Apical Membrane Expression of Distinct Sulfated Glycans Is a Characteristic Feature of Ductules and Their Reactive and Neoplastic Counterparts

Intrahepatic bile ducts transport bile between bile canaliculi and the extrahepatic bile duct. The luminal surface of this tract is lined by a layer of biliary epithelial cells, or cholangiocytes, which secrete mucins consisting of scaffold proteins and O-glycosidically linked carbohydrate side chains. Although mucin core proteins have been extensively investigated, the structure and function of carbohydrate side chains have not. Here, we demonstrate that distinct sulfated glycans positive for MECA-79, R-10G, and 297-11A, but not 5D4, monoclonal antibodies are expressed in the cytoplasm of cells of large-sized ducts and in the apical membrane of cells in ductules, and that R-10G immunolabeling is partially eliminated by endo-β-galactosidase digestion, supporting the presence of N-acetylglucosamine-6-O-sulfated N-acetyllactosamine structures. We observed comparable apical membrane-predominant staining in ductular reactions seen during regeneration that occurs in various liver diseases and in cholangiolocarcinoma, a subtype of small duct-type intrahepatic cholangiocarcinoma (iCCA). Apical membrane expression of distinct sulfated glycans in large duct-type iCCA was negligible. Intriguingly, under pathological conditions, endo-β-galactosidase digestion almost completely eliminated R-10G immunoreactivity. These findings suggest that apical membrane expression of distinct sulfated glycans is a characteristic feature of ductules and their reactive and neoplastic counterparts     

Two nuclear export signals specify the cytoplasmic localization of calcineurin B homologous protein 1

We previously showed that calcineurin B homologous protein 1 (CHP1) interacts with nuclear apoptosis-inducing protein kinase DRAK2, and that overexpression of DRAK2 induces the nuclear accumulation of CHP1, although CHP1 usually resides in the cytoplasm [Matsumoto et al. (2001) J. Biochem. 130, 217-225]. Here we show that CHP1 has two functional nuclear export signal (NES) sequences in its carboxyl-terminal region. Treatment of several cell lines with leptomycin B, a specific inhibitor of CRM1-dependent nuclear export, induces the nuclear accumulation of CHP1. Moreover, CHP1-GFP fusion proteins with deletions or point mutations affecting the two putative NES sequences accumulate in the nucleus to a greater extent than wild-type CHP1-GFP. Tagging glutathione S-transferase-GFP fusion protein with each NES sequence caused a shift in their intracellular localization from all over the cells to the cytoplasm. These results suggest that after CHP1 has entered the nucleus, it is exported to the cytoplasm in an NES-dependent manner.     

13C urea breath test with nondispersive isotope-selective infrared spectrometry: reproducibility and importance of the fasting status

Background. The ¹³C urea breath test (¹³C-UBT) is the most convenient method for diagnosing Helicobacter pylori infection noninvasively. Nondispersive isotope-selective infrared spectrometry (NDIRS) is an inexpensive and easy alternative to mass spectrometry. The objective of this study was to evaluate: (1) the reproducibility of the ¹³C-UBT as performed by using the NDIRS method; (2) the repeatability of bags analysis and the impact of delayed analysis; and (3) the need for fasting status for the ¹³C-UBT.
Methods. The ¹³C-UBT was performed with 75 mg urea labeled with ¹³C, with breath samples collected at times 0 and 30 minutes. Results are expressed as delta over baseline (0/00). Fifty-three patients underwent two successive ¹³C-UBTs with an interval of 48 to 72 hours. The 106 collected bags were randomly reanalyzed immediately or 72 hours later. In 26 volunteer subjects, the ¹³C-UBT was performed both in a fasting condition and after a nonstandardized meal. The reproducibility was assessed by the method of Bland and Altman.
Results. The mean of difference between two successive tests was 0.14 0/00 (standard deviation, 0.90), and the coefficient of repeatability was 1.80 (confidence interval, 95%). The difference between two successive analyses was always less than 2.2% of the initial value. The coefficient of variation between two successive tests for the influence of a meal was 11.24.
Conclusion. The ¹³C-UBT as performed by using NDIRS is reproducible, analyses can be delayed up to 72 hours, and the test must be performed in fasting conditions.     

Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development

BackgroundThe pervasive expression of circular RNA is a recently discovered feature of gene expression in highly diverged eukaryotes, but the functions of most circular RNAs are still unknown. Computational methods to discover and quantify circular RNA are essential. Moreover, discovering biological contexts where circular RNAs are regulated will shed light on potential functional roles they may play.ResultsWe present a new algorithm that increases the sensitivity and specificity of circular RNA detection by discovering and quantifying circular and linear RNA splicing events at both annotated and un-annotated exon boundaries, including intergenic regions of the genome, with high statistical confidence. Unlike approaches that rely on read count and exon homology to determine confidence in prediction of circular RNA expression, our algorithm uses a statistical approach. Using our algorithm, we unveiled striking induction of general and tissue-specific circular RNAs, including in the heart and lung, during human fetal development. We discover regions of the human fetal brain, such as the frontal cortex, with marked enrichment for genes where circular RNA isoforms are dominant.ConclusionsThe vast majority of circular RNA production occurs at major spliceosome splice sites; however, we find the first examples of developmentally induced circular RNAs processed by the minor spliceosome, and an enriched propensity of minor spliceosome donors to splice into circular RNA at un-annotated, rather than annotated, exons. Together, these results suggest a potentially significant role for circular RNA in human development.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0690-5) contains supplementary material, which is available to authorized users.     

Microglial transplantation increases amyloid-beta clearance in Alzheimer model rats

Immunization with amyloid-beta (Abeta) peptides, a therapeutic approach in Alzheimer's disease (AD), reduces brain Abeta, and microglial Abeta phagocytosis has been proposed as an Abeta-lowering mechanism. We transplanted rat microglia into the rat lateral ventricle just after intra-hippocampal Abeta injection, and then investigated the contribution of exogenous microglia to Abeta clearance. Migration of exogenous microglia from the lateral ventricle to Abeta plaque was detected by magnetic resonance imaging and histochemical analysis, and the clearance of Abeta was increased by transplantation. These results suggest the possible usefulness of exogenous microglia to the therapeutic approach in AD.     

Characterization of a hydroxyl-radical-producing glycoprotein and its presumptive genes from the white-rot basidiomycete Phanerochaete chrysosporium

During wood decay, the white-rot basidiomycete Phanerochaete chrysosporium secretes low-molecular-mass glycoproteins that catalyze a redox reaction between O(2) and electron donors to produce hydroxyl radical. This reaction accounts for most of the hydroxyl radical produced in wood-degrading cultures of P. chrysosporium. In combination with phenol oxidases, hydroxyl radical is believed to play a role in lignin degradation. The secreted glycoproteins also reduce Fe(III) to Fe(II) and strongly bind Fe(II). The partially purified glycoproteins contain 1-amino-1-deoxy-2-ketose (ketoamine) produced by the condensation of side-chain amino groups and carbohydrate. cDNAs and two putative genes encoding these glycoproteins, glp1 and glp2, have been isolated and sequenced. The 875bp glp1 and 864bp glp2 are found on scaffold 2 of the P. chrysosporium genome. These presumptive genes each consist of seven introns and eight exons. The latter encode a predicted protein of 138 amino acids and a 22-amino-acid signal sequence for secretion. The predicted protein sequences are nearly identical to N-terminal and internal sequences obtained from the partially purified glycoprotein. The molecular masses of the deduced mature proteins, 13,981 (glp1) and 13,970 (glp2), coincide with the molecular mass of the glycoprotein as determined by tricine-SDS-PAGE.     

Environmental risks posed by heavy metal contamination from mine waste: Case study from northwest Iran

Mining activities produce waste tailings that can be a significant source of pollution in the surrounding ecosystem. This study was designed to estimate the magnitude of Fe, As, Pb, Cd, Mn, Ni, Zn, and Cr in soil impacted by activities in the Moeil iron ore mine area of northwestern Iran and initially assess the potential risk to nearby residents and ecological habitats. For this, concentrations of elements in 24 samples from 8 locations were analyzed by inductivity coupled plasma optical emission spectrometry. Concentrations of heavy metals reported for samples collected from the area ranged from 50,247–466,200 mg/kg for Fe, 40–10,827 mg/kg for As, 9–84 mg/kg for Pb, 0.2–58.4 mg/kg for Cd, 32–424 mg/kg for Mn, 4–32 mg/kg for Ni, 37–60 mg/kg for Zn, and 32–337 mg/kg for Cr. Reported levels of Fe and As in particular are indicative of severe contamination and imply a high risk to ecological receptors. Reported levels of arsenic also imply elevated cancer and non-cancer health risks to residents who work in or pass through the area. Reported levels of Cd and Cr in soil samples also indicate an elevated cancer risk posed by these metals. The result of this study indicates it is important to estimate potential contamination of soils and drinking water wills in the vicinity of Moeil village to arsenic and heavy metals.