Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells

Custom-designed zinc finger nucleases (ZFNs), proteins designed to cut at specific DNA sequences, are becoming powerful tools in gene targeting—the process of replacing a gene within a genome by homologous recombination (HR). ZFNs that combine the non-specific cleavage domain (N) of FokI endonuclease with zinc finger proteins (ZFPs) offer a general way to deliver a site-specific double-strand break (DSB) to the genome. The development of ZFN-mediated gene targeting provides molecular biologists with the ability to site-specifically and permanently modify plant and mammalian genomes including the human genome via homology-directed repair of a targeted genomic DSB. The creation of designer ZFNs that cleave DNA at a pre-determined site depends on the reliable creation of ZFPs that can specifically recognize the chosen target site within a genome. The (Cys₂His₂) ZFPs offer the best framework for developing custom ZFN molecules with new sequence-specificities. Here, we explore the different approaches for generating the desired custom ZFNs with high sequence-specificity and affinity. We also discuss the potential of ZFN-mediated gene targeting for ‘directed mutagenesis’ and targeted ‘gene editing’ of the plant and mammalian genome as well as the potential of ZFN-based strategies as a form of gene therapy for human therapeutics in the future.     

Dosimetric impact of statistical uncertainty on Monte Carlo dose calculation algorithm in volumetric modulated arc therapy using Monaco TPS for three different clinical cases

AimTo study the dosimetric impact of statistical uncertainty (SU) per plan on Monte Carlo (MC) calculation in Monaco? treatment planning system (TPS) during volumetric modulated arc therapy (VMAT) for three different clinical cases.BackgroundDuring MC calculation SU is an important factor to decide dose calculation accuracy and calculation time. It is necessary to evaluate optimal acceptance of SU for quality plan with reduced calculation time.Materials and methodsThree different clinical cases as the lung, larynx, and prostate treated using VMAT technique were chosen. Plans were generated with Monaco? V5.11 TPS with 2% statistical uncertainty. By keeping all other parameters constant, plans were recalculated by varying SU, 0.5%, 1%, 2%, 3%, 4%, and 5%. For plan evaluation, conformity index (CI), homogeneity index (HI), dose coverage to PTV, organ at risk (OAR) dose, normal tissue receiving dose ≥5 Gy and ≥10 Gy, integral dose (NTID), calculation time, gamma pass rate, calculation reproducibility and energy dependency were analyzed.ResultsCI and HI improve as SU increases from 0.5% to 5%. No significant dose difference was observed in dose coverage to PTV, OAR doses, normal tissue receiving dose ≥5 Gy and ≥10 Gy and NTID. Increase of SU showed decrease in calculation time, gamma pass rate and increase in PTV max dose. No dose difference was seen in calculation reproducibility and dependent on energy.ConclusionFor VMAT plans, SU can be accepted from 1% to 3% per plan with reduced calculation time without compromising plan quality and deliverability by accepting variations in point dose within the target.     

In vitro interaction network of a synthetic gut bacterial community

A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM¹²) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM¹² interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM¹² interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.Subject terms: Microbiome, Microbial ecology     

Ligation of HLA class I molecules on endothelial cells induces phosphorylation of Src,paxillin, and focal adhesion kinase in an actin-dependent manner

The development of chronic rejection is the major limitation to long-term allograft survival. HLA class I Ags have been implicated to play a role in this process because ligation of class I molecules by anti-HLA Abs stimulates smooth muscle cell and endothelial cell proliferation. In this study, we show that ligation of HLA class I molecules on the surface of human aortic endothelial cells stimulates phosphorylation of Src, focal adhesion kinase, and paxillin. Signaling through class I stimulated Src phosphorylation and mediated fibroblast growth factor receptor (FGFR) translocation to the nucleus. In contrast, Src kinase activity was not involved in class I-mediated transfer of FGFR from cytoplasmic stores to the cell surface. Inhibition of Src protein kinase activity blocked HLA class I-stimulated tyrosine phosphorylation of paxillin and focal adhesion kinase. Furthermore, HLA class I-mediated phosphorylation of the focal adhesion proteins and FGFR expression was inhibited by cytochalasin D and latrunculin A, suggesting a role for the actin cytoskeleton in the signaling process. These findings indicate that anti-HLA Abs have the capacity to transduce activation signals in endothelial cells that may promote the development of chronic rejection.     

Photosynthetic flexibility in Pedilanthus tithymaloides poit,a CAM plant

The induction of CAM in Pedilanthus tithymaloides (Euphorbiaceae) under water-limited conditions was evaluated by following diurnal oscillations of CO2 fixation, titratable acidity and malic acid content in the leaf extracts. CAM induction was assessed by measuring the activities of phosphoenolpyruvate carboxylase (PEPC), NADH-malate dehydrogenase (MDH) and phosphoenolpyruvate caroxykinase (PEPCK) in the leaves as well. Drought resulted in large increases in the nocturnal acid accumulation and rates of CO2 uptake in the leaves of P. tithymaloides. The drought-induced CAM activity tended to be reversible after re-watering. Nevertheless, under well-watered conditions, plants of P. tithymaloides showed day time CO2 uptake patterns with less pronounced diurnal oscillations of organic acids. Our data indicate that although P. tithymaloides is a CAM plant, environmental variables like drought induce photosynthetic flexibility in this species. This type of plasticity in CAM and metabolic versatility in P. tithymaloides should be an adaptation for prolonged survival under natural adverse edaphic and microclimate situations.     

Decomposition patterns of unprocessed and processed lignocellulosics in a freshwater fish pond

In an attempt to recycle the lignocellulosic wastes like Eichhornia crassipes, Salvinia cucullata and rice (Oryza sativa) straw as manurial inputs in freshwater fish pond ecosystem, a decomposition experiment was carried out in litter bags in an oligotrophic freshwater fish pond environment, with the above mentioned three substrates in unprocessed and microbially processed forms. The loss rates, associated microbial groups, oxygen consumption patterns and other related parameters like carbon, nitrogen, phosphorus, cellulose, hemicellulose and lignin were analysed. The mean daily dry matter loss rates (unprocessed: 10.44>6.97>1.97 and processed: 11.03>8.21>3.67) and oxygen uptake rate (unprocessed: 0.675>0.571>0.568 mg O₂ g^–1 h^–1 and processed: 0.592>0.424>0.407 mg O₂ g^–1 h^–1) in raw and processed substrates were in the sequence Eichhornia > rice straw > Salvinia. The oxygen consumption pattern almost covariated with variations in temperature of pond water, daily dry matter loss rates and fungal counts on substrates. During the decay, the percentage of N and P increased whereas that of C decreased, resulting in lowering of C/N and C/P ratios of the substrates. The structural polymeric fractions like cellulose and hemicellulose decreased along with dry matter whereas the lignin content increased after an initial decrease due to loss of other structural carbohydrates resulting in apparent per cent gain of lignin. A higher number of different heterotrophic bacterial groups was observed in the processed substrates as compared to their raw counterparts. However, cellulolytic bacterial numbers were found to fluctuate through the study period. The fungal load was found to be decreasing gradually as the decay progressed. In this study, bacteria were found to be the prominent microbial group responsible for the decay. The nitrogen-fixing, phosphatase-producing and phosphorus-solubilising bacterial groups were observed to play an important role in lowering the C/N and C/P ratios of the decomposing substrates during decay.     

Glucocorticoids Suppress Renal Cell Carcinoma Progression by Enhancing Na,K-ATPase Beta-1 Subunit Expression

Glucocorticoids are commonly used as palliative or chemotherapeutic clinical agents for treatment of a variety of cancers. Although steroid treatment is beneficial, the mechanisms by which steroids improve outcome in cancer patients are not well understood. Na,K-ATPase beta-subunit isoform 1 (NaK-β₁) is a cell-cell adhesion molecule, and its expression is down-regulated in cancer cells undergoing epithelial-to mesenchymal-transition (EMT), a key event associated with cancer progression to metastatic disease. In this study, we performed high-throughput screening to identify small molecules that could up-regulate NaK-β₁ expression in cancer cells. Compounds related to the glucocorticoids were identified as drug candidates enhancing NaK-β₁ expression. Of these compounds, triamcinolone, dexamethasone, and fluorometholone were validated to increase NaK-β₁ expression at the cell surface, enhance cell-cell adhesion, attenuate motility and invasiveness and induce mesenchymal to epithelial like transition of renal cell carcinoma (RCC) cells in vitro. Treatment of NaK-β₁ knockdown cells with these drug candidates confirmed that these compounds mediate their effects through up-regulating NaK-β₁. Furthermore, we demonstrated that these compounds attenuate tumor growth in subcutaneous RCC xenografts and reduce local invasiveness in orthotopically-implanted tumors. Our results strongly indicate that the addition of glucocorticoids in the treatment of RCC may improve outcome for RCC patients by augmenting NaK-β₁ cell-cell adhesion function.     

Toxic effect of dimethoate on the crosslinking of gingival and uteral collagen in female albino rats fed with normal and high protein diets

The effect of dimethoate on gingival and uteral collagen crosslinking was studied in normal and high protein diets fed female albino rats. The gingival and uteral samples were collected from all the groups of rats and percent reversibility of neutral salt soluble collagen gel and the solubility of insoluble collagen in KCNS or urea were determined. The analysis of gingival and uteral samples showed alpha 1 and alpha 2 sub units of neutral salt soluble collagen appreciably increased beta chains and aldehyde content significantly decreased in dimethoate treated animals compared to controls. The results indicate that due to the effect of dimethoate, the crosslinking and maturation of collagen are impaired.