High resolution melting (HRM) analysis for the detection of ER22/23EK, BclI, and N363S polymorphisms of the glucocorticoid receptor gene

Polymorphisms in the glucocorticoid receptor (GR) gene have been associated with altered sensitivity to glucocorticoids. We designed a high-resolution melting (HRM) assay to detect, simultaneously, the three most intriguing GR polymorphisms, selected on the bases of clinical relevance and frequencies in caucasian population as described in literature. HRM enables the detection of ER22/23EK and N363S genotypes but fails to discriminate homozygous mutant for the BclI polymorphism from wild-type samples, however a simple spike experiment leads to a clear discrimination between these genotypes. The analyses were performed on a cohort of 70 healthy Caucasian subjects. The method was validated by restriction fragment length polymorphisms; HRM results were found to be in 100% concordance with those observed with the restriction enzymes. We also employed this method on a population of 40 Crohn Disease patients; the analysis demonstrated a significantly higher frequency of the BclI polymorphism in patients than in healthy volunteers.This is, at now, the less expensive and time-and work-saving method to detect GR mutations, providing precision, fast screening and high throughput capabilities.     

Partial monosomy 22 as result of an X/22 translocation in a newborn with DiGeorge syndrome

The case of a neonate with clinical symptoms of DiGeorge syndrome is reported. During pregnancy the measurements by ultrasonography revealed already a significant growth retardation of the fetus, for the first time obvious in the 20th week. The child died immediately after birth. A de novo translocation X/22 was observed with the translocation chromosome being late replicating in all mitoses analysed. The own observation is discussed regarding other cases with DiGeorge syndrome and taking the differential diagnoses into account. count.     

Increased prey vulnerability as a result of prey-prey interactions

This study examines indirect effects in a trophic system with three levels, consisting of two prey species, a top predator, and an intermediate predator. Qualitative data showed that the activity of both the top predator Aeshna juncea (Odonata) and the active prey Heterocope saliens, (Copepoda) caused bouts of swimming in the sedentary prey Sida crystallina (Cladocera). These swimming bouts caused encounters, reactions, attacks and captures of S. crystallina by the intermediate predator Coenagrion hastulatum (Odonata). Quantitative data showed that C. hastulatum had a higher encounter frequency and a higher attack frequency on the sedentary prey when the active prey was present. This result was an effect of encounters between the two prey which increased swimming activity of the sedentary S. crystallina. The results suggest that interactions between prey 1 and prey 2, and between prey and predators, could influence the structure of natural communities.     

Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status

Background

Expression of the oestrogen receptor (ER) in breast cancer predicts benefit from endocrine therapy. Minimising the frequency of false negative ER status classification is essential to identify all patients with ER positive breast cancers who should be offered endocrine therapies in order to improve clinical outcome. In routine oncological practice ER status is determined by semi-quantitative methods such as immunohistochemistry (IHC) or other immunoassays in which the ER expression level is compared to an empirical threshold[1], [2]. The clinical relevance of gene expression-based ER subtypes as compared to IHC-based determination has not been systematically evaluated. Here we attempt to reduce the frequency of false negative ER status classification using two gene expression approaches and compare these methods to IHC based ER status in terms of predictive and prognostic concordance with clinical outcome.

Methodology/Principal Findings

Firstly, ER status was discriminated by fitting the bimodal expression of ESR1 to a mixed Gaussian model. The discriminative power of ESR1 suggested bimodal expression as an efficient way to stratify breast cancer; therefore we identified a set of genes whose expression was both strongly bimodal, mimicking ESR expression status, and highly expressed in breast epithelial cell lines, to derive a 23-gene ER expression signature-based classifier. We assessed our classifiers in seven published breast cancer cohorts by comparing the gene expression-based ER status to IHC-based ER status as a predictor of clinical outcome in both untreated and tamoxifen treated cohorts. In untreated breast cancer cohorts, the 23 gene signature-based ER status provided significantly improved prognostic power compared to IHC-based ER status (P = 0.006). In tamoxifen-treated cohorts, the 23 gene ER expression signature predicted clinical outcome (HR = 2.20, P = 0.00035). These complementary ER signature-based strategies estimated that between 15.1% and 21.8% patients of IHC-based negative ER status would be classified with ER positive breast cancer.

Conclusion/Significance

Expression-based ER status classification may complement IHC to minimise false negative ER status classification and optimise patient stratification for endocrine therapies.     

Partial monosomy 22 as the result of an unbalanced translocation 5:22 in a patient with cri-du-chat syndrome

Summary Properdin factor B phenotypes were determined in 7 Bantu speaking Negroid populations, 1 Indian, and 1 Colored population of South Africa in a total of 1258 individuals. In the Negroid populations allele frequencies were: Bf^F 0.655, Bf^S 0.282, Bf^RARE 0.063, in the Indian population: Bf^F 0.322, Bf^S 0.645, Bf^RARE 0.033, and in the Colored population: Bf^F 0.513, Bf^S 0.435, Bf^RARE 0.052. In addition, 2 so far unknown F alleles and possibly 1 new S allele were discovered.     

Increased competition as a cost of specialization during the evolution of resource polymorphism

Identifying the factors that promote or preclude the evolution of resource polymorphism is essential for understanding the origins of diversity. Although such polymorphisms have long been viewed as an adaptive response to intraspecific competition, they are by no means ubiquitous, even in populations experiencing strong competition. In the present study, we examined a potentially important cost of resource polymorphism. Specifically, resource polymorphism typically entails the evolution of one or more resource‐use specialists, and these specialists may suffer more from competition with other specialists than generalists would with other generalists. Using spadefoot toad tadpoles as a model system, we combined stable isotope analyses with an experiment aiming to characterize dietary differences between alternative carnivore and omnivore morphs and to assess the potential ecological consequences of any such differences. We found that carnivores and omnivores represent alternative trophic specialists and generalists, respectively. We also established that the specialist morph (carnivores) experienced greater intramorph competition than the generalist morph (omnivores). We hypothesize that the greater intramorph competition faced by specialists stems ultimately from functional limitations associated with trophic specialization, which prevent specialists from switching to alternative resources when their resource is depleted. These costs may even preclude the evolution of distinct resource‐use specialists, and hence resource polymorphism, in certain populations. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Intra-individual polymorphism of human Y chromosome as a result of deletion in the heterochromatin region

Two equal cell populations with Y-heterochromatin of different lengths were found in a sterile male with azoospermia. There was no evidence for translocation of the heterochromatic material to other chromosomes. Both cell lines have the same Q-, C- and Ag-NOR patterns of chromosomal differential staining. The Y-chromosomes of both the father and brother were as long as the longest of the two populations in the proband. This intraindividual heteromorphism of Y-chromosome is, probably, a result of Y-heterochromatin deletion during the first mitotic division of the zygote, with the loss of a fragment as long as the difference between the long and the short Y populations in the proband. Intraindividual chromosomal heteromorphism is a convenient model to study reasons for variability in the heterochromatin regions of chromosomes.     

Decreases in yeast expression yields of the human adenosine A2a receptor are a result of translational or post-translational events

The human adenosine receptor (A2a), a G-protein-coupled receptor (GPCR), was C-terminally tagged with the green fluorescent protein (GFP) and expressed in the yeast Saccharomyces cerevisiae to gain an understanding of the expression limitations of this medically relevant class of membrane proteins. The A2a-GFP protein was able to bind adenosine analogs indicating that the GFP tag did not alter the ligand binding activity of the receptor. A screen based on whole cell fluorescence was developed and a library of clones with various gene copy numbers was screened via flow cytometry to isolate clones with the highest protein expression levels. All clones studied exhibited a decrease in the net A2a-GFP protein production rate over time as determined by whole cell fluorescence, Western blotting, confocal microscopy, and ligand binding. Quantitative PCR showed that A2a-GFP mRNA levels remained relatively high even as the protein production rate decreased. A cycloheximide chase experiment showed that the mature protein was stable over time and was not significantly degraded. Taken together, these results suggest that heterologous expression of GPCRs is limited by a translational or post-translational bottleneck that is unique from expression limitations seen for soluble proteins.     

Sense-overlapping lncRNA as a decoy of translational repressor protein for dimorphic gene expression

Long noncoding RNAs (lncRNAs) are vastly transcribed and extensively studied but lncRNAs overlapping with the sense orientation of mRNA have been poorly studied. We analyzed the lncRNA DAPALR overlapping with the 5´ UTR of the Doublesex1 (Dsx1), the male determining gene in Daphnia magna. By affinity purification, we identified an RNA binding protein, Shep as a DAPALR binding protein. Shep also binds to Dsx1 5´ UTR by recognizing the overlapping sequence and suppresses translation of the mRNA. In vitro and in vivo analyses indicated that DAPALR increased Dsx1 translation efficiency by sequestration of Shep. This regulation was impaired when the Shep binding site in DAPALR was deleted. These results suggest that Shep suppresses the unintentional translation of Dsx1 by setting a threshold; and when the sense lncRNA DAPALR is expressed, DAPALR cancels the suppression caused by Shep. This mechanism may be important to show dimorphic gene expressions such as sex determination and it may account for the binary expression in various developmental processes.     

Astrocytes as antigen-presenting cells: expression of IL-12/IL-23

Interleukin-12 (IL-12, p70) a heterodimeric cytokine of p40 and p35 subunits, important for Th1-type immune responses, has been attributed a prominent role in multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE). Recently, the related heterodimeric cytokine, IL-23, composed of the same p40 subunit as IL-12 and a unique p19 subunit, was shown to be involved in Th1 responses and EAE. We investigated whether astrocytes and microglia, CNS cells with antigen-presenting cell (APC) function can present antigen to myelin basic protein (MBP)-reactive T cells, and whether this presentation is blocked with antibodies against IL-12/IL-23p40. Interferon (IFN)-gamma-treated APC induced proliferation of MBP-reactive T cells. Anti-IL-12/IL-23p40 antibodies blocked this proliferation. These results support and extend our previous observation that astrocytes and microglia produce IL-12/IL-23p40. Moreover, we show that stimulated astrocytes and microglia produce biologically active IL-12p70. Because IL-12 and IL-23 share p40, we wanted to determine whether astrocytes also express IL-12p35 and IL-23p19, as microglia were already shown to express them. Astrocytes expressed IL-12p35 mRNA constitutively, and IL-23 p19 after stimulation. Thus, astrocytes, under inflammatory conditions, express all subunits of IL-12/IL-23. Their ability to present antigen to encephalitogenic T cells can be blocked by neutralizing anti-IL-12/IL-23p40 antibodies.     

Nucleolar retention of a translational C/EBPα isoform stimulates rDNA transcription and cell size

The messenger RNA of the intronless CEBPA gene is translated into distinct protein isoforms through the usage of consecutive translation initiation sites. These translational isoforms have distinct functions in the regulation of differentiation and proliferation due to the presence of different N‐terminal sequences. Here, we describe the function of an N‐terminally extended protein isoform of CCAAT enhancer‐binding protein α (C/EBPα) that is translated from an alternative non‐AUG initiation codon. We show that a basic amino‐acid motif within its N‐terminus is required for nucleolar retention and for interaction with nucleophosmin (NPM). In the nucleoli, extended‐C/EBPα occupies the ribosomal DNA (rDNA) promoter and associates with the Pol I‐specific factors u pstream‐b inding f actor 1 (UBF‐1) and SL1 to stimulate rRNA synthesis. Furthermore, during differentiation of HL‐60 cells, endogenous expression of extended‐C/EBPα is lost concomitantly with nucleolar C/EBPα immunostaining probably reflecting the reduced requirement for ribosome biogenesis in differentiated cells. Finally, overexpression of extended‐C/EBPα induces an increase in cell size. Altogether, our results suggest that control of rRNA synthesis is a novel function of C/EBPα adding to its role as key regulator of cell growth and proliferation.     

Modulation of the expression of ryanodine receptor mRNA from Plutella xylostella as a result of diamide insecticide application

Ryanodine receptors (RyRs), members of the largest family of calcium channel proteins, have been studied because of their key roles in calcium signalling within cells. With the development of diamide insecticides that exhibit a novel mode of action on the RyRs from Lepidoptera, research on insect RyRs has become more attractive in the field of plant protection. To enhance our understanding of the effects of diamides on RyRs, we cloned the Plutella xylostella RyR gene (Px-RyR), which is the most serious pest of Brassicaceae plants throughout the world. Furthermore, we investigated the modulation of the expression of Px-RyR as a result of the application of diamide insecticides. The full-length cDNAs of Px-RyR contain an open reading frame (ORF) of 15,372 bp with a predicted protein consisting of 5123 amino acids. Px-RyR possesses a high level of overall amino acid homology with other isoforms (77–92% identity with insect isoforms and 45–47% identity with vertebrate isoforms). The weight of Px. gradually decreased as the concentration of the diamides increased. However, the relative expression levels of the RyRs from larvae were dependent on the insecticide concentration and gradually increased with increasing insecticide concentrations.     

Increased rates of sugar transport in Saccharomyces cerevisiae a result of sugar metabolism

Preincubation of yeast cells with glucose or other metabolic energy sources increased the rate of sorbose efflux 2- or 3-fold. Stimulated rates persisted for several h, decreasing slowly. They were approximately halved by including K_m concentrations of highly competitive sugars such as deoxyglucose, glucose, fructose and mannose in sorbose efflux suspensions, and were greatly slowed at reduced temperatures. Inhibitors of energy metabolism blocked the rate stimulation, as did cycloheximide; added nitrogen sources increased the rate additionally. The rate of sorbose uptake was also increased, whereas that of dimethylsulfoxide, which enters the cell by simple diffusion, was not changed. Transport of arabinose and fucose also occurred at increased rates. The data indicate a change in the sorbose transport system rather than in membrane permeability. The change, apparently the synthesis of a transport system component, requires metabolic energy and involves protein synthesis.