A proteomic glimpse into human ureter proteome

Urine has evolved as one of the most important biofluids in clinical proteomics due to its noninvasive sampling and its stability. Yet, it is used in clinical diagnostics of several disorders by detecting changes in its components including urinary protein/polypeptide profile. Despite the fact that majority of proteins detected in urine are primarily originated from the urogenital (UG) tract, determining its precise source within the UG tract remains elusive. In this article, we performed a comprehensive analysis of ureter proteome to assemble the first unbiased ureter dataset. Next, we compared these data to urine, urinary exosome, and kidney mass spectrometric datasets. Our result concluded that among 2217 nonredundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48) that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease‐associated biomarkers such as ureter carcinoma. In addition, the ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery. All MS data have been deposited in the ProteomeXchange with identifier PXD002620 ( http://proteomecentral.proteomexchange.org/dataset/PXD002620 ).     

A new measure of time-varying association for shared frailty models with bivariate current status data

In this paper, a new measure for assessing the temporal variation in the strength of association in bivariate current status data is proposed. This novel measure is relevant for shared frailty models. We show that this measure is particularly convenient, owing to its connection with the relative frailty variance and its interpretability in suggesting appropriate frailty models. We introduce a method of estimation and standard errors for this measure. We discuss its properties and compare it to an existing measure of association applicable to current status data. Small sample performance of the measure in realistic scenarios is investigated using simulations. The methods are illustrated with bivariate serological survey data on a pair of infections, where the time-varying association is likely to represent heterogeneities in activity levels and/or susceptibility to infection.     

Modulation of the herpes simplex virus type-1 UL9 DNA helicase by its cognate single-strand DNA-binding protein, ICP8

The mechanism of stimulation of a DNA helicase by its cognate single-strand DNA-binding protein was examined using herpes simplex virus type-1 UL9 DNA helicase and ICP8. UL9 and ICP8 are two essential components of the viral replisome that associate into a complex to unwind the origins of replication. The helicase and DNA-stimulated ATPase activities of UL9 are greatly elevated as a consequence of this association. Given that ICP8 acts as a single-strand DNA-binding protein, the simplest model that can account for its stimulatory effect predicts that it tethers UL9 to the DNA template, thereby increasing its processivity. In contrast to the prediction, data presented here show that the stimulatory activity of ICP8 does not depend on its single-strand DNA binding activity. Our data support an alternative hypothesis in which ICP8 modulates the activity of UL9. Accordingly, the data show that the ICP8-binding site of UL9 constitutes an inhibitory region that maintains the helicase in an inefficient ground state. ICP8 acts as a positive regulator by neutralizing this region. ICP8 does not affect substrate binding, ATP hydrolysis, or the efficiency of translocation/DNA unwinding. Rather, we propose that ICP8 increases the efficiency with which substrate binding and ATP hydrolysis are coupled to translocation/DNA unwinding.     

Nitric oxide and endothelin relationship in intestinal ischemia/reperfusion injury (II).

Endothelins ( ETs ) are potent vasoconstrictors derived from vascular endothelium. They have primary roles in many pathophysiologic states including ischemia/reperfusion (I/R) injury. The relationships between nitric oxide (NO) and ETs are still under investigation. In this study on rats we want to focus on the interaction of NO and ET especially in I/R injury. For this purpose ET-1 and PD-156252, a nonselective ET receptor blocker, were given in a mesenteric I/R model and reactive oxygen species were detected directly using chemiluminescence of the ileal tissue. ET administrations to sham and I/R groups caused significant increases in NO concentrations whereas, in terms of peroxynitrite, which is a highly reactive group of free radicals, its increasing effects were seen only in I/R groups. This suggests that in I/R where superoxide levels increase together with NO, the conversion to peroxynitrite is likely and this effect is augmented with ET administration. On the other hand PD administration decreases superoxide and thereby peroxynitrite levels and this study shows that the effect of PD-156252 is established through this mode of action. These data suggest therapeutic approaches that may be beneficial in the treatment of I/R injury.     

The shadow of life: Psychosocial explanations for placenta rituals

Culturally determined patterns of behavior associated with placenta disposal are characteristic of many modern and ancient societies. This paper defines this type of placenta disposal as a ritual event that delimits a portion of reality; explanations are provided leading to the conclusion that placenta rituals operate as anxiety releasing mechanisms that provide a means of control over the future health and welfare of mother, child, and community. The question of why the placenta figures so prominently in folk beliefs and practices has previously been attributed to its morphological and physiological properties; this paper argues that attributes associated with it from a psychosocial model are equally important. The data for this study were drawn from a compilation of ethnographic reports of post-partum practices in African, Asian, European, and Latin American societies. Additional information on placenta disposal was derived from interviews with 1,859 Peruvian informants. Analysis of the data obtained from the Peruvian studies show a significant difference between rural and semi-urban patterns of placenta disposal.I am using the term ritual to refer to the culturally determined behavioral sequences that relate to the placenta. The basis of the explanatory system that I have proposed in this article to account for its cross-cultural importance is that these behavioral sequences are examples of secular rituals as defined by Moore and Meyerhoff 1977: 3–24.     

Evidence for induced fit in bacterial RNase P RNA-mediated cleavage

RNase P with its catalytic RNA subunit is involved in the processing of a number of RNA precursors with different structures. However, precursor tRNAs are the most abundant substrates for RNase P. Available data suggest that a tRNA is folded into its characteristic structure already at the precursor state and that RNase P recognizes this structure. The tRNA D-/T-loop domain (TSL-region) is suggested to interact with the specificity domain of RNase P RNA while residues in the catalytic domain interact with the cleavage site. Here, we have studied the consequences of a productive interaction between the TSL-region and its binding site (TBS) in the specificity domain using tRNA precursors and various hairpin-loop model substrates. The different substrates were analyzed with respect to cleavage site recognition, ground-state binding, cleavage as a function of the concentration of Mg(2+) and the rate of cleavage under conditions where chemistry is suggested to be rate limiting using wild-type Escherichia coli RNase P RNA, M1 RNA, and M1 RNA variants with structural changes in the TBS-region. On the basis of our data, we conclude that a productive TSL/TBS interaction results in a conformational change in the M1 RNA substrate complex that has an effect on catalysis. Moreover, it is likely that this conformational change comprises positioning of chemical groups (and Mg(2+)) at and in the vicinity of the cleavage site. Hence, our findings are consistent with an induced-fit mechanism in RNase P RNA-mediated cleavage.     

Mass spectrometry for the identification of the discriminating signals from metabolomics: current status and future trends

The metabolome is characterized by a large number of molecules exhibiting a high diversity of chemical structures and abundances, requiring complementary analytical platforms to reach its extensive coverage. Among them, atmospheric pressure ionization mass spectrometry (API-MS)-based technologies, and especially those using electrospray ionization are now very popular. In this context, this review deals with strengths, limitations and future trends in the identification of signals highlighted by API-MS-based metabolomics. It covers the identification process from the determination of the molecular mass and/or its elemental composition to the confirmation of structural hypotheses. Furthermore, some tools that were developed in order to address the MS signal redundancy and some approaches that could facilitate identification by improving the visualization and organization of complex data sets are also reported and discussed.     

Cellular munc18c levels can modulate glucose transport rate and GLUT4 translocation in 3T3L1 cells

Munc18c has been shown to bind syntaxin 4 and to play a role in GLUT4 translocation and glucose transport, although this role is as yet poorly defined. In the present study, the effects of modulating the available level of munc18c on glucose transport and GLUT4 translocation were examined. Over-expression of munc18c in 3T3L1 adipocytes inhibited insulin-stimulated glucose transport by approximately 50%. Basal glucose transport rates were also decreased by approximately 25%. In contrast, microinjection of a munc18c polyclonal antibody stimulated GLUT4 translocation by approximately 60% over basal levels without affecting insulin-stimulated GLUT4 levels. Microinjection of a control antibody had no effect. These data are consistent with the likelihood that antibody microinjection sequesters munc18c enabling translocation/fusion of GLUT4 vesicles. Mutagenesis of a potential proline-directed kinase phosphorylation site in munc18c, T569, that in previous studies of its neuronal counterpart munc18a caused its dissociation from its complex with syntaxin 1a, had no effect on munc18c's association with syntaxin 4 or its inhibition of glucose transport, indicative that phosphorylation of this residue is not important for insulin regulation of glucose transport. The over-expression and microinjection sequestration data support an inhibitory role for munc18c on translocation/fusion of GLUT4 vesicles. They further show that altering the level of available munc18c in 3T3L1 cells can modulate glucose transport rates, indicating its potential as a target for therapeutics in diabetes.     

Iodine biofortification and antioxidant capacity of lettuce: potential benefits for cultivation and human health

Iodine is considered an essential trace element for mammals, and its deficiency is related to numerous pathologies as severe as goitre, reproductive failure, mental retardation and brain damage, among others. Currently, about 30% of the world's population are affected by this deficiency, and thus, in an attempt to ameliorate these nutritional disorders, we propose a biofortification programme with iodine by an application of different dosages and forms of this element (iodide versus iodate) in lettuce plants. In this work, a study has been made of the iodine concentration in roots and edible leaves and their influence on nutritional quality through an analysis of its antioxidant capacity. The results showed that the most appropriate application rates in hydroponic cultivation were 40 μM or lower in the form I⁻ because these concentrations did not reduce biomass in the treated plants with respect to control plants and caused a foliar accumulation of this element that guarantees the viability of this type of programmes. Furthermore, these data are novel, given that the treated plants show a significant increase in antioxidant compounds after the application of iodine.     

Cyberknife: A double edged sword?

The Cyberknife represents a new, frameless stereotactic radiosurgery system which efficiently incorporates advance robotics with computerized image reconstruction to allow highly conformal image guided radiation delivery. This review focus is on the pros and cons of this new radiotherapy tool, its current indications, safety profile and future directions. A literature search of Medline, Pubmed, Biomed, Medscape and Cancer lit database were referred to retrieve relevant data/information. The authors conclude that the use of this system offers an invaluable solution to the treatment of selective tumours/lesions located close to critical structures, salvage of recurrent and metastatic lesions and potential of treatment of selective early stage malignancies like the carcinoma prostate and lung. However, it is still too premature, with insufficient follow up data to advocate it as the treatment of choice in any set up. There are several radiobiological issues that also remain in the greyzone.     

Studies on a Capillary-Rich Fraction Isolated from Brain: Histaminic Components and Characterization of the Histamine Receptors Linked to Adenylate Cyclase

Abstract: A fraction enriched in capillaries has been prepared from the guinea pig cerebral cortex. The purity of this fraction was checked by light- and electron-microscopic examination and by its high enrichment in alkaline phosphatase and γ-glutamyl transpeptidase. In the capillary-rich fraction, the endogenous level of histamine was 1.9%'of that measured in the initial hornogenate. The histamine-synthesizing enzyme, I-histidine decarboxylase, and the metabolizing enzyme, histamine-N-methyltransferase, were barely detectable. In addition, histamine elicits a twofold stimulation in the accumulation of cyclic AMP in this capillary fraction with an EC₅₀ of 5 γM. Agonists and antagonists of the two types of histamine receptors (H₁ and H₂) were used for the characterization of the receptors mediating this action: H₂-receptor agonists were able to activate the adenylate cyclase with "relative potencies" similar to that found on typical H₂-receptors, and cimetidine, a specific H₂-receptor antagonist, competitively inhibited the response to histamine with a K₁ value reflecting its interaction with a single population of H₂-receptors. On the contrary, data obtained with H₁-receptor agonists and antagonists reflect their interaction with H₂-receptors rather than H₁-receptors. Thus H₂-receptors are involved in the activation of adenylate cyclase of the capillary fraction.     

Behavioural responses to photographs by pictorially naïve baboons (Papio anubis), gorillas (Gorilla gorilla) and chimpanzees (Pan troglodytes)

This study assessed how pictorially naïve nonhuman primates understand pictures. Fifty-five baboons with no prior exposure to pictures were trained to grasp a slice of banana presented against a pebble in a two alternative forced choice task. Post-training testing involved three stimulus pairs: (1) real banana slice vs. its picture, (2) the banana picture vs. a real pebble and (3) banana picture vs. a pebble picture which were presented twice. Preliminary data were also collected on naïve gorillas (n = 4) and chimpanzees (n = 7) using the same procedure. Baboons revealed a preference for the food picture in (2) and (3) and often ate this stimulus, but the food item and its picture were accurately discriminated in (1). These results suggest that baboons mistook the pictorial stimulus and its referent, but processed the banana pictures as poor exemplars of the real banana category. Among apes, only gorillas ate the banana pictures, suggesting that picture–object confusion may also occur in this species. Findings are discussed as pertaining to the general issue of representational abilities in nonhuman primates, and its evolution.     

Overexpression of ubiquitin specific protease 44 (USP44) induces chromosomal instability and is frequently observed in human T-cell leukemia

Cdc20-anaphase promoting complex/cyclosome (Cdc20-APC/C) E3 ubiquitin ligase activity is essential for orderly mitotic progression. The deubiqituinase USP44 was identified as a key regulator of APC/C and has been proposed to suppress Cdc20-APC/C activity by maintaining its association with the inhibitory protein Mad2 until all chromosomes are properly attached to the mitotic spindle. However, this notion has been challenged by data in which a lysine-less mutant of Cdc20 leads to premature anaphase, suggesting that it's ubiquitination is not required for APC/C activation. To further evaluate its role in checkpoint function and chromosome instability, we studied the consequences of over-expression of mouse Usp44 in non-transformed murine embryonic fibroblasts. Here we show that cells with high Usp44 are prone to chromosome segregation errors and aneuploidization. We find that high Usp44 promotes association of Mad2 with Cdc20 and reinforces the mitotic checkpoint. Surprisingly, the APC/C-Cdc20 substrate cyclin B1 is stabilized in G2 when Usp44 is over-expressed, but is degraded with normal kinetics once cells enter mitosis. Furthermore, we show that USP44 expression is elevated in subset of T-cell leukemias. These data are consistent with an important role for USP44 in regulating Cdc20-APC/C activity and suggest that high levels of this enzyme may contribute to the pathogenesis of T-ALL.     

Promoter characterization and regulation of expression of an imprinted gene SLC22A18AS

The SLC22A18/SLC22A18AS genes are a sense-antisense pair located at human chromosome segment 11p15.5. These genes are paternally imprinted: paternal alleles are silenced and maternal alleles are expressed. Although SLC22A18 is a well-characterized gene, very little is known regarding its antisense partner SLC22A18AS. We therefore sought to identify the potential cis-regulating elements including the promoter of this gene, differentially methylated regions (DMRs) and the translation of its putative ORF. Dual promoters (P1 and P2) were identified for this gene and both are devoid of consensus TATA and CCAAT boxes. However, the P1 promoter harbors a putative Sp1 binding site. Sp1 binds to the P1 promoter in vivo and positively regulates its activity. Promoter and CpG II island regions showed heavy methylation of CpG sites, but no DMRs were observed. Treatment of a non-SLC22A18AS expressing HuH7 cells with the methyltransferase inhibitor 5-aza-2'-deoxycytidine restored expression of this gene. The histone deacetylase (HDAC) inhibitor Trichostatin-A, on the other hand, failed to induce its expression. We suggest that the expression of this gene is methylation-dependent, but histone acetylation-independent. This gene was found to be translated with a cytoplasmic localization. The present data will help to understand the regulation of this gene and its role in tumorigenesis.     

Substrate specificity and kinetic mechanism of human placental insulin receptor/kinase

The insulin receptor has been shown to be a protein kinase which phosphorylates its substrates on tyrosine residues. To examine the acceptor specificity of affinity-purified insulin receptor/kinase, hydroxyamino acid containing analogues of the synthetic peptide substrate Arg-Arg-Leu-Ile-Glu-Asp-Ala-Glu-Tyr-Ala-Ala-Arg-Gly were prepared. Substitution of serine, threonine, or D-tyrosine for L-tyrosine completely ablated the acceptor activity of the synthetic peptides. These peptides, along with a phenylalanine-containing analogue, did serve as competitive inhibitors of the insulin receptor/kinase with apparent Ki values in the range of 2-4 mM. These data suggest that the insulin receptor/kinase is specific for tyrosine residues in its acceptor substrate and imply that serine phosphate or threonine phosphate present in receptor is due to phosphorylation by other protein kinases. The kinetics of the phosphorylation of the L-tyrosine-containing peptide were examined by using prephosphorylated insulin receptor/kinase. Prephosphorylation of the receptor was necessary to maximally activate the kinase and to linearize the initial velocity of the peptide phosphorylation reaction. The data obtained rule out a ping-pong mechanism and are consistent with a random-order rapid-equilibrium mechanism for the phosphorylation of this peptide substrate. Additional experiments demonstrated that the autophosphorylated insulin receptor was not able to transfer the preincorporated phosphate to the synthetic peptide substrate. Thus, the insulin receptor/kinase catalyzes the reaction via a mechanism that does not involve transfer of phosphate from a phosphotyrosine-containing enzyme intermediate.     

The Hsp70 chaperone Ssq1p is dispensable for iron-sulfur cluster formation on the scaffold protein Isu1p

The specialized yeast mitochondrial chaperone system, composed of the Hsp70 Ssq1p, its co-chaperone J-protein Jac1p, and the nucleotide release factor Mge1p, perform a critical function in the biogenesis of iron-sulfur (Fe/S) proteins. Using a spectroscopic assay, we have analyzed the potential role of the chaperones in Fe/S cluster assembly on the scaffold protein Isu1p in vitro in the presence of the cysteine desulfurase Nfs1p. In the absence of chaperones, the kinetics of Fe/S cluster formation on Isu1p were compatible with a chemical reconstitution pathway with Nfs1p functioning as a sulfide donor. Addition of Ssq1p improved the rates of Fe/S cluster assembly 3-fold. However, this stimulatory effect of Ssq1p required neither ATP nor Jac1p and could be fully attributed to the activation of the Nfs1p desulfurase activity by Ssq1p. Furthermore, chaperone-stimulated Fe/S cluster assembly did not involve the specific interaction between Isu1p and Ssq1p, since the effect was observed with Isu1p mutant proteins defective in this interaction, suggesting that nonspecific binding of Ssq1p to Nfs1p helped to prevent its unfolding. Consistent with this idea, these Isu1p mutants were capable of binding an Fe/S cluster in vivo but failed to restore the growth and Fe/S cluster assembly defects of a Isu1p/Isu2p-deficient yeast strain. Taken together, these data suggest that Ssq1p/Jac1p/Mge1p are not important for Fe/S cluster synthesis on Isu1p. Hence, consistent with previous in vivo data, these chaperones likely function in steps subsequent to the de novo synthesis of the Fe/S cluster on Isu1p.