bluuebunny/crossref_metadata_2025 huggingface dataset:
Cognition and the evolution of camouflage
Authors: Skelhorn John , Rowe Candy
Published: February 2016

Camouflage is one of the most widespread forms of anti-predator defence and prevents prey individuals from being detected or correctly recognized by would-be predators. Over the past decade, there has been a resurgence of interest in both the evolution of prey camouflage patterns, and in understanding animal cognition in a more ecological context. However, these fields rarely collide, and the role of cognition in the evolution of camouflage is poorly understood. Here, we review what we currently know about the role of both predator and prey cognition in the evolution of prey camouflage, outline why cognition may be an important selective pressure driving the evolution of camouflage and consider how studying the cognitive processes of animals may prove to be a useful tool to study the evolution of camouflage, and vice versa. In doing so, we highlight that we still have a lot to learn about the role of cognition in the evolution of camouflage and identify a number of avenues for future research.
The genetic backburn: using rapid evolution to halt invasions
Authors: Phillips Ben L. , Shine Richard , Tingley Reid
Published: February 2016

The impact of an invasive species depends upon the extent of area across which it ultimately spreads. A powerful strategy for limiting impact, then, is to limit spread, and this can most easily be achieved by managing or reinforcing natural barriers to spread. Using a simulation model, we show that rapid evolutionary increases in dispersal can render permeable an otherwise effective barrier. On the other hand, we also show that, once the barrier is reached, and if it holds, resultant evolutionary decreases in dispersal rapidly make the barrier more effective. Finally, we sketch a strategy—the genetic backburn—in which low-dispersal individuals from the range core are translocated to the nearside of the barrier ahead of the oncoming invasion. We find that the genetic backburn—by preventing invasion front genotypes reaching the barrier, and hastening the evolutionary decrease in dispersal—can make barriers substantially more effective. In our simulations, the genetic backburn never reduced barrier strength, however, the improvement to barrier strength was negligible when there was substantial long-distance dispersal, or when there was no genetic variation for dispersal distance. The improvement in barrier strength also depended on the trade-off between dispersal and competitive ability, with a stronger trade-off conferring greater power to the genetic backburn.
Quality characteristics of cut kimchi cabbage during short-term storage depending on the packaging materials
Authors: Son Eun Ji , Hwang In-Wook , Chung Shin-Kyo
Published: February 2016

Fresh cut vegetables provide convenience and rapidity to consumers. However, they have a weakness with respect to their short shelf-life due to browning and quality degradation via increased respiration. To overcome this problem, the effect of packaging film on the short-term storage of cut kimchi cabbages was investigated. Polypropylene (PP), oriented polypropylene (OPP), and low-density polyethylene (LDPE) films were used as packaging film, and cut kimchi cabbages were stored in the packaging films at 5°C for 4 weeks. PP film packaging showed the least weight loss and soluble solids loss after 4 weeks. Titratable acidity increased during storage for all samples, however, the increase rate of titratable acidity in PP and OPP film packaging decreased, which was lower than that of LDPE film packaging. Color values decreased over time during storage. In appearance, PP film packaging was better than other films due to their high transparency. In a sensory test, there was no statistical difference among samples. Taken together, the transparent PP film packaging was more effective for short-term storage of cut kimchi cabbages. Thus, this study provides useful information for the selection of packaging materials for cut kimchi cabbage marketing.
Effect of moisture content on some physical properties of domestic wheat
Authors: Kim Oui-Woung , Kim Hoon , Kim Sang-Suk , Choi Eun-Jung
Published: February 2016

The physical properties of wheat kernels were determined as a function of moisture content to optimize the design of equipment for post-harvest management. Several properties, including bulk density, dynamic repose angle, one thousand-kernel weight, specific gravity, length, width, thickness, and area of two wheat cultivars (Baekjjung: B and Jogyeong: J ), were studied in the moisture range from approximately 9% to 30% wet basis. As moisture increased, length increased linearly from 6.42 to 7.20 mm (B) and 8.71 to 9.15 mm (J), width increased from 2.90 to 3.49 mm (B) and 4.12 to 4.43 mm (J), thickness from 2.94 to 3.20 mm (B) and 3.29 to 3.63 mm (J), and area from 14.13 to 19.44 mm2 (B) and 27.75 to 31.25 mm2 (J). Additionally, the dynamic repose angle and one thousand-kernel weight increased linearly from 46.3° to 54.0° (B) and 46.3° to 54.5° (J) and from 32.26 to 41.51 g (B) and 45.30 to 63.07 g (J), respectively, as the moisture content increased. Based on the experimental measurements, only the bulk density and specific gravity decreased from 754.0 to 664.1 kgm-3 (B) and 776.1 to 660.0 kgm-3 (J) and from 1.2950 to 1.2265 (B) and 1.3379 to 1.2671 (J), respectively, as moisture content increased.
Quality characteristics of fermented vinegar prepared with the detoxified Rhus verniciflua extract
Authors: Baek Seong Yeol , Lee Choong Hwan , Park Yoo Kyoung , Choi Han-Seok , Mun Ji-Young , Yeo Soo-Hwan
Published: February 2016

In this study, vinegar was produced using urushiol-free fermented Rhus verniciflua extract to create a lacquer with added value. The effect of manufacturing conditions on the quality of vinegar using detoxified R. verniciflua extract for fermentation was investigated. The acidity of the vinegar for inoculations with various liquid starter contents was 4.8~4.9%, and it was similar among all treatment groups. The acidity of vinegar was higher when the initial alcohol content was high. The acetic acid yields were 82.8%, 84.4%, 77.7%, and 69.5%, and the maximum yield was observed when the initial alcohol content was 6%. For acetic acid fermentation using different amounts of detoxified R. verniciflua extracts, the acidity of the vinegar with the extract after fermentation was 5.3~5.9%. However, the acidity of vinegar without the extract was 5.5%. The intensity of the brown color was high for vinegar without the extract. Hunter’s L values were high for vinegar with an extract content of 2%. Acetic acid (53.3~65.8 mg/mL) was the predominant acid. Arginine (190.3~333.3 μg/mL), proline (125.6~290.8 μg/mL), alanine (126.1~270.9 μg/mL), and glutamic acid (159.0~262.4 μg/mL) were the predominant amino acids in detoxified R. verniciflua vinegar.
Effects of roasting conditions on the physicochemical properties of Coffea arabica beans
Authors: Suh Yeon-Soo , Lee Seung-Heon , Shang Yafang , Lee Won-Jong
Published: February 2016

Effects of roasting on physical (weight, volume, density and color) and chemical properties (total phenol, caffeine, chlorogenic acid and antioxidant properties) of three Arabica coffee beans (Brazil Bourbon, Indonesia Mandheling and Kenya Tatu) were investigated. A steady weight loss, volume increase, and bean density decrease were observed during the roasting process. The L*, a*, and b* values tended to decrease as the roasting temperature and time increased. Caffeine level was approximately 0.73% in green beans, and increased to 40-67% for darker roasts. Green beans contained the highest chlorogenic acid content, which decreased as the roasting temperature and time increased. The light- and medium-roasted coffee showed the highest total phenolol contents. The antioxidant activities were measured using DPPH and ABTS. The light-roasted coffee beans showed the highest antioxidant activities, and an approximately 36-51% loss in antioxidant activity was observed after further roasting. The flavor patterns of roasted coffee beans were analyzed using an electronic nose system based on gas chromatography. This analysis demonstrated that an electronic nose system can be applied to identify the green bean variety and the degree of roasting.
Physicochemical properties of Salvia miltiorrhiza Bunge following treatment with enzymes
Authors: Kim Sun-Hwa , Hwang In-Wook , Chung Shin-Kyo , Seo Young-Jin , Kim Jong-Soo , Jeong Yong-Jin , Kim Mi-Yeon
Published: February 2016

To improve the utilization of the domestic plant Salvia miltiorrhiza Bunge (Danshen), this study investigated changes in the physicochemical qualities of Danshen extracts obtained from low-temperature extraction using the enzymes amylase, cellulase, pectinase, and protease. Changes in the yield, pH, sugar content, and chromaticity were investigated. The changes were found to be highest in the amylase-treated extract with the following values: yield, 58.3%; pH, 6.04; sugar content, 5.97°Brix. With regard to antioxidant properties, Danshen extracts treated with amylase showed the highest DPPH and ABTS scavenging activities of 84.25% and 74.11% at 55 ppm. The total phenolic compound content was highest in the group subjected to enzyme treatment at 60 °C. The salvianolic acid B level of the Danshen extract was the highest in the amylase-treated group, with a value of 3,002.6 mg/100 g. Cryptotanshinone level was the highest in the amylase- and protease-treated group with a value of 3.8 mg/100 g. Tanshinone I was the highest in the protease-treated group, with a value of 14.2 mg/100 g. The results showed that the indicator components of Danshen were detected as stable in the extracts after using amylase for low-temperature extraction; therefore, it would be possible to use Danshen industrially as a functional ingredient through mass production. Furthermore, the enzyme-treatment extraction could be utilized for a variety of natural products.
Antioxidant capacities and β-glucan content of ethanol extract from Phellinus baumii
Authors: Bae Hyun-Kyung , Hwang In-Wook , Hong Hee-Do , Chung Shin-Kyo
Published: February 2016

Phellinus baumii has been used in traditional oriental medicine for the treatment of various cancer types, such as lung cancer, ovarian cancer and malignant melanoma. It has strong anti-cancer, anti-inflammatory and antioxidant activities due to its polysaccharides including glucan, schizophyllan, heteroglycan and lentinan, as well as its polyphenolics such as protocatechuic acid, caffeic acid, coumaric acid. β-Glucan and polyphenolics may be the most important activ ecompounds in P. baumii. Therefore, researchers have focused on these two compounds to improve their contents in extracts. In this study, P. baumii was extracted with hot-water and ethanol at different pH conditions, and their β-glucan contents, antioxidant activity and antioxidant contents were determined. Extraction yield was highest for the 60% ethanol extract at pH 4. The β-glucan contents of the hot-water extract at pH 7 was higher than those of the ethanol extracts. The antioxidant contents and antioxidant activities of the ethanol extracts were higher than those of the hot-water extracts. Extraction with 60% ethanol at pH 7 was appropriate with respect to the antioxidant capacities.
Physicochemical properties of rice varieties for manufacturing frozen fried rice
Authors: Youn Young , Kim Young-Soo
Published: February 2016

Physicochemical properties of five commercial rice products were investigated in order to select the appropriate rice varieties for the preparation of frozen fried rice. Among the evaluated rice varieties, Onnuri (16.06%) had the highest amylose content, while Beakjinju (11.83%) had the lowest. The water absorption index ranged from 1.45 to 1.65 g/g. Regarding the Hunter’s color values, the L and a values of all rice varieties decreased while the b value increased with freezing-storage following the cooking process. The initial pasting temperature showed no significant differences among the five rice varieties. The highest viscosity (peak, trough, and final) and setback were found in the Sindongjin, while the lowest breakdown was found in the Baekjinju variety. Hardness, chewiness, and cohesiveness of all five cooked rice varieties decreased while their adhesiveness increased after freezing-storage. Under electron microscopy scanning, pores were observed inside the tissue of frozen cooked rices manufactured from Baekjinju and Hopum varieties, while substantially smooth tissue structure was observed in Sindognjin, Onnuri, and Ilmi rice varieties.
Physicochemical properties of edible cricket (Gryllus bimaculatus) in different districts
Authors: Kim Eun-Mi , Kim Dae-Hyun , Lim Jeong-Ho , Chang Yoon-Je , Lee Yong-Hwan , Park Jin Ju , Ahn Mi-Young
Published: February 2016

Insects have gained increasing attention as an alternative protein and nutrient rich food source for humans. This study was conducted to investigate the physicochemical characteristics and harmful components of edible crickets (Gryllus bimaculatus) in the 6 districts of Yeonggwang (YG), Jeongseon (JS), Wonju (WJ), Hwaseong (HS), Geochang (GC), and Chungju (CJ). The average crude protein and crude lipid contents on a dry basis were 64.34% and 16.60%, respectively. The crude protein content of CJ was the highest (67.40%), whereas YG (59.42%) had the lowest content. On the other hand, the crude fat content of YG was the highest (20.61%), whereas CJ (14.04%) had the lowest content. The unsaturated fatty acid contents were 57.97-63.93 g/100 g of the total fatty acid content in the crickets of the 6 districts. The major fatty acids of the crickets in the 6 districts were palmitic acid, oleic acid, and linoleic acid. Among the essential amino acids, valine, leucine, and lysine were the most abundant. GC had the highest total amino acids (57.93 g/100 g), whereas YG (48.65 g/100 g) had the lowest. Major mineral contents included potassium (K, 0.92~1.01 mg/100 mg) and phosphorus (P, 0.74~0.88 mg/100 mg). The mineral composition was fairly similar among the crickets. Crickets in the 6 districts were verified to have safe levels of residual heavy metals according to the Korea Food & Drug Administration (KFDA) advisory levels.
삼채(Allium hookeri) 뿌리 추출물의 항산화 및 항염증 특성
Authors: Zhang Chengmei , Tong Tao , Kim Chong-Kyung , Liu Yajuan , Seo Hyuk-Jun , Kim Bo-Sup , Kang Seong-Gook
Published: February 2016

In this study, antioxidant and anti-inflammatory activities of water, methanol, and ethanol extracts obtained from Allium hookeri root were evaluated. The ethanol extract of A. hookeri was found to possess the strongest reducing power and also exhibited dominant effects on scavenging of nitrites, DPPH radicals, and superoxide radicals. The water extract showed more efficient DPPH and hydroxyl radical-scavenging activities than those of the methanol extract. Furthermore, the inhibitory activity against nitric oxide (NO) production in RAW 264.7 macrophages was evaluated to elucidate the anti-inflammatory properties of the extracts. Results indicated that all the extracts of A. hookeri exerted inhibitory activities against NO production, especially the ethanol extract (IC5029.13μg/mL). Total phenolic and total flavonoid contents were found to be abundant in the ethanol extract, with values of 24.96 mg gallic acid equivalent/g extract and 4.27 mg rutin equivalent/g extract, respectively. Total thiosulfinate content was determined for the first time and a high amount was present in the ethanol extract (14.2 μM/g extract). These results suggest that A. hookeri root has antioxidant and anti-inflammatory properties and could be used as a natural source for the development of pharmaceutical agents or functional foods.
Study of antioxidant activities of extracts from Metaplexis japonica leaf and stem
Authors: Hong Ju-Yeon , Shin Seung-Ryeul
Published: February 2016

The purpose of this study was to evaluate the antioxidant activity of Metaplexis japonica by using hot-water and ethanol extracts of its leaf and stem. Yields of hot-water and ethanol extracts of M. japonica leaf were high at 6.89 and 6.23%, respectively. The polyphenol and flavonoid contents in ethanol extracts of M. japonica leaf (ALEE) were high (86.96 and 60.73 mg/g, respectively). The electron-donating ability of all M. japonica extracts increased with an increase in extract concentration, with the highest electron-donating ability of 36.20~68.19% shown by hot-water extracts of M. japonica leaf (ALWE). The superoxide dismutase (SOD)-like activities of ALWE and ALEE increased with an increase in extract concentration. The nitrite-scavenging ability of the extracts was the highest at pH 1.2 and that of ALWE was higher than that of ALEE. The reducing power of 62.5 μg/mL ALEE was 0.09 and that of 1,000 μg/mL ALWE was 0.44. The inhibitory effect of an ethanol extract of M. japonica stem (ASEE) on tyrosinase was 13.81% at a concentration of 62.5 μg/mL and that of 1,000 μg/mL ALEE was 57.04%.
Effect of submerged culture of Ceriporia lacerata mycelium on GLUT4 protein in db/db mouse
Authors: Shin Eun Ji , Kim Ji-Eun , Kim Ji-Hye , Park Yong Man , Yoon Sung Kyoon , Jang Byeong-Churl , Lee Sam-Pin , Kim Byoung-Cheon
Published: February 2016

In this study, we evaluated the antidiabetic effect of a submerged culture of Ceriporia lacerata mycelium (CL01) on hematological indices, as well as protein and mRNA expression of the insulin-signaling pathway, in db/db mice. After CL01 was administrated for 4 weeks, blood glucose levels decreased consistently, and plasma insulin and c-peptide levels each decreased by roughly 55.8%, 40% of those in the negative control (p<0.05). With regard to HOMA-IR, an insulin resistance index, insulin resistance of the CL01-fed group improved over that of the negative control group by about 62% (p<0.05). In addition, we demonstrated that the protein expression levels of pIR, pAkt, pAMPK, and GLUT4 and the mRNA expression levels of Akt2, IRS1, and GLUT4 in the muscle cells of db/db mice increased in the CL01-fed group compared to the corresponding levels in the control group. These results demonstrate that CL01 affects glucose metabolism, upregulates protein and gene expression in the insulin-signaling pathway, and decreases blood glucose levels effectively by improving insulin sensitivity. More than 90% of those who suffer from type 2 diabetes are more likely to suffer from hyperinsulinemia, hypertension, obesity, and other comorbidities because of insulin resistance. Therefore, it is possible that CL01 intake could be used as a fundamental treatment for type 2 diabetes by lowering insulin resistance, and these results may prove be useful as basic evidence for further research into the mechanisms of a cure for type 2 diabetes.
Eco-evolutionary buffering: rapid evolution facilitates regional species coexistence despite local priority effects
Authors: Wittmann Meike J. , Fukami Tadashi
Published: February 2016

Inhibitory priority effects, in which early-arriving species exclude competing species from local communities, are thought to enhance regional species diversity via community divergence. Theory suggests, however, that these same priority effects make it difficult for species to coexist in the region unless individuals are continuously supplied from an external species pool, often an unrealistic assumption. Here we develop an eco-evolutionary hypothesis to solve this conundrum. We build a metacommunity model in which local priority effects occur between two species via interspecific interference. Within each species there are two genotypes: one is more resistant to interspecific interference than the other, but pays a fitness cost for its resistance. Because of this trade-off, species evolve to become less resistant as they become regionally more common. Rare species can then invade some local patches and consequently recover in regional frequency. This “eco-evolutionary buffering” enables the regional coexistence of species despite local priority effects, even in the absence of immigration from an external species pool. Our model predicts that eco-evolutionary buffering is particularly effective when local communities are small and connected by infrequent dispersal.
Multiscale simulations reveal key features of the proton pumping mechanism in cytochromecoxidase
Authors: Liang Ruibin , Swanson Jessica M. J. , Peng Yuxing , Wikström Mårten , Voth Gregory A.
Published: February 2016

Cytochromecoxidase (CcO) reduces oxygen to water and uses the released free energy to pump protons across the membrane, contributing to the transmembrane proton electrochemical gradient that drives ATP synthesis. We have used multiscale reactive molecular dynamics simulations to explicitly characterize (with free energy profiles and calculated rates) the internal proton transport events that enable pumping and chemistry during the A→PR→F transition in theaa3-type CcO. Our results show that proton transport from amino acid residue E286 to both the pump loading site (PLS) and to the binuclear center (BNC) are thermodynamically driven by electron transfer from hemeato the BNC, but that the former (i.e., pumping) is kinetically favored while the latter (i.e., transfer of the chemical proton) is rate-limiting. The calculated rates are in quantitative agreement with experimental measurements. The back flow of the pumped proton from the PLS to E286 and from E286 to the inner side of membrane are prevented by the fast reprotonation of E286 through the D-channel and large free energy barriers for the back flow reactions. Proton transport from E286 to the PLS through the hydrophobic cavity (HC) and from D132 to E286 through the D-channel are found to be strongly coupled to dynamical hydration changes in the corresponding pathways. This work presents a comprehensive description of the key steps in the proton pumping mechanism in CcO.

Significance

The long studied proton pumping mechanism in cytochromecoxidase (CcO) continues to be a source of debate. This work provides a comprehensive computational characterization of the internal proton transport dynamics, while explicitly including the role of Grotthuss proton shuttling, that lead to both pumping and catalysis. Focusing on the A to F transition, our results show that the transfer of both the pumped and chemical protons are thermodynamically driven by electron transfer, and explain how proton back leakage is avoided by kinetic gating. This work also explicitly characterizes the coupling of proton transport with hydration changes in the hydrophobic cavity and D-channel, thus advancing our understanding of proton transport in biomolecules in general.
Atomic structure of Hsp90:Cdc37:Cdk4 reveals Hsp90 regulates kinase via dramatic unfolding
Authors: Verba Kliment A. , Wang Ray Yu-Ruei , Arakawa Akihiko , Liu Yanxin , Shirouzu Mikako , Yokoyama Shigeyuki , Agard David A.
Published: February 2016

The Hsp90 molecular chaperone and its Cdc37 co-chaperone help stabilize and activate over half of the human kinome. However, neither the mechanism by which these chaperones assist their client kinases nor why some kinases are addicted to Hsp90 while closely related family members are independent is known. Missing has been any structural understanding of these interactions, with no full-length structures of human Hsp90, Cdc37 or either of these proteins with a kinase. Here we report a 3.9Å cryoEM structure of the Hsp90:Cdc37:Cdk4 kinase complex. Cdk4 is in a novel conformation, with its two lobes completely separated. Cdc37 mimics part of the kinase N-lobe, stabilizing an open kinase conformation by wedging itself between the two lobes. Finally, Hsp90 clamps around the unfolded kinase β5 strand and interacts with exposed N-and C-lobe interfaces, safely trapping the kinase in an unfolded state. Based on this novel structure and extensive previous data, we propose unifying conceptual and mechanistic models of chaperone-kinase interactions.

One Sentence Summary

The first structure of a chaperone:kinase complex reveals that the Hsp90 system modulates and stabilizes kinases via a functionally relevant, unfolded open state.
Genetic redundancies enhance information transfer in noisy regulatory circuits
Authors: Rodrigo Guillermo , Poyatos Juan F.
Published: February 2016

Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show instead how such intrinsic noise enhances information transfer in the presence of multiple circuit copies. The result is due to the contribution of noise to the generation of autonomous responses by each copy, which are altogether associated with a common decision. Moreover, factors that correlate the responses of the redundant units (extrinsic noise or regulatory cross-talk) contribute to reduce fidelity, while those that further uncouple them (heterogeneity within the copies) can lead to stronger information gain. Overall, our study emphasizes how the interplay of signal thresholding, redundancy, and noise influences the accuracy of cellular decision making. Understanding this interplay provides a basis to explain collective cell signaling mechanisms, and to engineer robust decisions with noisy genetic circuits.
Exploitation by cheaters facilitates the preservation of essential public goods in microbial communities
Authors: Moreno-Fenoll Clara , Cavaliere Matteo , Martínez-García Esteban , Poyatos Juan F.
Published: February 2016

How are public goods1-4maintained in bacterial cooperative populations? The presence of these compounds is usually threatened by the rise of cheaters that do not contribute but just exploit the common resource5,6. Minimizing cheater invasions appears then as a necessary maintenance mechanism7,8. However, that invasions can instead add to the persistence of cooperation is a prospect that has yet remained largely unexplored6. Here, we show that the detrimental consequences of cheaters can actually preserve public goods, at the cost of recurrent collapses and revivals of the population. The result is made possible by the interplay between spatial constraints and the essentiality of the shared resource. We validate this counter-intuitive effect by carefully combining theory and experiment, with the engineering of an explicit synthetic community in which the public compound allows survival to a bactericidal stress. Notably, the characterization of the experimental system identifies additional factors that can matter, like the impact of the lag phase on the tolerance to stress, or the appearance of spontaneous mutants. Our work emphasizes the unanticipated consequences of the eco-evolutionary feedbacks that emerge in microbial communities relying on essential public goods to function, feedbacks that reveal fundamental for the adaptive change of ecosystems at all scales.
Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree
Authors: Ansari M. Azim , Didelot Xavier
Published: February 2016

The distribution of a phenotype on a phylogenetic tree is often a quantity of interest. Many phenotypes have imperfect heritability, so that a measurement of the phenotype for an individual can be thought of as a single realisation from the phenotype distribution of that individual. If all individuals in a phylogeny had the same phenotype distribution, measured phenotypes would be randomly distributed on the tree leaves. This is however often not the case, implying that the phenotype distribution evolves over time. Here we propose a new model based on this principle of evolving phenotype distribution on the branches of a phylogeny, which is different from ancestral state reconstruction where the phenotype itself is assumed to evolve. We develop an efficient Bayesian inference method to estimate the parameters of our model and to test the evidence for changes in the phenotype distribution. We use multiple simulated datasets to show that our algorithm has good sensitivity and specificity properties. Since our method identifies branches on the tree on which the phenotype distribution has changed, it is able to break down a tree into components for which this distribution is unique and constant. We present two applications of our method, one investigating the association between HIV genetic variation and human leukocyte antigen, and the other studying host range distribution in a lineage ofSalmonella enterica, and we discuss many other potential applications. All the methods described in this paper are implemented in a software package called TreeBreaker which is freely available for download athttps://github.com/ansariazim/TreeBreaker
Pooled enrichment sequencing identifies diversity and evolutionary pressures at NLR resistance genes within a wild tomato population
Authors: Stam Remco , Scheikl Daniela , Tellier Aurélien
Published: February 2016

Nod-like Receptors (NLRs) are Nucleotide-binding domain and Leucine rich Repeats (NB-LRR)-containing proteins that are important in plant resistance signaling. Many of the known pathogen Resistance (R)-genes in plants are NLRs and they can recognise directly or indirectly pathogen molecules. As such, divergence and copy number variants at these genes is found to be high between species. Within populations, positive and balancing selection are to be expected if plants coevolve with their pathogens. In order to understand the complexity of R-gene coevolution in wild non-model species, it is necessary to identify the full range of NLRs and infer their evolutionary history.

Here we investigate and reveal polymorphism occurring at 220 NLR genes within one population of the partially selfing wild tomato speciesS. pennellii. We use a combination of enrichment sequencing and pooling of ten individuals, to specifically sequence NLR genes in a resource and cost-effective manner. We focus on the effects which different of mapping and SNP calling software and settings have on calling polymorphisms in customized pooled samples. Our results are accurately verified using Sanger sequencing of polymorphic gene fragments. Our results indicate that some NLRs, namely 13 out of 220, have maintained polymorphism within ourS. pennelliipopulation. These genes show a wide range of πN/πsratios and differing site frequency spectra. We compare our observed rate of heterozygosity to expectations for this selfing and bottlenecked population. We conclude that our method enables us to pinpoint NLR genes which have experienced natural selection in their habitat.
On the Regulator of Spike Activity in Cortical Neurons Under Hypothermic Conditions
Authors: Mednikova Yu. S. , Zakharova N. M. , Pasikova N. V. , Averina I. V.
Published: February 2016

In sensorimotor cortical slices of guinea pig in the course of cooling incubating fluid from 34 to 21-22°C it was shown that hypothermia exerted both increase and decrease of spontaneous activity in different neurons. On hypothermic increase of firing level spike responses of soma to iontophoretic application of glutamate to dendritic locus appeared with shorter latencies and with longer latencies – on hypothermic decrease of spontaneous activity. At the same time hypothermia did not influence on the evoked spike reactions to iontophoretic application of glutamate straight to the soma. It means that hypothermic disorders of neuronal activity are not connected with changes in sensitivity to glutamate but determined by changes of amplitude of glutamatergic excitation while propagating along dendritic branches. The changes in spontaneous activity began at 30°C along with the decreased spike reactions to iontophoretic applications of acetylcholine and efficacy of dendro-somatic propagation. At the same temperature the fall of spike amplitude was initiated and increased with further hypothermia. It is proposed that the basis for hypothermic changes of neuronal activity is the decreased rate of M-cholinergic process at 27-29°C which leads both to attenuation of conductive function of dendrites and imbalance of K+ion homeostasis. Peculiarities of hypothermic regulation of neuronal spike activity depend on individual functional properties of cortical neurons.
foxc1agenetically interacts withripply1to regulatemesp-baexpression and somitogenesis in the zebrafish embryo
Authors: Lavy Rotem , Allison W. Ted , Berry Fred B.
Published: February 2016

Somitogenesis is a fundamental segmentation process that forms the vertebrate body plan. A network of transcription factors is essential in establishing the spatial temporal order of this process. One such transcription factor is mesp-bawhich has an important role in determining somite boundary formation. Its expression in somitogenesis is tightly regulated by the transcriptional activator Tbx6 and the repressor Ripply1 via a feedback regulatory network. Loss offoxc1afunction in zebrafish leads to lack of anterior somite formation and reducedmesp-baexpression. Here we examine howfoxc1ainteracts with thetbx6-ripply1network to regulatemesp-baexpression. Infoxc1amorphants, anterior somites did not form at 12.5 hours post fertilization (hpf). At 22 hpf posterior somites formed, whereas anterior somites remained absent. Inripply1morphants, no somites were observed at any time point. The expression ofmesp-bawas reduced in thefoxc1amorphants and expanded anteriorly inripply1morphants. Thetbx6expression domain was smaller and shifted anteriorly in thefoxc1amorphants. Double knockdown offoxc1aandripply1resulted in absence of anterior somite formation while posterior somites did form, suggesting a partial rescue of theripply1phenotype. However, unlike the singlefoxc1amorphants, expression ofmesp-bawas restored in the anterior PSM. Expression oftbx6was expanded anteriorly in the double morphants. In conclusion, bothfoxc1aandripply1morphants displayed defects in somitogenesis, but their individual loss of function had opposing effects onmesp-baexpression. Loss ofripply1appears to have rescued themesp-ba expression in thefoxc1amorphant, suggesting that intersection of these parallel regulatory mechanisms is required for normalmesp-baexpression and somite formation.
Accurate promoter and enhancer identification in 127 ENCODE and Roadmap Epigenomics cell types and tissues by GenoSTAN
Authors: Zacher Benedikt , Michel Margaux , Schwalb Björn , Cramer Patrick , Tresch Achim , Gagneur Julien
Published: February 2016

Accurate maps of promoters and enhancers are required for understanding transcriptional regulation. Promoters and enhancers are usually mapped by integration of chromatin assays charting histone modifications, DNA accessibility, and transcription factor binding. However, current algorithms are limited by unrealistic data distribution assumptions. Here we propose GenoSTAN (Genomic STate ANnotation), a hidden Markov model overcoming these limitations. We map promoters and enhancers for 127 cell types and tissues from the ENCODE and Roadmap Epigenomics projects, today’s largest compendium of chromatin assays. Extensive benchmarks demonstrate that GenoSTAN consistently identifies promoters and enhancers with significantly higher accuracy than previous methods. Moreover, GenoSTAN-derived promoters and enhancers showed significantly higher enrichment of complex trait-associated genetic variants than current annotations. Altogether, GenoSTAN provides an easy-to-use tool to define promoters and enhancers in any system, and our annotation of human transcriptional cis-regulatory elements constitutes a rich resource for future research in biology and medicine.
Effectors and potential targets selectively upregulated in human KRAS-mutant lung adenocarcinomas
Authors: Li Jinyu , Sordella Raffaella , Powers Scott
Published: February 2016

Genetic and proteomic analysis of human tumor samples can provide an important compliment to information obtained from model systems. Here we examined protein and gene expression from the Cancer Genome and Proteome Atlases (TCGA and TCPA) to characterize proteins and protein-coding genes that are selectively upregulated inKRAS-mutant lung adenocarcinomas. Phosphoprotein activation of several MAPK signaling components was considerably stronger inKRAS-mutants than any other group of tumors, even those with activating mutations in receptor tyrosine kinases (RTKs) and BRAF. Co-occurring mutations inKRAS-mutants were associated with differential activation of PDK1 and PKC-alpha. Genes showing strong activation in RNA-seq data included negative regulators of RTK/RAF/MAPK signaling along with potential oncogenic effectors including activators of Rac and Rho proteins and the receptor protein-tyrosine phosphatase genes PTPRM and PTPRE. These results corroborate RAF/MAPK signaling as an important therapeutic target inKRAS-mutant lung adenocarcinomas and pinpoint new potential targets.
Natural selection driven by DNA binding proteins shapes genome-wide motif statistics
Authors: Qian Long , Kussell Edo
Published: February 2016

Ectopic DNA binding by transcription factors and other DNA binding proteins can be detrimental to cellular functions and ultimately to organismal fitness. The frequency of protein-DNA binding at non-functional sites depends on the global composition of a genome with respect to all possible short motifs, ork-mer words. To determine whether weak yet ubiquitous protein-DNA interactions could exert significant evolutionary pressures on genomes, we correlatein vitromeasurements of binding strengths on all 8-mer words from a large collection of transcription factors, in several different species, against their relative genomic frequencies. Our analysis reveals a clear signal of purifying selection to reduce the large number of weak binding sites genome-wide. This evolutionary process, which we callglobal selection, has a detectable hallmark in that similar words experience similar evolutionary pressure, a consequence of the biophysics of protein-DNA binding. By analyzing a large collection of genomes, we show that global selection exists in all domains of life, and operates through tiny selective steps, maintaining genomic binding landscapes over long evolutionary timescales.
X-ray and DFT-calculated structures of bis[N-(quinolin-8-yl)benzamidato-κ2N,N′]copper(II)
Authors: Chatturgoon Teshica , Akerman Matthew P.
Published: February 2016

The application of transition metal chelates as chemotherapeutic agents has the advantage that they can be used as a scaffold around which ligands with DNA recognition elements can be anchored. The facile substitution of these components allows for the DNA recognition and binding properties of the metal chelates to be tuned. Copper is a particularly interesting choice for the development of novel metallodrugs as it is an endogenous metal and is therefore less toxic than other transition metals. The title compound, [Cu(C16H11N2O)2], was synthesized by reactingN-(quinolin-8-yl)benzamide and the metal in a 2:1 ratio. Ligand coordination required deprotonation of the amide N—H group and the isolated complex is therefore neutral. The metal ion adopts a flattened tetrahedral coordination geometry with the ligands in a pseudo-transconfiguration. The free rotation afforded by the formal single bond between the amide group and phenyl ring allows the phenyl rings to rotate out-of-plane, thus alleviating nonbonded repulsion between the phenyl rings and the quinolyl groups within the complex. Weak C—H...O interactions stabilize a dimer in the solid state. Density functional theory (DFT) simulations at the PBE/6-311G(dp) level of theory show that the solid-state structure (C1 symmetry) is 79.33 kJ mol−1higher in energy than the lowest energy gas-phase structure (C2 symmetry). Natural bond orbital (NBO) analysis offers an explanation for the formation of the C—H...O interactions in electrostatic terms, but the stabilizing effect is insufficient to support the dimer in the gas phase.
A new arc-length control method based on the rates of the internal and the dissipated energy
Authors: May Stefan , Vignollet Julien , de Borst René
Published: February 2016

Purpose

– The purpose of this paper is to introduce a new arc-length control method for physically non-linear problems based on the rates of the internal and the dissipated energy.

Design/methodology/approach

– In this paper, the authors derive from the second law of thermodynamics the arc-length method based on the rate of the dissipated energy and from the time derivative of the energy density the arc-length method based on the rate of the internal energy.

Findings

– The method requires only two parameters and can automatically trace equilibrium paths which display multiple snap-through and/or snap-back phenomena.

Originality/value

– A fully energy-based control procedure is developed, which facilitates switching between dissipative and non-dissipative arc-length control equations in a natural way. The method is applied to a plate with an eccentric hole using the phase field model for brittle fracture and to a perforated beam using interface elements with decohesion.
Strategies for computationally feasible multi-objective simulation-driven design of compact RF/microwave components
Authors: Koziel Slawomir , Bekasiewicz Adrian
Published: February 2016

Purpose

– Strategies for accelerated multi-objective optimization of compact microwave and RF structures are investigated, including the possibility of exploiting surrogate modeling techniques for electromagnetic (EM)-driven design speedup for such components. The paper aims to discuss these issues.

Design/methodology/approach

– Two algorithmic frameworks are described that are based on fast response surface approximation models, structure decomposition, and Pareto front refinement. Numerical case studies are provided demonstrating feasibility of solving real-world problems involving multi-objective optimization of miniaturized microwave passives and expensive EM-simulation models of such structures.

Findings

– It is possible, through appropriate combination of the surrogate modeling techniques and response correction methods, to identify the set of alternative designs representing the best possible trade-offs between conflicting design objectives in a realistic time frame corresponding to a few dozen of high-fidelity EM simulations of the respective structures.

Research limitations/implications

– The present study sets a direction for further studied on expedited optimization of computationally expensive simulation models for miniaturized microwave components.

Originality/value

– The proposed algorithmic framework proved useful for fast design of microwave structures, which is extremely challenging when using conventional methods. To the authors’ knowledge, this is one of the first attempts to surrogate-assisted multi-objective optimization of compact components at the EM-simulation level.
Effects of economic and social satisfaction on partner trust
Authors: Ha Hong-Youl , Lee Myung-Soo , Janda Swinder
Published: February 2016

Purpose

– It has previously been noted that channel relationships are more richly understood when viewed over time. Moreover, there is a lack of research on how two types of satisfaction (economic and social satisfaction) have differential effects on partner trust over time. The purpose of this study is to investigate whether (and if so how) these two types of satisfaction have differential effects on partner trust from the initial stage of channel relationship to the subsequent relationship period.

Design/methodology/approach

– Longitudinal data are used in an effort to understand the dynamic process of channel relationships over time.

Findings

– It is found that over time, the strength of the relationship between economic satisfaction and partner trust decreases, while the effect of social satisfaction on partner trust increases. Interestingly, the direct effect of perceived value on partner trust dramatically decreases from time point T to T + 1, indicating that these relationships exhibit significant temporal effects.

Research limitations/implications

– The most relevant theoretical implication is that social satisfaction has a desirable role of bridging the relationship between perceived value and partner trust at time points T and T + 1. Thus, social satisfaction is a key factor in sustaining a channel partnership over time even after initial perceived value has been enhanced via the route of economic satisfaction. The main limitation is that data were collected in South Korea – further validation would require data from multiple cultural contexts.

Practical implications

– Results provide important implications for channel members aiming to enhance trust with partners. In initial stages of a relationship, channel members should concentrate their marketing resources on enhancing economic satisfaction, as it plays a key role in enhancing trust. As channel relationships evolve, the role of social satisfaction between perceived value and partner trust becomes more important. Thus, in the latter stages of a relationship, it would be prudent to focus more on activities which enhance social satisfaction.

Originality/value

– To the best of the authors’ knowledge, there is very little research focusing on temporal carryover effects. The authors thus contribute to the establishment and testing of temporal carryover effects of various business-to-business (B2B) relationship-related constructs, such as perceived value, economic and social satisfaction and partner trust.
Exploring the impact of employees’ self-concept, brand identification and brand pride on brand citizenship behaviors
Authors: Helm Sabrina Verena , Renk Uwe , Mishra Anubha
Published: February 2016

Purpose

– The purpose of this paper is to identify how employees’ perceived congruity of their employers’ corporate brand with their own actual and ideal self may affect their brand identification (BI), brand pride (BP) and brand citizenship behavior (BCB).

Design/methodology/approach

– This cross-sectional paper involved 283 employees in Germany who completed an online survey.

Findings

– Congruity of the brand with employees’ actual self and with their ideal self has similar effects on employees’ BI. However, effects differ with respect to the other outcome variables. BP is only affected by congruity of the brand with the ideal self, whereas BCB is only affected by congruity of the brand with the actual self. Brand identity is positively related to BP and BCB; BP also affects BCB.

Research limitations/implications

– Future studies could include different sources for evaluation of BI, BP and BCB; for temporally separate measurement of identification, pride and BCB; and for use of fictitious brands or experimental manipulations of pride to increase internal validity. The discrepant impacts of congruity of the brand with the actual self and the ideal self as detected in the paper could spark research interest in addressing motivations to increase self-esteem and self-consistency in a work context or in investigating specific mediators or moderators in the relationship between self-concept, (brand) identification and pride, as well as behaviors. Finally, research could address different kinds of pride, such as individual and collective forms of pride, as well as their interplay.

Practical implications

– Managers should be aware of the different effects of a corporate brand’s fit with employees’ actual and ideal self, and also should note that BI seems essential in augmenting BP and brand-related behaviors. The paper develops implications for internal branding and HRM strategies regarding employee selection, promotion and retention. Findings also indicate that BP motivates BCB in line with current assumptions in research and practice on individual forms of pride.

Originality/value

– This paper investigates employees’ perceptions of “their” brand’s fit with their actual and ideal self separately, and determines the differences in impact on BP and BCB, extending existing knowledge on drivers of brand-building behaviors. It also develops the concept of BP in the context of social identity theory and the need for distinction; it further provides initial empirical insights into the role of employees’ BP, including the development of a measure.