners was significantly concentrated in "Oocyte meiosis", "Cell cycle", "Ubiquitin mediated proteolysis", and "Progesterone-mediated oocyte maturation". Moreover, ESCA and HNSC tissues having the higher expression of PTTG3P were found to have lower promoter methylation levels of PTTG3P and higher CD8+ T immune cells level. Additionally, PTTG3P expression-regulatory drugs were also explored in the current manuscript for designing appropriate treatment strategies for ESCA and HNSC with respect to PTTG3P expression. CONCLUSION: Our pan-cancer based findings provided a comprehensive account of the oncogenic role and utilization of PTTG3P as a novel molecular biomarker of ESCA and HNSC.

Bioinformatics, RNA sequencing, and targeted bisulfite sequencing analyses identify the role of PROM2 as a diagnostic and prognostic biomarker.

OBJECTIVES: Prominin 2 (PROM2) gene has been reported as a molecular biomarker of human cancers; however, its role is still controversial. This study was therefore arranged to seek the role of PROM2 in different cancers with Bioinformatics and in vitro analyses. METHODS: A combination of bioinformatics and molecular experiments. RESULTS: Through the utilization of Bioinformatics analysis, it was observed that in 19 out of the 24 human cancers studied, there was a significant increase in the expression of PROM2 compared to the respective control samples. Additionally, the overexpression of PROM2 was linked specifically to a decrease in overall survival (OS) among breast cancer (BRCA), lung adenocarcinoma (LUAD), and uterine corpus endometrial carcinoma (UCEC) patients. Furthermore, advanced molecular investigations were conducted, encompassing RNA sequencing (RNA-seq) as well as targeted bisulfite sequencing (bisulfite-seq) assessments of PROM2. These analyses were performed across an array of lung cancer cell lines (A549, ABC-1, EBC-1, and LK-2) and a normal control lung cell line (MRC-9). Results of these analysis revealed overexpression and reduced methylation of PROM2 within lung cancer cell lines, relative to the corresponding control cell line. This suggests that PROM2 assumes a substantial function in the advancement and course of BRCA, LUAD, and UCEC cancers. Subsequent pathway analysis revealed that genes enriched by PROM2 are actively engaged in four pivotal pathways. Additionally, intriguing associations were observed between PROM2 expression, tumor purity, infiltration of CD8+ T immune cells, and genetic modifications. Moreover, we also predicted a few MicroRNAs (miRNAs), transcription factors (TFs), and potential drugs that could help to understand and better manage these cancers via designing appropriate therapies targeting PROM2. CONCLUSION: Via this study, we effectively revealed PROM2 overexpression as a potential diagnostic and prognostic biomarker of survival in BRCA, LUAD, and UCEC.

Phytoremediation of bauxite wastewater potentiality by Jatropa curcas.

Bauxite wastewater creates soil contamination and produces toxic effects on human health such as respiratory and skin rash problems. In this study, we investigated the phytoremediation ability of Jatropha curcas to remove bauxite wastewater from soil. Pot experiments were conducted to investigate the bauxite wastewater on the phytoremediation potential of J. curcas grown in contaminated soils. J. curcas exhibited a significant increase in plant growth leaf, root activity, plant height, and plant shoot when grown in bauxite contaminated soils compared with J. curcas grown in uncontaminated soils after 30 d treatment. Under bauxite exposure, a higher aluminium removal (88.5%) was observed in soils planted with J. curcas than unplanted soils (39.6%). The bioconcentration factor was also found to be 5.62, indicating that J. curcas have great tolerance and hyperaccumulator of aluminium under high aluminium concentrations and are capable of phytoextraction of soil contaminated with bauxite wastewater.

Role of extremophilic Bacillus cereus KH1 and its lipopeptide in treatment of organic pollutant in wastewater.

An effective biosurfactant producer and extremophiles bacteria, Bacillus cereus KH1, was isolated from textile effluent and the biosurfactant was produced using molasses as the sole carbon source. Growth parameters such as pH, temperature, salinity and concentration of molasses were optimised for decolourising the textile effluent with 24-h incubation. The biosurfactant property of B. cereus KH1 was evaluated based on haemolytic activity, oil displacement technique, drop-collapsing test and emulsification index. The results of the produced biosurfactant showed a positive reaction in haemolytic activity, oil displacement technique, drop-collapsing test and exhibiting a 67% emulsification index. The cell-free broth was stable in 40 °C pH 7, 7% salinity and 7% molasses. Thin-Layer Chromatography and Fourier Transform Infrared Spectroscopy analysis revealed that the biosurfactant was a lipopeptide with a yield 2.98 g L-1. These findings proved the synergistic action of B. cereus KH1 with lipopeptide biosurfactant may accelerated the decolourisation efficiency to 87%.

Health risk assessment by toxic metals in little egrets (Egretta garzetta) and food chain contaminations.

This study analysed heavy metals from little egret (Egretta garzetta). Egret's Eggs, egg shells, food (fish and insects), blood, meat samples (thigh, liver, and chest), water, soil and sediments samples were collected from the two selected sites of the study area. Samples were analysed on flame atomic absorption spectrometer after acid digestion. Detected metals were found almost inline of concentrations when compared with the both sites. Among detected metals Mn was found higher in concentration (µg/g) i.e. 18.509 followed by Zn i.e. 9.383, Ni, Cu, Pb and Cd. Sediment exhibited higher levels (µg/g) of metals (25.061) followed by the meat (19.044) egrets food (18.825), excreta (16.26), blood serums (4.577), eggs (3.626) and water samples (2.432).The level of metals in sediments of the study are showed environmental concerns. Health risks were also investigated that were compared to guidelines of WHO and FAO threshold limits. It was found a marginal health risk to life through detected metals. This study revealed that little egret are good bio-indicator for the screening and investigation of contaminates presence in the environment.

Adsorption of copper and nickel by using sawdust chitosan nanocomposite beads - A kinetic and thermodynamic study.

The adsorption behavior of biomaterial activated Sawdust-Chitosan nanocomposite beads (SDNCB) powder was investigated along with synthesis and experimental techniques approaches to study the removal efficiency of some heavy metal ions including Ni (II) and Cu (II) ions from aqueous solutions by assessing the surface-modified activated carbon by the cost-effective non-conventional method. Structural analysis of the entitled compound was evaluated by the PXRD techniques and its surface morphology was inferred by the following techniques: TEM, EDAX. The behavior of the functional group presents in the compound was discussed using the FTIR technique. Such parameters like dosage, pH, time, temperature, and initial concentration of copper and nickel were associated with this to examine the effect of adsorption of heavy elements that exist in the portable solution. Further, the cellulose and chitosan beads complex material have an appropriate surface area, it demonstrated metal ions removal efficiency was more appreciable due to the action of activated carbon, where this showed fast rate sorption kinetics due to strong involvement of Cu+ & Ni+ towards cellulose and chitosan's functional groups in the bio composite. The isotherm model so-called Langmuir, Freundlich, and Temkin model was utilized to plot the experimental adsorption dataset to infer the maximum adsorption capacity. Based on this model, the adsorption properties of the beads treated compound was determined by plotting the graphs in which sorption intensity (n) which implies expected sorption, and the correlation value are 1.989, 0.998, and 0,981 respectively.

Gum mediated synthesis and characterization of CuO nanoparticles towards infectious disease-causing antimicrobial resistance microbial pathogens.

BACKGROUND: In this work biologically active CuO nanoparticle were discussed. The literature suggests that CuO shows very good antibacterial activity on both Gram positive and Gram-negative bacterial strains. Further, it is used in antibacterial coatings on various substrates to prevent various kinds of medical equipment's. Here CuO NPs was prepared via greener approach and almond gum is used as a reducing agent. Almond gum is nontoxic and contains huge amount of polysaccharides. Hence, the gum mediated CuO NPs can be used to treat urinary tract infection (UTI). METHOD: The CuO NPs were characterized using UV, FTIR, XRD and HESEM with EDX analysis. The antibacterial (both Gram positive and Gram negative) effects of CuO NPs were determined with agar well diffusion method. RESULTS: The CuO NPs were characterized by X-ray diffraction pattern result indicates that the monoclinic structure with average crystallite size about 12.91 nm. Straight line model in Scherrer method results found to be crystallite size. The crystallite size and microstrain were estimated in W-H analysis. Lorentz polarization factor, size-strain plot (SSP), morphological index (M-I) and dislocation density were calculated based on x-ray diffraction data. The FTIR analysis confirms presence of Cu and O band. From the absorption spectrum of CuO NPs, it was found to be cutoff wavelength of 230 nm and direct bandgap was found to be 4.97 eV. Morphology analysis shows that the synthesized of CuO NPs reveals agglomerated and spherical in shape. It was found to be 16 nm-25 nm. Energy dispersive spectroscopy (EDX) result indicates percentages of Cu and O element present in the sample. Antimicrobial studies reveal zone of inhibition of CuO NPs. This was used in different pathogens such as gram-positive and Gram-negative bacteria. This study shows exhibit excellent antimicrobial effects of CuO NPs. CONCLUSION: Hence, in this article the novel and cost-effective method to prepare CuO NPs was discussed. The prepared CuO NPs can be used as an antifungal and antibacterial reagent.

Functionalization of gold nanoparticles by ß-cyclodextrin as a probe for the detection of heavy metals in water and photocatalytic degradation of textile dye.

Gold nanoparticles (AuNPs) and AuNPs functionalized by ß-cyclodextrin (ß-CD/AuNPs) were prepared successfully through chemical reduction method. The structural, morphological, optical, compositional and vibrational studies for the AuNPs and ß-CD/AuNPs were carried out. Functionalization of AuNPs by ß-CD was confirmed with FT-IR results. The UV-visible absorption spectra exhibit a red-shift with decreasing average particle size. This sustains the enhancement in surface area (SA) to volume (V) ratio that is one of the peculiar characteristics of nanoparticles. TEM results show that ß-CD/AuNPs formed were monodispersed and self assembled. Also it shows a decrease in average particle size and improved distribution. The use of ß-CD in the synthesis of AuNPs are revealed not only create uniform small sized nanoparticles but these water soluble nanoparticles have very good antibacterial action by inhibiting the growth of bacteria commonly found in water and sensing activity for sensing the concentration of toxic metals in water. The sensitivity of the system towards copper (Cu) concentration was found as 1.788/mM for ß-CD/AuNPs and 1.333/mM for AuNPs. The photocatalytic action of the obtained nanoparticles increases with decreasing average particle size. The kapp value of this photocatalytic degradation of textile dyeing waste water in presence of AuNPs was 0.002/min and ß-CD/AuNPs was 0.005/min. This is a non-toxic and eco-friendly approach.

Improved photocatalytic activity for degradation of textile dyeing waste water and thiazine dyes using PbWO4 nanoparticles synthesized by co-precipitation method.

The coloured dyes released from the textile industrial effluents into water resources cause non-aesthetic pollution and aquatic life toxicity. Thus textile waste water treatment has been studied globally for many years. Photocatalytic properties of lead tungstate (PbWO4) nanoparticles (NPs) were analyzed for thiazine dyes and textile waste water under ultraviolet light conditions. XRD result showed the tetragonal scheelite structure of PbWO4 NPs. The crystallinity of the sample was confirmed from the SAED and XRD pattern. The existence of stretch vibration of Pb-O and O-W-O confirmed from FTIR results. EDAX displays optical absorption signals of Pb, W and O, and confirm the formation of PbWO4. Optical studies reveal that the band gap of the obtained nanoparticles increases with respect to their bulk counterparts that may be attributed to reduction in particle size. TEM images of PbWO4 powder consists of hexagonal particles and relatively uniform and smooth surface rod shaped prism-like structures. The photocatalytic activity of the prepared nanoparticles was analyzed through the degradation of textile waste water under UV light irradiation. The photocatalytic reaction rate constant was found to be 0.014/min. The small sized PbWO4 particles can adsorb more OH groups and oxidatively degrade the pollutants in the textile waste water.

In silico prediction of silver nitrate nanoparticles and Nitrate Reductase A (NAR A) interaction in the treatment of infectious disease causing clinical strains of E. coli.

BACKGROUND: The interaction of specially designed nanoparticles with proteins is the basis of formation of a nanoparticle-protein corona. Silver nanoparticles and molecules have been used in many fields due to their strong antimicrobial activity against pathogenic microorganisms such as bacteria, yeast and fungi. E. coli is a Gram-negative bacteria that has the genome completely sequenced and determined majority of its protein 3D structures. Nitrate Reductase A is a cellular protein often found in many bacteria that uses nitrate as an electron acceptor during anaerobic growth. The enzyme is composed of three different chains α, ß and γ, all having properties of metal binding regions and domains. METHODS: Bioinformatics tools were used to investigate the structure, domains, interactomes, and docking sites of E. coli Nitrate Reductase A in order to predict the possible site of interaction of silver nitrate AgNO3 with the protein. The 3D structure of the NAR A protein was predicted with the Phyre2 protein modeling software. The generated structures from Phyre2 were validated and evaluated by analysis of Ramachandran plots using RAMPAGE online software. To understand the evolutionary relationships between the subunits of Nitrate Reductase A, a phylogenetic tree was constructed using Phylogeny.fr. RESULTS: All cysteine and histidine residues in amino acid sequences were identified; 3D structure of subunits predicted together with Ramachandran plots, and the electrostatic potential was computed using various bioinformatics tools. The reactive cationic property of silver ion leads to attachment to specific anionic regions and active sites of the three subunits causing in many prokaryotic cells deactivation of nitrate reductase. Obtained results showed the possible sites of attachment of silver ions and their reactivity with domains that have metal bonding properties. In silico analysis of silver nanoparticles and nitrate reductase is helpful to treat various infections diseases caused by E. coli.

Interactome Analysis and Docking Sites of MutS Homologs Reveal New Physiological Roles in Arabidopsis thaliana.

Due to their sedentary lifestyle, plants are constantly exposed to different stress stimuli. Stress comes in variety of forms where factors like radiation, free radicals, "replication errors, polymerase slippage", and chemical mutagens result in genotoxic or cytotoxic damage. In order to face "the base oxidation or DNA replication stress", plants have developed many sophisticated mechanisms. One of them is the DNA mismatch repair (MMR) pathway. The main part of the MMR is the MutS homologue (MSH) protein family. The genome of Arabidopsis thaliana encodes at least seven homologues of the MSH family: AtMSH1, AtMSH2, AtMSH3, AtMSH4, AtMSH5, AtMSH6, and AtMSH7. Despite their importance, the functions of AtMSH homologs have not been investigated. In this work, bioinformatics tools were used to obtain a better understanding of MSH-mediated DNA repair mechanisms in Arabidopsis thaliana and to understand the additional biological roles of AtMSH family members. In silico analysis, including phylogeny tracking, prediction of 3D structure, interactome analysis, and docking site prediction, suggested interactions with proteins were important for physiological development of A. thaliana. The MSH homologs extensively interacted with both TIL1 and TIL2 (DNA polymerase epsilon catalytic subunit), proteins involved in cell fate determination during plant embryogenesis and involved in flowering time repression. Additionally, interactions with the RECQ protein family (helicase enzymes) and proteins of nucleotide excision repair pathway were detected. Taken together, the results presented here confirm the important role of AtMSH proteins in mismatch repair and suggest important new physiological roles.

Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis.

Plant malate dehydrogenase (MDH) isoforms are found in different cell compartments and function in key metabolic pathways. It is well known that the chloroplastic NADP-dependent MDH activities are strictly redox regulated and controlled by light. However, redox dependence of other NAD-dependent MDH isoforms have been less studied. Here, we show by in vitro biochemical characterization that the major cytosolic MDH isoform (cytMDH1) is sensitive to H2O2 through sulfur oxidation of cysteines and methionines. CytMDH1 oxidation affects the kinetics, secondary structure, and thermodynamic stability of cytMDH1. Moreover, MS analyses and comparison of crystal structures between the reduced and H2O2-treated cytMDH1 further show that thioredoxin-reversible homodimerization of cytMDH1 through Cys330 disulfide formation protects the protein from overoxidation. Consistently, we found that cytosolic thioredoxins interact specifically with cytMDH in a yeast two-hybrid system. Importantly, we also show that cytosolic and chloroplastic, but not mitochondrial NAD-MDH activities are sensitive to H2O2 stress in Arabidopsis. NAD-MDH activities decreased both in a catalase2 mutant and in an NADP-thioredoxin reductase mutant, emphasizing the importance of the thioredoxin-reducing system to protect MDH from oxidation in vivo. We propose that the redox switch of the MDH activity contributes to adapt the cell metabolism to environmental constraints.

Evolution of redoxin genes in the green lineage.

The availability of the Arabidopsis genome revealed the complexity of the gene families implicated in dithiol disulfide exchanges. Most non-green organisms present less dithiol oxidoreductase genes. The availability of the almost complete genome sequence of rice now allows a systematic search for thioredoxins, glutaredoxins and their reducers. This shows that all redoxin families previously defined for Arabidopsis have members in the rice genome and that all the deduced rice redoxins fall within these families. This establishes that the redoxin classification applies both to dicots and monocots. Nevertheless, within each redoxin type the number of members is not the same in these two higher plants and it is not always possible to define orthologues between rice and Arabidopsis. The sequencing of two unicellular algae (Chlamydomonas and Ostreococcus) genomes are almost finished. This allowed us to follow the origin of the different gene families in the green lineage. It appears that most thioredoxin and glutaredoxin types, their chloroplastic, mitochondrial and cytosolic reducers are always present in these unicellular organisms. Nevertheless, striking differences appear in comparison to higher plant redoxins. Some thioredoxin types are not present in these algal genomes including thioredoxins o, clot and glutaredoxins CCxC. Numerous redoxins, including the cytosolic thioredoxins, do not fit with the corresponding higher plant classification. In addition both algae present a NADPH-dependent thioredoxin reductase with a selenocysteine which is highly similar to the animal thioredoxin reductases, a type of thioredoxin reductase not present in higher plants.