Chris T. Jones

Functional Subpopulations of V3 Interneurons in the Mature Mouse Spinal Cord

V3 interneurons (INs) are a major group of excitatory commissural interneurons in the spinal cord, and they are essential for producing a stable and robust locomotor rhythm. V3 INs are generated from the ventral-most progenitor domain, p3, but migrate dorsally and laterally during postmitotic development. At birth, they are located in distinctive clusters in the ventral horn and deep dorsal horn. To assess the heterogeneity of this genetically identified group of spinal INs, we combined patch-clamp recording and anatomical tracing with cluster analysis. We examined electrophysiological and morphological properties of mature V3 INs identified by their expression of tdTomato fluorescent proteins in Sim1Cre/+; Rosafloxstop26TdTom mice. We identified two V3 subpopulations with distinct intrinsic properties and spatial distribution patterns. Ventral V3 INs, primarily located in lamina VIII, possess a few branching processes and were capable of generating rapid tonic firing spikes. By contrast, dorsal V3 INs exhibited a more complex morphology and relatively slow average spike frequency with strong adaptation, and they also displayed large sag voltages and post-inhibitory rebound potentials. Our data suggested that hyperpolarization-activated cation channel currents and T-type calcium channel currents may account for some of the membrane properties of V3 INs. Finally, we observed that ventral and dorsal V3 INs were active in different ways during running and swimming, indicating that ventral V3 INs may act as premotor neurons and dorsal V3 INs as relay neurons mediating sensory inputs. Together, we detected two physiologically and topographically distinct subgroups of V3 INs, each likely playing different roles in locomotor activities.

Sim1 is required for the migration and axonal projections of V3 interneurons in the developing mouse spinal cord

V3 spinal interneurons (INs) are a group of excitatory INs that play a crucial role in producing balanced and stable gaits in vertebrate animals. In the developing mouse spinal cord, V3 INs arise from the most ventral progenitor domain and form anatomically distinctive subpopulations in adult spinal cords. They are marked by the expression of transcription factor Sim1 postmitotically, but the function of Sim1 in V3 development remains unknown. Here, we used Sim1Cre;tdTomato mice to trace the fate of V3 INs in a Sim1 mutant versus control genetic background during development. In Sim1 mutants, V3 INs are produced normally and maintain a similar position and organization as in wild types before E12.5. Further temporal analysis revealed that the V3 INs in the mutants failed to migrate properly to form V3 subgroups along the dorsoventral axis of the spinal cord. At birth, in the Sim1 mutant the number of V3 INs in the ventral subgroup was normal, but they were significantly reduced in the dorsal subgroup with a concomitant increase in the intermediate subgroup. Retrograde labeling at lumbar level revealed that loss of Sim1 led to a reduction in extension of contralateral axon projections both at E14.5 and P0 without affecting ipsilateral axon projections. These results demonstrate that Sim1 is essential for proper migration and the guidance of commissural axons of the spinal V3 INs.

Curvature in models of the photosynthesis-irradiance response

An equation for the rate of photosynthesis as a function of irradiance introduced by T. T. Bannister included an empirical parameter b to account for observed variations in curvature between the initial slope and the maximum rate of photosynthesis. Yet researchers have generally favored equations with fixed curvature, possibly because b was viewed as having no physiological meaning. We developed an analytic photosynthesis‐irradiance equation relating variations in curvature to changes in the degree of connectivity between photosystems, and also considered a recently published alternative, based on changes in the size of the plastoquinone pool. When fitted to a set of 185 observed photosynthesis‐irradiance curves, it was found that the Bannister equation provided the best fit more frequently compared to either of the analytic equations. While Bannisters curvature parameter engendered negligible improvement in the statistical fit to the study data, we argued that the parameter is nevertheless quite useful because it allows for consistent estimates of initial slope and saturation irradiance for observations exhibiting a range of curvatures, which would otherwise have to be fitted to different fixed‐curvature equations. Using theoretical models, we also found that intra‐ and intercellular self‐shading can result in biased estimates of both curvature and the saturation irradiance parameter. We concluded that Bannisters is the best currently available equation accounting for variations in curvature precisely because it does not assign inappropriate physiological meaning to its curvature parameter, and we proposed that b should be thought of as the expression of the integration of all factors impacting curvature.

Using mass reconstruction along a four-site transect as a method to interpret PM10 in west-central Scotland, United Kingdom.

Abstract Concurrent 24-hr samples of particulate matter of median aerodynamic diameter less than 10 µm (PM10) were collected over a 10-day period in August 2000 at four sites along a transect in west-central Scotland, UK (passing from the coast through the city of Glasgow) in line with the prevailing southwesterly wind. Each sample was analyzed for chloride (Cl−), nitrate (NO3 −), sulfate (SO4 2+), ammonium (NH4 +), calcium (Ca2+), iron (Fe), and organic hydrocarbon material (OHM). The contribution from elemental carbon (EC) was estimated. Sampling days were categorized according to local wind direction, synoptic flow, and air mass back trajectories. Chemical mass balance (CMB) reconstruction of the following PM10 com ponents was derived for each wind direction group and at each transect location: ammonium sulfate ((NH4)2SO4), ammonium nitrate (NH4NO3), sodium chloride (NaCl), gypsum (CaSO4), OHM, EC, soil/surface dusts, and particle-bound water. The results showed that PM10 at the coastal site was dominated by the marine background (NaCl) compared with the urban sites, which were dominated by local primary (EC and soil/resuspension) and secondary sources (NH4NO3, (NH4)2SO4, and OHM). There was evidence of Cl− depletion as NaCl aerosol passes over urban areas. There was also evidence of long-range transport of primary PM10 (EC and OHM); for example, at the coastal site from transport from Ireland. The work demonstrates how the general approach of combining mass reconstruction along a transect with other information such as wind/air-mass direction generates insight into the sources contributing to PM10 over a more extended spatial scale than at a single receptor.

A novel statistical approach for ocean colour estimation of inherent optical properties and cyanobacteria abundance in optically complex waters

Eutrophication is an increasing problem in coastal waters of the Baltic Sea. Moreover, algal blooms, which occur every summer in the Gulf of Gdansk can deleteriously impact human health, the aquatic environment, and economically important fisheries, tourism, and recreation industries. Traditional laboratory-based techniques for water monitoring are expensive and time consuming, which usually results in limited numbers of observations and discontinuity in space and time. The use of hyperspectral radiometers for coastal water observation provides the potential for more detailed remote optical monitoring. A statistical approach to develop local models for the estimation of optically significant components from in situ measured hyperspectral remote sensing reflectance in case 2 waters is presented in this study. The models, which are based on empirical orthogonal function (EOF) analysis and stepwise multilinear regression, allow for the estimation of parameters strongly correlated with phytoplankton (pigment concentration, absorption coefficient) and coloured detrital matter abundance (absorption coefficient) directly from reflectance spectra measured in situ. Chlorophyll a concentration, which is commonly used as a proxy for phytoplankton biomass, was retrieved with low error (median percent difference, MPD = 17%, root mean square error RMSE = 0.14 in log10 space) and showed a high correlation with chlorophyll a measured in situ (R = 0.84). Furthermore, phycocyanin and phycoerythrin, both characteristic pigments for cyanobacteria species, were also retrieved reliably from reflectance with MPD = 23%, RMSE = 0.23, R2 = 0.77 and MPD = 24%, RMSE = 0.15, R2 = 0.74, respectively. The EOF technique proved to be accurate in the derivation of the absorption spectra of phytoplankton and coloured detrital matter (CDM), with R2 (?) above 0.83 and RMSE around 0.10. The approach was also applied to satellite multispectral remote sensing reflectance data, thus allowing for improved temporal and spatial resolution compared with the in situ measurements. The EOF method tested on simulated Medium Resolution Imaging Spectrometer (MERIS) or Ocean and Land Colour Instrument (OLCI) data resulted in RMSE = 0.16 for chl-a and RMSE = 0.29 for phycocyanin. The presented methods, applied to both in situ and satellite data, provide a powerful tool for coastal monitoring and management.

Shifting Balance on a Static Mutation–Selection Landscape: A Novel Scenario of Positive Selection

A version of the mechanistic mutation-selection (MutSel) model that accounts for temporal dynamics at a site is presented. This is used to show that the rate ratio dN/dS at a site can be transiently >1 even when fitness coefficients are fixed or the fitness landscape is static. This occurs whenever a site drifts away from its fitness peak and is then forced back by selection, a process reminiscent of shifting balance. Shifting balance is strongest when the substitution process is not dominated by selection or drift, but admits interplay between the two. Under this condition, site-specific changes in dN/dS were inferred in 78-100% of trials, and positive selection (i.e., dN/dS>1) in 10-40% of trials, when sequence alignments generated under MutSel were fitted to two popular phenomenological branch-site models. These results demonstrate that positive selection can occur without a change in fitness regime, and that this is detectable by branch-site models. In addition, MutSel is used to show that a site can be occupied by a sub-optimal amino acid for long periods on a fixed landscape when selection is stringent. This has implications for the interpretation of constant-but-different site patterns typically attributed to changes in fitness. Furthermore, a version of MutSel with episodic changes in fitness coefficients is used to illustrate systematic differences between parameters used to generate data under MutSel and their counterparts estimated by a simple codon model. Motivated by a discrepancy in the literature, interpretation of dN/dS in the context of MutSel is also discussed.

V3 interneuron subpopulations in the mouse spinal cord undergo distinctive postnatal maturation processes.

Mice develop weight-bearing locomotion within the first 2-3 weeks of birth, a period during which motoneurons (MNs) and interneurons (INs) that control locomotor activities undergo rapid maturation. In this study, we investigate the maturation of two subpopulations of V3 INs in the mouse spinal cord during this period. To do this, we conducted whole-cell patch-clamp recordings of tdTomato fluorescent protein-expressing spinal V3 INs from Sim1(Cre/+);tdTom mice at post-natal day (P) 0, P4, P9 and P14 and compared their properties to those at P21. Combining electrophysiology with computational analyses, we show that dorsal and ventral V3 subpopulations are physiologically distinct at birth, but the electrophysiological properties of V3 INs change significantly during the first three post-natal weeks. We further reveal that there are multiple developmental phases of both V3 subpopulations during the maturation process. The different developmental trajectories of physiological properties also coincide with changes in an animals locomotor behavior. These properties likely reflect the differential functions of V3 subpopulations in maturing spinal locomotor circuits.

Phenomenological Load on Model Parameters Can Lead to False Biological Conclusions

Abstract When a substitution model is fitted to an alignment using maximum likelihood, its parameters are adjusted to account for as much site‐pattern variation as possible. A parameter might therefore absorb a substantial quantity of the total variance in an alignment (or more formally, bring about a substantial reduction in the deviance of the fitted model) even if the process it represents played no role in the generation of the data. When this occurs, we say that the parameter estimate carries phenomenological load (PL). Large PL in a parameter estimate is a concern because it not only invalidates its mechanistic interpretation (if it has one) but also increases the likelihood that it will be found to be statistically significant. The problem of PL was not identified in the past because most off‐the‐shelf substitution models make simplifying assumptions that preclude the generation of realistic levels of variation. In this study, we use the more realistic mutation‐selection framework as the basis of a generating model formulated to produce data that mimic an alignment of mammalian mitochondrial DNA. We show that a parameter estimate can carry PL when 1) the substitution model is underspecified and 2) the parameter represents a process that is confounded with other processes represented in the data‐generating model. We then provide a method that can be used to identify signal for the process that a given parameter represents despite the existence of PL.