GOPred: GO Molecular Function Prediction by Combined Classifiers

Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines different methods to better represent protein function. First, we formulated the function annotation problem as a classification problem defined on 300 different Gene Ontology (GO) terms from molecular function aspect. We presented a method to form positive and negative training examples while taking into account the directed acyclic graph (DAG) structure and evidence codes of GO. We applied three different methods and their combinations. Results show that combining different methods improves prediction accuracy in most cases. The proposed method, GOPred, is available as an online computational annotation tool (http://kinaz.fen.bilkent.edu.tr/gopred).     

Influence of nitrate and COD on phosphorus, nitrogen and dinitrotoluene (DNT) removals under batch anaerobic and anoxic conditions

In this study, the effects of COD to NO(3)-N ratio in the feed on PO(4)-P removal was investigated. Maximum PO(4)-P uptake was obtained in the anoxic reactor when the COD to NO(3)-N ratios were between 2 and 3.75. With the influent COD of 800-1500 mg COD/L a total of the maximum removable PO(4)-P was 56 mg PO(4)-P/L through 20 days of anaerobic/anoxic incubation, indicating 98% P removal in the anoxic reactor. Similarly, for the COD to NO(3)-N ratios varying between 2 and 3.75 maximum denitrification was observed. Through anoxic operation the poly-P bacteria are capable of removing NO(3)-N using VFA, COD as carbon source and NO(3)-N as the electron acceptor after methanogenesis has been completed. High NO(3)-N concentrations stopped significantly the P uptake. A total of 97-99% dinitrotoluene removal efficiencies in the reactors containing COD to NO(3)-N ratio of 2 and 3.75 after 20 days of incubation period. For maximum NO(3)-N and PO(4)-P removals optimal COD to NO(3)-N ratios, COD and NO(3)-N concentrations were 2-3.75, 2000-4000 mg COD/L and, 800-1500 mg NO(3)-N/L, respectively.     

Balancing in- and out-breeding by the predatory mite <Emphasis Type="Italic">Phytoseiulus persimilis</Emphasis>

In- and out-breeding depressions are commonly observed phenomena in sexually reproducing organisms with a patchy distribution pattern, and spatial segmentation and/or isolation of groups. At the genetic level, inbreeding depression is due to increased homozygosity, whereas outbreeding depression is due to inferior genetic compatibility of mates. Optimal outbreeding theory suggests that intermediate levels of mate relatedness should provide for the highest fitness gains. Here, we assessed the fitness consequences of genetic relatedness between mates in plant-inhabiting predatory mites Phytoseiulus persimilis, which are obligatory sexually reproducing but haplo-diploid. Both females and males arise from fertilized eggs but males lose the paternal chromosome set during embryogenesis, dubbed pseudo-arrhenotoky. Phytoseiulus persimilis are highly efficacious in reducing crop-damaging spider mite populations and widely used in biological control. Using iso-female lines of two populations, from Sicily and Greece, we assessed the fecundity of females, and sex ratio of their offspring, that mated with either a sibling, a male from the same population or a male from the other population. Additionally, we recorded mating latency and duration. Females mating with a male from the same population produced more eggs, with a lower female bias, over a longer time than females mating with a sibling or with a male from the other population. Mating latency was unaffected by mate relatedness; mating duration was disproportionally long in sibling couples, likely indicating female reluctance to mate and sub-optimal spermatophore transfer. Our study provides a rare example of in- and out-breeding depression in a haplo-diploid arthropod, supporting the optimal outbreeding theory.     

Exploring strategies to prevent post-lobectomy space: transient diaphragmatic paralysis using Botulinum Toxin Type A (BTX-A)

Objective

Various techniques to reduce air space after pulmonary lobectomy especially for lung cancer have been an important concern in thoracic surgical practice. The aim of this study was to assess the effectiveness of Botulinum toxin A (BTX-A) injection into the diaphragm to reduce air space after right lower pulmonary lobectomy in an animal model.

Methods

Twelve male New Zealand rabbits were randomly allocated into two groups. All animals underwent right lower lobectomy. Then, normal saline of 0,1 ml and 10 units of 0,1 ml Botulinum toxin type A were injected into the muscular part of the right hemidiaphragm in control (n = 6) and BTX-A groups (n = 6) respectively. Residual air space and diaphragmatic elevation were evaluated with chest X-ray pre- and postoperatively. Diaphragmatic elevation was measured as a distance in millimetre from the line connecting the 10th ribs to the midpoint of the right hemidiaphragm.

Results

The mean diaphragmatic elevation in BTX-A and control groups were 7.0 ± 2.5 and 1.3 ± 1.2 millimetres respectively. Diaphragmatic elevations were significantly higher in BTX-A group (p = 0.0035).

Conclusion

Intraoperative Botulinum toxin type A injection may reduce postlobectomy spaces effectively via hemidiaphragmatic paralysis in rabbits. Further studies are needed to validate the safe use of Botulinum toxin type A in human beings.

     

Implicit motif distribution based hybrid computational kernel for sequence classification

MOTIVATION: We designed a general computational kernel for classification problems that require specific motif extraction and search from sequences. Instead of searching for explicit motifs, our approach finds the distribution of implicit motifs and uses as a feature for classification. Implicit motif distribution approach may be used as modus operandi for bioinformatics problems that require specific motif extraction and search, which is otherwise computationally prohibitive. RESULTS: A system named P2SL that infer protein subcellular targeting was developed through this computational kernel. Targeting-signal was modeled by the distribution of subsequence occurrences (implicit motifs) using self-organizing maps. The boundaries among the classes were then determined with a set of support vector machines. P2SL hybrid computational system achieved approximately 81% of prediction accuracy rate over ER targeted, cytosolic, mitochondrial and nuclear protein localization classes. P2SL additionally offers the distribution potential of proteins among localization classes, which is particularly important for proteins, shuttle between nucleus and cytosol. AVAILABILITY: http://staff.vbi.vt.edu/volkan/p2sl and http://www.i-cancer.fen.bilkent.edu.tr/p2sl CONTACT: rengul@bilkent.edu.tr.     

A Case Discussion on Market‐Based Extended Producer Responsibility: The Minnesota Electronics Recycling Act

In this article, we analyze the Minnesota Electronics Recycling Act to explore the benefits and potential drawbacks of a market‐based extended producer responsibility (EPR) legislation implementation with operational flexibility for manufacturers. Based on publicly available reports and stakeholder interviews, we find that the Minnesota Act attains two key goals of market‐based EPR (i.e., higher cost efficiencies and substantial landfill diversion); however, this may come at the expense of selective collection and recycling, an increased burden on local governments, and a loss of balance in contractual power between stakeholders. We observe that these concerns arise because of specific flexibility provisions afforded to manufacturers that allow them to operationalize their EPR compliance with a cost‐efficiency focus. Thus, we conclude that EPR goals must be carefully translated into operating rules in order to achieve goals while avoiding unintended consequences.     

Synergistic larvicidal and repellent effects of essential oils of three Origanum species on Rhipicephalus annulatus tick

Ticks are of great economic importance worldwide, both because they represent major obstacles to livestock productivity and because of their ability to transmit diseases to humans and animals. Although synthetic acaricides are the most common method for tick control, their overuse has led to the development of resistance as well as unacceptable residual levels in animal products and in the environment in general. There is therefore an urgent need to identify alternative treatments. Among such alternative approaches for tick control is plant essential oil (EO) therapy. In the present study, we investigated the synergistic effect of EOs of three oregano species—Origanum onites, O. majorana and O. minutiflorum—against Rhipicephalus annulatus larvae. Gas chromatography–mass spectrometry profiles of the three EOs revealed that carvacrol was their major component, with a concentration of 86.2% in O. majorana, 79.1% in O. minutiflorum and 77.4% in O. onites. The results of larvicidal assays revealed that the doses that lead to the death of 50% of the ticks (LC₅₀) were 22.99, 25.08 and 27.06 µL/mL for O. majorana, O. minutiflorum and O. onites EOs, respectively, whereas the doses that lead to the death of 99% (LC₉₉) were 41.26, 43.62 and 48.96 µL/mL. In addition, the LC₅₀ and LC₉₉ of the three oils combined was lower (viz., 4.01 and 6.97 µL/mL) than that of each oil alone. The tested EOs were also able to repel larvae of R. annulatus to varying degrees, with O. onites oil exhibiting the greatest repellent effect, as shown by the lowest RC₅₀ dose, followed by O. minutiflorum and O. majorana. Interestingly, this means that the oil that was least effective in killing the larvae was the most effective in repelling them. The calculated synergistic factor of any combination was higher than 1 which means that combinations have a synergistic effect. In conclusion, the combination of all three oils showed higher toxic and repellent activities than either oil separately or combinations of any two oils, suggesting synergistic effects with low doses. Further studies including field trials and the establishment of the mode of action and side effects are urgently needed to expand on these findings, and other tick stages such as adults should also be tested.