Real-time PCR assay is superior to other methods for the detection of mycoplasma contamination in the cell lines of the National Cell Bank of Iran

Mycoplasmas are the most important contaminants of cell cultures throughout the world. They are considered as a major problem in biological studies and biopharmaceutical economic issues. In this study, our aim was to find the best standard technique as a rapid method with high sensitivity, specificity and accuracy for the detection of mycoplasma contamination in the cell lines of the National Cell Bank of Iran. Thirty cell lines suspected to mycoplasma contamination were evaluated by five different techniques including microbial culture, indirect DNA DAPI staining, enzymatic mycoalert^® assay, conventional PCR and real-time PCR. Five mycoplasma-contaminated cell lines were assigned as positive controls and five mycoplasma-free cell lines as negative controls. The enzymatic method was performed using the mycoalert^® mycoplasma detection kit. Real-time PCR technique was conducted by PromoKine diagnostic kits. In the conventional PCR method, mycoplasma genus-specific primers were designed to analyze the sequences based on a fixed and common region on 16S ribosomal RNA with PCR product size of 425 bp. Mycoplasma contamination was observed in 60, 56.66, 53.33, 46.66 and 33.33 % of 30 different cell cultures by real-time PCR, PCR, enzymatic mycoalert^®, indirect DNA DAPI staining and microbial culture methods, respectively. The analysis of the results of the different methods showed that the real-time PCR assay was superior the other methods with the sensitivity, specificity, accuracy, predictive value of positive and negative results of 100 %. These values were 94.44, 100, 96.77, 100 and 92.85 % for the conventional PCR method, respectively. Therefore, this study showed that real-time PCR and PCR assays based on the common sequences in the 16S ribosomal RNA are reliable methods with high sensitivity, specificity and accuracy for detection of mycoplasma contamination in cell cultures and other biological products.     

Translational models of tumor angiogenesis: A nexus of in silico and in vitro models

Emerging evidence shows that endothelial cells are not only the building blocks of vascular networks that enable oxygen and nutrient delivery throughout a tissue but also serve as a rich resource of angiocrine factors. Endothelial cells play key roles in determining cancer progression and response to anti-cancer drugs. Furthermore, the endothelium-specific deposition of extracellular matrix is a key modulator of the availability of angiocrine factors to both stromal and cancer cells. Considering tumor vascular network as a decisive factor in cancer pathogenesis and treatment response, these networks need to be an inseparable component of cancer models. Both computational and in vitro experimental models have been extensively developed to model tumor-endothelium interactions. While informative, they have been developed in different communities and do not yet represent a comprehensive platform. In this review, we overview the necessity of incorporating vascular networks for both in vitro and in silico cancer models and discuss recent progresses and challenges of in vitro experimental microfluidic cancer vasculature-on-chip systems and their in silico counterparts. We further highlight how these two approaches can merge together with the aim of presenting a predictive combinatorial platform for studying cancer pathogenesis and testing the efficacy of single or multi-drug therapeutics for cancer treatment.     

Interleukin-1 α and β genes: linkage on chromosome 2 in the mouse

Two interleukin-1 polypeptides, and , are known, and cDNAs corresponding to each have been described. Genomic cloning and Southern blotting experiments suggest that in the mouse each is encoded by a gene present in one copy per haploid genome. Analysis of a panel of somatic cell hybrids carrying various mouse chromosomes on a constant Chinese hamster background indicates that both genes map to mouse chromosome 2. Further, analysis of the inheritance of DNA restriction fragment length polymorphisms associated with each gene in recombinant inbred strains of mice shows the two loci to be tightly linked to one another, and to lie approximately 4.7 centimorgans distal to B2m (beta-2 microglobulin). We have named the locus encoding IL-1 Il-1 and the locus encoding IL-1 Il-1b.     

Cytogenetic changes of mesenchymal stem cells in the neoplastic bone marrow niche in leukemia

Background

Bone marrow mesenchymal stromal cells (BM-MSCs) are an essential cell type in the hematopoietic microenvironment. The question of whether MSCs from patients with different leukemias have cytogenetic abnormalities is controversial. In this study, we attempted to review the cytogenetic profiles of MSCs in patients with leukemia, and verify whether these profiles were related to different ex vivo culture conditions or to chronic or acute disease states. This information could be useful in clarifying the origin of MSCs and developing clinical applications for this cell type.

Methods

A systematic literature search was performed using the PubMed search engine. Studies published over the past 15 years, i.e., between 1995 and January 2015, were considered for review. The following keywords were used: “cytogenetic,” “leukemia,” “bone marrow,” and “mesenchymal stromal cells.”

Results

Some studies demonstrated that BM-MSCs are cytogenetically normal, whereas others provided evidence of aberrations in these cells

Conclusions

Studying cytogenetic changes of MSCs in a variety of leukemias will help researchers understand the nature of these tumors and ensure the safety of human stem cells in clinical applications.

     

Utilizing bacterial flagellins against infectious diseases and cancers

The flagellum is the organelle providing motility to bacterial cells and its activity is coupled to the cellular chemotaxis machinery. The flagellar filament is the largest portion of the flagellum, which consists of repeating subunits of the protein flagellin. Receptors of the innate immune system including Toll like receptor 5, ICE protease activating factor, and neuronal apoptosis inhibitory protein 5 signal in response to bacterial flagellins. In addition to inducing innate immune responses, bacterial flagellins mediate the development of adaptive immune responses to both flagellins and coadministered antigens. Therefore, these proteins have intensively been investigated for the vaccine development and the immunotherapy. This review describes the utilization of bacterial flagellins for the construction of vaccines against infectious diseases and cancer immunotherapy. Furthermore, the key factors affecting the performance of these systems are highlighted.     

Effect of tomato fruit cultivar and ripening stage on Bactrocera tryoni (Froggatt) egg and larval survival

In studies of frugivorous tephritids, determining when offspring (i.e. egg and three larval instars) mortality occurs within the fruit can greatly improve the mechanistic understanding of the fly/host interaction. Previous research has demonstrated that the Queensland fruit fly, Bactrocera tryoni, has differential offspring performance in two tomato cultivars Cherry and Roma, but when juvenile mortality was occurring was not determined. We examined B. tryoni egg and larval survival in three different ripening stages (immature-green (IG), colour-break (CB) and fully-ripe (FR)) of Cherry and Roma tomato cultivars through destructive fruit sampling at 72 and 120 hr for eggs, and 48 (1st instar), 96 (2nd instar) and 120 hr (3rd instar) after fruit inoculation with neonates for larvae. Cultivar and ripening stage had no significant effect on egg survival, nor larval survival at 48 hr: the overall percentage of egg survival was at least 80% across all treatments, while 1st-instar larval was less than 52% across all treatments. In immature-green tomatoes of both varieties, nearly all mortality occurred during the first and second instars, but at 96 and 120 hr, there were significant interaction effects between cultivar and ripening stage on larval survival. In both colour-break Cherry and Roma tomatoes, there was significant larval mortality between 96 and 120 hr. However, in fully-ripe Cherry, no further significant larval mortality happened after 48 hr, while in fully-ripe Roma significant larval mortality occurred between the first and second larval instars but not thereafter. The difference in timing of larval mortality with ripening stage provides indirect evidence of active fruit defence which is strongest in immature-green fruit, less in colour-break fruit and absent in fully-ripe fruit.     

Loss of Cytosolic Phosphoglucose Isomerase Affects Carbohydrate Metabolism in Leaves and Is Essential for Fertility of Arabidopsis

Carbohydrate metabolism in plants is tightly linked to photosynthesis and is essential for energy and carbon skeleton supply of the entire organism. Thus, the hexose phosphate pools of the cytosol and the chloroplast represent important metabolic resources that are maintained through action of phosphoglucose isomerase (PGI) and phosphoglucose mutase interconverting glucose 6-phosphate, fructose 6-phosphate, and glucose 1-phosphate. Here, we investigated the impact of disrupted cytosolic PGI (cPGI) function on plant viability and metabolism. Overexpressing an artificial microRNA targeted against cPGI (amiR-cpgi) resulted in adult plants with vegetative tissue essentially free of cPGI activity. These plants displayed diminished growth compared with the wild type and accumulated excess starch in chloroplasts but maintained low sucrose content in leaves at the end of the night. Moreover, amiR-cpgi plants exhibited increased nonphotochemical chlorophyll a quenching during photosynthesis. In contrast to amiR-cpgi plants, viable transfer DNA insertion mutants disrupted in cPGI function could only be identified as heterozygous individuals. However, homozygous transfer DNA insertion mutants could be isolated among plants ectopically expressing cPGI. Intriguingly, these plants were only fertile when expression was driven by the ubiquitin10 promoter but sterile when the seed-specific unknown seed protein promoter or the Cauliflower mosaic virus 35S promoter were employed. These data show that metabolism is apparently able to compensate for missing cPGI activity in adult amiR-cpgi plants and indicate an essential function for cPGI in plant reproduction. Moreover, our data suggest a feedback regulation in amiR-cpgi plants that fine-tunes cytosolic sucrose metabolism with plastidic starch turnover.Starch and Suc turnover are major pathways of primary metabolism in all higher plants. As such, they are essential for carbohydrate storage and the energy supply of sink tissues and as building blocks for amino acid, fatty acid, or cell wall biosynthesis (Stitt and Zeeman, 2012).A core reaction in both starch and Suc biosynthesis is the reversible interconversion of the hexose phosphate pool metabolites Fru 6-phosphate (Fru6P) and Glc 6-phosphate (Glc6P), which is mediated by phosphoglucose isomerase (PGI). Arabidopsis (Arabidopsis thaliana) contains two isoforms of PGI, one in the plastids and one in the cytosol (Caspar et al., 1985).During the light period, the plastid isoform of PGI (PGI1) is involved in starch biosynthesis by generating Glc6P from the primary photosynthetic product Fru6P. Glc6P is further converted to Glc 1-phosphate (Glc1P) and ADP-glucose via action of phosphoglucomutase (PGM) and ADP-glucose pyrophosphorylase (AGPase), respectively (Stitt and Zeeman, 2012). Finally, transfer of the glucosyl moiety of ADP-glucose to the growing carbohydrate chain of starch is mediated by starch synthases. Any of the enzymatic reactions of this linear pathway is essential for starch synthesis, as illustrated by the virtual absence of transitory starch in chloroplasts of mutant plant lines with impaired function of PGI1 (Yu et al., 2000; Kunz et al., 2010), PGM (Caspar et al., 1985; Kofler et al., 2000), or AGPase (Lin et al., 1988). Interestingly, in a few specific cell types, e.g. leaf guard cells and root columella cells, loss of PGI1 activity can be bypassed by the presence of the plastid Glc6P/phosphate translocator GPT1 (Niewiadomski et al., 2005; Kunz et al., 2010).The cytosolic isoform of PGI (cPGI) is involved in anabolism and catabolism of Suc, the major transport form of carbohydrates in plants. Glc6P and Fru6P interconversion is necessary for both Suc synthesis during the day and during the night. During the day, Suc synthesis in source leaves is fueled mainly by triose phosphates exported from chloroplasts that are eventually converted to Fru6P in the cytosol. However, Fru6P is only one substrate for the Suc-generating enzyme Suc phosphate synthase. The second substrate, UDP-glucose, is synthesized from Fru6P via Glc6P and Glc1P by the cytosolic isoenzymes of PGI1 and PGM as well as UDP-glucose pyrophosphorylase.Because Suc is the major long-distance carbon transport form, its synthesis has to continue throughout the night to supply energy and carbohydrates to all tissues. The nocturnal synthesis of Suc is dependent on breakdown and mobilization of transitory starch from chloroplasts (Zeeman et al., 2007) via export of maltose and Glc (Weber et al., 2000; Niittylä et al., 2004; Weise et al., 2004; Cho et al., 2011). Exported maltose is temporarily integrated into cytosolic heteroglycans (Fettke et al., 2005) mediated by disproportionating enzyme2 (DPE2; Chia et al., 2004; Lu and Sharkey, 2004) yielding Glc and a heteroglycan molecule elongated by an α1-4-bound glucosyl residue. Cytosolic Glc can directly be phosphorylated to Glc6P by the action of hexokinase, while temporarily stored Glc in heteroglycans is released as Glc1P mediated by cytosolic glucan phosphorylase2 (PHS2; Fettke et al., 2004; Lu et al., 2006). Both Glc6P and Glc1P can then be converted to UDP-glucose as during the day.Generation of Fru6P, the second substrate for Suc synthesis, can proceed only to a limited extent from triose phosphates during the night. This limitation is caused mainly by the nocturnal inactivation of Fru 1,6-bisphosphatase (Cséke et al., 1982; Stitt, 1990), a key enzyme in Suc biosynthesis during the day. Hence, in contrast to the situation in the light, cPGI activity is now crucial for providing Fru6P from Glc6P.On the catabolic side, degradation of Suc into its monosaccharides in sink tissues yields both Glc6P and Fru6P, of which only Fru6P can be utilized in glycolytic degradation. Therefore, cPGI is also required for Glc6P conversion to Fru6P in glycolysis, which, in combination with respiration, is the major path of energy production in heterotrophic tissues.Impairment or loss of function of enzymes contributing to the cytosolic hexose phosphate pool has recently been investigated for the Glc1P-forming enzyme PGM (Egli et al., 2010). The Arabidopsis genome encodes three PGM isoforms, with PGM1 localized to plastids and PGM2 and PGM3 localized to the cytosol (Caspar et al., 1985; Egli et al., 2010). Analyses of transfer DNA (T-DNA) mutants showed that homozygous pgm2/pgm3 double mutants were nonviable because of impaired gametophyte development. However, pgm2 and pgm3 single mutants grew like ecotype Columbia (Col-0) wild-type plants, indicating overlapping functions of PGM2 and PGM3 (Egli et al., 2010).By contrast, cPGI is encoded only by a single locus in Arabidopsis (Kawabe et al., 2000). Higher plant mutants reduced in cPGI activity have so far been characterized only in ethyl methanesulfonate-mutagenized Clarkia xantiana (Jones et al., 1986a; Kruckeberg et al., 1989; Neuhaus et al., 1989). The C. xantiana genome encodes for two isoenzymes of cPGI, and homozygous point mutations in each individual cPGI led to significant decrease in cPGI enzyme activity, which was further reduced to a residual activity of 18% in cpgi2/cpgi3 double mutants, where the cPGI3 locus was heterozygous for the mutation (Jones et al., 1986a; Kruckeberg et al., 1989). Detailed physiological analyses of these mutants indicated a negative impact on Suc biosynthesis and elevated starch levels when cPGI activity was decreased at least 3- to 5-fold (Kruckeberg et al., 1989).The physiological impact of decreased or even absent cPGI activity has not been characterized in the genetic model organism Arabidopsis. Here, we show that homozygous T-DNA insertion mutants in the cPGI locus are nonviable and present data from analyses of mature Arabidopsis plants constitutively expressing artificial microRNAs (amiRNAs) targeted against cPGI. These mutants reveal altered photosynthesis, a strong impact on nocturnal leaf starch degradation, and impaired Suc metabolism.