Molecular dynamics and molecular docking studies on E166A point mutant,R274N/R276N double mutant,and E166A/R274N/R276N triple mutant forms of class A β-lactamases

Bacterial resistance to β-lactams antibiotics is a serious threat to human health. The most common cause of resistance to the β-lactams is the production of β-lactamase that inactivates β-lactams. Specifically, class A extended-spectrum β-lactamase produced by antibiotic resistant bacteria is capable of hydrolyzing extended-spectrum Cephalosporins and Monobactams. Mutations in class A β-lactamases play a crucial role in substrate and inhibitor specificity. In this present study, the E166A point mutant, R274N/R276N double mutant, and E166A/R274N/R276N triple mutant class A β-lactamases are analyzed. Molecular dynamics (MD) simulations are done to understand the consequences of mutations in class A β-lactamases. Root mean square deviation, root mean square fluctuation, radius of gyration, solvent accessibility surface area, hydrogen bond, and essential dynamics analysis results indicate notable loss in stability for mutant class A β-lactamases. MD simulations of native and mutant structures clearly confirm that the substitution of alanine at the position of 166, Asparagine at 274 and 276 causes more flexibility in 3D space. Molecular docking results indicate the mutation in class A β-lactamases which decrease the binding affinity of Cefpirome and Ceftobiprole which are third and fifth generation Cephalosporins, respectively. MD simulation of Ceftobiprole-native and mutant type Class A β-lactamases complexes reveal that E166A/R274N/R276N mutations alter the structure and notable loss in the stability for Ceftobirole-mutant type Class A β-lactamases complexes. Ceftobiprole is currently prescribed for patients with serious bacterial infections; this phenomenon is the probable cause for the effectiveness of Ceftobiprole in controlling bacterial infections.     

Regulating the response to targeted MEK inhibition in melanoma: Enhancing apoptosis in NRAS- and BRAF-mutant melanoma cells with Wnt/β-catenin activation

The limitations of revolutionary new mutation-specific inhibitors of BRAF^V600E include the universal recurrence seen in melanoma patients treated with this novel class of drugs. Recently, our lab showed that simultaneous activation of the Wnt/β-catenin signaling pathway and targeted inhibition of BRAF^V600E by PLX4720 synergistically induces apoptosis across a spectrum of BRAF^V600E melanoma cell lines. As a follow-up to that study, treatment of BRAF-mutant and NRAS-mutant melanoma lines with WNT3A and the MEK inhibitor AZD6244 also induces apoptosis. The susceptibility of BRAF-mutant lines and NRAS-mutant lines to apoptosis correlates with negative regulation of Wnt/β-catenin signaling by ERK/MAPK signaling and dynamic decreases in abundance of the downstream scaffolding protein, AXIN1. Apoptosis-resistant NRAS-mutant lines can sensitize to AZD6244 by pretreatment with AXIN1 siRNA, similar to what we previously reported in BRAF-mutant cell lines. Taken together, these findings indicate that NRAS-mutant melanoma share with BRAF-mutant melanoma the potential to regulate apoptosis upon MEK inhibition through WNT3A and dynamic regulation of cellular AXIN1. Understanding the cellular context that makes melanoma cells susceptible to this combination treatment will contribute to the study and development of novel therapeutic combinations that may lead to more durable responses.     

Do cities simulate climate change? A comparison of herbivore response to urban and global warming

Cities experience elevated temperature, CO₂, and nitrogen deposition decades ahead of the global average, such that biological response to urbanization may predict response to future climate change. This hypothesis remains untested due to a lack of complementary urban and long‐term observations. Here, we examine the response of an herbivore, the scale insect Melanaspis tenebricosa, to temperature in the context of an urban heat island, a series of historical temperature fluctuations, and recent climate warming. We survey M. tenebricosa on 55 urban street trees in Raleigh, NC, 342 herbarium specimens collected in the rural southeastern United States from 1895 to 2011, and at 20 rural forest sites represented by both modern (2013) and historical samples. We relate scale insect abundance to August temperatures and find that M. tenebricosa is most common in the hottest parts of the city, on historical specimens collected during warm time periods, and in present‐day rural forests compared to the same sites when they were cooler. Scale insects reached their highest densities in the city, but abundance peaked at similar temperatures in urban and historical datasets and tracked temperature on a decadal scale. Although urban habitats are highly modified, species response to a key abiotic factor, temperature, was consistent across urban and rural‐forest ecosystems. Cities may be an appropriate but underused system for developing and testing hypotheses about biological effects of climate change. Future work should test the applicability of this model to other groups of organisms.     

Fructose and uric acid as drivers of a hyperactive foraging response: A clue to behavioral disorders associated with impulsivity or mania?

Several behavioral disorders, including attention deficit hyperactivity disorder (ADHD), bipolar disorder, and aggressive behaviors are linked with sugar intake and obesity. The reason(s) for this association has been unclear. Here we present a hypothesis supporting a role for fructose, a component of sugar and high fructose corn syrup (HFCS), and uric acid (a fructose metabolite), in increasing the risk for these behavioral disorders. Recent studies have shown that the reason fructose intake is strongly associated with development of metabolic syndrome is that fructose intake activates an evolutionary-based survival pathway that stimulates foraging behavior and the storage of energy as fat. While modest intake may aid animals that would like to store fat as a protective response from food shortage or starvation, we propose that high intake of sugar and HFCS causes a hyperactive foraging response that stimulates craving, impulsivity, risk taking and aggression that increases the risk for ADHD, bipolar disease and aggressive behavior. High glycemic carbohydrates and salty foods may also contribute as they can be converted to fructose in the body. Some studies suggest uric acid produced during fructose metabolism may mediate some of these effects. Chronic stimulation of the pathway could lead to desensitization of hedonic responses and induce depression. In conclusion, a hyperactive foraging response driven by high glycemic carbohydrates and sugars may contribute to affective disorders.     

A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life

Most genomes are much more complex than required for the minimum chemistry of life. Evolution has selected sophistication more than life itself. Could this also apply to bioenergetics? We first examine mechanisms through which bioenergetics could deliver sophistication. We illustrate possible benefits of the turbo-charging of catabolic pathways, of loose coupling, low-gear catabolism, automatic transmission in energy coupling, and of homeostasis. Mechanisms for such phenomena may reside at the level of individual proton pumps, or consist of rerouting of electrons over parallel pathways. The mechanisms may be confined to preexisting components, or involve the plasticity of gene expression that is so characteristic of most living organisms. These possible benefits lead us to the conjecture that also bioenergetics has evolved more for sophistication than for necessity. We next discuss a hitherto unresolved enigma, i.e. that bioenergetics does not seem to be critical for the physiological state. To decide on how critical bioenergetics is, we quantified the control exerted by catabolism on important physiological functions such as growth rate and growth yield. We also determined whether a growth inhibition mostly affected bioenergetics (catabolism) or anabolism; if ATP increases with growth rate, then growth should be considered energy (catabolism) limited. The experimental results for Escherichia coli pinpoint the enigma: its energy metabolism (catabolism) is not critical for growth rate. These results might suggest that because it has no direct control over cell function, bioenergetics is unimportant. Paradoxically however, in biology, highly important mechanisms tend to have little control on cell function, precisely because of that importance. Sophistication in terms of homeostatic mechanisms has evolved to guarantee robustness of the most important functions: The most important mechanisms are redundant in biology. Bioenergetics may be an excellent example of this paradox, in line with the above conjecture. It may be highly important and sophisticated. We then discuss work that has begun to focus on the sophistication of bioenergetics. Homeostasis of the energetics of DNA structure in E. coli is extensive. It relies both on preexisting components and on responsive gene expression. The vastly parallel electron-transfer network of Paracoccus denitrificans engages in sophisticated dynamic and hierarchical regulation. The growth yield of the organism can depend on which terminal oxidases are active. Effective proton translocation may vary due to rerouting of electrons. We conclude that much sophistication of bioenergetics will be discovered in this era of functional genomics.     

A substrate cycling model for nitrate uptake byPisum sativum seedlings: A key to sensitivity of response of net flux to substrate and effectors?

Summary Net nitrate uptake (J) intoPisum sativum L. seedlings has been investigated. J was high initially, but declined with time as NO ₃ ^– efflux (E) approached that of NO ₃ ^– influx (I). Both I and E were higher in plants which had been grown without N. J could be reversibly and immediately inhibited by 5 mmol m^–3 NH ₄ ⁺ , although plants grown in the presence of nitrate were less sensitive. A theoretical model which involves substrate cycling across the plasmalemma is shown to increase the sensitivity to substrate and effectors. It predicts that during growth of Pisum in N free media the cycling rate (E/I) is increased and the sensitivity of net flux of inhibition by NH ₄ ⁺ is highest. The model also provides a means for control of cytoplasmic nitrate pool size [NO ₃ ^– ] c.     

Should I pick that? A scoring tool to prioritize and valuate native wild seed for restoration

Commercial sources of native seed are often unavailable for ecological restoration projects or do not have a suitable provenance. Local collection of wild seed is an option, but it can be challenging to collect seed for a variety of species and set fair seed prices. Our aim was to quantify the relative effort to collect, clean, store, and propagate seed to better prioritize species and assess the value of their seed. For 57 species native to the Canadian subarctic and typical of upland habitats, we evaluated 13 poorly correlated attributes in the field and lab or using the literature. For collection attributes, regional occurrence, local abundance, seed collection rate, and collection window were normally or log‐normally distributed. Most species were easy to identify and posed few collection obstacles. Cleaning effort was evenly distributed across species and the majority could be cleaned to more than 95% purity. We only encountered orthodox seed and most species had seed longevity exceeding a year. Seed viability mostly exceeded 80%, pre‐treatment requirements were evenly distributed and the majority of species could be germinated under standard conditions. We propose a standard worksheet, in which we assign relative effort scores to the distribution of each attribute. We illustrate this approach for the revegetation planning of a remote mine site. We also propose a seed lot certificate to ensure high seed quality. This tool can be applied to various restoration applications to assess relative effort, to plan and prioritize species for restoration projects and to help set fair seed pricing.     

Separate generators with distinct orientations for N20 and P22 somatosensory evoked potentials to finger stimulation?

Sequential spatial maps of scalp potentials, obtained with a 16-channel montage, were used in 12 healthy subjects in order to assess the temporal and spatial distribution of early cortical SEPs to single finger stimulation. It was found that when the contralateral parietal N20 negativity peaks there is a synchronous frontal P20 positivity, supporting the view of a tangentially orientated dipolar generator for this couple of scalp SEPs components. It was not possible to show a distribution of N20 peak on the scalp that would parallel the somatotopic finger representations in area S1; however, the orientation of the putative dipolar source of the N20/P20 complex was found to change according to the finger stimulated. A central P22 component was also constantly obtained without any synchronous negativity on the scalp surface corresponding to the electrode array; a clear somatotopic organisation was found for P22. These features favour the hypothesis that this latter component has a radially orientated generator situated in the prerolandic motor cortex, close to the scalp surface. Because of overlapping between the P20 and P22 components, the determination of P22 onset latency was hazardous in some cases, and spatial mapping was then essential to identify this component. The conclusion that the contralateral parietal N20 and central P22 could be generated by separate dipolar generators with distinct orientations is supported by recent data from combined electrical and magnetic field recording.     

Do PTK2 gene polymorphisms contribute to the interindividual variability in muscle strength and the response to resistance training? A preliminary report

The protein tyrosine kinase-2 (PTK2) gene encodes focal adhesion kinase, a structural protein involved in lateral transmission of muscle fiber force. We investigated whether single-nucleotide polymorphisms (SNPs) of the PTK2 gene were associated with various indexes of human skeletal muscle strength and the interindividual variability in the strength responses to resistance training. We determined unilateral knee extension single repetition maximum (1-RM), maximum isometric voluntary contraction (MVC) knee joint torque, and quadriceps femoris muscle specific force (maximum force per unit physiological cross-sectional area) before and after 9 wk of knee extension resistance training in 51 untrained young men. All participants were genotyped for the PTK2 intronic rs7843014 A/C and 3'-untranslated region (UTR) rs7460 A/T SNPs. There were no genotype associations with baseline measures or posttraining changes in 1-RM or MVC. Although the training-induced increase in specific force was similar for all PTK2 genotypes, baseline specific force was higher in PTK2 rs7843014 AA and rs7460 TT homozygotes than in the respective rs7843014 C- (P = 0.016) and rs7460 A-allele (P = 0.009) carriers. These associations between muscle specific force and PTK2 SNPs suggest that interindividual differences exist in the way force is transmitted from the muscle fibers to the tendon. Therefore, our results demonstrate for the first time the impact of genetic variation on the intrinsic strength of human skeletal muscle.     

How integrated are behavioral and endocrine stress response traits? A repeated measures approach to testing the stress-coping style model

It is widely expected that physiological and behavioral stress responses will be integrated within divergent stress‐coping styles (SCS) and that these may represent opposite ends of a continuously varying reactive–proactive axis. If such a model is valid, then stress response traits should be repeatable and physiological and behavioral responses should also change in an integrated manner along a major axis of among‐individual variation. While there is some evidence of association between endocrine and behavioral stress response traits, few studies incorporate repeated observations of both. To test this model, we use a multivariate, repeated measures approach in a captive‐bred population of Xiphophorus birchmanni. We quantify among‐individual variation in behavioral stress response to an open field trial (OFT) with simulated predator attack (SPA) and measure waterborne steroid hormone levels (cortisol, 11‐ketotestosterone) before and after exposure. Under the mild stress stimulus (OFT), (multivariate) behavioral variation among individuals was consistent with a strong axis of personality (shy–bold) or coping style (reactive–proactive) variation. However, behavioral responses to a moderate stressor (SPA) were less repeatable, and robust statistical support for repeatable endocrine state over the full sampling period was limited to 11‐ketotestosterone. Although post hoc analysis suggested cortisol expression was repeatable over short time periods, qualitative relationships between behavior and glucocorticoid levels were counter to our a priori expectations. Thus, while our results clearly show among‐individual differences in behavioral and endocrine traits associated with stress response, the correlation structure between these is not consistent with a simple proactive–reactive axis of integrated stress‐coping style. Additionally, the low repeatability of cortisol suggests caution is warranted if single observations (or indeed repeat measures over short sampling periods) of glucocorticoid traits are used in ecological or evolutionary studies focussed at the individual level.     

Can the functional response to prey predict invasiveness? A comparison of native fishes and alien poeciliids in Hong Kong

Biological invasion is globally pervasive and an increasing threat to biodiversity. We need to be able to predict the ecological impacts of alien species, in order to prioritize management of those expected to be most damaging. Comparisons of functional response (FR) between invaders and trophically similar natives has been proposed as useful for predicting invader impacts, as interaction intensity tends to be reflected in higher FRs. We undertook feeding trials comparing FRs of four invasive poeciliids (mosquitofish [Gambusia affinis], guppy [Poecilia reticulata], liberty molly [P. salvatoris] and swordtail [Xiphophorus hellerii]) in Hong Kong with three similar-sized native fishes (ricefish [Oryzias curvinotus: Adrianichthyidae]; predaceous chub [Parazacco spilurus] and half-banded barb [Puntius semifasciolatus: Cyprinidae]). We tested whether FRs correctly reflected known impacts of the mosquitofish and guppy locally, and used FRs to forecast potential impacts of the molly and swordtail. Overall, the swordtail and molly consumed more prey and had higher FRs than the other five fishes, owing to their shorter prey handling time and/or higher attack rate. Mosquitofish and guppy had similar FRs to native fishes. All fishes showed type-II FRs, and had some potential to destabilize prey populations. Such results predict that the molly and swordtail could have strong ecological effects in Hong Kong freshwaters. However, FR alone was not highly predictive of known impacts of mosquitofish and guppy. It is suggested a more holistic approach incorporating estimates of field abundance and parameterization of other niche dimensions of the invader will be needed.