Evolutionary modelling of feed forward loops in gene regulatory networks

Feed forward loops (FFLs) are gene regulatory network motifs. They exist in different types, defined by the signs of the effects of genes in the motif on one another. We examine 36 feed forward loops in Escherichia coli, using evolutionary simulations to predict the forms of FFL expected to evolve to generate the pattern of expression of the output gene. These predictions are tested using likelihood ratios, comparing likelihoods of the observed FFL structures with their likelihoods under null models. The very high likelihood ratios generated, of over 10(11), suggest that evolutionary simulation is a valuable component in the explanation of FFL structure.     

MicroRNA-regulated feed forward loop network

Comment on: Cohen EE, et al. A feed-forward loop involving protein kinase Calpha and microRNAs regulates tumor cell cycle. Cancer Res 2009; 69:65-74.     

Sentence alignment using feed forward neural network

Parallel corpora have become an essential resource for work in multi lingual natural language processing. However, sentence aligned parallel corpora are more efficient than non-aligned parallel corpora for cross language information retrieval and machine translation applications. In this paper, we present a new approach to align sentences in bilingual parallel corpora based on feed forward neural network classifier. A feature parameter vector is extracted from the text pair under consideration. This vector contains text features such as length, punctuate score, and cognate score values. A set of manually prepared training data has been assigned to train the feed forward neural network. Another set of data was used for testing. Using this new approach, we could achieve an error reduction of 60% over length based approach when applied on English-Arabic parallel documents. Moreover this new approach is valid for any language pair and it is quite flexible approach since the feature parameter vector may contain more/less or different features than that we used in our system such as lexical match feature.     

Perception of left and right by a feed forward net

In studying the ability of feed forward networks to perform perceptual tasks, we train a network to master a specific task, that of deciding whether a given object is to the left or to the right of another object. We discuss in general terms such issues as architecture, drilling, generalization, abstraction, learning from small examples, and versatility.     

Specialized conservation of surface loops of myosin: evidence that loops are involved in determining functional characteristics

The molecular motor myosin has been the focus of considerable structure-function analysis. Of key interest are the portions of the protein that control the rate of ATP hydrolysis, the affinity for actin, and the velocity at which myosin moves actin. Two regions that have been implicated in determining these parameters are the "loop" regions at the junctions of the 25 kDa and 50 kDa domains and the 50 kDa and 20 kDa domains of the protein. However, the sequences of these regions are poorly conserved between different myosin families, suggesting that they are not constrained evolutionarily, and thus are relatively unimportant for myosin function. In order to address this apparent incongruity, we have performed an analysis of relative rates of observed evolutionary change. We found that the sequences of these loop regions appear to be actually more constrained than the sequences of the rest of the myosin molecule, when myosins are compared that are known to be kinetically or developmentally similar. This suggests that these loop regions could play an important role in myosin function and supports the idea that they are involved in modulating the specific kinetic characteristics that functionally differentiate one myosin isoform from another. Apparently "unconserved" loops may generally play a role in determining kinetic properties of enzymes, and similar analyses of relative rates of evolution may prove useful for the study of structure-function relationships in other protein families.     

Noise characteristics of a plasma relativistic microwave amplifier

Reasons for the occurrence of microwave noise at the output of a plasma relativistic amplifier have been analyzed. It is found that, in the absence of an input signal, the emission spectrum of the plasma relativistic microwave amplifier is similar to that of an electron beam in vacuum. It is concluded that microwave noise at the output of the amplifier appears as a result of amplification of the intrinsic noise of the electron beam. The emission characteristics of a relativistic electron beam formed in a magnetically insulated diode with an explosive emission cathode in vacuum have been studied experimentally for the first time. An important point is that, in this case, there is no virtual cathode in the drift space.     

Natively unstructured loops differ from other loops

Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions) differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%–70% of all worm proteins observed to have more than seven protein–protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested that long unstructured loops are a major part of unstructured regions in molecular networks.     

Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops.

Thermodynamic parameters for internal loops of unpaired adenosines in oligoribonucleotides have been measured by optical melting studies. Comparisons are made between helices containing symmetric and asymmetric loops. Asymmetric loops destabilize a helix more than symmetric loops. The differences in free energy between symmetric and asymmetric loops are roughly half the magnitude suggested from a study of parameters required to give accurate predictions of RNA secondary structure [Papanicolaou, C., Gouy, M., & Ninio, J. (1984) Nucleic Acids Res. 12, 31-44]. Circular dichroism spectra indicate no major structural difference between helices containing symmetric and asymmetric loops. The measured sequence dependence of internal loop stability is not consistent with approximations used in current algorithms for predicting RNA secondary structure.     

Bovine serum albumin-hemoglobin fractionation: significance of ultrafiltration system and feed solution characteristics

This work investigates the fractionation of similar molecular weight proteins bovine serum albumin (69 kD) and bovine hemoglobin (67 kD) by ultrafiltration. Three different membranes, viz. regenerated cellulose, poly(sulfone) and surface modified poly(acrylonitrile), each with a nominal molecular cutoff rating of 100 kD, were examined. The experiments were conducted in dead end, crossflow and vortex flow filtration modes and the separation was studied as a function of feed pH and ionic strength. Under similar system hydrodynamics, the surface modified poly(acrylonitrile) membrane displayed the highest resolution with minimum membrane fouling. The separation could be improved further by operating at low applied pressure (40 kPa) and high mass transfer (> 20 × 10^–6 m/s) in a vortex flow module. Under these conditions, the highest separation factor of 40 was obtained at the pI of hemoglobin.     

Movement characteristics of bovine epididymal spermatozoa: effects of forward motility protein and epididymal maturation

Movement characteristics of untreated bovine caudal epididymal spermatozoa were compared by high-speed cinemicrography with those of theophylline-activated caput epididymal spermatozoa with and without added forward motility protein (FMP). Comparison of individual movement characteristics clearly established the importance of FMP in converting the nonprogressive motility of theophylline-activated caput sperm into the progressive swimming of mature caudal sperm. Although the total or curvilinear distance traveled in 1 sec by theophylline-activated caput sperm was not changed by the addition of FMP, the linear progression was doubled and the percentage of progressively motile sperm was tripled by this protein. Untreated caudal sperm were 80% motile and theophylline-activated caput sperm were nearly 50% motile; the percentage of motile sperm that were progressive was the same for theophylline-activated caput sperm with FMP and for untreated caudal sperm. Caput sperm without FMP roll infrequently, if at all, but caput sperm with FMP and caudal sperm roll at 4.7 Hz. The beat frequency increases significantly with the addition of FMP and is even higher for caudal sperm. The hydrodynamic power output rises concomitantly with the beat frequency. Perhaps the most striking difference between caput sperm without FMP and those with it is in the swimming paths they follow. Caput sperm without FMP exhibit frequent reversals in direction, or yawing of the sperm heads as they loop back and cross over their tails in an apparently very flexible bending. Their average swimming paths are circles. Caput sperm with FMP and caudal sperm do not show this behavior, but swim in average paths which are linear. The minimum radius of curvature of the tail of caput sperm without FMP is much smaller than that for the other two cell types. These studies clarify the role of FMP in epididymal development of sperm motility.     

Effect of feed composition and upflow velocity on aggregate characteristics in anaerobic upflow reactors

Two upflow anaerobic hybrid reactors treated lactose and a mixture of ethanol, propionate and butyrate, respectively, at a volumetric loading rate of 3.7 kg chemical oxygen demand (COD) m⁻³day⁻¹, a hydraulic retention time of 5 days and a liquid upflow velocity of 0.01 m/h. Under steady-state conditions, the lactose-fed sludge had much higher (20%–100%) specific methanogenic conversion rates than the volatile-fatty acid␣(VFA)/ethanol-fed sludge for all substrates tested, including VFA. In both reactors, a flocculant sludge developed, although a much higher content of extracellular polysaccharide was measured in the lactose-fed sludge [1900 μg compared to 305 μg uronic acid/g volatile suspended solids (VSS)]. When the liquid upflow velocity of a third, VFA/ethanol-fed reactor was increased to 0.5 m/h, granulation of the sludge occurred, accompanied by a large increase (200%–500%) in the specific methanogenic conversion rates for the syntrophic and methanogenic substrates studied. Granulation reduced the susceptibility of the sludge to flotation. Glucose was degraded at a high rate (100 mg glucose gVSS⁻¹h⁻¹) by the sludge from the third reactor, despite not having been exposed to a sugar-containing influent for 563␣days. Received: 7 June 1996 / Received revision: 23 September 1996 / Accepted: 29 September 1996