PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB

Background

One of the recent challenges of computational biology is development of new algorithms, tools and software to facilitate predictive modeling of big data generated by high-throughput technologies in biomedical research.

Results

To meet these demands we developed PROPER - a package for visual evaluation of ranking classifiers for biological big data mining studies in the MATLAB environment.

Conclusion

PROPER is an efficient tool for optimization and comparison of ranking classifiers, providing over 20 different two- and three-dimensional performance curves.

     

Concentration of air-borne pheromone required for long-lasting peripheral adaptation in the obliquebanded leafroller, Choristoneura rosaceana

Abstract. Electroantennogram (EAG) responses of male obliquebanded leafrollers, Choristoneura rosaceana (Harris), to the main component of its pheromone blend and traces of geometric isomer ((Z)11‐14:Ac and (E)11‐14:Ac, respectively) were recorded before and after 1 h of continuous exposure to pheromone in laboratory experiments, and 24 h of exposure under field conditions. Concentrations of pheromone ranging from 56 to below 1 ng mL^?1 air in Teflon chambers with regulated air exchange reduced peripheral sensory responses by 40–60% as measured by amplitudes of the EAG. Adaptation did not increase in a dosage‐dependent fashion over most of this range; an identical reduction of responsiveness was observed at each exposure to an effective concentration. Exposure of C. rosaceana at a loading dosage of 1 ng of pheromone in 100 µL of mineral oil (air concentration below the GLC detection limit) did not induce measurable adaptation. Caging C. rosaceana in apple trees adjacent to one, two or four Isomate OBLR/PLR Plus polyethylene pheromone dispensers for 24 h resulted in long‐lasting adaptation similar to that seen in laboratory experiments. Adaptation was not observed for C. rosaceana caged at a distance of 2 m from Isomate dispensers in 1‐ha plots treated with 500 dispensers per ha. Whenever observed, this type of adaptation was expressed for more than 5 min after exposure to pheromone ceased. Collectively, this adaptation phenomenon in C. rosaceana is consistent with the third of Zufall & Leinders‐Zufall's types of olfactory adaptation that is ‘long‐lasting’. Although the dosage of pheromone required to induce long‐lasting adaptation in this moth is judged high relative to that for normal sexual communication, we suggest this type of adaptation may come into play for some but not all moths under pest‐control regimes using the tactic of pheromone‐disruption, particularly those using high‐dosage release technologies like pheromone rope dispensers or Microsprayers.     

MQAPsingle: A quasi single‐model approach for estimation of the quality of individual protein structure models

We present a Model Quality Assessment Program (MQAP), called MQAPsingle, for ranking and assessing the absolute global quality of single protein models. MQAPsingle is quasi single‐model MQAP, a method that combines advantages of both “pure” single‐model MQAPs and clustering MQAPs. This approach results in higher accuracy compared to the state‐of‐the‐art single‐model MQAPs. Notably, the prediction for a given model is the same regardless if this model is submitted to our server alone or together with other models. Proteins 2016; 84:1021–1028. © 2015 Wiley Periodicals, Inc.     

Heparan Sulfate Proteoglycans Mediate Factor XIIa Binding to the Cell Surface

Hageman factor (FXIIa) initiates the intrinsic coagulation pathway and triggers the kallikrein-kinin and the complement systems. In addition, it functions as a growth factor by expressing promitogenic activities toward several cell types. FXIIa binds to the cell surface via a number of structurally unrelated surface receptors; however, the underlying mechanisms are not yet fully understood. Here, we demonstrate that FXIIa utilizes cell membrane-bound glycosaminoglycans to interact with the cell surface of human lung fibroblasts (HLF). The combination of enzymatic, inhibitory, and overexpression approaches identified a heparan sulfate (HS) component of proteoglycans as an important determinant of the FXIIa binding capacity of HLF. Moreover, cell-free assays and competition experiments revealed preferential binding of FXIIa to HS and heparin over dextran sulfate, dermatan sulfate, and chondroitin sulfate A and C. Finally, we demonstrate that fibroblasts isolated from the lungs of the patients suffering from idiopathic pulmonary fibrosis (IPF) exhibit enhanced FXIIa binding capacity. Increased sulfation of HS resulting from elevated HS 6-O-sulfotransferase-1 expression in IPF HLF accounted, in part, for this phenomenon. Application of RNA interference technology and inhibitors of intracellular sulfation revealed the cooperative action of cell surface-associated HS and urokinase-type plasminogen activator receptor in the accumulation of FXIIa on the cell surface of IPF HLF. Moreover, FXIIa stimulated IPF HLF migration, which was abrogated by pretreatment of cells with heparinase I. Collectively, our study uncovers a novel role of HS-type glycosaminoglycans in a local accumulation of FXIIa on the cell membrane. The enhanced association of FXIIa with IPF HLF suggests its contribution to fibrogenesis.     

VHH characterization. Comparison of recombinant with chemically synthesized anti‐HER2 VHH

In the continuous exploration of the VHH chemistry, biochemistry and therapeutic future use, we investigated two different production strategies of this small antibody‐like protein, using an anti‐HER2 VHH as a model. The total chemical synthesis of the 125 amino‐acid peptide was performed with reasonable yield, even if optimization will be necessary to upgrade this kind of production. In parallel, we expressed the same sequence in two different hosts: Escherichia coli and Pichia pastoris. Both productions were successful and led to a fair amount of VHHs. The integrity and conformation of the VHH were characterized by complementary mass spectrometry approaches, while surface plasmon resonance experiments were used to assess the VHH recognition capacity and affinity toward its “antigen.” Using this combination of orthogonal techniques, it was possible to show that the three VHHs—whether synthetic or recombinant ones—were properly and similarly folded and recognized the “antigen” HER2 with similar affinities, in the nanomolar range. This opens a route toward further exploration of modified VHH with unnatural amino acids and subsequently, VHH‐drug conjugates.     

Metallochaperone function of the self-subunit swapping chaperone involved in the maturation of subunit-fused cobalt-type nitrile hydratase

The transition metal (iron or cobalt) is a mandatory part that constitutes the catalytic center of nitrile hydratase (NHase). The incorporation of the cobalt ion into cobalt-containing NHase (Co-NHase) was reported to depend on self-subunit swapping and the activator of the Co-NHase acts as a self-subunit swapping chaperone for subunit exchange. Here we discovered that the activator acting as a metallochaperone transferred the cobalt ion into subunit-fused Co-NHase. We successfully isolated two activators, P14K and NhlE, which were the activators of NHases from Pseudomonas putida NRRL-18668 and the activator of low-molecular-mass NHase from Rhodococcus rhodochrous J1, respectively. Cobalt content determination demonstrated that NhlE and P14K were two cobalt-containing proteins. Substitution of the amino acids involved in the C-terminus of the activators affected the activity of the two NHases, indicating that the potential cobalt-binding sites might be located at the flexible C-terminal region. The cobalt-free NHases could be activated by either of the two activators, and both the two activators activated their cognate NHase more efficiently than did the noncognate ones. This study provided insights into the maturation of subunit-fused NHases and confirmed the metallochaperone function of the self-subunit swapping chaperone.     

Exploring thermal imaging variables for the detection of stress responses in grapevine under different irrigation regimes

Temperatures of leaves or canopies can be used as indicators of stomatal closure in response to soil water deficit. In 2 years of field experiments with grapevines (Vitis vinifera L., cvs Castel?o and Aragonês), it was found that thermal imaging can distinguish between irrigated and non-irrigated canopies, and even between deficit irrigation treatments. Average canopy temperature was inversely correlated with stomatal conductance measured with a porometer. Variation of the distribution of temperatures within canopies was not found to be a reliable indicator of stress. A large degree of variation between images was found in reference 'wet' and 'dry' leaves used in the first year for the calculation of an index proportional to stomatal conductance. In the second year, fully irrigated (FI) (100% Et(c)) and non-irrigated (NI) canopies were used as alternatives to wet and dry leaves. A crop water stress index utilizing these FI and NI 'references', where stressed canopies have the highest values and non-stressed canopies have the lowest values, was found to be a suitable measure for detecting stress. It is suggested that the average temperatures of areas of canopies containing several leaves may be more useful for distinguishing between irrigation treatments than the temperatures of individual leaves. Average temperatures over several leaves per canopy may be expected to reduce the impact of variation in leaf angles. The results are discussed in relation to the application of thermal imaging to irrigation scheduling and monitoring crop performance.