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The Multiple Roles of Genetics on Freshwater Macrophyte Functional Traits in the Interplay With the Environment: A Review.

The study of functional trait variation is increasingly used to understand macrophyte adaptation, as traits reflect organismal performance under different ecosystem conditions. Phenotypic expression results from the interplay of genetic and environmental factors: genetics provides the molecular basis for heritable traits and constrains potential phenotypes, while the environment acts as a selective and modulatory force. However, the genetic insight into traits has rarely been addressed in freshwater macrophyte studies. This review examines the different ways in which the DNA of macrophytes interplays with the environment and contributes to the variation in their functional traits, outlining main approaches, gaps, and future challenges. Only 21 studies explicitly combined genetics with functional traits and environment in the last fifteen years. The most common approach was the use of common garden experiments to explore acclimation and adaptation in a few model species. Current studies mainly focus on morphological and growth traits that best describe macrophytes' economic strategies, with limited attention to other trait categories, while the genetic and DNA traits studied are more variable. Across studies, environmental factors generally explained a larger proportion of functional trait variation, highlighting the dominant role of phenotypic plasticity for macrophyte acclimatation, whereas genetic contribution increased under experimentally manipulated conditions. Genome size and epigenetic variation influenced phenotypic plasticity; however, the effect was different and inconsistent on traits and depended on phylogenetic relationships and geographical environment variation. In field studies of natural populations, life history traits and hydrology had a strong effect on the geographic distribution of genetic diversity and the response to selection, as well as on our ability to distinguish selection from genetic drift. Future research should enhance molecular analyses, adopt multifactorial and long-term experimental designs, develop conceptual frameworks to address the relationships between genomics, environment and functional traits and integrate emerging tools to capture macrophyte adaptation better.

adaptation↗

Simple methods for assessing haplotype-environment interactions in case-only and case-control studies.

For investigating haplotype-environment interactions in case-control studies, one can implement statistical methods based either on a retrospective likelihood (modeling the probability of haplotype and environment conditional on disease status) or a prospective likelihood (modeling the probability of disease status conditional on haplotype and environment). Retrospective approaches are generally more powerful than prospective approaches, but require an explicit model of the joint distribution of haplotype and environmental factors in the sample with the latter being particularly unattractive to specify. To resolve this issue, we propose a number of simple retrospective procedures for haplotype-environment interaction analysis that do not require explicit modeling of environmental covariates in the sample. We first consider a cases-only procedure, followed by a simple likelihood for case-control data that is proportional to the full-retrospective likelihood. Finally, we consider a retrospective procedure for inference on haplotype-environment interaction effects in matched or finely-stratified case-control studies. Our methods are based on the assumptions that haplotypes and environmental covariates are independent in the target population and that disease is rare. We illustrate our approaches using case-control data from the Finland-United States Investigation of Non-Insulin Dependent Diabetes Mellitus (FUSION) genetic study and simulated data.

Case-Control Studies↗

The effects of test environment and cyclic stretching on the failure properties of human patellar tendons.

There is a need to document the mechanical properties of patellar tendon allografts used for reconstructive surgery of the damaged anterior cruciate ligament, especially the effects of irradiation sterilization. The purpose of this study was to investigate the influences of in vitro test environment and low-level cyclic stretching prior to failure tests on nonirradiated and irradiated human graft tissues. Bilateral patellar tendons were split and each half processed accordingly. Some graft tissues were stretched cyclically at 2.5 mm deformation before failure. Experiments were performed in a 37 degrees C saline bath or with tissues moistened with a drip of the same. The irradiated grafts relaxed less and generated less slack length in the drip environment than the nonirradiated controls. Cyclic stretching did not alter failure characteristics of either graft tissue. While no significant differences in the tensile responses or failure characteristics were noted for irradiated and nonirradiated grafts in the drip, in the bath environment the nonirradiated tissues had greater strength and modulus. This resulted in there being a significant difference between irradiated and nonirradiated tissue responses in a heated saline bath environment. These experimental results exemplify the need to control in vitro test environments in the evaluation of various sterilization and preservation protocols for soft tissue allografts.

Adult↗

Occupational therapy adaptation of the home environment in Sweden for people with asthma.

The purpose of this study was to evaluate changes of lung function, respiratory symptoms and indoor air quality after reducing allergens and indoor pollutants in the home environment of people with asthma (n = 21). A quasi-experimental pre-/post-test design with one group of participants was implemented. The interventions included removal of wall-to-wall carpets (n = 14) or improvement of indoor air exchange (n = 7). Participants' lung function, symptoms, medication and type-1 allergy were recorded before and after the intervention. The indoor environment was monitored at house calls by an occupational therapist using conventional physical, biological and chemical methods. There was an improvement of lung function evidenced by an increased mean Forced Expiratory Volume (FEV(1) %) and a reduction of airway obstruction (reversibility, % of baseline value), which indicate an improved asthmatic condition. Lung function assessed by vital capacity, bronchial hyper-responsiveness, mean of Peak Expiratory Flow, symptom score and medicine consumption did not change significantly. There was a tendency that the amount of airborne dust (p=0.06) was reduced in the indoor environment. Relative humidity, carbon dioxide, formaldehyde and house dust mite levels had decreased after the intervention, but not significantly. Asthma symptoms related to the home environment are probably caused by several factors. When people with asthma suffer from increased symptoms in the home, house calls should be performed routinely. Dust samples from beds and carpets for analysis of allergens give information about exposure, and environmental assessments should be performed before interventions. Occupational therapists can make a valuable contribution in evaluating the home environment and suggesting ergonomic adaptations for individuals with asthma.

Adult↗

Design and testing of a virtual environment to train stroke patients with unilateral spatial neglect to cross a street safely.

Virtual reality (VR) entails the use of advanced technologies, including computers and various multimedia peripherals, to produce a simulated (that is, virtual) environment that users perceive as comparable to real world objects and events. In recent years, virtual reality technologies have begun to be used as an assessment and treatment tool in occupational therapy, in part because of the ability to create environments that provide patients with opportunities to engage in meaningful, purposeful tasks that are related to real-life interests and activities. The objective of this study was to determine the suitability and feasibility of using a PC-based, non-immersive, VR system (that is, a system in which the user has a reduced sense of actual presence in and control over the simulated environment) for training individuals with unilateral spatial neglect to cross streets in a safe and vigilant manner. A virtual environment, consisting of a typical city street, was programmed using Superscape's 3D-Webmaster, a 3D web-authoring tool. Twelve subjects, aged 55 to 75 years, participated in the initial feasibility study and, to date, a further eight subjects have participated in the intervention study. Six of the initial subjects and all eight of the intervention subjects had sustained a right hemispheric stroke at least 6 weeks prior to the study. The remaining subjects were healthy age-matched adults who were independently mobile and had no difficulty in crossing streets. The results show that this virtual environment was suitable in both its cognitive and motor demands for the targeted population and indicate that the virtual reality training is likely to prove beneficial to people who have difficulty with crossing streets. The generalizability of these results, and recommendations regarding the use of virtual reality as an occupational therapy intervention, must be substantiated by further studies using a range of VR platforms with people with different cognitive and motor disabilities.

Accidents, Traffic↗

The three-dimensional profile method using residue preference as a continuous function of residue environment.

In the 3-dimensional profile method, the compatibility of an amino acid sequence for a given protein structure is scored as the sum of the preferences of the residues for their environments in the 3D structure. In the original method (Bowie JU, Lüthy R, Eisenberg D, 1991, Science 253:164-170), residue environments were quantized into 18 discrete environmental classes. Here, amino acid residue preferences are expressed as a continuous function of environmental variables (residue area buried and fractional area buried by polar atoms). This continuous representation of residue preferences, expressed as a Fourier series, avoids the abrupt change of preference of residues in slightly different environments, as encountered in the original method with its 18 discrete environmental classes. When compared with the discrete 18-class representation of residue environments, this continuous 3D profile is found to be more sensitive in identifying sequences that fold into the profiled structure but share with it little sequence identity. The continuous 3D profile is also less sensitive to errors in environmental variables than is the discrete 3D profile. The continuous 3D profile can also be used to detect wrong folds or incorrectly modeled segments in an otherwise correct structure, as could the discrete 3D profile (Lüthy R, Bowie JU, Eisenberg D, 1992, Nature 356:83-85). Moreover, the progress of structure improvement during atomic refinement can also be monitored by examining the profile scores in a moving-window scan. Finally, by defining a functional form for profile scores, we open the way to profile atomic refinement in which an atomic structure adjusts to produce residue environments more compatible with the protein side chains.

Amino Acids↗

The host environment drives HIV-1 fitness.

Viral fitness is defined by the ability of an individual genotype to produce infectious progeny in a specific environment. For HIV the environment is never constant but rather fluctuates in time and space. For instance, environmental factors that determine viral fitness during transmission from host to host are different to the pressures from either cytotoxic T-lymphocytes (CTLs) or antiviral drugs. Consequently, viral fitness is highly dependent on the environment and the accurate determination of this value therefore depends strongly on the chosen environmental setting. This review describes how the host environment imposes selective pressures on the virus that shape its genotype and fitness. The most important environments that the virus encounters throughout its life cycle and during natural infection are discussed. In order of appearance, CTLs are discussed, followed by neutralising antibodies and antiretroviral drug treatment. It then goes on to describe receptor molecules that mediate viral entry and intracellular restriction factors, which represent selective pressures that are present directly from the start of a natural infection. It concludes by discussing the complexity of viral fitness and how an accurate measure of viral fitness eventually may, for example, contribute to the improvement of antiretroviral therapy or help in the formulation of an optimal vaccination strategy.

Adaptation, Biological↗

Low calcium environment effects osteoprotegerin ligand/osteoclast differentiation factor.

In coculture with osteoblastic cell line MC3T3-E1 (E1) and mouse bone marrow cells, we reported that numbers of osteoclasts rose significantly on exposure to a low-calcium environment. Here we examined how osteoblasts influence osteoclastogenesis under a low-calcium environment. Comparing low extracellular calcium with a regular calcium environment, osteoprotegerin ligand (OPGL)/osteoclast differentiation factor (ODF) mRNA expression show more increase in the culture of low-calcium environment than in that of a regular calcium environment. Calcium-sensing receptor (CaSR), which was supposed as one of the mechanisms of recognizing extracellular calcium, existedon the surface of E1 cells. When E1 cells stimulated with agonists of CaSR, gadolinium, and neomycin, OPGL/ODF mRNA expression decreased. Moreover, these agonists reduced osteoclast formation in coculture. Taken together, it is possible that osteoblasts may recognize extracellular calcium via CaSR and regulate osteoclastogenesis.

3T3 Cells↗

What can abnormal environments tell us about normal people? Polar stations as natural psychology laboratories.

The psychological effects of unusual environments reveal different aspects of behaviour from those seen in more customary situations. Such environments provide natural laboratories in which many questions of psychological interest, varying with the specific environment, may be studied. This paper uses isolated polar stations to illustrate this point. In such settings, the usual parameters that control a variety of psychological processes are drastically changed, and confounding variables are stripped away. Consequently, the environment offers unique perspectives on environmental perception and cognition; adaptation to and use of the environment; environmental bonding; social interaction; and coping with environmental challenge.

Adaptation, Psychological↗

Scientific principles for evaluating the potential for adverse effects from chlorinated organic chemicals in the environment.

The term chlorinated chemicals is used to describe diverse groups of chemicals of varying chemical structure, including those used in water disinfection, as well as numerous aliphatic, aromatic, and polycyclic chlorinated substances. This report elaborates a number of scientific principles that govern the evaluation of the potential for chlorinated organic chemicals to cause adverse effects on the environment and to human health. The purpose of the report is to demonstrate the importance of applying these scientific principles in the evaluation of potential adverse effects of chlorinated organic chemicals. The four major principles upon which such a scientific analysis must be based are: (1) the fate and biological activity of a compound are determined by the chemical properties of the compound; (2) compounds do not show adverse effects below certain threshold concentrations, and the magnitude of response is related to dose; (3) inherent metabolic processes allow organisms to accommodate low doses of chlorinated organic chemicals; (4) observations associated with the presence of a certain compound must be biologically plausible effects, based on the specificity of the compound's activity in experimental systems. With respect to the first of these principles, there is abundant scientific evidence that the physical and chemical properties of chlorinated organic chemicals govern their bioaccumulative potential, toxicological properties, and thus their potential behavior and effects in the environment. Chemicals that have low solubility in water are highly lipophilic and have low vapor pressure, tend to accumulate in biological systems, and degrade slowly in the environment. Chlorinated organic chemicals that possess these characteristics include those having a carbon ring structure and multiple chlorine substitution. Other chlorinated organic chemicals with lesser degrees of chlorine substitution, such as 2,4-dichlorophenoxyacetic acid (2,4-D), trichlorophenol, chloroform, and dichloroethane, do not share the physical and chemical properties of the high molecular weight, cyclic, polychlorinated compounds and, as such, do not have the same potential to bioaccumulate. These differences among chlorinated organic chemicals with respect to their physical and chemical properties and behavior in the environment preclude the generalization that all organic chemicals containing chlorine behave similarly in the environment and act as persistent, bioaccumulative chemicals. The reactivity of chlorinated organic chemicals and hence their potential to produce biological effects depends on their specific molecular features. The substitution of chlorine into an organic molecule may increase or may reduce its biological activity.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

Treatment environment and staff ideology in two British mental hospitals.

Hypotheses were derived from assumptions inherent in two contrasting conceptions of a treatment environment, attitudinal and ecological. Research was conducted in two different British mental hospitals, using scales from the OMI and the CTE. As predicted, the OMI scales were related only to staff attributes and did not discriminate among environments of institutions or units that differed in program, philosophy, organization, or type of patients. CTE scales distinguished between hospital treatment environments and wards. There was slight evidence that observed attributes influenced ecological measures of the objective treatment environment, or that staff ideology had any substantial impact upon treatment environments.

Adult↗

Resolution-enhanced Fourier transform infrared spectroscopy study of the environment of phosphate ions in the early deposits of a solid phase of calcium-phosphate in bone and enamel, and their evolution with age. I: Investigations in the upsilon 4 PO4 domain.

In order to investigate the possible existence in biological and poorly crystalline synthetic apatites of local atomic organizations different from that of apatite, resolution-enhanced, Fourier transform infrared spectroscopy studies were carried out on chicken bone, pig enamel, and poorly crystalline synthetic apatites containing carbonate and HPO4(2-) groups. The spectra obtained were compared to those of synthetic well crystallized apatites (stoichiometric hydroxyapatite, HPO4(2-)-containing apatite, type B carbonate apatite) and nonapatitic calcium phosphates which have been suggested as precursors of the apatitic phase [octacalcium phosphate (OCP), brushite, and beta tricalcium phosphate and whitlockite]. The spectra of bone and enamel, as well as poorly crystalline, synthetic apatite in the upsilon 4 PO4 domain, exhibit, in addition to the three apatitic bands, three absorption bands that were shown to be independent of the organic matrix. Two low-wave number bands at 520-530 and 540-550 cm-1 are assigned to HPO4(2-). Reference to known calcium phosphates shows that bands in this domain also exist in HPO4(2-)-containing apatite, brushite, and OCP. However, the lack of specific absorption bands prevents a clear identification of these HPO4(2-) environments. The third absorption band (610-615 cm-1) is not related to HPO4(2-) or OH- ions. It appears to be due to a labile PO4(3-) environment which could not be identified with any phosphate environment existing in our reference samples, and thus seems specific of poorly crystalline apatites. Correlation of the variations in band intensities show that 610-615 cm-1 band is related to an absorption band at 560 cm-1 superimposed on an apatite band. All the nonapatitic phosphate environments were shown to decrease during aging of enamel, bone, and synthetic apatites. Moreover, EDTA etching show that the labile PO4(3-) environment exhibited a heterogeneous distribution in the insoluble precipitate.

Aging↗

Gene-environment interplay in neurogenesis and neurodegeneration.

Factors associated with predisposition and vulnerability to neurodegenerative disorders may be described usefully within the context of gene-environment interplay. There are many identified genetic determinants for so-called genetic disorders, and it is possible to duplicate many elements of recognized human neurodegenerative disorders in either knock-in or knock-out mice. However, there are similarly, many identifiable environmental influences on outcomes of the genetic defects; and the course of a progressive neurodegenerative disorder can be greatly modified by environmental elements. Constituent cellular defense mechanisms responsive to the challenge of increased reactive oxygen species represent only one crossroad whereby environment can influence genetic predisposition. In this paper we highlight some of the major neurodegenerative disorders and discuss possible links of gene-environment interplay. The process of adult neurogenesis in brain is also presented as an additional element that influences gene-environment interplay. And the so-called priming processes (i.e., production of receptor supersensitization by repeated drug dosing), is introduced as yet another process that influences how genes and environment ultimately and co-dependently govern behavioral ontogeny and outcome. In studies attributing the influence of genetic alteration on behavioral phenotypy, it is essential to carefully control environmental influences.

Alzheimer Disease↗

QTLs for straw quality characteristics identified in recombinant inbred lines of a Hordeum vulgare x H. spontaneum cross in a Mediterranean environment.

Barley straw is commonly used as animal feed in many developing countries. Even a small increase in its nutritive value can have a large impact on animal production, and hence, on rural livelihood and human nutrition. Straw quality is strongly affected by environmental factors and is, therefore, difficult to improve with empirical breeding. The objective of this study was to identify molecular markers to facilitate the improvement of straw quality in barley. For this purpose, we have used the genetic linkage map that was already developed for recombinant inbred lines (RILs) of the cross between a Hordeum vulgare cultivar ('Arta') and a H. spontaneum line (H. spontaneum 41-1), covering a total of 890 cM. Straw parameters from RILs grown at Tel Hadya and Breda (ICARDA's research stations) in 2 years (1996/1997 and 1997/1998) were analyzed by NIRS for predicted nutritional characteristics including neutral detergent fiber, acid detergent fiber, lignin, digestible organic matter in dry matter, voluntary intake, crude protein, and straw morphology (the percentage of blades, sheaths, and stems). Localization of QTLs was performed using Windows QTL Cartographer, version 2.0. Seventy-three QTLs were identified, the majority of which (17) in the driest of the four environments. Only six QTLs were identified in two environments; in five cases, one of the two was the wettest environment. This is discussed in relation to the possibility of improving straw quality in favorable environments where yields are higher, rather than in dry environments where straw quality is already relatively good.

Animal Feed↗

Empirical method for prediction of the coordination environment of Eu(III) by time-resolved laser-induced fluorescence spectroscopy.

The number of water molecules in the inner-sphere (N(H2O)) was determined for Eu(III) and the strength of ligand field (R(E/M)) was evaluated for a variety of coordination environments from the luminescence lifetime and the relative intensity at 615 nm and at 592 nm, by time-resolved laser-induced fluorescence spectroscopy. When R(E/M) and deltaN(H2O) for Eu(III) with a known coordination environment were plotted clear regularity was apparent between the location of the R(E/M)-deltaN(H2O) plot and the coordination environment of Eu(III). Here, deltaN(H2O) was calculated by use of the equation, deltaN(H2O)=9-N(H2O). Unknown coordination environments of Eu(III) can, in turn, be characterized, including both the inner- and the outer-sphere, simply by plotting R(E/M) and deltaN(H2O) for Eu(III) on the diagram. This empirical method is effective for prediction of the coordination environment of hydrated and complexed Eu(III) in solutions and that of the adsorbed Eu(III) on ion-exchange resins and by microorganisms.

Journal Article↗

Fate of Cryptosporidium oocysts and Giardia cysts in the Norwegian aquatic environment over winter.

We investigated the survival of Cryptosporidium oocysts and Giardia cysts during winter in an aquatic environment (approximate temperature measurements between 1 and 7 degrees C) in Norway, using morphology and uptake of dyes as indicators of viability. Previous research has shown that in the terrestrial environment, shear forces caused by freeze and thaw cycles probably cause the parasites to be inactivated. Such forces occurred infrequently in the aquatic environment, as freezing of the water around the parasites was not observed during the study period (although freezing of the water surface did occur). The rate of decline in viability (log(10) N (t)/N (0)) was similar in control and experimental environments for both parasites; no Cryptosporidium oocysts with viable morphology were detected after approximately 20 weeks and no Giardia cysts with apparently viable morphology could be detected after 1 month. These results suggest that infection with these parasites in Norway is not usually from transmission stages that have over-wintered in the Norwegian environment.

Animals↗

Use of loglinear models to assess factors influencing concern for the natural environment.

Since it is necessary to isolate the most significant factors influencing personal concern for the environment, this paper utilizes loglinear models for identifying the interactions and interrelationships underlying multidimensional environmental survey data. A field study in Guyana conducted face-to-face interviews with 1600 citizens. Acquired categorical data were then subjected to loglinear modeling techniques to determine what significance the factors education, age, residential location, and gender have on personal concern for the environment. The loglinear models obtained from the five-dimensional contingency table suggest that there is a direct relationship between education and personal concern for the environment. Age has an interaction with education, and some influence on environmental concern, with younger respondents expressing higher concern for the environment than older respondents. Other results from the loglinear model demonstrate that residential location and the gender of the respondents do not have any statistically significant association with personal concern for the environment.

Adolescent↗

Spatial relations between floodplain environments and land use - land cover of a large lowland tropical river valley: Pánuco basin, México.

Large lowland river valleys include a variety of floodplain environments that represent opportunities and constraints for human activities. This study integrates extensive field observations and geomorphic data with analysis of satellite remote sensing data to examine spatial relations between land use/land cover (LULC) and floodplain environments in the lower Pánuco basin of eastern Mexico. The floodplain of the lower Pánuco basin was delineated by combining a digital elevation model with a satellite image of a large flood event. The LULC was classified by combining a hybrid classification strategy with image stratification, applied to 15-m-resolution ASTER data. A geomorphic classification of floodplain environments was performed using a dry-stage image (ASTER data) and a 1993 Landsat image acquired during a large flood event. Accuracy assessment was based on aerial photographs (1:38,000), global positioning satellite ground-truthing, and a Landsat 7ETM(+) image from 2000, which resulted in an overall accuracy of 82.9% and a KHAT of 79.8% for the LULC classification. The geomorphic classification yielded 83.5% overall accuracy, whereas the KHAT was 81.5%. LULC analysis was performed for the entire floodplain and individually within four valley segments. The analysis indicates that the study area is primarily utilized for grazing and farming. Agriculture is primarily associated with coarse-grained (sandy/silty) natural levee and point bar units close to the river channel, whereas cattle grazing occurs in distal and lower-lying reaches dominated by cohesive fine-grained (clayey) deposits, such as backswamps. In the Pánuco valley, wetlands and lakes occur within backswamp environments, whereas in the Moctezuma segments, wetlands and lakes are associated with relict channels. This study reveals considerable variation in LULC related to spatial differences in floodplain environments and illustrates the importance of considering older anthropogenic influences on the landscape. The research design should be applicable for other large lowland coastal plain river valleys where agriculture is a major component of the floodplain landscape.

Agriculture↗