Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: Applications in secondary structure analyses

Circular dichroism (CD) spectroscopy is a valuable method for defining canonical secondary structure contents of proteins based on empirically‐defined spectroscopic signatures derived from proteins with known three‐dimensional structures. Many proteins identified as being “Intrinsically Disordered Proteins” have a significant amount of their structure that is neither sheet, helix, nor turn; this type of structure is often classified by CD as “other”, “random coil”, “unordered”, or “disordered”. However the “other” category can also include polyproline II (PPII)‐type structures, whose spectral properties have not been well‐distinguished from those of unordered structures. In this study, synchrotron radiation circular dichroism spectroscopy was used to investigate the spectral properties of collagen and polyproline, which both contain PPII‐type structures. Their native spectra were compared as representatives of PPII structures. In addition, their spectra before and after treatment with various conditions to produce unfolded or denatured structures were also compared, with the aim of defining the differences between CD spectra of PPII and disordered structures. We conclude that the spectral features of collagen are more appropriate than those of polyproline for use as the representative spectrum for PPII structures present in typical amino acid‐containing proteins, and that the single most characteristic spectroscopic feature distinguishing a PPII structure from a disordered structure is the presence of a positive peak around 220nm in the former but not in the latter. These spectra are now available for inclusion in new reference data sets used for CD analyses of the secondary structures of soluble proteins.     

Rethinking trophic niches: Speed and body mass colimit prey space of mammalian predators

1. Realized trophic niches of predators are often characterized along a one‐dimensional range in predator–prey body mass ratios. This prey range is constrained by an “energy limit” and a “subdue limit” toward small and large prey, respectively. Besides these body mass ratios, maximum speed is an additional key component in most predator–prey interactions.
2. Here, we extend the concept of a one‐dimensional prey range to a two‐dimensional prey space by incorporating a hump‐shaped speed‐body mass relation. This new “speed limit” additionally constrains trophic niches of predators toward fast prey.
3. To test this concept of two‐dimensional prey spaces for different hunting strategies (pursuit, group, and ambush predation), we synthesized data on 63 terrestrial mammalian predator–prey interactions, their body masses, and maximum speeds.
4. We found that pursuit predators hunt smaller and slower prey, whereas group hunters focus on larger but mostly slower prey and ambushers are more flexible. Group hunters and ambushers have evolved different strategies to occupy a similar trophic niche that avoids competition with pursuit predators. Moreover, our concept suggests energetic optima of these hunting strategies along a body mass axis and thereby provides mechanistic explanations for why there are no small group hunters (referred to as “micro‐lions”) or mega‐carnivores (referred to as “mega‐cheetahs”).
5. Our results demonstrate that advancing the concept of prey ranges to prey spaces by adding the new dimension of speed will foster a new and mechanistic understanding of predator trophic niches and improve our predictions of predator–prey interactions, food web structure, and ecosystem functions.

     

EFFECT OF SESAME LEAF DIET ON DETOXIFICATION ACTIVITIES OF INSECTS WITH DIFFERENT FEEDING BEHAVIOR

Three diverse insects, a polyphagous “leaf chewer” (Atractomorpha lata), a polyphagous “sap feeder” (Myzus persicae), and a “restrictive feeder” (Plutella xylostella) responded differently when fed with eight cultivars of sesame either as whole leaf or via artificial diet. There was limited or no correlation in induction between detoxifying enzyme substrates (esterase, glutathione s‐transferase [GST], and mixed function oxidase [MFO] activities) when activity toward various substrates α‐naphthyl acetate, 1‐chloro‐2,4‐dinitrobenzene, 1,2‐dichloro‐4‐nitrobenzene, and p‐nitroanisole (pNA), were compared although they were generally elevated in the tissues from insects on sesame than a reference fed with radish seedlings. In A. lata, esterase activity for the cultivar 11Pusan and 45Laos were three‐fold higher compared to the reference, while other cultivars, 24Nanbu‐twasaki and 56S‐radiatum were—two‐ to three‐fold lower than the reference. In M. persicae, the esterase activity was as much as five‐fold higher than the reference in one test cultivar. GST activities of the sesame cultivars were generally higher (≈two‐fold) than the reference in all insects and at variable ratios among the cultivars. The MFO activity toward pNA in grasshoppers feeding on these sesame cultivars was either highly expressed or nonexistent. These results indicate that although the cultivars belong to the same species, they might have undergone changes in secondary phytochemicals in response to varying biogeographical distribution. Each insect species is suspected to target a specific plant chemical burden that it tries to overcome in each cultivar through enzyme activation.     

Directional change in upland tundra plant communities 20‐30 years after seismic exploration in the Canadian low‐arctic

Question: What is the disturbance response of low‐arctic plant communities two to three decades after seismic exploration. Location: Mackenzie River Delta, low‐arctic, northwestern Canada. Methods: Plant communities in two upland tundra vegetation types were compared between winter seismic lines, created between 1970 and 1986, and adjacent “reference” tundra. Also, we used aerial surveys to quantify the total area impacted by visible linear features. Results: Vascular plant cover was significantly higher, and lichen cover significantly lower, on seismic lines than in reference tundra. The increase in vascular plant cover was attributable to deciduous shrubs and graminoids. There were significant differences in plant community composition between seismic lines and reference tundra but no differences in species diversity or richness. Betula glandulosa and Arctagrostis latifolia were significant indicator species for seismic lines, while Saussurea angustifolia was a significant indicator for reference tundra. Based on the aerial surveys, these effects apply to at least 90% of seismic lines from two‐dimensional programs in these habitat types during the 1970s. Conclusions: Vegetation composition and structure on 20‐30‐year‐old seismic lines differs from reference upland tundra despite no persistent differences in organic layer depth or depth to permafrost. We propose that this reflects: (1) successional redevelopment following changes in soil conditions and nutrient availability arising from the disturbance, and/or (2) disturbance‐initiated succession towards a community reflecting current climatic conditions.     

A critique of the “ultra‐high risk” and “transition” paradigm

The transdiagnostic expression of psychotic experiences in common mental disorder (anxiety/depression/substance use disorder) is associated with a poorer prognosis, and a small minority of people may indeed develop a clinical picture that meets criteria for schizophrenia. However, it appears neither useful nor valid to observe early states of multidimensional psychopathology in young people through the “schizo”‐prism, and apply misleadingly simple, unnecessary and inefficient binary concepts of “risk” and “transition”. A review of the “ultra‐high risk” (UHR) or “clinical high risk” (CHR) literature indicates that UHR/CHR samples are highly heterogeneous and represent individuals diagnosed with common mental disorder (anxiety/depression/substance use disorder) and a degree of psychotic experiences. Epidemiological research has shown that psychotic experiences are a (possibly non‐causal) marker of the severity of multidimensional psychopathology, driving poor outcome, yet notions of “risk” and “transition” in UHR/CHR research are restrictively defined on the basis of positive psychotic phenomena alone, ignoring how baseline differences in multidimensional psychopathology may differentially impact course and outcome. The concepts of “risk” and “transition” in UHR/CHR research are measured on the same dimensional scale, yet are used to produce artificial diagnostic shifts. In fact, “transition” in UHR/CHR research occurs mainly as a function of variable sample enrichment strategies rather than the UHR/CHR “criteria” themselves. Furthermore, transition rates in UHR/CHR research are inflated as they do not exclude false positives associated with the natural fluctuation of dimensional expression of psychosis. Biological associations with “transition” thus likely represent false positive findings, as was the initial claim of strong effects of omega‐3 polyunsatured fatty acids in UHR samples. A large body of UHR/CHR intervention research has focused on the questionable outcome of “transition”, which shows lack of correlation with functional outcome. It may be more productive to consider the full range of person‐specific psychopathology in all young individuals who seek help for mental health problems, instead of “policing” youngsters for the transdiagnostic dimension of psychosis. Instead of the relatively inefficient medical high‐risk approach, a public health perspective, focusing on improved access to a low‐stigma, high‐hope, small scale and youth‐specific environment with acceptable language and interventions may represent a more useful and efficient strategy.     

The Challenge to Restore Processes in Face of Nonlinear Dynamics—On the Crucial Role of Disturbance Regimes

Increasingly, restoration ecologists and managers are challenged to restore ecological processes that lead to self‐sustaining ecosystem dynamics. Due to changing environmental conditions, however, restoration goals need to include novel regimes beyond prior reference conditions or reference dynamics. In face of these fundamental challenges in process‐based restoration ecology, disturbance ecology can offer useful insights. Here, I discuss the contribution of disturbance ecology to understanding assembly rules, ecosystem dynamics, regime shifts, and nonlinear dynamics. Using the patch and multipatch concept, all insights are organized according to two spatial and two temporal categories: “patch–event,”“patch–multievent,”“multipatch–event,” and “multipatch–multievent.” This concept implies the consideration of both spatial patterns and temporal rhythms inside and outside of a restoration site. Emerging issues, such as uncoupling of internal and external dynamics, are considered.     

Progress in scaffold‐free bioprinting for cardiovascular medicine

Biofabrication of tissue analogues is aspiring to become a disruptive technology capable to solve standing biomedical problems, from generation of improved tissue models for drug testing to alleviation of the shortage of organs for transplantation. Arguably, the most powerful tool of this revolution is bioprinting, understood as the assembling of cells with biomaterials in three‐dimensional structures. It is less appreciated, however, that bioprinting is not a uniform methodology, but comprises a variety of approaches. These can be broadly classified in two categories, based on the use or not of supporting biomaterials (known as “scaffolds,” usually printable hydrogels also called “bioinks”). Importantly, several limitations of scaffold‐dependent bioprinting can be avoided by the “scaffold‐free” methods. In this overview, we comparatively present these approaches and highlight the rapidly evolving scaffold‐free bioprinting, as applied to cardiovascular tissue engineering.     

Signification differentielle des photoperiodes pour l'horloge biologique de Pieris brassicae (Lepidoptera)

Abstract

Photoperiodic insects are able to distinguish between long days and short days. In various models the long day response is classifically considered the “actively” induced state. The short day response is thought to be “passive”, caused by failure of light to coincide with a photosensitive part of the night or failure of coincidence of constituent oscillators. The photoperiodic response curve of Pieris brassicae showed that diapause is induced by short days (4–14 h), and non‐diapause state by several conditions (natural and non‐natural): long days (16 h or more), LL, DD and ultrashort days (0.1 h). By reciprocal transfers of larvae between non‐diapausing determining and diapause determining conditions, it was proved possible to estimate the differential capacity of four non‐diapausing conditions vs. the diapausing action of LD 8: 16 in decreasing sequence: LD 16:8 > LL > DD = LD 0.1: 23.9. DD may be considered a “neutral” condition. In darkness the development seems to be determined by an endogenous program without external influence. LL, although beingan aperiodic signal as DD, has a weak antidiapausingeffect.Thebiological clock of Pieris differentiates between two constant conditions. The four non‐diapausing conditions have the same effect on the development when applied during the entire larval life, but have different effects when only applied during a few days. Both ecological conditions LD 16:8 and LD 8:16 have an action on the development but in an opposite way. There was not a “passive” state caused by failure of another inductive photoperiod. Ultra‐short days, DD and LL are without ecological meaning. Nevertheless, in these experiments, they provided informations in attempts to determine the mechanism of the time measurement. The external coincidence model of Pittendrigh and Minis (1964) was the more adequate to explain theearlier results on the biological clock of Pieris. However, this model has to be modified to account for the differential significance of several non‐diapausing conditions.     

Multivariate Data Analysis Methodology to Solve Data Challenges Related to Scale‐Up Model Validation and Missing Data on a Micro‐Bioreactor System

Multivariate data analysis (MVDA) is a highly valuable and significantly underutilized resource in biomanufacturing. It offers the opportunity to enhance understanding and leverage useful information from complex high‐dimensional data sets, recorded throughout all stages of therapeutic drug manufacture. To help standardize the application and promote this resource within the biopharmaceutical industry, this paper outlines a novel MVDA methodology describing the necessary steps for efficient and effective data analysis. The MVDA methodology is followed to solve two case studies: a “small data” and a “big data” challenge. In the “small data” example, a large‐scale data set is compared to data from a scale‐down model. This methodology enables a new quantitative metric for equivalence to be established by combining a two one‐sided test with principal component analysis. In the “big data” example, this methodology enables accurate predictions of critical missing data essential to a cloning study performed in the ambr15 system. These predictions are generated by exploiting the underlying relationship between the off‐line missing values and the on‐line measurements through the generation of a partial least squares model. In summary, the proposed MVDA methodology highlights the importance of data pre‐processing, restructuring, and visualization during data analytics to solve complex biopharmaceutical challenges.     

Digitalis receptor desensitization in rat ventricle: Ouabain produces two inotropic effects

In rat ventricular strips at 35° and 37°C, at 1 Hz and 3 Hz stimulation rate and in Krebs-Henseleit and Tyrode solution, cumulative dose/response curves of ouabain revealed two apparent positive inotropic effects, a “low-dose” effect with a half maximal increase in contractile force (ED₅₀) of 0.5 μM ouabain representing about 30% of the total inotropy and a “high-dose” effect of 19 to 35 μM ouabain representing about 70% of total inotropy. The overall or combined ED₅₀ was 16 μM ouabain. The “low-dose” effect was not prevented by α or β adrenergic blockade, by reserpinization, or by histamine H₂ antagonist. However, when the tissue preparations were washed for 60 to 120 min after completion of the first dose/response experiment, a second dose/response curve with ouabain revealed an absence or disappearance of the “low-dose” effect and a normal “high-dose” effect. The “low-dose” effect is apparently related to pretreatment with ouabain. We refer to this phenomenon as “desensitization”.     

Contrasting patterns of density‐dependent selection at different life stages can create more than one fast–slow axis of life‐history variation

There has been much recent research interest in the existence of a major axis of life‐history variation along a fast–slow continuum within almost all major taxonomic groups. Eco‐evolutionary models of density‐dependent selection provide a general explanation for such observations of interspecific variation in the "pace of life." One issue, however, is that some large‐bodied long‐lived “slow” species (e.g., trees and large fish) often show an explosive “fast” type of reproduction with many small offspring, and species with “fast” adult life stages can have comparatively “slow” offspring life stages (e.g., mayflies). We attempt to explain such life‐history evolution using the same eco‐evolutionary modeling approach but with two life stages, separating adult reproductive strategies from offspring survival strategies. When the population dynamics in the two life stages are closely linked and affect each other, density‐dependent selection occurs in parallel on both reproduction and survival, producing the usual one‐dimensional fast–slow continuum (e.g., houseflies to blue whales). However, strong density dependence at either the adult reproduction or offspring survival life stage creates quasi‐independent population dynamics, allowing fast‐type reproduction alongside slow‐type survival (e.g., trees and large fish), or the perhaps rarer slow‐type reproduction alongside fast‐type survival (e.g., mayflies—short‐lived adults producing few long‐lived offspring). Therefore, most types of species life histories in nature can potentially be explained via the eco‐evolutionary consequences of density‐dependent selection given the possible separation of demographic effects at different life stages.     

The SER Standards,cultural ecosystems,and the nature‐culture nexus—a reply to Evans and Davis

Evans and Davis claim the SER Standards use a “pure naturalness” model for restoration baselines and exclude most cultural ecosystems from the ecological restoration paradigm. The SER Standards do neither. The SER Standards consider both “natural” ecosystems (that are unequivocally not cultural) and “similar” cultural ecosystems as suitable reference models. Furthermore, Evans and Davis propose assessing whether a cultural ecosystem exhibits “good, bad, or neutral impacts from humans on ecosystems” as the basis for reference models. We argue that such an approach would overlook the indispensability of native ecosystem benchmarks to measure human impacts and provide a springboard for social‐ecological restoration.     

On ROC analysis with nonbinary reference standard

Statistical methods for the evaluation of the accuracy of diagnostic tests usually assume a binary true disease status. However, this assumption may not be realistic in practical settings in which “disease” is defined by dichotomizing continuous or ordinal categorical measures using a pre‐specified threshold value. In this paper, we focus on the analysis of studies in which both the diagnostic test and the reference standard are reported as continuous measures. We propose a semiparametric model for estimating the sensitivity, specificity, and the ROC curve as functions of reference standard thresholds. Under suitable order restrictions on the mean of the test result variable, fitting is done via two alternative approaches: isotonic regression and monotone smoothing splines. The model provides the basis to assess the effect of varying reference standard threshold on the performance of a diagnostic test. An example to evaluate the ability of the maximal SUV‐lean (standardized uptake value normalized to lean body mass) in predicting axillary node involvement in women diagnosed with breast cancer is presented.     

The Genomic Code: A Pervasive Encoding/Molding of Chromatin Structures and a Solution of the “Non‐Coding DNA” Mystery

Recent investigations have revealed 1) that the isochores of the human genome group into two super‐families characterized by two different long‐range 3D structures, and 2) that these structures, essentially based on the distribution and topology of short sequences, mold primary chromatin domains (and define nucleosome binding). More specifically, GC‐poor, gene‐poor isochores are low‐heterogeneity sequences with oligo‐A spikes that mold the lamina‐associated domains (LADs), whereas GC‐rich, gene‐rich isochores are characterized by single or multiple GC peaks that mold the topologically associating domains (TADs). The formation of these “primary TADs” may be followed by extrusion under the action of cohesin and CTCF. Finally, the genomic code, which is responsible for the pervasive encoding and molding of primary chromatin domains (LADs and primary TADs, namely the “gene spaces”/“spatial compartments”) resolves the longstanding problems of “non‐coding DNA,” “junk DNA,” and “selfish DNA” leading to a new vision of the genome as shaped by DNA sequences.     

Tropicality and abjection: What do we really mean by “Neglected Tropical Diseases”?

Neglected tropical diseases are defined operationally as diseases that prevail in “tropical” regions and are under‐researched, under‐funded, and under‐treated compared with their disease burden. By analysing the adjectives “tropical” and “neglected,” I expose and interrogate the discourses within which the term “neglected tropical disease” derives its meaning. First, I argue that the term “tropical” conjures the notion of “tropicality,” a form of Othering which erroneously explains the disease‐prevalence of “tropical” regions by reference to environmental determinism, rather than colonialism and neocolonialism. Second, I examine the way in which this Othering enables the abjection of tropical regions and their peoples, leading to neglect. I recommend that the term “neglected tropical diseases” be more carefully contextualised within health scholarship, education, and policy.     

THE CONTRIBUTION OF SPONTANEOUS MUTATIONS TO THERMAL SENSITIVITY CURVE VARIATION IN DROSOPHILA SERRATA

Many traits studied in ecology and evolutionary biology change their expression in response to a continuously varying environmental factor. One well‐studied example are thermal performance curves (TPCs); continuous reaction norms that describe the relationship between organismal performance and temperature and are useful for understanding the trade‐offs involved in thermal adaptation. We characterized curves describing the thermal sensitivity of voluntary locomotor activity in a set of 66 spontaneous mutation accumulation lines in the fly Drosophila serrata. Factor‐analytic modeling of the mutational variance–covariance matrix, M , revealed support for three axes of mutational variation in males and two in females. These independent axes of mutational variance corresponded well to the major axes of TPC variation required for different types of thermal adaptation; “faster‐slower” representing changes in performance largely independent of temperature, and the “hotter‐colder” and “generalist‐specialist” axes, representing trade‐offs. In contrast to its near‐absence from standing variance in this species, a “faster‐slower” axis, accounted for most mutational variance (75% in males and 66% in females) suggesting selection may easily fix or remove these types of mutations in outbred populations. Axes resembling the “hotter‐colder” and “generalist‐specialist” modes of variation contributed less mutational variance but nonetheless point to an appreciable input of new mutations that may contribute to thermal adaptation.     

Selection on the morphology–physiology‐performance nexus: Lessons from freshwater stickleback morphs

Conspecifics inhabiting divergent environments frequently differ in morphology, physiology, and performance, but the interrelationships amongst traits and with Darwinian fitness remains poorly understood. We investigated population differentiation in morphology, metabolic rate, and swimming performance in three‐spined sticklebacks (Gasterosteus aculeatus L.), contrasting a marine/ancestral population with two distinct freshwater morphotypes derived from it: the “typical” low‐plated morph, and a unique “small‐plated” morph. We test the hypothesis that similar to plate loss in other freshwater populations, reduction in lateral plate size also evolved in response to selection. Additionally, we test how morphology, physiology, and performance have evolved in concert as a response to differences in selection between marine and freshwater environments. We raised pure‐bred second‐generation fish originating from three populations and quantified their lateral plate coverage, burst‐ and critical swimming speeds, as well as standard and active metabolic rates. Using a multivariate Q_ST‐F_ST framework, we detected signals of directional selection on metabolic physiology and lateral plate coverage, notably demonstrating that selection is responsible for the reduction in lateral plate coverage in a small‐plated stickleback population. We also uncovered signals of multivariate selection amongst all bivariate trait combinations except the two metrics of swimming performance. Divergence between the freshwater and marine populations exceeded neutral expectation in morphology and in most physiological and performance traits, indicating that adaptation to freshwater habitats has occurred, but through different combinations of traits in different populations. These results highlight both the complex interplay between morphology, physiology and performance in local adaptation, and a framework for their investigation.     

“Saddle-shaped” dose-survival effect,is it a general and valuable phenomenon in microbes in response to heavy ion beam irradiation?

We aimed to verify the “saddle-shaped” dose-survival effect of microbes in response to heavy ion beam irradiation (HI), and further determine the radiation parameter that affects saddle shape formation, and the relationship between the saddle region and the positive mutation rate. A bibliometric analysis was performed based on literature containing the dose-survival effect of microbes in response to HI, from which the data on the particle energies, ionic types, irradiated microbes, survival curves, and maximum positive mutation rates were assembled. Articles reporting a “saddle-shaped” survival curve accounted for 64% of the total relevant articles and possessed a high cited frequency. The predominant articles, authors, and institutions that reported the dose-survival effect of microbes in response to HI proposed the “saddle-shaped” survival curve. It was customarily low-energy (but not moderate- or high-energy) HI that induced the “saddle-shaped” dose-survival effect. In addition, the “saddle-shaped” dose-survival effect was general among ~ 30-genera microbes. More importantly, most of the saddle regions contained the survival fractions within 10–30%, which are customarily used to screen mutants due to a high positive mutation rate. Further, 87% of the maximum positive mutation rates were associated with the saddle region, and 58% were located in the peak of the saddle region. “Saddle-shaped” dose-survival effect is a reliable and general phenomenon among varieties of microbes customarily in response to low-energy HI. Meanwhile, saddle region is always accompanied with high positive mutation rates. Thus, this study will aid in microbial mutation breeding practices.

     

Insect photoperiodism: effects of temperature on the induction of insect diapause and diverse roles for the circadian system in the photoperiodic response

This review considers the effects of temperature on insect diapause induction and the photoperiodic response, and includes constant temperature, temperature cycles, pulses and steps in daily light–dark cycles, constant darkness and in constant light, all with reference to various circadian‐based “clock” models. Although it is a comparative survey, it concentrates on two species, the flesh fly Sarcophaga argyrostoma and its pupal parasite Nasonia vitripennis, which possess radically different photoperiodic mechanisms, although both are based upon the circadian system. Particular attention is given to the effects of daily thermoperiod in darkness and to low and high temperature pulses in conjunction with a daily light–dark cycle, treatments that suggest that S. argyrostoma “measures” night length with a “clock” of the external coincidence type. However, N. vitripennis responds to seasonal changes in photoperiod with an internal coincidence device involving both “dawn” and “dusk” oscillators. Other species may show properties of both external and internal coincidence. Although the precepts of external coincidence have been well formulated and supported experimentally, those for internal coincidence remain obscure.