Photoperiodic Mediation of Seasonal Breeding and Immune Function In Rodents: A Multi-Factorial Approach

SYNOPSIS. Winter is energetically-demanding; thermoregulatorydemands increase when food availability usually decreases. Physiologicaland behavioral adaptations, including termination of breeding,have evolved among nontropical animals to cope with winter energyshortages. Presumably, selection for mechanisms that permitphysiological and behavioral anticipation of seasonal ambientchanges have led to current seasonal breeding patterns for manypopulations. Energetically—challenging winter conditionscan directly induce death via hypothermia, starvation, or shock;surviving these demanding conditions likely evokes significantstress responses. The stress of coping with energetically-demandingconditions may increase adrenocortical steroid levels to theextent that immune function is compromised. Individuals wouldenjoy a survival advantage if seasonally-recurring stressorscould be anticipated and countered by shunting energy reservesto bolster immune function. The primary environmental cue thatpermits physiological anticipation of season is daily photoperiod,a cue that is mediated by melatonin. However, other environmentalfactors, such as low food availability and ambient temperatures,may interact with photoperiod to affect immune function anddisease processes. Laboratory studies of seasonal changes inmammalian immune function consistently report that immune functionis enhanced in short day lengths. Prolonged melatonin treatmentmimics short days, and also enhances immune function in rodents.In sum, melatonin may be part of an integrative system to coordinatereproductive, immunologic, and other physiological processesto cope successfully with energetic stressors during winter.Social factors influence immune function and changes in socialinteractions may also contribute to seasonal changes in immunefunction. The mechanisms by which social factors are transducedinto immune responses are largely unspecified. In order to understandthe optimization of immune function it is necessary to understandthe interaction of factors, on both mechanistic and functionallevels, that affect immunity.     

Transmission of the Subthalamic Nucleus Oscillatory Activity to the Cortex: A Computational Approach

Parkinsonian tremor is most likely due to oscillatory neuronal activities of central oscillators such as the subthalamic nucleus (STN)-external segment of the globus pallidus (GPe) pacemaker within the basal ganglia (BG). Activity from the central oscillator is proposed to be transmitted via transcortical pathways to the periphery. A computational model of the BG is proposed for simulating the transmission of the STN oscillatory activity to the cortex, based closely on known anatomy and physiology of the BG. According to the results of the simulation, for transmission of the STN oscillatory activity to the cortex, the STN oscillatory activity has to be transmitted simultaneously to the thalamus via STN-internal segment of the globus pallidus (GPi)-thalamus and STN-GPe-GPi-thalamus pathways. This transmission is controlled by the various factors such as the phase between the STN and GPe oscillatory activities, the STN oscillatory activity frequency, the low-threshold calcium spike bursts of the thalamus and the GPi spontaneous activity.     

A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation

Subcellular compartmentation of the ubiquitous second messenger cAMP has been widely proposed as a mechanism to explain unique receptor-dependent functional responses. How exactly compartmentation is achieved, however, has remained a mystery for more than 40 years. In this study, we developed computational and mathematical models to represent a subcellular sarcomeric space in a cardiac myocyte with varying detail. We then used these models to predict the contributions of various mechanisms that establish subcellular cAMP microdomains. We used the models to test the hypothesis that phosphodiesterases act as functional barriers to diffusion, creating discrete cAMP signaling domains. We also used the models to predict the effect of a range of experimentally measured diffusion rates on cAMP compartmentation. Finally, we modeled the anatomical structures in a cardiac myocyte diad, to predict the effects of anatomical diffusion barriers on cAMP compartmentation. When we incorporated experimentally informed model parameters to reconstruct an in silico subcellular sarcomeric space with spatially distinct cAMP production sites linked to caveloar domains, the models predict that under realistic conditions phosphodiesterases alone were insufficient to generate significant cAMP gradients. This prediction persisted even when combined with slow cAMP diffusion. When we additionally considered the effects of anatomic barriers to diffusion that are expected in the cardiac myocyte dyadic space, cAMP compartmentation did occur, but only when diffusion was slow. Our model simulations suggest that additional mechanisms likely contribute to cAMP gradients occurring in submicroscopic domains. The difference between the physiological and pathological effects resulting from the production of cAMP may be a function of appropriate compartmentation of cAMP signaling. Therefore, understanding the contribution of factors that are responsible for coordinating the spatial and temporal distribution of cAMP at the subcellular level could be important for developing new strategies for the prevention or treatment of unfavorable responses associated with different disease states.     

Stab Wound Injury of the Zebrafish Adult Telencephalon: A Method to Investigate Vertebrate Brain Neurogenesis and Regeneration

Adult zebrafish have an amazing capacity to regenerate their central nervous system after injury. To investigate the cellular response and the molecular mechanisms involved in zebrafish adult central nervous system (CNS) regeneration and repair, we developed a zebrafish model of adult telencephalic injury.In this approach, we manually generate an injury by pushing an insulin syringe needle into the zebrafish adult telencephalon. At different post injury days, fish are sacrificed, their brains are dissected out and stained by immunohistochemistry and/or in situ hybridization (ISH) with appropriate markers to observe cell proliferation, gliogenesis, and neurogenesis. The contralateral unlesioned hemisphere serves as an internal control. This method combined for example with RNA deep sequencing can help to screen for new genes with a role in zebrafish adult telencephalon neurogenesis, regeneration, and repair.     

An Approach to a Function of Photorespiration in C3 Plants

Intact attached leaves of wheat were illuminated at 2000 μmol m-2·s-1 in CO2-free gas for 3 hours, inhibition percentage of photosynthesis in these leaves by illumination was related lo oxygen concentration in the gas. (1) The damage to the leaves became less gradually when oxygen concentration rose from 0 to 10%. (2) Almost no damage occurred between 10%–50% O2. (3) The damage appeared again when oxygen concentration exceeded 50%. The duration of CO2 outburst of wheat leaves in CO2-free gas containing 8%–11% O2 was 0nly about 15–30 min. However, no photoinhibition could be observed under this condition. Oxygen also could prevent isolated chloroplasts from the damage by strong light. No matter what concentration of oxygen in CO2-free gas was during photoinhibition treatment, the photodamaged site was always in PSⅡ. It is concluded from the results that the way in which photoinhibition was alleviated by oxygen seems not only to be photorespiration, but also the other unknown mechanisms waich may play more important part in it.     

Arabidopsis Trichome Morphogenesis: A Genetic Approach to Studying Cytoskeletal Function

   apd: 3 July 2001     

A Novel Genetic Score Approach Using Instruments to Investigate Interactions between Pathways and Environment: Application to Air Pollution

Air pollution has been associated with increased systemic inflammation markers. We developed a new pathway analysis approach to investigate whether gene variants within relevant pathways (oxidative stress, endothelial function, and metal processing) modified the association between particulate air pollution and fibrinogen, C-reactive protein (CRP), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1). Our study population consisted of 822 elderly participants of the Normative Aging Study (1999–2011). To investigate the role of biological mechanisms and to reduce the number of comparisons in the analysis, we created pathway-specific scores using gene variants related to each pathway. To select the most appropriate gene variants, we used the least absolute shrinkage and selection operator (Lasso) to relate independent outcomes representative of each pathway (8-hydroxydeoxyguanosine for oxidative stress, augmentation index for endothelial function, and patella lead for metal processing) to gene variants. A high genetic score corresponds to a higher allelic risk profile. We fit mixed-effects models to examine modification by the genetic score of the weekly air pollution association with the outcome. Among participants with higher genetic scores within the oxidative stress pathway, we observed significant associations between particle number and fibrinogen, while we did not find any association among participants with lower scores (p_interaction = 0.04). Compared to individuals with low genetic scores of metal processing gene variants, participants with higher scores had greater effects of particle number on fibrinogen (p_interaction = 0.12), CRP (p_interaction = 0.02), and ICAM-1 (p_interaction = 0.08). This two-stage penalization method is easy to implement and can be used for large-scale genetic applications.     

Recognition Mechanism of siRNA by Viral p19 Suppressor of RNA Silencing: A Molecular Dynamics Study

The p19 protein (p19) encoded from Tombusvirus is involved in various activities such as pathogenicity and virus transport. Recent studies have found that p19 is a plant suppressor of RNA silencing, which binds to short interfering RNAs (siRNAs) with high affinity. We use molecular dynamics (MD) simulations of the wild-type and mutant p19 protein (W39 and W42G) binding with a 21-nt siRNA duplex to study the p19-siRNA recognition mechanism and mutation effects. Our simulations with standard MD and steered molecular dynamics have shown that the double mutant structure is indeed much less stable than the wild-type, consistent with the recent experimental findings. Comprehensive structural analysis also shows that the W39/42G mutations first induce the loss of stacking interactions between p19 and siRNA, Trp⁴²-Cyt1 (Cyt1 from the 5′ to 3′ strand) and Trp³⁹-Gua′19 (Gua19 from the 3′ to 5′ strand), and then breaks the hydrophobic core formed by W39-W42 with nucleotide basepairs in the wild-type. The steered molecular dynamics simulations also show that the mutant p19 complex is “decompounded” very fast under a constant separation force, whereas the wild-type remains largely intact under the same steering force. Moreover, we have used the free energy perturbation to predict a binding affinity loss of 6.98 ± 0.95 kcal/mol for the single mutation W39G, and 12.8 ± 1.0 kcal/mol loss for the double mutation W39/42G, with the van der Waals interactions dominating the contribution (∼90%). These results indicate that the W39/42G mutations essentially destroy the important p19-siRNA recognition by breaking the strong stacking interaction between Cyt1 and Gua′19 with end-capping tryptophans. These large scale simulations might provide new insights to the interactions and co-evolution relationship between RNA virus proteins and their hosts.     

Low-Moisture Food: A Physicochemical Approach to Investigate the Origin of Their Physical Instability versus Water or Sucrose

Low-moisture biopolymer-based systems are commonly encountered in food. Obviously, understanding the physical basis of their quality [texture, or performance over time or as a function of their composition (water or other added solutes)] is of primary importance. A polymer science approach using physical chemistry concepts based on physical state, phase transitions and molecular mobility can be applied to investigate the performances of food in particular versus moisture. Based on the example of starch-based samples and their texture property changes versus composition, the role of water and sucrose is considered through different aspects. The relations existing between the observed changes and physical state are investigated. While the motions associated with the glass transition were observed at high temperature, secondary relaxations are observed below Tg (at T _β): T _β decreased with water content and increased with increasing sucrose content. These local motions are suggested to contribute to the observed texture modifications versus water. Moreover, the stability of the glassy state was investigated by differential scanning calorimetry through the study of enthalpy relaxation (physical ageing). The amplitude of enthalpy relaxation decreased with both increasing sucrose and water content. All in all, this study strengthened the hypotheses that sub-Tg mobility could contribute to texture instability versus moisture or sugar content.     

GLOBIO3: A Framework to Investigate Options for Reducing Global Terrestrial Biodiversity Loss

The GLOBIO3 model has been developed to assess human-induced changes in biodiversity, in the past, present, and future at regional and global scales. The model is built on simple cause–effect relationships between environmental drivers and biodiversity impacts, based on state-of-the-art knowledge. The mean abundance of original species relative to their abundance in undisturbed ecosystems (MSA) is used as the indicator for biodiversity. Changes in drivers are derived from the IMAGE 2.4 model. Drivers considered are land-cover change, land-use intensity, fragmentation, climate change, atmospheric nitrogen deposition, and infrastructure development. GLOBIO3 addresses (i) the impacts of environmental drivers on MSA and their relative importance; (ii) expected trends under various future scenarios; and (iii) the likely effects of various policy response options. GLOBIO3 has been used successfully in several integrated regional and global assessments. Three different global-scale policy options have been evaluated on their potential to reduce MSA loss. These options are: climate-change mitigation through expanded use of bio-energy, an increase in plantation forestry, and an increase in protected areas. We conclude that MSA loss is likely to continue during the coming decades. Plantation forestry may help to reduce the rate of loss, whereas climate-change mitigation through the extensive use of bioenergy crops will, in fact, increase this rate of loss. The protection of 20% of all large ecosystems leads to a small reduction in the rate of loss, provided that protection is effective and that currently degraded protected areas are restored. Author Contributions  RA—Writing, study design, data analyses; MvO—Writing, research; LM— Writing, data analyses; CN—Contribution to method; MB—Research, data analyses; BtB—Contribution to method.     

A Modeling Approach to Investigate Epizootic Outbreaks and Enzootic Maintenance of Rift Valley Fever Virus

We propose a mathematical model to investigate the transmission dynamics of Rift Valley fever (RVF) virus among ruminants. Our findings indicate that in endemic areas RVF virus maintains at a very low level among ruminants after outbreaks and subsequent outbreaks may occur when new susceptible ruminants are recruited into endemic areas or abundant numbers of mosquitoes emerge when herd immunity decreases. Many factors have been shown to have impacts on the severity of RVF outbreaks; a higher probability of death due to RVF among ruminants, a higher mosquito:ruminant ratio, or a shorter lifespan of animals can amplify the magnitude of the outbreaks; vaccination helps to reduce the magnitude of RVF outbreaks and the loss of animals efficiently, and the maximum vaccination effort (a high vaccination rate and a larger number of vaccinated animals) is recommended before the commencement of an outbreak but can be reduced later during the enzootic.     

Antilymphocyte Serum and Tissue Culture Used to Investigate Role of Cell-mediated Response in Viral Encephalitis in Mice

Antilymphocyte serum given to suppress selectively the cell response to Langat virus in Swiss albino mice prolonged the average survival times. In vitro, lymph-node cells from virus-immunized mice were strongly cytotoxic for syngenic non-neuronal brain cells infected with virus. The implications of these findings are discussed, with particular reference to the concept of autoimmunity.     

A New Bioinformatics Approach to Natural Protein Collections: Permutation Structure Contrasts of Viral and Cellular Systems

Biological cells and viruses operate by different replication and symmetry paradigms. Cells are able to replicate independently and express little spatial symmetry; viruses require cells for replication while manifesting high symmetry. The author inquired whether different paradigms were reflected in the permutations of amino acid sequences. The hypothesis was that the permutation structure level and symmetry within viral protein collections exceed that of living cells. The rationale was that one symmetry aspect generally accompanies and promotes others in a system. The inquiry was readily answered given abundant sequence archives for proteins. The analysis of collections from diverse viral and cellular sources lends strong support. Additional insights into protein primary structure, the design of collections, and the role of information are provided as well.     

Using Association Mapping in Teosinte to Investigate the Function of Maize Selection-Candidate Genes

Background

Large-scale screens of the maize genome identified 48 genes that show the putative signature of artificial selection during maize domestication or improvement. These selection-candidate genes may act as quantitative trait loci (QTL) that control the phenotypic differences between maize and its progenitor, teosinte. The selection-candidate genes appear to be located closer in the genome to domestication QTL than expected by chance.

Methods and Findings

As a step toward defining the traits controlled by these genes, we performed phenotype-genotype association mapping in teosinte for 32 of the 48 plus three other selection-candidate genes. Our analyses assayed 32 phenotypic traits, many of which were altered during maize domestication or improvement. We observed several significant associations between SNPs in the selection-candidate genes and trait variation in teosinte. These included two associations that surpassed the Bonferroni correction and five instances where a gene significantly associated with the same trait in both of our association mapping panels. Despite these significant associations, when compared as a group the selection-candidate genes performed no better than randomly chosen genes.

Conclusions

Our results suggest association analyses can be helpful for identifying traits under the control of selection-candidate genes. Indeed, we present evidence for new functions for several selection-candidate genes. However, with the current set of selection-candidate genes and our association mapping strategy, we found very few significant associations overall and no more than we would have found with randomly chosen genes. We discuss possible reasons that a large number of significant genotype-phenotype associations were not discovered.     

The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks

Background  

This paper describes an automated method for finding clusters of interconnected proteins in protein interaction networks and retrieving protein annotations associated with these clusters.     

RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding

RNA interference (RNAi) is a promising gene regulatory approach in functional genomics that has significant impact on crop improvement which permits down-regulation in gene expression with greater precise manner without affecting the expression of other genes. RNAi mechanism is expedited by small molecules of interfering RNA to suppress a gene of interest effectively. RNAi has also been exploited in plants for resistance against pathogens, insect/pest, nematodes, and virus that cause significant economic losses. Keeping beside the significance in the genome integrity maintenance as well as growth and development, RNAi induced gene syntheses are vital in plant stress management. Modifying the genes by the interference of small RNAs is one of the ways through which plants react to the environmental stresses. Hence, investigating the role of small RNAs in regulating gene expression assists the researchers to explore the potentiality of small RNAs in abiotic and biotic stress management. This novel approach opens new avenues for crop improvement by developing disease resistant, abiotic or biotic stress tolerant, and high yielding elite varieties.     

A Comprehensive Approach to Identify Reliable Reference Gene Candidates to Investigate the Link between Alcoholism and Endocrinology in Sprague-Dawley Rats

Gender and hormonal differences are often correlated with alcohol dependence and related complications like addiction and breast cancer. Estrogen (E2) is an important sex hormone because it serves as a key protein involved in organism level signaling pathways. Alcoholism has been reported to affect estrogen receptor signaling; however, identifying the players involved in such multi-faceted syndrome is complex and requires an interdisciplinary approach. In many situations, preliminary investigations included a straight forward, yet informative biotechniques such as gene expression analyses using quantitative real time PCR (qRT-PCR). The validity of qRT-PCR-based conclusions is affected by the choice of reliable internal controls. With this in mind, we compiled a list of 15 commonly used housekeeping genes (HKGs) as potential reference gene candidates in rat biological models. A comprehensive comparison among 5 statistical approaches (geNorm, dCt method, NormFinder, BestKeeper, and RefFinder) was performed to identify the minimal number as well the most stable reference genes required for reliable normalization in experimental rat groups that comprised sham operated (SO), ovariectomized rats in the absence (OVX) or presence of E2 (OVXE2). These rat groups were subdivided into subgroups that received alcohol in liquid diet or isocalroic control liquid diet for 12 weeks. Our results showed that U87, 5S rRNA, GAPDH, and U5a were the most reliable gene candidates for reference genes in heart and brain tissue. However, different gene stability ranking was specific for each tissue input combination. The present preliminary findings highlight the variability in reference gene rankings across different experimental conditions and analytic methods and constitute a fundamental step for gene expression assays.