Phenotypic flexibility as a measure of health: the optimal nutritional stress response test

Nutrition research is struggling to demonstrate beneficial health effects, since nutritional effects are often subtle and long term. Health has been redefined as the ability of our body to cope with daily-life challenges. Physiology acts as a well-orchestrated machinery to adapt to the continuously changing environment. We term this adaptive capacity “phenotypic flexibility.” The phenotypic flexibility concept implies that health can be measured by the ability to adapt to conditions of temporary stress, such as physical exercise, infections or mental stress, in a healthy manner. This may offer a more sensitive way to assess changes in health status of healthy subjects. Here, we performed a systematic review of 61 studies applying different nutritional stress tests to quantify health and nutritional health effects, with the objective to define an optimal nutritional stress test that has the potential to be adopted as the golden standard in nutrition research. To acknowledge the multi-target role of nutrition, a relevant subset of 50 processes that govern optimal health, with high relevance to diet, was used to define phenotypic flexibility. Subsequently, we assessed the response of biomarkers related to this subset of processes to the different challenge tests. Based on the obtained insights, we propose a nutritional stress test composed of a high-fat, high-caloric drink, containing 60 g palm olein, 75 g glucose and 20 g dairy protein in a total volume of 400 ml. The use of such a standardized nutritional challenge test in intervention studies is expected to demonstrate subtle improvements of phenotypic flexibility, thereby enabling substantiation of nutritional health effects.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-015-0459-1) contains supplementary material, which is available to authorized users.     

Phenotypic flexibility of body composition associated with seasonal acclimatization in passerine birds

Improved winter cold tolerance is widespread among small birds overwintering in cold climates and is associated with improved shivering endurance and elevated summit metabolic rate (M_sum). Phenotypic flexibility resulting in elevated M_sum could result from either increased skeletal muscle mass (perhaps with support from similar adjustments in “nutritional organs”) and/or cellular metabolic intensity. We investigated seasonal changes in body composition of three species of passerine birds resident in cold winter climates, all of which show large seasonal variations in M_sum (>25%); white-breasted nuthatch (Sitta carolinensis), black-capped chickadee (Poecile atricapillus), and house sparrow (Passer domesticus). All three species displayed significant winter increases in pectoralis and heart masses, and supracoracoideus mass also increased in winter chickadees. Gizzard mass increased in winter for all three species, but masses of other nutritional organs did not vary consistently with season. These data suggest that winter increases in pectoralis and heart masses are important contributors to elevated thermogenic capacity and cold tolerance, but seasonal variation in nutritional organ masses, other than gizzard, which is likely associated with dietary changes, are not universally associated with seasonal phenotypes. The winter increases in pectoralis and heart masses are consistent with data from other small passerines showing marked seasonal changes in cold tolerance and support the Variable Maximum Model of seasonal phenotypic flexibility, where physiological adjustments that promote improved cold tolerance, also result in elevated M_sum.     

Between-population differences in digestive flexibility in the olivaceous field mouse

The flexibility of digestive traits characterizes a standard model of physiological flexibility, demonstrating that animals adjust their digestive attributes in order to maximize overall energy return. Using an intraspecific experimental study, we evaluated the amount of flexibility in digestive tract mass and length in individuals from field mouse populations inhabiting semi-arid and temperate rain forest habitats and acclimated for six months to diets of different qualities. In accordance with the predictions of the theory of digestion, we observed a highly significant relationship between dietary variability and digestive flexibility in both specific digestive chambers and in the total digestive tract mass and length. Specifically, we found higher digestive plasticity in response to diet quality in rodents inhabiting southern temperate ecosystems with higher dietary variability in comparison to individuals from northern semi-arid habitats.     

Phenotypic flexibility in the energetic strategy of the greater white-toothed shrew,Crocidura russula

The balance between energetic acquisition and expenditure depends on the amount of energy allocated to biological functions such as thermoregulation, growth, reproduction and behavior. Ambient temperature has a profound effect on this balance, with species inhabiting colder climates often needing to invest more energy in thermoregulation to maintain body temperature. This leads to local behavioral and physiological adaptations that increase energetic efficiency. In this study, we investigated the role of activity, behavior and thermogenic capacity in the ability of the greater white-toothed shrew, Crocidura russula, to cope with seasonal changes. Individuals were captured in the Sintra-Cascais Natural Park, a Mediterranean region, and separated into three experimental groups: a control group, acclimated to a 12L:12D photoperiod and temperature of 18–20 °C; a winter group, acclimatized to natural winter fluctuations of light and temperature; and a summer group, acclimatized to natural summer fluctuations of light and temperature. No differences were found in resting metabolic rate and nonshivering thermogenesis between the three groups. However, winter shrews significantly reduced their activity, particularly at night, compared to the control and summer groups. Differences in torpor use were also found between groups, with winter shrews entering torpor more frequently and during shorter periods of time than summer and control shrews. Our results indicate C. russula from Sintra relies on the flexibility of energy saving mechanisms, namely daily activity level and torpor use, to cope with seasonal changes in a Mediterranean climate, rather than mechanisms involving body heat production.     

The relationship between lumbopelvic flexibility and sitting posture in adult women

Clinical observations have suggested that limited hamstring flexibility may be associated with sagittal spinal curvatures in spine flexed postures. Thus, limited hamstring flexibility may be related to large amounts of spine flexion in “slumped” sitting postures which could contribute to low back pain and injury. The aim of this study was to determine if hamstring and pelvic flexibility are associated with flexed sitting postures using a backless office chair. Forty-one healthy female adults aged 18–69 years were recruited. Subjects performed the Sit-and-Reach test to determine maximum flexibility values and lumbar and pelvic angles were measured with accelerometers. Participants then completed a standardized typing task for a 10-minute sitting trial at an ergonomically adjusted workstation. The results showed no association between hamstring flexibility and seated lumbar spine and pelvic angles (p = 0.999, η² = 0.000; p = 0.901, η² = 0.006). Greater pelvic flexibility was associated with a more upright lumbar sitting posture (p = 0.023; η² = 0.132) but with no specific pelvic sitting posture (p = 0.660; η² = 0.005). Different movement strategies during the Sit-and-Reach test were detected: all participants moved through their lumbar spine; but only those with ‘excellent’ flexibility also used their pelvis. Individuals in the ‘excellent’ flexibility group were significantly shorter than those with ‘poor’ and ‘good’ flexibility (p = 0.020; η² = 0.190). In conclusion, hamstring flexibility does not influence sitting posture but pelvic flexibility does. Other factors such as acetabulofemoral joint limitations, consciousness of posture, or the seat itself may also influence sitting posture. Different movement strategies as well as height appear to contribute to the Sit-and-Reach test which should be researched further.     

Behavioral and physiological flexibility are used by birds to manage energy and support investment in the early stages of reproduction

Interest in phenotypic flexibility has increased dramatically over the last decade, but flexibility during reproduction hasreceived relatively little attention from avian scientists, despite its possible impact on fitness. Because most avian species maintainatrophied reproductive organs when not active, reproduction in birds requires major tissue remodeling in preparation for breeding.Females undergo rapid (days) recrudescence and regression of their reproductive organs at each breeding attempt, while m...     

Global profiling of proteolytically modified proteins in human metastatic hepatocellular carcinoma cell lines reveals CAPN2 centered network

Proteolysis affects every protein at some point in its life cycle. Many biomarkers of disease or cancer are stable proteolytic fragments in biological fluids. There is great interest and a challenge in proteolytically modified protein study to identify physiologic protease-substrate relationships and find potential biomarkers. In this study, two human hepatocellular carcinoma (HCC) cell lines with different metastasis potential, MHCC97L, and HCCLM6, were researched with a high-throughput and sensitive PROTOMAP platform. In total 391 proteins were found to be proteolytically processed and many of them were cleaved into persistent fragments instead of completely degraded. Fragments related to 161 proteins had different expressions in these two cell lines. Through analyzing these significantly changed fragments with bio-informatic tools, several bio-functions such as tumor cell migration and anti-apoptosis were enriched. A proteolysis network was also built up, of which the CAPN2 centered subnetwork, including SPTBN1, ATP5B, and VIM, was more active in highly metastatic HCC cell line. Interestingly, proteolytic modifications of CD44 and FN1 were found to affect their secretion. This work suggests that proteolysis plays an important role in human HCC metastasis.     

Protein flexibility is key to cisplatin crosslinking in calmodulin

Chemical crosslinking in combination with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) has significant potential for studying protein structures and protein-protein interactions. Previously, cisplatin has been shown to be a crosslinker and crosslinks multiple methionine (Met) residues in apo-calmodulin (apo-CaM). However, the inter-residue distances obtained from nuclear magnetic resonance structures are inconsistent with the measured distance constraints by crosslinking. Met residues lie too far apart to be crosslinked by cisplatin. Here, by combining FTICR MS with a novel computational flexibility analysis, the flexible nature of the CaM structure is found to be key to cisplatin crosslinking in CaM. It is found that the side chains of Met residues can be brought together by flexible motions in both apo-CaM and calcium-bound CaM (Ca(4) -CaM). The possibility of cisplatin crosslinking Ca(4) -CaM is then confirmed by MS data. Therefore, flexibility analysis as a fast and low-cost computational method can be a useful tool for predicting crosslinking pairs in protein crosslinking analysis and facilitating MS data analysis. Finally, flexibility analysis also indicates that the crosslinking of platinum to pairs of Met residues will effectively close the nonpolar groove and thus will likely interfere with the binding of CaM to its protein targets, as was proved by comparing assays for cisplatin-modified/unmodified CaM binding to melittin. Collectively, these results suggest that cisplatin crosslinking of apo-CaM or Ca(4) -CaM can inhibit the ability of CaM to recognize its target proteins, which may have important implications for understanding the mechanism of tumor resistance to platinum anticancer drugs.     

PhenUMA: a tool for integrating the biomedical relationships among genes and diseases

Background

Several types of genetic interactions in humans can be directly or indirectly associated with the causal effects of mutations. These interactions are usually based on their co-associations to biological processes, coexistence in cellular locations, coexpression in cell lines, physical interactions and so on. In addition, pathological processes can present similar phenotypes that have mutations either in the same genomic location or in different genomic regions. Therefore, integrative resources for all of these complex interactions can help us prioritize the relationships between genes and diseases that are most deserving to be studied by researchers and physicians.

Results

PhenUMA is a web application that displays biological networks using information from biomedical and biomolecular data repositories. One of its most innovative features is to combine the benefits of semantic similarity methods with the information taken from databases of genetic diseases and biological interactions. More specifically, this tool is useful in studying novel pathological relationships between functionally related genes, merging diseases into clusters that share specific phenotypes or finding diseases related to reported phenotypes.

Conclusions

This framework builds, analyzes and visualizes networks based on both functional and phenotypic relationships. The integration of this information helps in the discovery of alternative pathological roles of genes, biological functions and diseases. PhenUMA represents an advancement toward the use of new technologies for genomics and personalized medicine.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0375-1) contains supplementary material, which is available to authorized users.     

古尼拟青霉表型多样性及其与活性成分的关系

目的研究表型多样性与活性成分之间的联系。方法研究10株古尼拟青霉菌株的培养特性,观察菌落形态,测定其产孢量和粗蛋白、多糖、甘露醇、麦角甾醇、腺苷等主要活性成分含量。结果A类菌株菌落背面褶皱不平,中央为棕色环状,周边为淡黄色,是生长性状优良、活性成分含量高,适于大规模工业化生产的优质菌株。结论不同菌株具有不同的形态特征,且形态特征与其产孢量及主要活性成分存在一定内在联系。     

Phenotypic plasticity and nutrition in a phytophagous insect: consequences of colonizing a new host

The European rose-hip fruit fly Rhagoletis alternata (Diptera, Tephritidae) infests hips of Rosa species. This fly includes R. rugosa, an Asian species now cultivated all over Europe, in its host range. Differences in size and biomass of hips between the ancestral host R. canina and the new host translate into better growth, shorter larval development of larvae within hips of R. rugosa and larger body size and fertility of flies which developing in the new host. In turn this causes different interactions with other organisms of the food-web centred on the host plant. The importance of nutrition and phenotypic plasticity is twofold: they generate a considerable part of life-history diversity within a species and reinforce differences in the ecological context of the ancestral and new host.     

Physiological flexibility in the Andean lizard <Emphasis Type="Italic">Liolaemus bellii</Emphasis>: seasonal changes in energy acquisition,storage and expenditure

According to the “barrel model”, an organism may be represented by a container, with input energy constraints (foraging, digestion, and absorption) symbolized by funnels connected in tandem, and energy outputs (maintenance, growth, and reproduction) symbolized by a series of spouts arranged in parallel. Animals can respond to changes in environmental conditions, through adjustments in the size of the funnels, the fluid stored inside the barrel, or the output flow through the spouts. In the present study, we investigate the interplay among these processes through the analysis of seasonal changes in organ size and metabolic rate in a lizard species (Liolaemus bellii) that inhabits extremely seasonal environments in the Andes range. We found that digestive organ size showed the greatest values during spring and summer, that is, during the foraging seasons. Energy reserves were larger during summer and autumn, and then decreased through winter and spring, which was correlated with overwintering maintenance and reproductive costs. Standard metabolic rate was greater during the high-activity seasons (spring and summer), but this increase was only noticeable at higher environmental temperatures. The ability of many lizard species to reduce their maintenance cost during the cold months of the year, beyond what is expected from temperature decrease, is probably related to their success in coping with highly fluctuating environments. Here, we demonstrate that this ability is correlated with high physiological flexibility, which allows animals to adjust energy acquisition, storing and expenditure processes according to current environmental conditions.     

Phenotypic heterogeneity as key factor for growth and survival under oligotrophic conditions

Productivity-poor oligotrophic environments are plentiful on earth. Yet it is not well understood how organisms maintain population sizes under these extreme conditions. Most scenarios consider the adaptation of a single microorganism (isogenic) at the cellular level, which increases their fitness in such an environment. However, in oligotrophic environments, the adaptation of microorganisms at population level – that is, the ability of living cells to differentiate into subtypes with specialized attributes leading to the coexistence of different phenotypes in isogenic populations – remains a little-explored area of microbiology research. In this study, we performed experiments to demonstrate that an isogenic population differentiated to two subpopulations under low energy-flux in chemostats. Fluorescence cytometry and turnover rates revealed that these subpopulations differ in their nucleic acid content and metabolic activity. A mechanistic modelling framework for the dynamic adaptation of microorganisms with the consideration of their ability to switch between different phenotypes was experimentally calibrated and validated. Simulation of hypothetical scenarios suggests that responsive diversification upon a change in energy availability offers a competitive advantage over homogenous adaptation for maintaining viability and metabolic activity with time.     

肠道菌群代谢作用与人体健康关系的研究进展

人体肠道内寄居的大量共生微生物可以通过多方面作用影响人体健康,特别是肠道内菌群的代谢作用,及与人体自身代谢的交互作用在人类的健康促进与疾病的发生、发展中起着重要作用。本文从正反两面讨论了肠道菌群代谢作用对人体健康的影响,并进一步探讨了肠道菌群代谢在健康监测、疾病的预防与治疗,以及个体化医疗方面的运用。     

An integrated approach for inference and mechanistic modeling for advancing drug development

An important challenge facing researchers in drug development is how to translate multi-omic measurements into biological insights that will help advance drugs through the clinic. Computational biology strategies are a promising approach for systematically capturing the effect of a given drug on complex molecular networks and on human physiology. This article discusses a two-pronged strategy for inferring biological interactions from large-scale multi-omic measurements and accounting for known biology via mechanistic dynamical simulations of pathways, cells, and organ- and tissue level models. These approaches are already playing a role in driving drug development by providing a rational and systematic computational framework.     

系统生物学(Systems Biology)的几大重要问题

近几年来,系统生物学从正式提出到受到普遍关注和研究,对生物学的研究发展起了革命性的变化。主要从系统生物学的发展及其内容进行分析,讨论了生物数据整合,模型建立和模拟分析等几点关键性的问题,并展望了系统生物学的研究。     

A computational model of the human thyroid

The thyroid, the largest gland in the endocrine system, secretes hormones that help promote bodily growth and development. This gland regulates hormonal secretion rate in spite of changes in dietary iodine which is a key ingredient in the hormone's biosynthesis. The thyroid relies on several feedback mechanisms for this regulation, and in this paper we use recent molecular-level and clinical observations to engineer a computational thyroid model. We use simulation and analysis to show that this models captures known aspects of thyroid physiology. We identify features in the model that are responsible for hormonal regulation, and use the model to identify and evaluate competing hypotheses associated with Wolff-Chaikoff escape.