DICER1 Hotspot Mutations in Pleuropulmonary Blastoma: A Case Series From a Tertiary Center.

Pleuropulmonary blastoma (PPB) is a potentially aggressive, rare childhood neoplasia. We investigated histopathological features, survival, and DICER1 hotspot mutations among PPB patients. Archive records at our institution were reviewed, covering a 20-year period. Thirteen children (6 males and 7 females) with a mean age of 30.5 (range 6-83) months were included. The tumor subtypes were type I in 6 (46%), type II in 4 (31%), and type III in 3 (23%). Only tumors with type II and type III histology showed anaplasia (4/7, 57%). Median follow-up was 28 (range 9-216) months. Three-year overall survival rate was 83.3% and 3-year progression-free survival rate was 25%. Progression was seen in 60% (3/5) of type I and 66.7% (4/6) of type II and type III cases. Two patients died of disseminated disease at 9 and 44 months. Hotspot missense mutations on DICER1 gene were detected in all 11 patients with available tumor tissue. We found an additional novel germline loss-of-function mutation (c.5436dupT; p.E1813*) in 1 case. To the best of our knowledge, this is the first study to investigate hotspot missense mutations on DICER1 gene among the largest series of Turkish children with PPB.

Sex-specific genotype-by-environment interactions for cuticular hydrocarbon expression in decorated crickets, Gryllodes sigillatus: implications for the evolution of signal reliability.

Phenotypic traits that convey information about individual identity or quality are important in animal social interactions, and the degree to which such traits are influenced by environmental variation can have profound effects on the reliability of these cues. Using inbred genetic lines of the decorated cricket, Gryllodes sigillatus, we manipulated diet quality to test how the cuticular hydrocarbon (CHC) profiles of males and females respond across two different nutritional rearing environments. There were significant differences between lines in the CHC profiles of females, but the effect of diet was not quite statistically significant. There was no significant genotype-by-environment interaction (GEI), suggesting that environmental effects on phenotypic variation in female CHCs are independent of genotype. There was, however, a significant effect of GEI for males, with changes in both signal quantity and content, suggesting that environmental effects on phenotypic expression of male CHCs are dependent on genotype. The differential response of male and female CHC expression to variation in the nutritional environment suggests that these chemical cues may be under sex-specific selection for signal reliability. Female CHCs show the characteristics of reliable cues of identity: high genetic variability, low condition dependence and a high degree of genetic determination. This supports earlier work showing that female CHCs are used in self-recognition to identify previous mates and facilitate polyandry. In contrast, male CHCs show the characteristics of reliable cues of quality: condition dependence and a relatively higher degree of environmental determination. This suggests that male CHCs are likely to function as cues of underlying quality during mate choice and/or male dominance interactions.

Toxicity of urban highway runoff with respect to storm duration.

The toxicity of stormwater runoff during various time-based stages was measured in both grab and composite samples collected from three highly urbanized highway sites in Los Angeles, California between 2002 and 2005. Stormwater runoff samples were tested for toxicity using three freshwater species (the water flea Ceriodaphnia dubia, the fathead minnow Pimephales promelas, and the green algae Pseudokirchneriella subcapitatum) and two marine species (the purple sea urchin Strongylocentrotus purpuratus, and the luminescent bacteria Photobacterium phosphoreum using Microtox. Toxicity results varied substantially throughout the storm events for both freshwater and marine species toxicity tests. In general, however, the first few samples were found to be more toxic compared with those collected during later stages of each storm event. In most cases, more than 40% of the toxicity was associated with the first 20% of discharged runoff volume. Furthermore, on average, 90% of the toxicity was observed during the first 30% of storm duration. Toxicity identification evaluation results found copper and zinc to be the primary cause of toxicity in about 90% of the samples evaluated with these procedures. Surfactants were also found to be the cause of toxicity in less than 10% of the samples.

A fully synthetic immunogen carrying a carcinoma-associated carbohydrate for active specific immunotherapy.

Aberrant glycosylation of mucins leads to the exposure of cryptic carbohydrate antigens at the surface of carcinoma cells, which, therefore, represent potent targets for anticancer therapeutic vaccines. To date, the development of immunogens to stimulate immune response to such saccharidic antigens is based on carbohydrate conjugation to carrier proteins. However, these traditional protein conjugates are poorly defined in chemical composition and structure. As an alternative, we synthesized a multiple antigenic O-linked glycopeptide (MAG) carrying the carbohydrate Tn antigen associated with a CD4+ T-cell epitope (MAG:Tn-PV). This fully synthetic immunogen is highly defined in composition and carries a high saccharidic epitope ratio over the entire molecule. The MAG:Tn-PV was able to induce anti-Tn IgG antibodies that recognize human tumor cell lines. A therapeutic immunization protocol performed with this fully synthetic immunogen increased the survival of tumor-bearing mice. Thus, the accurately defined and versatile MAG system represents an efficient strategy to induce carbohydrate-specific antitumor immune responses but may also be applicable to the prevention of infectious diseases, if it is based on bacterial oligosaccharides.

Analysis of the fine specificity of Tn-binding proteins using synthetic glycopeptide epitopes and a biosensor based on surface plasmon resonance spectroscopy.

Using synthetic Tn (GalNAc-O-Ser/Thr) glycopeptide models and a biosensor based on surface plasmon resonance spectroscopy we have determined that isolectin B4 from Vicia villosa (VVLB4) binds to one Tn determinant whereas the anti-Tn monoclonal antibodies 83D4 and MLS128 require at least two Tn residues for recognition. When an unglycosylated amino acid is introduced between the Tn residues, both antibodies do not bind. MLS128 affinity was higher on a glycopeptide with three consecutive Tn residues. These results indicate that Tn residues organized in clusters are essential for the binding of these antibodies and indicate a different Tn recognition pattern for VVLB4.

Temporal aggregation bias and inference of causal regulatory networks.

Time course experiments with microarrays have begun to provide a glimpse into the dynamic behavior of gene expression. In a typical experiment, scientists use microarrays to measure the abundance of mRNA at discrete time points after the onset of a stimulus. Recently, there has been much work on using these data to infer causal regulatory networks that model how genes influence each other. However, microarray studies typically have slow sampling rates that can lead to temporal aggregation of the signal. That is, each successive sampling point represents the sum of all signal changes since the previous sample. In this paper, we show that temporal aggregation can bias algorithms for causal inference and lead them to discover spurious relations that would not be found if the signal were sampled at a much faster rate. We discuss the implications of temporal aggregation on inference, the problems it creates, and potential directions for solutions.

Enzymatic synthesis of some O-beta-D-digalactosyl glycopeptides, using beta-D-galactosidase.

Disaccharide-peptide conjugates were obtained in yields of 30-50% from o-nitrophenyl beta-D-galactopyranoside by employing beta-D-galactosidase from E. coli as catalyst. Two series of beta-D-galactosyldipeptides were examined as galactosyl acceptors. They both contain an L-serine residue beta-linked to the anomeric carbon of galactose. In the first series, serine is in the N-terminal position of the dipeptide; in the second series, serine is in the C-terminal position. The second amino acid is L-alanine or glycine. Some of our substrates gave a high yield of beta-(1-->3)-digalactosyldipeptide derivatives and all gave very little of the beta-(1-->6) regioisomer. The conditions and the limitations of the transgalactosylation reaction are discussed.

Synthesis of alpha- and beta-biotinylated T-antigen.

The T-antigen [beta-D-Gal-(1-->3)-D-Ga1NAc] has been linked to biotin through a C6 spacer arm for the detection of a specific 'T-antigen-lectin' complex at the surface and/or on the migration pathway of melanoma cells. When 4,6-di-O-acetyl-2-azido-2-deoxy-3-O-(2,3,4, 6-tetra-O-acetyl-beta-D-galactopyranosyl)-alpha- or -beta-D-galactopyranosyl halides were treated with N-benzyloxycarbonyl or N-fluorenylmethoxycarbonyl protected aminohexanols (used as the spacer arm), unusual stereoselectivities were observed for the synthesis of the alpha and beta anomers. The synthesis of the alpha anomer could only be achieved, in reasonable yields, with the Schiff base of aminohexanol.

Unusual lactam formation occurring in the synthesis of a biotinylated T-antigen-serine derivative.

Synthesis of the biotinylated T-antigens, linked to a serine by an alpha (7 alpha) or a beta (7 beta) 2-acetamido-2-deoxy-D-galactoside bond, is described. These derivatives were needed for the detection of a specific endogenous lectin at the surface and/or on the migration pathway of melanoma cells. In the course of the synthesis, an unusual lactam formation was observed with the beta anomer of the azido-disaccharide 5 beta.

A monoclonal antibody, MIN/3/60, that recognizes the sulpho-Lewis(x) and sulpho-Lewis(a) sequences detects a sub-population of epithelial glycans in the crypts of human colonic epithelium.

Monoclonal antibodies (MAbs) directed to Lewis(x) (Le(x)) and related carbohydrate sequences have been invaluable in anticipating biological roles for these oligosaccharides by detecting the remarkable changes that occur in their expression from the earliest stages of embryogenesis, through development and sequential stages of cell differentiation and maturation. A notable impact has been in the molecular dissection of ligand-receptor interactions in key cell adhesion events at the initial stages of leukocyte recruitment in inflammation, and almost certainly in the metastasis of epithelial tumours. Antibodies that recognise Le(x) and the 3'-sialyl forms were observed to identify leukocyte subsets; these were subsequently found to match those recognized by the leukocyte-endothelium adhesion molecules, the E- and P-selectins. We now describe a MAb (rat hybridoma MIN/3/60) raised to 3'-sulpho-Le(x), a carbohydrate sequence which, in vitro, is bound not only by the E-, L-, and P-selectins, but also by the cysteine-rich domain of the macrophage endocytosis receptor. We observe that MIN/3/60 is bispecific, however; it binds 3'-sulpho-Le(a) as well as 3'-sulpho-Le(x). Nevertheless, our exploratory studies reveal that it may be a useful histochemical reagent when used in conjunction with a monospecific antibody to 3'-sulpho-Le(a). The MIN/3/60 antibody reveals a sub-population of epithelial glycans in the crypts of Lieberkühn in normal human colon.

Production and functional characterization of two mouse/human chimeric antibodies with specificity for the tumor-associated Tn-antigen.

In this work, we have constructed two functional mouse/human chimeric antibodies (IgMkappa and IgG1kappa isotypes) by inserting genomic DNA fragments encoding VH and Vkappa variable regions of the murine monoclonal antibody IgMK-83D4 into mammalian expression vectors containing human mu, gamma1, and kappa constant exons, and by transfecting them into the nonsecreting mouse myeloma X-63 cell line. In previous works, we have demonstrated that 83D4 murine mAb reacts with Tn determinant (GalNAcalpha-O-Ser/Thr) expressed in 90% of breast, ovary, and colon carcinomas. Both expressed chimeric antibodies were purified from the transfected cell line supernatant by affinity chromatography, and their reactivities against Tn antigen were confirmed by ELISA on asialo ovine submaxilar mucin and immunofluorescence studies on MCF-7 breast carcinoma cell line. We have demonstrated by gel filtration chromatography, that the principal secreted forms were monomers for IgG1kappa and pentamers for IgMkappa. The binding affinities of these chimeric antibodies against synthetic Tn glycopeptides, were evaluated by surface plasmon resonance showing an affinity constant similar to that of 83D4 native antibody for IgMkappa and a lower affinity constant for IgG1kappa chimeric antibody. On the other hand, the replacement of mouse C regions with human C regions confers both chimeric antibodies the ability to activate human complement. These mouse/human chimeric antibodies should be much less immunogenic and could play an important role in the lysis of tumor cell expressing Tn-antigen. Therefore, these anti-Tn chimeric antibodies could be considered as potential tools for human in vivo studies.

Concentrations of methyl- tert-butyl ether (MTBE) in inputs and receiving waters of Southern California.

The occurrence and concentration of the fuel additive methyl-tert-butyl ether (MTBE) were measured in dry weather runoff, municipal wastewater and industrial effluents, and coastal receiving waters in southern California. Combined, refineries and sewage treatment plants release approximately 214 kg day(-1) of MTBE into the marine environment, with Santa Monica Bay receiving most (98%) of this discharge. Dry weather urban runoff was analysed for samples collected from 25 streams and rivers, and accounted for less than 0.5% of the mass of MTBE discharged to coastal waters. Receiving water samples were collected from 23 stations in Santa Monica Bay, Los Angeles Harbour and Mission Bay or San Diego Bay. MTBE was detected at low concentrations near effluent discharges, however there was no evidence of baywide MTBE contamination related to these outfalls. Marinas and areas used intensively for recreational boating had the highest average MTBE concentration (8.8 microg l(-1)). Surface water contamination was most widespread in San Diego Bay and Mission Bay, areas with no refinery or sewage treatment plant inputs.

Induction of a melanoma-specific antibody response by a monovalent, but not a divalent, synthetic GM2 neoglycopeptide.

The GM2 ganglioside represents an important target for specific anticancer immunotherapy. We designed and synthesized a neoglycopeptide immunogen displaying one or two copies of the GM2 tetrasaccharidic moiety. These glycopeptides were prepared using the Huisgen cycloaddition, which enables the efficient ligation of the alkyne-functionalized biosynthesized GM2 with an azido CD4(+) T cell epitope peptide. It is worth noting that the GM2 can be produced on a gram scale in bacteria, which can be advantageous for a scale-up of the process. We show here for the first time that a fully synthetic glycopeptide, which is based on a ganglioside carbohydrate moiety, can induce human tumor cell-specific antibodies after immunization in mice. Interestingly, the monovalent, but not the divalent, form of GM2 peptide construct induced antimelanoma antibodies. Unlike traditional vaccines, this vaccine is a pure chemically-defined entity, a key quality for consistent studies and safe clinical evaluation. Therefore, such carbohydrate-peptide conjugate represents a promising cancer vaccine strategy for active immunotherapy targeting gangliosides.

Effects of dietary selenomethionine on larval rainbow trout (Oncorhynchus mykiss).

Increased selenium (Se) concentrations in water (>10 microg/L) have been measured in the San Diego Creek, which is a tributary of the Upper Newport Bay in Orange County, CA. The objective of this study was to develop tissue- and dietary-based thresholds for Se in resident fish species in San Diego Creek. A 90-day dietary experiment was conducted to determine the effects of seleno-L-methionine (SeMe) on the growth, survival, and whole-body Se accumulation in larval (24-day-old) rainbow trout. Decreased and oxidized glutathione (GSH-to-GSSG ratio) and thiobarbituric acid-reactive substances (TBARS) were also measured in livers of exposed animals to assess oxidative damage caused by Se. Fish food was spiked with SeMe to contain 4.6, 12, and 18 microg/g (dry weight) of Se. Fish exposed to SeMe for 90 days exhibited a significant decrease in body weight and fork length in the 4.6 and 12 microg/g Se treatments compared with controls. Whole-body total Se concentrations increased significantly in fish fed 12 and 18 microg/g SeMe after 90 days compared with controls. Lipid peroxidation (TBARS) and GSH-to-GSSG ratios were unchanged by SeMe treatment. Based on decreased growth after 90 days, a dietary Se lowest observed-effect concentration (LOEC) value of 4.6 microg/g and a Se body burden LOEC of 1.20 microg/g (wet weight) were estimated.

Sodium-taurine cotransport in reptilian renal brush-border membrane vesicles.

The coupled transport of Na+ with taurine into snake renal brush-border membrane vesicles (BBMV) was studied using 5-s uptake conditions. Taurine transport into snake renal BBMV involved two parallel processes, one saturable (Na(+)-dependent) and one (Na(+)-independent) that behaved like passive diffusion. Below 1 mM taurine concentration, the Na(+)-dependent system accounted for 60% of total taurine uptake. Over both low (0.001-0.80 mM) and high (0.8-5.0 mM) taurine concentration ranges, the Na(+)-dependent taurine uptake within each range showed Michaelis-Menten kinetics, suggesting the presence of two independent saturable Na(+)-dependent transport systems for taurine. The high-affinity, low-capacity system saturated above 100 microM with a Km of 71.4 +/- 45.7 microM and a maximum velocity (Vmax) of 21.9 +/- 3.77 pmol (mg protein)-1 (5 s)-1. The low-affinity, high-capacity system saturated above 1 mM, with a Km of 1.11 +/- 0.63 mM and a Vmax of 252 +/- 47 pmol (mg protein)-1 (5 s)-1. The stoichiometric relationship between external Na+ concentration and taurine uptake (at 10 microM) by the high-affinity BBMV transport system was examined by the activation method under short-circuited conditions. The 5-s rate of taurine transport was a sigmoid function of increasing extravesicular Na+ concentration. Kinetic analysis of the interaction of Na+ with the high-affinity taurine transport system suggested that 3 Na+ ions (3.2 +/- 0.7) may be involved with 1 taurine molecule in the transport event.(ABSTRACT TRUNCATED AT 250 WORDS)

Toxicity of parking lot runoff after application of simulated rainfall.

Stormwater runoff is an important source of toxic substances to the marine environment, but the effects of antecedent dry period, rainfall intensity, and duration on the toxicity of runoff are not well understood. In this study, simulated rainfall was applied to parking lots to examine the toxicity of runoff while controlling for antecedent period, intensity, and duration of rainfall. Parking areas were divided into high and low use and maintained and unmaintained treatments. The parking stalls were cleaned by pressure washing at time zero. Simulated rainfall was then applied to subplots of the parking lots so that antecedent periods of 1, 2, and 3 months were achieved, and all of the runoff was collected for analysis. On a separate parking lot, rainfall was applied at a variety of intensities and durations after a 3-month antecedent period. Runoff samples were tested for toxicity using the purple sea urchin fertilization test. Every runoff sample tested was found to be toxic. Mean toxicity for the sea urchin fertilization test ranged from 2.0 to 12.1 acute toxic units. The toxicity increased rapidly during the first month but then decreased approximately to precleaning levels and remained there. No difference in toxicity was found between the different levels of use or maintenance treatments. The intensity and duration of rainfall were inversely related to degree of toxicity. For all intensities tested, toxicity was always greatest in the first sampling time interval. Dissolved zinc was most likely the primary cause of toxicity based on toxicant characterization of selected runoff samples.

Synthesis of alpha and beta-glycopyranosyl-serine derivatives by enzymic transglycosylation.

The transglycosylation from raffinose and lactose to Aloc-Ser-OMe is catalyzed respectively by alpha and beta galactosidases. Transglycosylation from cellobiose has been achieved with beta-glucosidase. The simplicity of the enzymatic synthesis, the stereospecificity of the condensations in one-pot reactions and the ease of purification give the method value for large scale preparation of beta-linked derivatives. The protective groups of the serine residue can be cleaved under mild conditions: the ester group has been removed quantitatively by papain catalyzed hydrolysis and the Aloc group by a Pd (0) hydrostannolytic cleavage.

Basolateral taurine transport system in reptilian renal cells.

The characteristics of taurine transport across renal basolateral membranes were examined, using basolateral membrane vesicles (BLMV) isolated from garter snake (Thamnophis spp.) kidneys. BLMV fraction exhibited high enrichment for the basolateral marker enzyme, Na(+)-K(+)-adenosinetriphosphatase (23-fold), with approximately 10% contamination by brush-border membranes. Taurine uptake into BLMV was specifically stimulated by inwardly directed Na+ gradient in the presence of Cl-. Equilibrium NaCl condition and replacement of NaCl gradient by KCl, choline chloride, NaSCN, sodium gluconate, or mannitol inhibited taurine uptake. Unlike brush-border membrane vesicles (BBMV), taurine uptake into BLMV was not stimulated by a Cl- gradient. In further contrast to BBMV, BLMV taurine uptake was smaller in magnitude and not electrogenic. The stoichiometric relationship between Na+ and BLMV taurine uptake, determined by activation method, indicated a 1 Na+:1 taurine interaction, in contrast to the 3 Na+:1 taurine stoichiometry for BBMV taurine transport. Bromcresol green inhibited BBMV taurine transport but had no effect on BLMV taurine uptake. Efflux of taurine from BLMV was faster than that from BBMV. Unlike BBMV, the BLMV efflux was stimulated by external taurine. The observed characteristics of taurine transport on both membranes would integratively result in net transepithelial reabsorption of taurine across renal cells of the garter snake, a species that demonstrates both net reabsorption and secretion of taurine in vivo.

Revising regulatory networks: from expression data to linear causal models.

Discovering the complex regulatory networks that govern mRNA expression is an important but difficult problem. Many current approaches use only expression data from microarrays to infer the likely network structure. However, this ignores much existing knowledge because for a given organism and system under study, a biologist may already have a partial model of gene regulation. We propose a method for revising and improving these initial models, which may be incomplete or partially incorrect, with expression data. We demonstrate our approach by revising a model of photosynthesis regulation proposed by a biologist for Cyanobacteria. Applied to wild type expression data, our system suggested several modifications consistent with biological knowledge. Applied to a mutant strain, our system correctly modified the disabled gene. Power experiments with synthetic data that indicate that reliable revision is feasible even with a small number of samples.

Effect of total percent polyacrylamide in capillary gel electrophoresis for DNA sequencing of short fragments. A phenomenological model.

Polyacrylamide capillary gels were prepared with constant (5% C) cross-linker concentration and with total acrylamide concentration ranging from 2.5 to 6% T. At each acrylamide concentration, peak spacing was constant for DNA sequencing fragments ranging from 25 to 250 nucleotides in length. Peak spacing increased linearly with the total acrylamide concentration. The intercept of the retention time vs. fragment length plot was independent of % T. Ferguson plots were constructed for short DNA fragments; the polyacrylamide pore size falls in the 2.5 to 3.5 nm range for the gels studied. Theoretical plate count is independent of total acrylamide concentration; longitudinal diffusion, and not thermal gradients, limit the plate count. A phenomenological model is presented that predicts retention time, plate count, and resolution for sequencing fragments ranging in size from 25 to 250 bases and gels that range from 2.5 to 6% total acrylamide.