TCRJ and BCRJ gene segments contain 5′ D-segment sequences that contribute to repertoire diversity

T cell receptor (TCR) and B cell receptors (BCR) junctions, also known as the CDR3, are where the V, D, and J gene segments converge, coding for a loop structure important for contacting ligands. J segments contribute to the formation of the CDR3 loop through their 5′ ends that vary in length and show high sequence variability. The 5′ ends of J segments of TCRα genes show nucleotide sequence similarities to TCRDδ segments as high as 89% and show a preponderance of murine TCRDδ2 or human TCRDδ3 amino acid sequence similarities. Surprisingly, most of the 5′ ends of TCRJγ segments show nucleotide and amino acid sequence similarities with TCRDβ segments. All murine and human BCRJH segments and most TCRJδ segments contain amino acid sequences at their 5′ ends that resemble their own D segments, a finding that is not seen with TCRJβ segments. TCRα and TCRγ genes thus make up for their lack of separate D segments with distinct D-like segments that are built into the 5′ ends of their J segments. Additionally, in some cases, TCR and BCR genes that utilize separate D segments also receive additional D-like contributions though the 5′ ends of their J segments to add additional diversity to their CDR3 loops.     

Anticipation in myotonic dystrophy: new light on an old problem.

The concept of anticipation, the occurrence of a genetic disorder at progressively earlier ages in successive generations, has been debated from the early years of this century, with myotonic dystrophy as the most striking example. Throughout most of this period there has been controversy as to whether the phenomenon resulted from observational and ascertainment biases or reflected a more fundamental mechanism. The recent discovery of inherited unstable DNA sequences, first in fragile-X mental retardation and now in myotonic dystrophy, not only confirms that anticipation indeed has a true biological basis but provides a specific molecular mechanism for it; this discovery can explain many of the puzzling anomalies in the inheritance of myotonic dystrophy and may prove relevant to comparable problems in other genetic disorders.     

Analytical validation of a prognostic prostate cancer gene expression assay using formalin fixed paraffin embedded tissue

Background

There is a clear need for assays that can predict the risk of metastatic prostate cancer following curative procedures. Importantly these assays must be analytically robust in order to provide quality data for important clinical decisions. DNA microarray based gene expression assays measure several analytes simultaneously and can present specific challenges to analytical validation. This study describes the analytical validation of one such assay designed to predict metastatic recurrence in prostate cancer using primary formalin fixed paraffin embedded tumour material.

Methods

Accuracy was evaluated with a method comparison study between the assay development platform (Prostate Disease Specific Array) and an alternative platform (Xcel? microarray) using 50 formalin-fixed, paraffin-embedded prostate cancer patient samples. An additional 70 samples were used to establish the assay reportable range. Determination of assay precision and sensitivity was performed on multiple technical replicates of three prostate cancer samples across multiple variables (operators, days, runs, reagent lots, and equipment) and RNA/cDNA inputs respectively using the appropriate linear mixed model.

Results

The overall agreement between the development and alternative platform was 94.7% (95% confidence interval, 86.9–98.5%). The reportable range was determined to be 0.150 to 1.107 for core needle biopsy samples and???0.214 to 0.844 for radical prostatectomy samples. From the precision study, the standard deviations for assay repeatability and reproducibility were 0.032 and 0.040 respectively. The sensitivity study demonstrated that a total RNA input and cDNA input of 50?ng and 3.5?μg respectively was conservative.

Conclusion

The Metastatic Assay was found to be highly reproducible and precise. In conclusion the studies demonstrated an acceptable analytical performance for the assay and support its potential use in the clinic.

     

Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids

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Electroantennogram measurements of atmospheric pheromone concentration after aerial and ground application of gypsy moth mating disruptants

Abstract:  A portable electroantennogram (EAG) sensor was used to measure relative atmospheric pheromone concentration in forest plots treated with aerial and ground applications of gypsy moth, Lymantria dispar (L.) (Lep., Lymantriidae), mating-disruption formulations. Five treatments (Disrupt II flakes with sticker, Disrupt II flakes without sticker, Disrupt II flakes in a sticker slurry, microcapsules and hand-applied Luretape), all applied at 75 g active ingredient per hectare and an untreated control were evaluated. Gypsy moth male catch in pheromone-baited traps and fertilization of deployed females were suppressed in all treatments, and no females deployed in treated plots produced more than 5% fertile eggs. Relative pheromone concentrations were significantly higher in the two treatments in which flakes were aerially applied with sticker and in the microcapsule treatment. Pheromone concentration measurements in the flakes without sticker and hand-applied treatments were not significantly different from those in the control. Mating success was negatively correlated with relative pheromone concentration. The ability of the EAG to detect differences in pheromone concentration that are correlated with mating success suggests that this could be a useful method for predicting the effectiveness of mating-disruption treatments.     

Radiation-induced Release of Transforming Growth Factor α Activates the Epidermal Growth Factor Receptor and Mitogen-activated Protein Kinase Pathway in Carcinoma Cells, Leading to Increased Proliferation and Protection from Radiation-induced Cell Death

Exposure of A431 squamous and MDA-MB-231 mammary carcinoma cells to ionizing radiation has been associated with short transient increases in epidermal growth factor receptor (EGFR) tyrosine phosphorylation and activation of the mitogen-activated protein kinase (MAPK) and c-Jun NH(2)-terminal kinase (JNK) pathways. Irradiation (2 Gy) of A431 and MDA-MB-231 cells caused immediate primary activations (0-10 min) of the EGFR and the MAPK and JNK pathways, which were surprisingly followed by later prolonged secondary activations (90-240 min). Primary and secondary activation of the EGFR was abolished by molecular inhibition of EGFR function. The primary and secondary activation of the MAPK pathway was abolished by molecular inhibition of either EGFR or Ras function. In contrast, molecular inhibition of EGFR function abolished the secondary but not the primary activation of the JNK pathway. Inhibition of tumor necrosis factor alpha receptor function by use of neutralizing monoclonal antibodies blunted primary activation of the JNK pathway. Addition of a neutralizing monoclonal antibody versus transforming growth factor alpha (TGFalpha) had no effect on the primary activation of either the EGFR or the MAPK and JNK pathways after irradiation but abolished the secondary activation of EGFR, MAPK, and JNK. Irradiation of cells increased pro-TGFalpha cleavage 120-180 min after exposure. In agreement with radiation-induced release of a soluble factor, activation of the EGFR and the MAPK and JNK pathways could be induced in nonirradiated cells by the transfer of media from irradiated cells 120 min after irradiation. The ability of the transferred media to cause MAPK and JNK activation was blocked when media were incubated with a neutralizing antibody to TGFalpha. Thus radiation causes primary and secondary activation of the EGFR and the MAPK and JNK pathways in autocrine-regulated carcinoma cells. Secondary activation of the EGFR and the MAPK and JNK pathways is dependent on radiation-induced cleavage and autocrine action of TGFalpha. Neutralization of TGFalpha function by an anti-TGFalpha antibody or inhibition of MAPK function by MEK1/2 inhibitors (PD98059 and U0126) radiosensitized A431 and MDA-MB-231 cells after irradiation in apoptosis, 3-[4, 5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT), and clonogenic assays. These data demonstrate that disruption of the TGFalpha-EGFR-MAPK signaling module represents a strategy to decrease carcinoma cell growth and survival after irradiation.     

Chromate and selenate hydrocalumite solid solutions and their applications in waste treatment

Hydrocalumite, a calcium aluminate hydrate phase, consists of positively-charged structure units, and is therefore an ideal candidate for accommodating anionic contaminants. In this study, a series of batch experiments was carried out to examine the uptake of chromate and selenate by hydrocalumite. To determine the uptake capacity and long-term stability, hydro-calumite solid solutions between chromate/selenate and hydroxyl were synthesized over a reaction time of more than one year. At a ratio of water to initial solids added (CaAl2O4+CaO) of 75 : 1, the maximum uptake capacities were over 77 and 114 g/kg for Cr and Se, respectively. These values are very close to the theoretical uptake capacities of chromate and selenate hydrocalumite end-members (81 and 118 g/kg, respectively). The oxyanion removal efficiency from solution was above 95%. Due to the high uptake capacity and anion removal efficiency of hy-drocalumites, their application in wastewater treatment is promising. Hydrocalumites are also impor     

Vegetative Community Compositional Gradients of Tropical Hardwood Hammocks along the Florida Keys

Tropical hardwood hammocks, among the rarest and most threatened vegetative communities in the United States, occur throughout the 225-km Florida Keys archipelago as it extends toward the Caribbean from the southeast tip of peninsular Florida. Compounding their critical conservation status, tropical hardwood hammocks and the dynamics that support their peculiar species diversity in the region are poorly understood. The goal of this study was to explore the dynamics of the species compositional gradient of the hammocks along the Florida Keys, and to identify significant ecological units within the gradient. The primary data for this research were assembled from the Institute for Regional Conservation's floristic database of South Florida. We were able to extract presence/absence data for 295 species from comprehensive surveys of 23 study sites. Nonmetric multidimensional scaling was used to deconstruct the compositional trends into a reduced ordination space. Cluster analysis was subsequently used to identify discrete ecological units. Additionally, we used vector fitting to interpret the significant correlated ancillary variables. Our main results were three well-fitted nonmetric multidimensional scaling axes with three nonoverlapping ecological units. Of the ancillary variables, latitude, longitude, percent composition from biogeographical regions, richness, and area were correlated to the nonmetric multidimensional scaling results. These results increase our understanding of the community structure of the hammocks along the Florida Keys, and can contribute to increasing our ability to adequately protect and restore tropical hardwood hammocks and other similar tropical dry forest communities throughout the Caribbean.