Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity.

even-skipped is a homeobox gene important in controlling segment patterning in the embryonic fruit fly. Its homeobox encodes a DNA binding domain which binds with similar affinities to two DNA consensus sequences, one AT-rich, the other GC-rich. We describe a crystallographic analysis of the Even-skipped homeodomain complexed to an AT-rich oligonucleotide at 2.0 A resolution. The structure reveals a novel arrangement of two homeodomains bound to one 10 bp DNA sequence in a tandem fashion. This arrangement suggests a mechanism for the homeoproteins' regulatory specificity. In addition, the functionally important residue Gln50 is observed in multiple conformations making direct and water-mediated hydrogen bonds with the DNA bases.     

Disease-associated pathophysiologic structures in pediatric rheumatic diseases show characteristics of scale-free networks seen in physiologic systems: implications for pathogenesis and treatment

Background

Tamoxifen (TAM) is a well characterized breast cancer drug and selective estrogen receptor modulator (SERM) which also has been associated with a small increase in risk for uterine cancers. TAM's partial agonist activation of estrogen receptor has been characterized for specific gene promoters but not at the genomic level in vivo.Furthermore, reducing uncertainties associated with cross-species extrapolations of pharmaco- and toxicogenomic data remains a formidable challenge.

Results

A comparative ligand and species analysis approach was conducted to systematically assess the physiological, morphological and uterine gene expression alterations elicited across time by TAM and ethynylestradiol (EE) in immature ovariectomized Sprague-Dawley rats and C57BL/6 mice. Differential gene expression was evaluated using custom cDNA microarrays, and the data was compared to identify conserved and divergent responses. 902 genes were differentially regulated in all four studies, 398 of which exhibit identical temporal expression patterns.

Conclusion

Comparative analysis of EE and TAM differentially expressed gene lists suggest TAM regulates no unique uterine genes that are conserved in the rat and mouse. This demonstrates that the partial agonist activities of TAM extend to molecular targets in regulating only a subset of EE-responsive genes. Ligand-conserved, species-divergent expression of carbonic anhydrase 2 was observed in the microarray data and confirmed by real time PCR. The identification of comparable temporal phenotypic responses linked to related gene expression profiles demonstrates that systematic comparative genomic assessments can elucidate important conserved and divergent mechanisms in rodent estrogen signalling during uterine proliferation.     

One dimensional approximations of neuronal dynamics reveal computational strategy

The relationship between neuronal activity and computations embodied by it remains an open question. We develop a novel methodology that condenses observed neuronal activity into a quantitatively accurate, simple, and interpretable model and validate it on diverse systems and scales from single neurons in C. elegans to fMRI in humans. The model treats neuronal activity as collections of interlocking 1-dimensional trajectories. Despite their simplicity, these models accurately predict future neuronal activity and future decisions made by human participants. Moreover, the structure formed by interconnected trajectories—a scaffold—is closely related to the computational strategy of the system. We use these scaffolds to compare the computational strategy of primates and artificial systems trained on the same task to identify specific conditions under which the artificial agent learns the same strategy as the primate. The computational strategy extracted using our methodology predicts specific errors on novel stimuli. These results show that our methodology is a powerful tool for studying the relationship between computation and neuronal activity across diverse systems.     

Locus minimization in breed prediction using artificial neural network approach

Molecular markers, viz. microsatellites and single nucleotide polymorphisms, have revolutionized breed identification through the use of small samples of biological tissue or germplasm, such as blood, carcass samples, embryos, ova and semen, that show no evident phenotype. Classical tools of molecular data analysis for breed identification have limitations, such as the unavailability of referral breed data, causing increased cost of collection each time, compromised computational accuracy and complexity of the methodology used. We report here the successful use of an artificial neural network (ANN) in background to decrease the cost of genotyping by locus minimization. The webserver is freely accessible ( http://nabg.iasri.res.in/bisgoat ) to the research community. We demonstrate that the machine learning (ANN) approach for breed identification is capable of multifold advantages such as locus minimization, leading to a drastic reduction in cost, and web availability of reference breed data, alleviating the need for repeated genotyping each time one investigates the identity of an unknown breed. To develop this model web implementation based on ANN, we used 51 850 samples of allelic data of microsatellite‐marker‐based DNA fingerprinting on 25 loci covering 22 registered goat breeds of India for training. Minimizing loci to up to nine loci through the use of a multilayer perceptron model, we achieved 96.63% training accuracy. This server can be an indispensable tool for identification of existing breeds and new synthetic commercial breeds, leading to protection of intellectual property in case of sovereignty and bio‐piracy disputes. This server can be widely used as a model for cost reduction by locus minimization for various other flora and fauna in terms of variety, breed and/or line identification, especially in conservation and improvement programs.     

Tumor necrosis factors alpha and beta differ in their capacities to generate interleukin 1 release from human endothelial cells

The capacity of the tumor necrosis factors, TNF-alpha and TNF-beta, products of activated macrophages and lymphocytes, respectively, to stimulate interleukin 1 (IL-1) release from endothelial cells derived from human umbilical veins was examined in vitro. Recombinant TNF-alpha caused IL-1 release by 4 hr with maximal levels of 17 U/ml by 24 hr; half-maximal stimulation occurred at approximately 80 pM. In contrast, recombinant TNF-beta was a relatively poor stimulus for IL-1 release. Even at concentrations as high as 600 pM, only 3 U of IL-1/ml were recovered; maximal IL-1 release (10 to 12 U/ml) required up to 5 nM TNF-beta. Natural, glycosated human TNF-beta was comparable in activity to recombinant TNF-beta. TNF-beta did not directly inhibit the IL-1 comitogenesis assay, nor was there evidence that TNF-beta induced the release of an IL-1 inhibitor, in that supernatants generated in the presence of TNF-beta did not inhibit thymocyte proliferation to a recombinant IL-1 standard. Binding of the recombinant TNF to endothelial monolayers was assessed by using [125I]TNF-alpha in competition studies with cold TNF-alpha and TNF-beta. Binding of TNF-alpha was half-maximal at 80 pM with an average of 664 receptors/cell and Kd = 0.043 nM. Although TNF-beta was capable of fully competing for [125I]TNF-alpha binding, half-maximal binding occurred at 800 pM TNF-beta. These data suggest that the TNF receptors on human endothelial cells may reflect the structural differences between these two homologous cytokines.     

Impact of Endobronchial Ultrasound (EBUS) Training on the Diagnostic Yield of Conventional Transbronchial Needle Aspiration for Lymph Node Stations 4R and 7

BackgroundThere is sparse literature on whether training in endobronchial ultrasound (EBUS)-guided transbronchial needle aspiration (TBNA) improves the diagnostic yield of conventional TBNA (cTBNA).ObjectivesThe aim of this study was to evaluate the diagnostic yield of cTBNA before and after the introduction of EBUS.MethodsThis was a retrospective analysis of patients who underwent cTBNA at our center. The study was divided into two periods, before and after the introduction of EBUS at our facility. The diagnostic yield of cTBNA was compared between the study periods. Rapid on-site cytological examination was not available.ResultsA total of 1,050 patients (61.6% men; mean age 45.6 years) underwent cTBNA during the study period (849 before EBUS; 201 after EBUS). Sarcoidosis (n = 527) followed by bronchogenic carcinoma (n = 222) formed the most common indications for performing cTBNA. There was a significant increase in both the success of obtaining a representative sample (from 71% to 85%), and the diagnostic yield (from 33% to 49.5%) of cTBNA, after the introduction of EBUS. The increase in the diagnostic yield of cTBNA after introduction of EBUS remained significant even after adjusting for years of performing cTBNA and the type of anesthesia (topical vs. sedation and topical) on a multivariate analysis.ConclusionThe diagnostic yield of cTBNA at our facility increased after the introduction of EBUS-TBNA. However, given the retrospective nature of the study, prospective studies are required to confirm our findings.     

Human interleukin 1 is a cytocidal factor for several tumor cell lines

Highly purified interleukin 1 (IL 1) obtained from stimulated human monocytes appeared to be growth inhibitory and cytocidal for a human melanoma cell line, A375. Although IL 1 did not have an immediate cytolytic effect, with time in culture the growth of the target cells was irreversibly inhibited. The cells eventually lysed and decreased markedly in number; the IL 1 effect can therefore be said to be cytocidal. IL 1 activity could not be separated from the cytocidal activity by a variety of chromatography procedures by using conventional and high-performance liquid chromatography (HPLC). The A375 melanoma cell line was also sensitive to another human cytokine alpha-lymphotoxin (alpha-LT) derived from a human B cell line. IL 1 also appeared to be partially growth inhibitory and cytocidal for a LT-sensitive mouse fibroblast cell line, L929; but not for LT-resistant cells, including a subline of L929; a human epithelial carcinoma cell line, HeLa; a human osteosarcoma cell line, HOS; and a mouse SV40-transformed kidney cell line, TU5. However, the LT-sensitive mouse fibroblast cell line, L-M, was resistant to IL 1. Therefore, the cytocidal activity of IL 1 only partially overlapped the target cell selectivity of alpha-LT. Although natural IFN-alpha and recombinant IFN-beta were appreciably growth inhibitory for the A375 cell line, natural and recombinant IFN-alpha and recombinant IFN-beta and IFN-gamma exhibited little cytocidal activity. Purified IL 1 did not have any antiviral activity, and conversely, IFN and alpha-LT were not co-mitogenic for thymocytes. Furthermore, by ELISA and radioimmunoassays, antibodies against human alpha-LT, tumor necrosis factor, and IFN-gamma did not react with IL 1, indicating that IL 1 is antigenically distinct from these other cytokines. These in vitro results suggest that IL 1 may play a role in host defense against some tumors as a cytocidal factor.