Cyanuric acid hydrolase: evolutionary innovation by structural concatenation

The cyanuric acid hydrolase, AtzD, is the founding member of a newly identified family of ring‐opening amidases. We report the first X‐ray structure for this family, which is a novel fold (termed the ‘Toblerone’ fold) that likely evolved via the concatenation of monomers of the trimeric YjgF superfamily and the acquisition of a metal binding site. Structures of AtzD with bound substrate (cyanuric acid) and inhibitors (phosphate, barbituric acid and melamine), along with mutagenesis studies, allowed the identification of the active site. The AtzD monomer, active site and substrate all possess threefold rotational symmetry, to the extent that the active site possesses three potential Ser–Lys catalytic dyads. A single catalytic dyad (Ser85–Lys42) is hypothesized, based on biochemical evidence and crystallographic data. A plausible catalytic mechanism based on these observations is also presented. A comparison with a homology model of the related barbiturase, Bar, was used to infer the active‐site residues responsible for substrate specificity, and the phylogeny of the 68 AtzD‐like enzymes in the database were analysed in light of this structure–function relationship.     

Thickness profiling of formaldehyde-fixed cells by transmission-through-dye microscopy

Conventional light microscopy techniques are poorly suited for imaging the vertical cell dimension. This can be accomplished using transmission-through-dye (TTD) imaging, in which cell thickness is directly converted into image intensity in the presence of extracellular dye with strong absorption. We have previously described applications of TTD to living cells using the dye Acid Blue 9 (AB9) to generate contrast. In this work, we investigated the possibility of extending TTD to chemically fixed cells. This would depend on preservation of cell impermeability to the dye; by using a method based on fluorescence quenching, we found that formaldehyde-fixed cells remain impermeable to AB9. Fixation enables imaging of cell surfaces in the presence of high concentrations of AB9, bringing the vertical resolution to several nanometers per pixel; that is at least an order of magnitude better than resolution achievable with live cells. TTD images collected with high-NA objectives are often contaminated by Becke lines resulting from intracellular organelles, and we show how to distinguish them from features on the cell surface. Quantification of cell thickness and volume on fixed cells is also possible during the early stages of fixation; this can be useful, for example, for measuring volume kinetics following rapid introduction of a stimulus.     

Chemistry of costunolide and biological activity of the derived lactones

Costunolide and its derived C-16 germacranolides on oxidation with selenium dioxide-t-butyl hydroperoxide afforded two melampolides, an aldehydolactone and the corresponding hydroxylactone, in each case. Structures were assigned to these melampolides on the basis of spectral data and chemical correlation. The aldehydolactones were significantly more active root promotors than their parent lactones. Costunolide and related germacranolides underwent cyclization on treatment with iodine and pyridinium chlorochromate to afford interesting products. (?)-β-Frullanolide has been synthesized and shown to be biologically more active when compared with its parent trans-lactone.     

Identification of Double-stranded Genomic DNA Spanning All Chromosomes with Mutated KRAS and p53 DNA in the Serum Exosomes of Patients with Pancreatic Cancer

Exosomes are small vesicles (50–150 nm) of endocytic origin that are released by many different cell types. Exosomes in the tumor microenvironment may play a key role in facilitating cell-cell communication. Exosomes are reported to predominantly contain RNA and proteins. In this study, we investigated whether exosomes from pancreatic cancer cells and serum from patients with pancreatic ductal adenocarcinoma contain genomic DNA. Our results provide evidence that exosomes contain >10-kb fragments of double-stranded genomic DNA. Mutations in KRAS and p53 can be detected using genomic DNA from exosomes derived from pancreatic cancer cell lines and serum from patients with pancreatic cancer. In addition, using whole genome sequencing, we demonstrate that serum exosomes from patients with pancreatic cancer contain genomic DNA spanning all chromosomes. These results indicate that serum-derived exosomes can be used to determine genomic DNA mutations for cancer prediction, treatment, and therapy resistance.     

Macrophage migration inhibitory factor mediates hypoxia-induced pulmonary hypertension

Pulmonary hypertension (PH) is a devastating disease leading to progressive hypoxemia, right ventricular failure, and death. Hypoxia can play a pivotal role in PH etiology, inducing pulmonary vessel constriction and remodeling. These events lead to increased pulmonary vessel wall thickness, elevated vascular resistance and right ventricular hypertrophy. The current study examined the association of the inflammatory cytokine macrophage migration inhibitory factor (MIF) with chronic lung disease and its role in the development of hypoxia-induced PH. We found that plasma MIF in patients with primary PH or PH secondary to interstitial lung disease (ILD) was significantly higher than in the control group (P = 0.004 and 0.007, respectively). MIF involvement with hypoxia-induced fibroblast proliferation was examined in both a human cell-line and primary mouse cells from wild-type (mif ^+/+) and MIF-knockout (mif ^−/−) mice. In vitro, hypoxia-increased MIF mRNA, extracellular MIF protein accumulation and cell proliferation. Inhibition of MIF inflammatory activity reduced hypoxia-induced cell proliferation. However, hypoxia only increased proliferation of mif ^−/− cells when they were supplemented with media from mif ^+/+ cells. This growth increase was suppressed by MIF inhibition. In vivo, chronic exposure of mice to a normobaric atmosphere of 10% oxygen increased lung tissue expression of mRNA encoding MIF and accumulation of MIF in plasma. Inhibition of the MIF inflammatory active site, during hypoxic exposure, significantly reduced pulmonary vascular remodeling, cardiac hypertrophy and right ventricular systolic pressure. The data suggest that MIF plays a critical role in hypoxia-induced PH, and its inhibition may be beneficial in preventing the development and progression of the disease.     

Immunocytochemical localization of binding 'sites' for LH and hCG in preimplantation mouse embryos.

By using an immunoperoxidase antibody method, mouse blastocysts were found to bind specifically hCG and ovine LH but not FSH or the beta unit of hCG. Brown peroxidase reaction products were present in the morula and increased with the formation of the blastocoele. The LH/hCG binding 'sites' may be related to the initiation of steroidogenesis in the embryo.     

Pod photosynthesis and seed dark CO2 fixation support oil synthesis in developingBrassica seeds

Rate of photosynthesis and activities of photosynthetic carbon reduction cycle enzymes were determined in pods (siliqua), whereas rate of dark CO₂ fixation, oil content and activities of enzymes involved in dark CO₂ metabolism were measured in seeds ofBrassica campestris L. cv. Toria at different stages of pod/seed development. The period between 14 and 35 days after anthesis corresponded to active phase of seed development during which period, seed dry weight and oil content increased sharply. Rate of pod photosynthesis and activities of photosynthetic carbon reduction cycle enzymes were maximum in younger pods but sufficiently high levels were retained up to 40 days after anthesis. The rate of dark¹⁴CO₂ fixation in seeds increased up to 21 days after anthesis and declined thereafter but maintaining sufficiently high rates till 35 days after anthesis. Similarly various enzymes viz., phosphoenolpyruvate carboxylase, NAD⁺-malate dehydrogenase and NADP⁺-malic enzyme, involved in dark CO₂ metabolism retained sufficient activities during the above period. These enzyme activities were more than adequate to maintain the desired supply of malate which mainly arises from dark CO₂ fixation in seeds and further translocated to leucoplasts for onward synthesis of fatty acids. Enzyme localization experiments revealed phosphoenolpyruvate carboxylase and enzymes of sucrose metabolism to be present only in cytosol, whereas enzymes of glycolysis were present both in cytosolic and leucoplastic fractions. These results indicated that oil synthesis in developingBrassica seeds is supported by pod photosynthesis and dark CO₂ fixation in seeds as the former serves as the source of sucrose and the latter as a source of malate     

In vitro and in vivo immunosuppressive effects of supernatants from human choriocarcinoma cell lines

Local immunosuppression mediated by placental suppressor factors may contribute to the absence of consistently demonstrable cellular immunity against the fetus. In this context, we have investigated the immunosuppressive capabilities of supernatants from human trophoblastic choriocarcinoma cell lines (HCS) by testing the effects of HCS on immune responses in vitro and in vivo in the human and murine systems. HCS suppresses mitogen-induced proliferation and mixed lymphocyte reactions in humans and in mice, as well as antigen-induced T cell proliferation in mice. HCS also suppresses the in vivo response of mice to allogeneic cells. Furthermore, HCS when injected intraperitoneally causes the induction of suppressor cells in mice which in turn prevent the mounting of an allogeneic response in other strains of mice. These results indicate that human choriocarcinoma cell lines secrete a suppressor factor(s) which induces suppression in vitro as well as in vivo through the generation of suppressor cells.