Marker‐based estimates of relatedness and inbreeding coefficients: an assessment of current methods

Inbreeding (F) of and relatedness (r) between individuals are now routinely calculated from marker data in studies in the fields of quantitative genetics, conservation genetics, forensics, evolution and ecology. Although definable in terms of either correlation coefficient or probability of identity by descent (IBD) relative to a reference, they are better interpreted as correlations in marker‐based analyses because the reference in practice is frequently the current sample or population whose F and r are being estimated. In such situations, negative estimates have a biological meaning, a substantial proportion of the estimates are expected to be negative, and the average estimates are close to zero for r and equivalent to F_IS for F. I show that although current r estimators were developed from the IBD‐based concept of relatedness, some of them conform to the correlation‐based concept of relatedness and some do not. The latter estimators can be modified, however, so that they estimate r as a correlation coefficient. I also show that F and r estimates can be misleading and become biased and marker dependent when a sample containing a high proportion of highly inbred and/or closely related individuals is used as reference. In analyses depending on the comparison between r (or F) estimates and a priori values expected under ideal conditions (e.g. for identifying genealogical relationship), the estimators should be used with caution.     

Is post-contrast MRI a valuable method for the study of the nutrition of the intervertebral disc?

Decreased nutrition has been proposed as a potential mechanism leading to intervertebral disc degeneration. A method to investigate it in vivo is the MRI evaluation of the transport of a paramagnetic contrast agent, which is assumed to diffuse through the endplate to the disc using the same mechanisms as the cell nutrients. However, previous numerical studies questioned the value of this method as a model to investigate disc nutrition. To assess its validity, a parametric osmoporoelastic finite element model of a lumbar intervertebral disc incorporating diffusion and convection of a solute (representing the contrast agent) was developed. A Taguchi sensitivity analysis was performed in order to assess the relevance of various parameters which influence the solute transport. Subsequently, a full-factorial sensitivity analysis was used to investigate specifically the diffusion coefficients of the contrast agent. The most important parameters in determining the results were the disc height, the diffusion coefficients and the pharmacokinetic of the contrast agent. However, diffusion coefficients values as measured in in vitro studies would lead to insubstantial enhancement of the MRI signal. Thus, transport mechanisms other than pure diffusion should be active in in vivo transport of the contrast agent. In conclusion, the study showed that post-contrast MRI may not be suited for a quantitative analysis, but only for a qualitative examination aimed for example to detect endplate lesions. Open questions remain on the use of post-contrast MRI for the investigation of the relevance of reduced nutrition as a trigger to disc degeneration.     

Continuous infusion of substance P into rat striatum alleviates nociceptive behavior via phosphorylation of extracellular signal‐regulated kinase 1/2

Intraplantar injection of 0.4% formalin into the rat hind paw leads to a biphasic nociceptive response; an ‘acute’ phase (0–15 min) and ‘tonic’ phase (16–120 min), which is accompanied by significant phosphorylation of extracellular signal‐regulated kinase (ERK)1/2 in the contralateral striatum at 120 min post‐formalin injection. To uncover a possible relationship between the slow‐onset substance P (SP) release and increased ERK1/2 phosphorylation in the striatum, continuous infusion of SP into the striatum by reverse microdialysis (0.4 μg/mL in microdialysis fiber, 1 μL/min) was performed to mimic volume neurotransmission of SP. Continuous infusion for 3 h of SP reduced the duration of ‘tonic’ phase nociception, and this SP effect was mediated by neurokinin 1 (NK1) receptors since pre‐treatment with NK1 receptor antagonist CP96345 (10 μM) blocked the effect of SP infusion. However, formalin‐induced ‘tonic’ phase nociception was significantly prolonged following acute injection of the MAP/ERK kinase 1/2 inhibitor PD0325901 (100 pmol) by microinjection. The coinfusion of SP and PD0325901 significantly increased the ‘tonic’ phase of nociception. These data demonstrate that volume transmission of striatal SP triggered by peripheral nociceptive stimulation does not lead to pain facilitation but a significant decrease of tonic nociception by the activation of the SP‐NK1 receptor–ERK1/2 system.

     

Choline‐mediated modulation of hippocampal sharp wave–ripple complexes in vitro

The cholinergic system is critically involved in the modulation of cognitive functions, including learning and memory. Acetylcholine acts through muscarinic (mAChRs) and nicotinic receptors (nAChRs), which are both abundantly expressed in the hippocampus. Previous evidence indicates that choline, the precursor and degradation product of Acetylcholine, can itself activate nAChRs and thereby affects intrinsic and synaptic neuronal functions. Here, we asked whether the cellular actions of choline directly affect hippocampal network activity. Using mouse hippocampal slices we found that choline efficiently suppresses spontaneously occurring sharp wave–ripple complexes (SPW‐R) and can induce gamma oscillations. In addition, choline reduces synaptic transmission between hippocampal subfields CA3 and CA1. Surprisingly, these effects are mediated by activation of both mAChRs and α7‐containing nAChRs. Most nicotinic effects became only apparent after local, fast application of choline, indicating rapid desensitization kinetics of nAChRs. Effects were still present following block of choline uptake and are, therefore, likely because of direct actions of choline at the respective receptors. Together, choline turns out to be a potent regulator of patterned network activity within the hippocampus. These actions may be of importance for understanding state transitions in normal and pathologically altered neuronal networks.

     

Intestinal MUC2 Mucin Supramolecular Topology by Packing and Release Resting on D3 Domain Assembly

MUC2 is the major gel-forming mucin of the colon forming a protective gel barrier organized into an inner stratified and an outer loose layer. The MUC2 N-terminus (D1-D2-D′D3 domains) has a dual function in building a net-like structure by disulfide-bonded trimerization and packing the MUC2 polymer into an N-terminal concatenated polygonal platform with the C-termini extending perpendicularly by pH- and calcium-dependent interactions. We studied the N-terminal D′D3 domain by producing three recombinant variants, with or without Myc tag and GFP (green fluorescent protein), and analyzed these by gel filtration, electron microscopy and single particle image processing. The three variants were all trimers when analyzed upon denaturing conditions but eluted as hexamers upon gel filtration under native conditions. Studies by electron microscopy and three-dimensional maps revealed cage-like structures with 2- and 3-fold symmetries. The structure of the MUC2 D3 domain confirms that the MUC2 mucin forms branched net-like structures. This suggests that the MUC2 mucin is stored with two N-terminal concatenated ring platforms turned by 180° against each other, implicating that every second unfolded MUC2 net in mature mucus is turned upside down.     

Can plants serve as a vector for prions causing chronic wasting disease?

Prions, the causative agent of chronic wasting disease (CWD) enter the environment through shedding of bodily fluids and carcass decay, posing a disease risk as a result of their environmental persistence. Plants have the ability to take up large organic particles, including whole proteins, and microbes. This study used wheat (Triticum aestivum L.) to investigate the uptake of infectious CWD prions into roots and their transport into aerial tissues. The roots of intact wheat plants were exposed to infectious prions (PrP^TSE) for 24 h in three replicate studies with PrP^TSE in protein extracts being detected by western blot, IDEXX and Bio-Rad diagnostic tests. Recombinant prion protein (PrP^C) bound to roots, but was not detected in the stem or leaves. Protease-digested CWD prions (PrP^TSE) in elk brain homogenate interacted with root tissue, but were not detected in the stem. This suggests wheat was unable to transport sufficient PrP^TSE from the roots to the stem to be detectable by the methods employed. Undigested PrP^TSE did not associate with roots. The present study suggests that if prions are transported from the roots to the stems it is at levels that are below those that are detectable by western blot, IDEXX or Bio-Rad diagnostic kits.     

Inheritance and Sequence Homology Analysis of the Maize DNA Introgressed into the Wheat Doubled Haploid Plant Through Wheat×Maize Cross

A maize (Zea mays L.) genome-specific repeated DNA sequence (clone MR64) has been transferred into one DH line of wheat through wheat (Triticum persicum Vav. ex Zhuk.) and maize cross. In the present study by RFLP analysis the authors proved that this DNA sequence could stably transmit into DH3 plants, the next generation derived from DH2 self-crossing. A similarity search in all DNA databases using BLASTN program showed that the DNA sequence of MR64 had as high as 93% identity to PREM-2 and 79% to Opie-2 in nucleotides. Both PREM-2 and Opie-2 are known as retrotransposons in maize genome, suggesting that MR64 likely is the partial sequence of a maize retrotransposon. Therefore, the results indicate that some retrotransposon might involve the DNA introgression from maize to wheat genome through wide fertilization. Stable inheritance of this maize genome-specific retrotransposon-like DNA in the wheat genome opens up the possibility of using retrotransposon as a new tool for gene tagging, function analysis, and insertional mutagenesis in wheat genome.     

Control of transpiration in three coffee cultivars: the role of hydraulic and crown architecture

Water use and hydraulic architecture were studied in the coffee (Coffea arabica) cultivars San Ramon, Yellow Caturra and Typica growing in the field under similar environmental conditions. The cultivars differed in growth habit, crown architecture, basal sapwood area and total leaf surface area. Transpiration per unit leaf area (E), stomatal conductance (g _s), crown conductance (g _c), total hydraulic conductance of the soil/leaf pathway (G _t) and the stomatal decoupling coefficient, omega (Ω) (Jarvis and McNaughton 1986) were assessed over a range of soil moisture and during partial defoliation treatments. The relationship between sap flow and sapwood area was linear and appeared to be similar for the three cultivars. Variation in g _c, E, and G _t of intact plants and leaf area-specific hydraulic conductivity (k _l) of excised lateral branches was negatively correlated with variation in the ratio of leaf area to sapwood area. Transpiration, g _c, and g _s were positively correlated with G _t. Transpiration and G _t varied with total leaf area and were greatest at intermediate values (10 m²) of leaf area. Omega was greatest in Yellow Caturra, the cultivar with the greatest leaf area and a dense crown, and was smallest in Typica, the cultivar with an open crown. Differences in omega were attributable primarily to differences in leaf boundary layer conductance among the cultivars. Plants of each cultivar that were 40% defoliated maintained sap flows comparable to pretreatment plants, but expected compensatory increases in g _s were not consistently observed. Despite their contrasting crown morphologies and hydraulic architecture, the three cultivars shared common relationships between water use and hydraulic architectural traits. Received: 17 February 1999 / Accepted: 28 July 1999