Crop improvement efforts have benefited greatly from advances in available data, computing technology, and methods for targeting genotypes to environments. These advances support the analysis of genotype by environment interactions (GEI) to understand how well a genotype adapts to environmental conditions. This paper reviews the use of spatial analysis to support crop improvement research aimed at matching genotypes to their most appropriate environmental niches. Better data sets are now available on soils, weather and climate, elevation, vegetation, crop distribution, and local conditions where genotypes are tested in experimental trial sites. The improved data are now combined with spatial analysis methods to compare environmental conditions across sites, create agro-ecological region maps, and assess environment change. Climate, elevation, and vegetation data sets are now widely available, supporting analyses that were much more difficult even 5 or 10 years ago. While detailed soil data for many parts of the world remains difficult to acquire for crop improvement studies, new advances in digital soil mapping are likely to improve our capacity. Site analysis and matching and regional targeting methods have advanced in parallel to data and technology improvements. All these developments have increased our capacity to link genotype to phenotype and point to a vast potential to improve crop adaptation efforts.
spatial analysis; genotype-by-environment interaction; geographic targeting
Insects have evolved obligate, mutualistic interactions with bacteria without further transmission to other eukaryotic organisms. Such long-term obligate partnerships between insects and bacteria have a profound effect on various physiological functions of the host. Here we provide an overview of the effects of endosymbiotic bacteria on the insect immune system as well as on the immune response of insects to pathogenic infections. Potential mechanisms through which endosymbionts can affect the ability of their host to resist an infection are discussed in the light of recent findings. We finally point out unresolved questions for future research and speculate how the current knowledge can be employed to design and implement measures for the effective control of agricultural insect pests and vectors of diseases.
insect; infection; immunity; endosymbiont; Wolbachia; Spiroplasma
The mouse is one of the most important model organisms for understanding human genetic function and disease. This includes characterization of the factors that influence energy expenditure and dysregulation of energy balance leading to obesity and its sequelae. Measuring energy metabolism in the mouse presents a challenge because the animals are small, and in this respect it presents similar challenges to measuring energy demands in many other species of small mammal. This paper considers some theoretical, practical, and analytical considerations to be considered when measuring energy expenditure in mice. Theoretically total daily energy expenditure is comprised of several different components: basal or resting expenditure, physical activity, thermoregulation, and the thermic effect of food. Energy expenditure in mice is normally measured using open flow indirect calorimetry apparatus. Two types of system are available – one of which involves a single small Spartan chamber linked to a single analyzer, which is ideal for measuring the individual components of energy demand. The other type of system involves a large chamber which mimics the home cage environment and is generally configured with several chambers/analyzer. These latter systems are ideal for measuring total daily energy expenditure but at present do not allow accurate decomposition of the total expenditure into its components. The greatest analytical challenge for mouse expenditure data is how to account for body size differences between individuals. This has been a matter of some discussion for at least 120 years. The statistically most appropriate approach is to use analysis of covariance with individual aspects of body composition as independent predictors.
energy metabolism; indirect calorimetry; mouse models; energy balance; obesity; physical activity; basal metabolic rate; energy expenditure
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects elderly persons, evolving with age to reach severe cognitive impairment. Amyloid deposits and neurofibrillary tangles constitute the main pathological hallmarks of AD. Amyloid deposits are initiated by the excessive production and accumulation of beta-amyloid (Aβ) peptides in the brain. The dysfunction of the Neurovascular Unit (NVU) has been proposed to be causative in AD development, due to an impaired clearance of Aβ from the brain. Cells forming the NVU express several Adenosine Triphosphate ATP-Binding Cassette (ABC) transporters, among which ABCB1 and ABCA1 play an important role in Aβ processing. The drug transporter ABCB1 directly transports Aβ from the brain into the blood circulation, whereas the cholesterol transporter ABCA1 neutralizes Aβ aggregation capacity in an Apolipoprotein E (ApoE)-dependent manner, facilitating Aβ subsequent elimination from the brain. In the present minireview, we will summarize the contribution of ABCB1, and ABCA1 at the NVU in Aβ clearance. Moreover, we will outline and discuss the possible collaboration of ABCB1, and ABCA1 at the NVU in mediating an efficient clearance of Aβ from the brain.
Alzheimer's disease; blood-brain barrier; neurovascular unit; ABCB1; ABCA1; apolipoprotein E; beta-amyloid clearance
Genotype-by-environment interaction (GEI) is an important phenomenon in plant breeding. This paper presents a series of models for describing, exploring, understanding, and predicting GEI. All models depart from a two-way table of genotype by environment means. First, a series of descriptive and explorative models/approaches are presented: Finlay–Wilkinson model, AMMI model, GGE biplot. All of these approaches have in common that they merely try to group genotypes and environments and do not use other information than the two-way table of means. Next, factorial regression is introduced as an approach to explicitly introduce genotypic and environmental covariates for describing and explaining GEI. Finally, QTL modeling is presented as a natural extension of factorial regression, where marker information is translated into genetic predictors. Tests for regression coefficients corresponding to these genetic predictors are tests for main effect QTL expression and QTL by environment interaction (QEI). QTL models for which QEI depends on environmental covariables form an interesting model class for predicting GEI for new genotypes and new environments. For realistic modeling of genotypic differences across multiple environments, sophisticated mixed models are necessary to allow for heterogeneity of genetic variances and correlations across environments. The use and interpretation of all models is illustrated by an example data set from the CIMMYT maize breeding program, containing environments differing in drought and nitrogen stress. To help readers to carry out the statistical analyses, GenStat® programs, 15th Edition and Discovery® version, are presented as “Appendix.”
adaptation; genotype by environment interaction; multi-environment trials; QTL by environment interaction; QTL mapping methodology; REML
Post-translational modification of proteins in diabetes, including formation of advanced glycation end products (AGEs) are believed to contribute to vascular dysfunction and disease. Impaired function of the endothelium is an early indicator of vascular dysfunction in diabetes and as many endothelial cell processes are dependent upon intracellular [Ca2+] and Ca2+ signaling, the aim of this study was to examine the acute effects of AGEs on Ca2+ signaling in bovine aortic endothelial cells (BAEC). Ca2+ signaling was studied using the fluorescent indicator dye Fura-2-AM. AGEs were generated by incubating bovine serum albumin with 0–250 mM glucose or glucose-6-phosphate for 0–120 days at 37°C. Under all conditions, the main AGE species generated was carboxymethyl lysine (CML) as assayed using both gas-liquid chromatograph-mass spectroscopy and high-performance liquid chromatography. In Ca2+-replete solution, exposure of BAEC to AGEs for 5 min caused an elevation in basal [Ca2+] and attenuated the increase in intracellular [Ca2+] caused by ATP (100 μM). In the absence of extracellular Ca2+, exposure of BAEC to AGEs for 5 min caused an elevation in basal [Ca2+] and attenuated subsequent intracellular Ca2+ release caused by ATP, thapsigargin (0.1 μM), and ionomycin (3 μM), but AGEs did not affect extracellular Ca2+ entry induced by the re-addition of Ca2+ to the bathing solution in the presence of any of these agents. The anti-oxidant α-lipoic acid (2 μM) and NAD(P)H oxidase inhibitors apocynin (500 μM) and diphenyleneiodonium (1 μM) abolished these effects of AGEs on BAECs, as did the IP3 receptor antagonist xestospongin C (1 μM). In summary, AGEs caused an acute depletion of Ca2+ from the intracellular store in BAECs, such that the Ca2+ signal stimulated by the subsequent application other agents acting upon this store is reduced. The mechanism may involve generation of reactive oxygen species from NAD(P)H oxidase and possible activation of the IP3 receptor.
calcium signaling; endothelium; advanced glycation end products; reactive oxygen species
Evidence suggests differences between African Americans (AAs) and Caucasian Americans (CAs) in cardiovascular responsiveness to physiological stressors. This study tested the hypothesis that carotid baroreflex (CBR) control of heart rate (HR) and blood pressure is reduced in AAs compared to CAs during exercise. Mean arterial pressure (MAP) and HR were continuously recorded at rest and during leg cycling in 23 non-hypertensive male subjects (12 AA; 11 CA; age 19–26 years). CBR control of HR and MAP was assessed with 5-s pulses of neck pressure (NP, simulated hypotension) and neck suction (NS, simulated hypertension) ranging from +45 to −80 Torr. Across all NS stimuli (−20, −40, −60, −80 Torr) at rest, the AA group demonstrated attenuated CBR-mediated reductions in HR (AA, −8.9 ± 1.9 vs. CA, −14.1 ± 2.3 bpm; P < 0.001) and MAP (AA, −6.4 ± 1 vs. CA, −7.8 ± 0.8 mmHg; P < 0.05). Despite similar gain and magnitude of resetting observed in the modeled stimulus response curves, an attenuation among AAs persisted in HR (AA, −8.2 ± 1.6 vs. CA, −11.8 ± 3 bpm; P < 0.05) and MAP (AA, −6.8 ± 0.9 vs. CA, −8.2 ± 1.1 mmHg; P < 0.05) responses to NS during exercise. No differences in CBR-mediated HR and MAP responses to NP were detected between groups at rest or during exercise. These data suggest impairment in the ability to defend against a hypertensive challenge among AAs during steady-state exercise compared to their CA counterparts.
blood pressure; heart rate; racial differences; hypertension; exercise
Attraction of female Aedes aegypti mosquitoes to 1-octen-3-ol (octenol), CO2, lactic acid, or ammonia emitted by vertebrate hosts is not only contingent on the presence of odorants in the environment, but is also influenced by the insect’s physiological state. For anautogenous mosquito species, like A. aegypti, newly emerged adult females neither respond to host odors nor engage in blood-feeding; the bases for these behaviors are poorly understood. Here we investigated detection of two components of an attractant blend emitted by vertebrate hosts, octenol, and CO2, by female A. aegypti mosquitoes using electrophysiological, behavioral, and molecular approaches. An increase in sensitivity of octenol olfactory receptor neurons (ORNs) was correlated with an increase in odorant receptor gene (Or) expression and octenol-mediated attractive behavior from day 1 to day 6 post-emergence. While the sensitivity of octenol ORNs was maintained through day 10, behavioral responses to octenol decreased as did the ability of females to discriminate between octenol and octenol + CO2. Our results show differing age-related roles for the peripheral receptors for octenol and higher order neural processing in the behavior of female mosquitoes.
odorant receptor; gustatory receptor; octenol; CO2; olfaction; Aedes aegypti; development
Common beans (Phaseolus vulgaris L.) originated in the New World and are the grain legume of greatest production for direct human consumption. Common bean production is subject to frequent droughts in highland Mexico, in the Pacific coast of Central America, in northeast Brazil, and in eastern and southern Africa from Ethiopia to South Africa. This article reviews efforts to improve common bean for drought tolerance, referring to genetic diversity for drought response, the physiology of drought tolerance mechanisms, and breeding strategies. Different races of common bean respond differently to drought, with race Durango of highland Mexico being a major source of genes. Sister species of P. vulgaris likewise have unique traits, especially P. acutifolius which is well adapted to dryland conditions. Diverse sources of tolerance may have different mechanisms of plant response, implying the need for different methods of phenotyping to recognize the relevant traits. Practical considerations of field management are discussed including: trial planning; water management; and field preparation.
Phaseolus; field technique; abiotic stress; breeding; stress physiology
Genetic variability has a profound effect on the development of cardiac hypertrophy in response to stress. Consequently, using a variety of inbred mouse strains with known genetic profiles may be powerful models for studying the response to cardiovascular stress. To explore this approach we looked at male C57BL/6J and 129/SvJ mice. Hemodynamic analyses of left ventricular pressures (LVPs) indicated significant differences in 129/SvJ and C57BL/6J mice that implied altered Ca2+ handling. Specifically, 129/SvJ mice demonstrated reduced rates of relaxation and insensitivity to dobutamine (Db). We hypothesized that altered expression of genes controlling the influx and efflux of Ca2+ from the sarcoplasmic reticulum (SR) was responsible and investigated the expression of several genes involved in maintaining the intracellular and sarcoluminal Ca2+ concentration using quantitative real-time PCR analyses (qRT-PCR). We observed significant differences in baseline gene expression as well as different responses in expression to isoproterenol (ISO) challenge. In untreated control animals, 129/SvJ mice expressed 1.68× more ryanodine receptor 2(Ryr2) mRNA than C57BL/6J mice but only 0.37× as much calsequestrin 2 (Casq2). After treatment with ISO, sarco(endo)plasmic reticulum Ca2+-ATPase(Serca2) expression was reduced nearly two-fold in 129/SvJ while expression in C57BL/6J was stable. Interestingly, β (1) adrenergic receptor(Adrb1) expression was lower in 129/SvJ compared to C57BL/6J at baseline and lower in both strains after treatment. Metabolically, the brain isoform of creatine kinase (Ckb) was up-regulated in response to ISO in C57BL/6J but not in 129/SvJ. These data suggest that the two strains of mice regulate Ca2+ homeostasis via different mechanisms and may be useful in developing personalized therapies in human patients.
mouse; heart; hypertrophy; Ca2+-handling; gene expression; hemodynamics
The ubiquitin proteasome system (UPS) is critical for the regulation of many intracellular processes necessary for cell function and survival. The absolute requirement of the UPS for the maintenance of protein homeostasis and thereby for the regulation of protein quality control is reflected by the fact that deviation of proteasome function from the norm was reported in cardiovascular pathologies. Inflammation is a major factor contributing to cardiac pathology. Herein, cytokines induce protein translation and the production of free radicals, thereby challenging the cellular protein equilibrium. Here, we discuss current knowledge on the mechanisms of UPS-functional adaptation in response to oxidative stress in cardiac inflammation. The increasing pool of oxidant-damaged degradation-prone proteins in cardiac pathology accounts for the need for enhanced protein turnover by the UPS. This process is accomplished by an up-regulation of the ubiquitylation machinery and the induction of immunoproteasomes. Thereby, the inflamed heart muscle is cleared from accumulating misfolded proteins. Current advances on immunoproteasome-specific inhibitors in this field question the impact of the proteasome as a therapeutic target in heart failure.
proteasome; oxidative stress; inflammation; protein quality control; cytokines
We describe our development of the diffusion tensor imaging modality for the bovine ocular lens. Diffusion gradients were added to a spin-echo pulse sequence and the relevant parameters of the sequence were refined to achieve good diffusion weighting in the lens tissue, which demonstrated heterogeneous regions of diffusive signal attenuation. Decay curves for b-value (loosely summarizes the strength of diffusion weighting) and TE (determines the amount of magnetic resonance imaging-obtained signal) were used to estimate apparent diffusion coefficients (ADC) and T2 in different lens regions. The ADCs varied by over an order of magnitude and revealed diffusive anisotropy in the lens. Up to 30 diffusion gradient directions, and 8 signal acquisition averages, were applied to lenses in culture in order to improve maps of diffusion tensor eigenvalues, equivalent to ADC, across the lens. From these maps, fractional anisotropy maps were calculated and compared to known spatial distributions of anisotropic molecular fluxes in the lens. This comparison suggested new hypotheses and experiments to quantitatively assess models of circulation in the avascular lens.
ocular lens; MRI; diffusion tensor imaging; fractional anisotropy; micro-circulation
A retrospective case-control study was conducted to investigate the risk factors for pre-eclampsia – including the protective effect of placenta previa – at Medani Maternity Hospital, Sudan. Medical files of the patients during the period 2003–2010 were reviewed for age, parity, education level, prenatal care, placenta previa, and hemoglobin level. Women with pre-eclampsia were the cases, and women with normal pregnancy were the controls. There were 54,339 singleton deliveries and 1765 women with pre-eclampsia in the hospital, giving the incidence of pre-eclampsia of 3.2%. The risk factors for pre-eclampsia were; women with age >35 years (OR = 1.4, 95% CI: 1.1–1.8), primiparity (OR = 3.3, 95% CI: 2.7–4.0), para >5 (OR = 3.1, 95% CI: 2.4–4.0), and anemia (OR = 3.3, 95% CI: 2.8–3.9). The risk of pre-eclampsia was inversely increased with education level and prenatal care attendance. The prevalence of placenta previa was 0 (0%) and 55 (3.3%), P < 0.001 in pre-eclamptic and control women, respectively. Placenta previa was a significant protective factor of pre-eclampsia (OR = 0.3, 95% CI: 0.1–0.7). Although, the socio-demographic risk factors for pre-eclampsia observed among women at Medani hospital were similar to those found in other settings; placenta previa was associated with decreased incidence of pre-eclampsia.
placenta previa; pre-eclampsia; pregnancy; vascular; Sudan
The plasma membrane of eukaryotic cells contains several types of lipids displaying high biochemical variability in both their apolar moiety (e.g., the acyl chain of glycerolipids) and their polar head (e.g., the sugar structure of glycosphingolipids). Among these lipids, cholesterol is unique because its biochemical variability is almost exclusively restricted to the oxidation of its polar −OH group. Although generally considered the most rigid membrane lipid, cholesterol can adopt a broad range of conformations due to the flexibility of its isooctyl chain linked to the polycyclic sterane backbone. Moreover, cholesterol is an asymmetric molecule displaying a planar α face and a rough β face. Overall, these structural features open up a number of possible interactions between cholesterol and membrane lipids and proteins, consistent with the prominent regulatory functions that this unique lipid exerts on membrane components. The aim of this review is to describe how cholesterol interacts with membrane lipids and proteins at the molecular/atomic scale, with special emphasis on transmembrane domains of proteins containing either the consensus cholesterol-binding motifs CRAC and CARC or a tilted peptide. Despite their broad structural diversity, all these domains bind cholesterol through common molecular mechanisms, leading to the identification of a subset of amino acid residues that are overrepresented in both linear and three-dimensional membrane cholesterol-binding sites.
cholesterol; CH-Pi; lipid-protein interaction; lipid raft; neurotransmitter; receptor structure; alpha-synuclein; Alzheimer
Exposure to second hand smoke is a major cause of chronic obstructive pulmonary disease (COPD) in the non-smoker. In this review we explore the use of animal smoke exposure models and their insight into disease pathogenesis. The methods of smoke exposure, including exposure delivery systems, are described. Key findings from the acute and chronic smoke exposure models are outlined, including descriptions of the inflammation processes, proteases involved, oxidative stress, and apoptosis. Finally, alternatives to rodent models of lung disease are presented.
emphysema; COPD; animal models; cigarette smoke; inflammation; apoptosis; proteases
Hepatocellular carcinomas (HCCs) have different etiology and heterogenic genomic alterations lead to high complexity. The molecular features of HCC have largely been studied by gene expression and proteome profiling focusing on the correlations between the expression of specific markers and clinical data. Integration of the increasing amounts of data in databases has facilitated the link of genomic and proteomic profiles of HCC to disease state and clinical outcome. Despite the current knowledge, specific molecular markers remain to be identified and new strategies are required to establish novel-targeted therapies. In the last years, mathematical models reconstructing gene and protein networks based on experimental data of HCC have been developed providing powerful tools to predict candidate interactions and potential targets for therapy. Furthermore, the combination of dynamic and logical mathematical models with quantitative data allows detailed mechanistic insights into system properties. To address effects at the organ level, mathematical models reconstructing the three-dimensional organization of liver lobules were developed. In the future, integration of different modeling approaches capturing the effects at the cellular up to the organ level is required to address the complex properties of HCC and to enable the discovery of new targets for HCC prevention or treatment.
HCC; mathematical modeling; network analysis; gene expression profile; proteomic; hepatocytes; liver
The Wnt/β-catenin pathway is involved in the regulation of a multitude of physiological processes by controlling the differential expression of target genes. In certain tissues such as the adult liver, the Wnt/β-catenin pathway can attain different levels of activity due to gradients of Wnt ligands and/or intracellular pathway components like APC. How graded pathway activity is converted into regionally distinct patterns of Wnt/β-catenin target gene expression is largely unknown. Here, we apply a mathematical modeling approach to investigate the impact of different regulatory mechanisms on target gene expression within Wnt or APC concentration gradients. We develop a minimal model of Wnt/β-catenin signal transduction and combine it with various mechanisms of target gene regulation. In particular, the effects of activation, inhibition, and an incoherent feedforward loop (iFFL) are compared. To specify activation kinetics, we analyze experimental data that quantify the response of β-catenin/TCF reporter constructs to different Wnt concentrations, and demonstrate that the induction of these constructs occurs in a cooperative manner with Hill coefficients between 2 and 5. In summary, our study shows that the combination of specific gene regulatory mechanisms with a time-independent gradient of Wnt or APC is sufficient to generate distinct target gene expression patterns as have been experimentally observed in liver. We find that cooperative gene activation in combination with a TCF feedback can establish sharp borders of target gene expression in Wnt or APC gradients. In contrast, the iFFL renders gene expression independent of gradients of the upstream signaling components. Our subsequent analysis of carcinogenic pathway mutations reveals that their impact on gene expression is determined by the gene regulatory mechanism and the APC concentration of the cell in which the mutation occurs.
mathematical modeling; gradients; gene expression; Wnt/β-catenin signaling; liver; zonation; mutation; feedback
Endothelin-1 (ET-1) is a peptide signaling molecule serving diverse functions in many different tissues such as the vasculature and the kidney. The primary mechanism thought to control ET-1 bioavailability is the rate of transcription from the ET-1 gene (EDN1), but recent research suggests that EDN1 expression is attenuated by microRNA (miRNA)—mediated regulation. The action of specific miRNAs on EDN1 mRNA appears to vary greatly in a tissue specific manner. This review provides a summary of our current understanding of miRNA-EDN1 interaction.
microRNA; endothelin-1; endothelin signaling; EDN1 mRNA; ET-1
Palatal fusion is a tightly controlled process which comprises multiple cellular events, including cell movement and differentiation. Midline epithelial seam (MES) degradation is essential to palatal fusion. In this study, we analyzed the function of Snail1 during the degradation of the MES. We also analyzed the mechanism regulating the expression of the Snail1 gene in palatal shelves. Palatal explants treated with Snail1 siRNA did not degrade the MES and E-cadherin was not repressed leading to failure of palatal fusion. Transforming growth factor beta 3 (Tgfβ3) regulated Snail1 mRNA, as Snail1 expression decreased in response to Tgfβ3 neutralizing antibody and a PI-3 kinase (PI3K) inhibitor. Twist1, in collaboration with E2A factors, regulated the expression of Snail1. Twist1/E47 dimers bond to the Snail1 promoter to activate expression. Without E47, Twist1 repressed Snail1 expression. These results support the hypothesis that Tgfβ3 may signal through Twist1 and then Snail1 to downregulate E-cadherin expression during palatal fusion.
palatal fusion; Snail1; Twist1; E-cadherin; Tgfβ3; E-proteins; epithelial-mesenchymal transition
This paper reviews methods for analyzing plant performance and its genetic variability under a range of environmental conditions. Biomass accumulation is linked every day to available light in the photosynthetically active radiation (PAR) domain, multiplied by the proportion of light intercepted by plants and by the radiation use efficiency. Total biomass is cumulated over the duration of the considered phase (e.g., plant cycle or vegetative phase). These durations are essentially constant for a given genotype provided that time is corrected for temperature (thermal time). Several ways of expressing thermal time are reviewed. Two alternative equations are presented, based either on the effect of transpiration, or on yield components. Their comparative interests and drawbacks are discussed. The genetic variability of each term of considered equations affects yield under water deficit, via mechanisms at different scales of plant organization and time. The effect of any physiological mechanism on yield of stressed plants acts via one of these terms, although the link is not always straightforward. Finally, I propose practical ways to compare the productivity of genotypes in field environments, and a “minimum dataset” of environmental data and traits that should be recorded for that.
stress; drought; temperature; intercepted light; plant performance