MMpred: functional miRNA – mRNA interaction analyses by miRNA expression prediction

Background: MicroRNA (miRNA) directed gene repression is an important mechanism of posttranscriptional regulation. Comprehensive analyses of how microRNA influence biological processes requires paired miRNA-mRNA expression datasets. However, a review of both GEO and ArrayExpress repositories revealed few such datasets, which was in stark contrast to the large number of messenger RNA (mRNA) only datasets. It is of interest that numerous primary miRNAs (precursors of microRNA) are known to be co-expressed with coding genes (host genes). Results: We developed a miRNA-mRNA interaction analyses pipeline. The proposed solution is based on two miRNA expression prediction methods – a scaling function and a linear model. Additionally, miRNA-mRNA anticorrelation analyses are used to determine the most probable miRNA gene targets (i.e. the differentially expressed genes under the influence of up- or down-regulated microRNA). Both the consistency and accuracy of the prediction method is ensured by the application of stringent statistical methods. Finally, the predicted targets are subjected to functional enrichment analyses including GO, KEGG and DO, to better understand the predicted interactions. Conclusions: The MMpred pipeline requires only mRNA expression data as input and is independent of third party miRNA target prediction methods. The method passed extensive numerical validation based on the binding energy between the mature miRNA and 3’ UTR region of the target gene. We report that MMpred is capable of generating results similar to that obtained using paired datasets. For the reported test cases we generated consistent output and predicted biological relationships that will help formulate further testable hypotheses

A Genetic Locus Regulates the Expression of Tissue-Specific mRNAs from Multiple Transcription Units

129 GIX- mice, unlike animals of the congeneic partner strain GIX+, do not express significant amounts of the retroviral antigens gp70 and p30. Evidence is presented indicating that the GIX phenotype is specified by a distinct regulatory gene acting on multiple transcription units to control the levels of accumulation of specific mRNA species. The steady-state levels of retroviral-homologous mRNA from the tissues of GIX+ and GIX- mice were examined by blot hybridization using as probes DNA fragments from cloned murine leukemia viruses. RNA potentially encoding viral antigens was reduced or absent in GIX- mice, even though no differences in integrated viral genomes were detected between these congeneic strains by DNA blotting. Tissue-specific patterns of accumulation of these RNA species were detected in brain, epididymis, liver, spleen, and thymus, and several distinct RNA species were found to be coordinately regulated with the GIX phenotype. Measurements of RNA synthesis suggest a major role for transcriptional control in the regulation of some retroviral messages

The Syntactic and Semantic Atoms of the Spray/load Alternation

What is the relationship between the word spray in the sentence John sprayed the paint onto the wall and its identically pronounced counterpart in John sprayed the wall with the paint? At some level, we recognize these two uses of spray as the same word. But the fact that they combine with their arguments in different ways means they cannot be identical. The relationship between these two uses of spray—called the spray/load alternation—is productive in a way that a descriptively adequate grammar of English should capture. Other verbs show the same pattern, adults and children extend it to novel verbs, and children learning English overextend the pattern to non-alternating verbs. For these and other reasons, precisely how to describe and explain the spray/load alternation has been well-studied.I discuss two kinds of novel evidence that bear on the correct analysis of the spray/load alternation. First, I wield the adverb again as a diagnostic of the syntactic and semantic decomposition of spray/load verbs, which reveals a syntactic bracketing paradox. Second, I dive deep into hitherto little explored facts that reveal striking asymmetries between the two kinds of objects of spray/load verbs. Goal objects are subject to restrictions on movement and nominalization that theme objects are not.To account for these data, I propose an analysis that makes two theoretical contributions. First, the bracketing paradox revealed by again can be neatly resolved by a theory of syntax that allows multidominance. Second, the asymmetries between theme and goal objects suggests goal objects are derived in English by the conflation of a phonologically null preposition with the verb root, which reduces the asymmetries to facts about the syntax of prepositions.Finally, I compare my analysis to others empirically and theoretically. Empirically, my analysis loses no significant ground to others\u27 and has the advantage of accounting for the novel evidence discussed above. Theoretically, my approach requires only a simple and independently motivated syntax and semantics; my analysis\u27 compatibility with this architectural simplicity constitutes an explanatory advantage compared to accounts that require more theoretical machinery to achieve similar or lesser levels of descriptive adequacy

In vitro effect of canine hyperimmune sera on TNFa activity

[Introduction]: Septic shock in dogs is caused by cardiovascular and vasomotor failure associated with an uncontrolled intrinsic release of inflammatory mediators [1–5]. The syndrome is characterized by cardiovascular dysfunction, vascular permeability alterations, pulmonary oedema and tissue hypoxia resulting from microthrombi which may culminate in disseminated intravascular coagulation and catastrophic multiple organ failure [6,7]. Systemic bacterial infection, particularly by Gram-negative enterobacteria, haemorrhagic trauma, gastric dilation/volvulus and pancreatitis are the major underlying causes leading tosepsis [8,9]. Because of haemodynamic instability and associated hypovolemia, fluid replacement therapy is generally applied to restore effective circulating volume. The use of fresh frozen plasma has been recommended in cases of coagulopathies as it has been recognized to assist restoration of haemodynamic stability [1,5,10,11]. There is increasing evidence that the drivers of the haemodynamic instability are inflammatory mediators (particularly TNFa) activated primarily by bacterial endotoxin [3,4,12,13]

ASSESSING THE EFFECT OF ECR ON FINANCIAL AND OPERATING PERFORMANCE

A debate has emerged in the literature and trade press whether the adoption of Efficient Consumer Response (ECR), the supply chain management initiatives for the food industry, leads to improved inventory and financial performance. Using regression analysis, the financial performance for adopters of ECR is about 3 to 4% higher than for non-adopters. However, the growth in profit does not appear to come from improved performance for traditional inventory measures (such as inventory turnover, inventory-to-sales, or inventory-to-assets). The driving force behind these improved financial measures can be attributed to changes leading to a shorter cash conversion cycle. In addition, size matters; ECR is more effective due to economies of scale, information technology, and buying power.Industrial Organization,

Non-Equilibrium Properties from Equilibrium Free Energy Calculations

Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments

Pesticides Registered for Mosquito Control in South Dakota

Pesticides alone will not eliminate all mosquitoes. The use of pesticides to control mosquitoes around the home and yard must be part of a multifaceted approach that includes the following non-chemical tactics: • Eliminate standing water. • Fix broken window screens. • Use outdoor bug lights. • Installing carbon dioxide-baited traps. Some mosquitoes will always “get through.” If you will be outdoors, it is recommended that you wear a mosquito repellent of your choice, avoid being outdoors around sunset and sunrise, and cover as much skin as possible with appropriate clothing. For more information on selection and use of insect repellents, refer to FS 920 Personal Mosquito Repellents available at your local Extension office or online at http://sdces.sdstate.edu/westnile/publications.htm. This publication lists the most common insecticides that are registered in South Dakota for use around the house and yard. The products are arranged by the active ingredient. The active ingredient is usually listed prominently in the first section of the label. This section will list the chemical name and/or the common name of the pesticide and also the concentration. This list was current as of June 2004, but label uses and registrations change. Before using any pesticide, be sure to read the entire label to ensure that the product can be used for mosquitoes, can be applied around the home and yard, and to be sure all safety restrictions are followed. For more information, refer to FS 923 Controlling Mosquitoes Around the Home and Yard