Enhancer evolution across 20 mammalian species.

The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution.

Reliability of gaze-contingent perimetry.

Standard automated perimetry, a psychophysical task performed routinely in eyecare clinics, requires observers to maintain fixation for several minutes at a time in order to measure visual field sensitivity. Detection of visual field damage is confounded by eye movements, making the technique unreliable in poorly attentive individuals and those with pathologically unstable fixation, such as nystagmus. Microperimetry, which utilizes 'partial gaze-contingency' (PGC), aims to counteract eye movements but only corrects for gaze position errors prior to each stimulus onset. Here, we present a novel method of visual field examination in which stimulus position is updated during presentation, which we refer to as 'continuous gaze-contingency' (CGC). In the first part of this study, we present three case examples that demonstrate the ability of CGC to measure the edges of the physiological blind spot in infantile nystagmus with greater accuracy than PGC and standard 'no gaze-contingency' (NoGC), as initial proof-of-concept for the utility of the paradigm in measurements of absolute scotomas in these individuals. The second part of this study focused on healthy observers, in which we demonstrate that CGC has the lowest stimulus positional error (gaze-contingent precision: CGC = ± 0.29°, PGC = ± 0.54°, NoGC = ± 0.81°). CGC test-retest variability was shown to be at least as good as both PGC and NoGC. Overall, CGC is supported as a reliable method of visual field examination in healthy observers. Preliminary findings demonstrate the spatially accurate estimation of visual field thresholds related to retinal structure using CGC in individuals with infantile nystagmus.

Minimal reporting guideline for research involving eye tracking (2023 edition).

A guideline is proposed that comprises the minimum items to be reported in research studies involving an eye tracker and human or non-human primate participant(s). This guideline was developed over a 3-year period using a consensus-based process via an open invitation to the international eye tracking community. This guideline will be reviewed at maximum intervals of 4 years.

Neural modeling of antisaccade performance of healthy controls and early Huntington's disease patients.

Huntington's disease (HD), a genetically determined neurodegenerative disease, is positively correlated with eye movement abnormalities in decision making. The antisaccade conflict paradigm has been widely used to study response inhibition in eye movements, and reliable performance deficits in HD subjects have been observed, including a greater number and timing of direction errors. We recorded the error rates and response latencies of early HD patients and healthy age-matched controls performing the mirror antisaccade task. HD participants displayed slower and more variable antisaccade latencies and increased error rates relative to healthy controls. A competitive accumulator-to-threshold neural model was then employed to quantitatively simulate the controls' and patients' reaction latencies and error rates and uncover the mechanisms giving rise to the observed HD antisaccade deficits. Our simulations showed that (1) a more gradual and noisy rate of accumulation of evidence by HD patients is responsible for the observed prolonged and more variable antisaccade latencies in early HD; (2) the confidence level of early HD patients making a decision is unaffected by the disease; and (3) the antisaccade performance of healthy controls and early HD patients is the end product of a neural lateral competition (inhibition) between a correct and an erroneous decision process, and not the end product of a third top-down stop signal suppressing the erroneous decision process as many have speculated.

An automated segmentation approach to calibrating infantile nystagmus waveforms.

Infantile nystagmus (IN) describes a regular, repetitive movement of the eyes. A characteristic feature of each cycle of the IN eye movement waveform is a period in which the eyes are moving at minimal velocity. This so-called "foveation" period has long been considered the basis for the best vision in individuals with IN. In recent years, the technology for measuring eye movements has improved considerably, but there remains the challenge of calibrating the direction of gaze in tracking systems when the eyes are continuously moving. Identifying portions of the nystagmus waveform suitable for calibration typically involves time-consuming manual selection of the foveation periods from the eye trace. Without an accurate calibration, the exact parameters of the waveform cannot be determined. In this study, we present an automated method for segmenting IN waveforms with the purpose of determining the foveation positions to be used for calibration of an eye tracker. On average, the "point of regard" was found to be within 0.21° of that determined by hand-marking by an expert observer. This method enables rapid clinical quantification of waveforms and the possibility of gaze-contingent research paradigms being performed with this patient group.

Effect of Stimulus Type and Motion on Smooth Pursuit in Adults and Children.

PURPOSE: This study presents a two-degree customized animated stimulus developed to evaluate smooth pursuit in children and investigates the effect of its predetermined characteristics (stimulus type and size) in an adult population. Then, the animated stimulus is used to evaluate the impact of different pursuit motion paradigms in children. METHODS: To study the effect of animating a stimulus, eye movement recordings were obtained from 20 young adults while the customized animated stimulus and a standard dot stimulus were presented moving horizontally at a constant velocity. To study the effect of using a larger stimulus size, eye movement recordings were obtained from 10 young adults while presenting a standard dot stimulus of different size (1° and 2°) moving horizontally at a constant velocity. Finally, eye movement recordings were obtained from 12 children while the 2° customized animated stimulus was presented after three different smooth pursuit motion paradigms. Performance parameters, including gains and number of saccades, were calculated for each stimulus condition. RESULTS: The animated stimulus produced in young adults significantly higher velocity gain (mean: 0.93; 95% CI: 0.90-0.96; P = .014), position gain (0.93; 0.85-1; P = .025), proportion of smooth pursuit (0.94; 0.91-0.96, P = .002), and fewer saccades (5.30; 3.64-6.96, P = .008) than a standard dot (velocity gain: 0.87; 0.82-0.92; position gain: 0.82; 0.72-0.92; proportion smooth pursuit: 0.87; 0.83-0.90; number of saccades: 7.75; 5.30-10.46). In contrast, changing the size of a standard dot stimulus from 1° to 2° did not have an effect on smooth pursuit in young adults (P > .05). Finally, smooth pursuit performance did not significantly differ in children for the different motion paradigms when using the animated stimulus (P > .05). CONCLUSIONS: Attention-grabbing and more dynamic stimuli, such as the developed animated stimulus, might potentially be useful for eye movement research. Finally, with such stimuli, children perform equally well irrespective of the motion paradigm used.

Saccades and fixations in children with delayed reading skills.

PURPOSE: Previous studies have reported that eye movements differ between good/average and poor readers. However, these studies have been limited to investigating eye movements during reading related tasks, and thus, the differences found could arise from deficits in higher cognitive processes involved in reading rather than oculomotor performance. The purpose of the study is to determine the extent to which eye movements in children with delayed reading skills are different to those obtained from children with good/average reading skills in non-reading related tasks. METHODS: After a screening optometric assessment, eye movement recordings were obtained from 120 children without delayed reading skills and 43 children with delayed reading skills (4 to 11 years) using a Tobii TX300 eye tracker. Cartoon characters were presented horizontally from -20° to +20° in steps of 5° to study saccades. An animated stimulus in the centre of the screen was presented for 8 seconds to study fixation stability. Saccadic main sequences, and the number and amplitude of the saccades during fixation were obtained for each participant. Children with delayed reading skills (n = 43) were unmasked after data collection was completed. Medians and quartiles were calculated for each eye movement parameter for children without (n = 120) and with (n = 43) delayed reading skills. RESULTS: Independent t-tests with Bonferroni correction showed no significant differences in any of the saccadic main sequence parameters (Slope, Intercept, A, n and Q ratio) between children without and with delayed reading (p > 0.01). Similarly, no significant differences were found in the number of saccades and their amplitude during the fixation task between the two groups (p > 0.05). Further, none of the gross optometric parameters assessed (visual acuity, refractive error, ocular alignment, convergence, stereopsis and accommodation accuracy) were found to be associated with delayed reading skills (p > 0.05). CONCLUSIONS: Eye movements in children with delayed reading skills are quantitatively similar to those found in children without delayed reading skills. These findings suggest that, in these children, delayed reading skills are not associated with eye movements and further question interventions targeted at improving eye movement control.

Fornical and nonfornical projections from the rat hippocampal formation to the anterior thalamic nuclei.

The hippocampal formation and anterior thalamic nuclei form part of an interconnected network thought to support memory. A central pathway in this mnemonic network comprises the direct projections from the hippocampal formation to the anterior thalamic nuclei, projections that, in the primate brain, originate in the subicular cortices to reach the anterior thalamic nuclei by way of the fornix. In the rat brain, additional pathways involving the internal capsule have been described, linking the dorsal subiculum to the anteromedial thalamic nucleus, as well as the postsubiculum to the anterodorsal thalamic nucleus. Confirming such pathways is essential in order to appreciate how information is transferred from the hippocampal formation to the anterior thalamus and how it may be disrupted by fornix pathology. Accordingly, in the present study, pathway tracers were injected into the anterior thalamic nuclei and the dorsal subiculum of rats with fornix lesions. Contrary to previous descriptions, projections from the subiculum to the anteromedial thalamic nucleus overwhelmingly relied on the fornix. Dorsal subiculum projections to the majority of the anteroventral nucleus also predominantly relied on the fornix, although postsubicular inputs to the lateral dorsal part of the anteroventral nucleus, as well as to the anterodorsal and laterodorsal thalamic nuclei, largely involved a nonfornical pathway, via the internal capsule.

The irregular firing properties of thalamic head direction cells mediate turn-specific modulation of the directional tuning curve.

Head direction cells encode an animal's heading in the horizontal plane. However, it is not clear why the directionality of a cell's mean firing rate differs for clockwise, compared with counterclockwise, head turns (this difference is known as the "separation angle") in anterior thalamus. Here we investigated in freely behaving rats whether intrinsic neuronal firing properties are linked to this phenomenon. We found a positive correlation between the separation angle and the spiking variability of thalamic head direction cells. To test whether this link is driven by hyperpolarization-inducing currents, we investigated the effect of thalamic reticular inhibition during high-voltage spindles on directional spiking. While the selective directional firing of thalamic neurons was preserved, we found no evidence for entrainment of thalamic head direction cells by high-voltage spindle oscillations. We then examined the role of depolarization-inducing currents in the formation of separation angle. Using a single-compartment Hodgkin-Huxley model, we show that modeled neurons fire with higher frequencies during the ascending phase of sinusoidal current injection (mimicking the head direction tuning curve) when simulated with higher high-threshold calcium channel conductance. These findings demonstrate that the turn-specific encoding of directional signal strongly depends on the ability of thalamic neurons to fire irregularly in response to sinusoidal excitatory activation. Another crucial factor for inducing phase lead to sinusoidal current injection was the presence of spike-frequency adaptation current in the modeled neurons. Our data support a model in which intrinsic biophysical properties of thalamic neurons mediate the physiological encoding of directional information.

Neurodevelopmental dimensional assessment of young children at high genomic risk of neuropsychiatric conditions.

Background: Individuals with 22q11.2 deletion are at considerably increased risk of neurodevelopmental and psychiatric conditions. There have been very few studies investigating how this risk manifests in early childhood and what factors may underlie developmental variability. Insights into this can elucidate transdiagnostic markers of risk that may underlie later development of neuropsychiatric outcomes. Methods: Thirty two children with 22q11.2 Deletion Syndrome (22q11.2DS) (mean age = 4.1 [SD = 1.2] years) and 12 sibling controls (mean age = 4.1 [SD = 1.5] years) underwent in-depth dimensional phenotyping across several developmental domains selected as being potential early indicators of neurodevelopmental and psychiatric liability. Comparisons were conducted of the dimensional developmental phenotype of 22q11.2DS and sibling controls. For autistic traits, both parents and children were phenotyped using the Social Responsiveness Scale. Results: Young children with 22q11.2DS exhibited large impairments (Hedge's g ≥ 0.8) across a range of developmental domains relative to sibling controls, as well as high rates of transdiagnostic neurodevelopmental and psychiatric traits. Cluster analysis revealed a subgroup of children with 22q11.2DS (n = 16; 53%) in whom neurodevelopmental and psychiatric liability was particularly increased and who differed from other children with 22q11.2DS and non-carrier siblings. Exploratory analyses revealed that early motor and sleep impairments indexed liability for neurodevelopmental and psychiatric outcomes. Maternal autism trait scores were predictive of autism traits in children with 22q11.2DS (intraclass correlation coefficients = 0.47, p = 0.046, n = 31). Conclusions: Although psychiatric conditions typically emerge later in adolescence and adulthood in 22q11.2DS, our exploratory study was able to identify a range of early risk indicators. Furthermore, findings indicate the presence of a subgroup who appeared to have increased neurodevelopmental and psychiatric liability. Our findings highlight the scope for future studies of early risk mechanisms and early intervention within this high genetic risk patient group.

Theta-modulated head direction cells in the rat anterior thalamus.

A major tool in understanding how the brain processes information is the analysis of neuronal output at each hierarchical level along the pathway of signal propagation. Theta rhythm and head directionality are the two main signals found across all levels of Papez's circuit, which supports episodic memory formation. Here, we provide evidence that the functional interaction between both signals occurs at a subcortical level. We show that there is population of head direction cells (39%) in rat anteroventral thalamic nucleus that exhibit rhythmic spiking in the theta range. This class of units, termed HD-by-theta (head direction-by-theta) cells, discharged predominantly in spike trains at theta frequency (6-12 Hz). The highest degree of theta rhythmicity was evident when the animal was heading/facing in the preferred direction, expressed by the Gaussian peak of the directional tuning curve. The theta-rhythmic mode of spiking was closely related to the firing activity of local theta-bursting cells. We also found that 32% of anteroventral theta-bursting cells displayed a head-directional modulation of their spiking. This crossover between theta and head-directional signals indicates that anterior thalamus integrates information related to heading and movement, and may therefore actively modulate hippocampo-dencephalic information processing.

Visual and Refractive Status of Children With Down's Syndrome and Nystagmus.

Purpose: Children with Down's syndrome (DS) are known to have poorer visual acuity than neurotypical children. One report has shown that children with DS and nystagmus also have poor acuity when compared to typical children with nystagmus. What has not been established is the extent of any acuity deficit due to nystagmus and whether nystagmus affects refractive error within a population with DS. Methods: Clinical records from the Cardiff University Down's Syndrome Vision Research Unit were examined retrospectively. Binocular visual acuity and refraction data were available for 50 children who had DS and nystagmus and 176 children who had DS but no nystagmus. Data were compared between the two groups and with published data for neurotypical children with nystagmus. Results: The study confirms the deficit in acuity in DS, compared to neurotypical children, of approximately 0.2 logMAR and shows a deficit attributable to nystagmus of a further 0.2 logMAR beyond the first year of life. Children with both DS and nystagmus clearly have a significant additional impairment. Children with DS have a wide range of refractive errors, but nystagmus increases the likelihood of myopia. Prevalence and axis direction of astigmatism, on the other hand, appear unaffected by nystagmus. Conclusions: Nystagmus confers an additional visual impairment on children with DS and must be recognized as such by families and educators. Children with both DS and nystagmus clearly need targeted support.

Oscillatory entrainment of thalamic neurons by theta rhythm in freely moving rats.

The anterior thalamic nuclei are assumed to support episodic memory with anterior thalamic dysfunction a core feature of diencephalic amnesia. To date, the electrophysiological characterization of this region in behaving rodents has been restricted to the anterodorsal nucleus. Here we compared single-unit spikes with population activity in the anteroventral nucleus (AV) of freely moving rats during foraging and during naturally occurring sleep. We identified AV units that synchronize their bursting activity in the 6-11 Hz range. We show for the first time in freely moving rats that a subgroup of AV neurons is strongly entrained by theta oscillations. This feature together with their firing properties and spike shape suggests they be classified as "theta" units. To prove the selectivity of AV theta cells for theta rhythm, we compared the relation of spiking rhythmicity to local field potentials during theta and non-theta periods. The most distinguishable non-theta oscillations in rodent anterior thalamus are sleep spindles. We therefore compared the firing properties of AV units during theta and spindle periods. We found that theta and spindle oscillations differ in their spatial distribution within AV, suggesting separate cellular sources for these oscillations. While theta-bursting neurons were related to the distribution of local field theta power, spindle amplitude was independent of the theta units' position. Slow- and fast-spiking bursting units that are selectively entrained to theta rhythm comprise 23.7% of AV neurons. Our results provide a framework for electrophysiological classification of AV neurons as part of theta limbic circuitry.

Selective disconnection of the hippocampal formation projections to the mammillary bodies produces only mild deficits on spatial memory tasks: implications for fornix function.

It is now clear that the integrity of the fornix is important for normal mnemonic function. The fornix, however, is a major white matter tract, carrying numerous hippocampal formation afferents and efferents, and it is not known which specific components support memory processes. Established theories of extended hippocampal function emphasize the sequential pathway from the hippocampal formation (i.e., subicular complex) to the mammillary bodies and, thence, to the anterior thalamus, as pathology in each of these structures is implicated in anterograde amnesia in humans and spatial memory deficits in rats. The specific importance of the hippocampal formation projections that just innervate the mammillary bodies has, however, never been tested. This study isolated these specific projections in the rat by selectively cutting the descending component of the postcommissural fornix. Two successive, cohorts of rats with these tract lesions were tested on working memory tasks in the water-maze, T-maze, and radial-arm maze. Disconnecting the descending postcommissural fornix had only a mild effect or sometimes no apparent effect on the performance of these spatial memory tasks, even though tracing experiments confirmed the loss of hippocampal formation-mammillary projections. One implication is that the spatial deficits found in rats following standard fornix lesions are only partly attributable to the loss of projections from the hippocampal formation to the mammillary bodies. Perhaps more surprising, the behavioral impact of cutting the descending postcommissural fornix in rats appeared appreciably less than the effect of either mammillary body or mammillothalamic tract lesions. The present experiments show that the mammillary bodies can still effectively support spatial memory in the absence of their dense subicular complex inputs, so revealing the importance of the other afferents for sustaining mammillary body function. This new evidence for independent functions shows that the mammillary bodies are more than just a hippocampal relay.

Differential regulation of synaptic plasticity of the hippocampal and the hypothalamic inputs to the anterior thalamus.

The hippocampus projects to the anterior thalamic nuclei both directly and indirectly via the mammillary bodies, but little is known about the electrophysiological properties of these convergent pathways. Here we demonstrate, for the first time, the presence of long-term plasticity in anterior thalamic nuclei synapses in response to high- and low-frequency stimulation (LFS) in urethane-anesthetized rats. We compared the synaptic changes evoked via the direct vs. the indirect hippocampal pathways to the anterior thalamus, and found that long-term potentiation (LTP) of the thalamic field response is induced predominantly through the direct hippocampal projections. Furthermore, we have estimated that that long-term depression (LTD) can be induced only after stimulation of the indirect connections carried by the mammillothalamic tract. Interestingly, basal synaptic transmission mediated by the mammillothalamic tract undergoes use-dependent, BDNF-mediated potentiation, revealing a distinct form of plasticity specific to the diencephalic region. Our data indicate that the thalamus does not passively relay incoming information, but rather acts as a synaptic network, where the ability to integrate hippocampal and mammillary body inputs is dynamically modified as a result of previous activity in the circuit. The complementary properties of these two parallel pathways upon anterior thalamic activity reveal that they do not have duplicate functions.

Involvement of the CD200 receptor complex in microglia activation in experimental glaucoma.

The interaction of the myeloid restricted molecule CD200R with its widely expressed ligand CD200 is involved in the down-regulation of microglia activation. In the present study, we examined the involvement of CD200R in microglia activation in experimental ocular hypertension to determine the role of microglia activation in retinal ganglion cell (RGC) death, the key pathological event in glaucoma. Experimental glaucoma was induced in adult Brown Norway rats by sclerosis of the episcleral veins with the injection of hypertonic saline. Immunohistochemical methods were used to determine the involvement of microglia using GFAP, CD45, OX42 and OX41 and the involvement of CD200 and CD200R in the optic nerve head. Our data demonstrate the increased presence of microglia within the optic nerve head during ocular hypertension, identified by positive staining with OX42 and OX41. The peak of microglia correlates with peak in RGC death at days 20-27 (T3) post OHT induction. In addition, CD200 and CD200R positive cells were increased in ocular hypertensive eyes. Increased expression of CD200 was detected in the early phase (days 1-7; T1) of OHT and decreased over time, whilst the expression of CD200R was detected in the middle phase (days 20-27; T3) of OHT, correlating with the increase in microglia markers. Changes in the expression of CD200R/CD200 occur early in experimental glaucoma and precede the peak in microglia infiltration and RGC death, suggesting that CD200R-positive microglia play an important role in the initiation of RGC death during OHT, indicating a potential area for therapeutic intervention in treating glaucoma.

Pre-treatment choroidal thickness is not predictive of susceptibility to form-deprivation myopia in chickens.

PURPOSE: Chicks developing experimentally-induced myopia show profound thinning of the choroid. We observed a wide range of choroidal thicknesses in a sample of normal chicks prior to their use in a pedigree-based study of form-deprivation myopia. Hence, we tested whether pre-treatment choroidal thickness predicted susceptibility to myopia. METHODS: Retinal, choroidal and scleral thickness were measured using A-scan ultrasonography in normal White Leghorn chicks (n= 891) aged 4 days old, and again (n=498) after 4 days of monocular form-deprivation at age 8 days of age. Refractive error was assessed by retinoscopy. Relationships between pre-treatment choroidal thickness and other variables were investigated using general linear models and variance components analysis. RESULTS: Untreated 4 day-old male chicks had choroids approximately 10% thinner than females (p<0.001), but sex explained <2% of the overall variability in choroidal thickness. Axial eye length in these untreated chicks was not significantly associated with choroidal thickness (p=0.25). Moreover, pre-treatment choroidal thickness was not predictive of susceptibility to form-deprivation myopia (p=0.89). Heritability analysis suggested that at least 50% of the variation in pre-treatment choroidal thickness was determined by additive genetic effects (p<0.001). CONCLUSIONS: Parental choroidal thickness is the major determinant of choroidal thickness in untreated 4-day old chicks. Despite choroidal thickness potentially being indicative of ongoing emmetropisation to innate refractive errors, in this study it was not predictive of subsequent susceptibility to form-deprivation myopia.

Hippocampal-anterior thalamic pathways for memory: uncovering a network of direct and indirect actions.

This review charts recent advances from a variety of disciplines that create a new perspective on why the multiple hippocampal-anterior thalamic interconnections are together vital for human episodic memory and rodent event memory. Evidence has emerged for the existence of a series of parallel temporal-diencephalic pathways that function in a reciprocal manner, both directly and indirectly, between the hippocampal formation and the anterior thalamic nuclei. These extended pathways also involve the mammillary bodies, the retrosplenial cortex and parts of the prefrontal cortex. Recent neuropsychological findings reveal the disproportionate importance of these hippocampal-anterior thalamic systems for recollective rather than familiarity-based recognition, while anatomical studies highlight the precise manner in which information streams are kept separate but can also converge at key points within these pathways. These latter findings are developed further by electrophysiological stimulation studies showing how the properties of the direct hippocampal-anterior thalamic projections are often opposed by the indirect hippocampal projections via the mammillary bodies to the thalamus. Just as these hippocampal-anterior thalamic interactions reflect an interdependent system, so it is also the case that pathology in one of the component sites within this system can induce dysfunctional changes to distal sites both directly and indirectly across the system. Such distal effects challenge more traditional views of neuropathology as they reveal how extensive covert pathology might accompany localised overt pathology, and so impair memory.

Ex vivo magnetic resonance imaging of crystalline lens dimensions in chicken.

PURPOSE: A reduction in the power of the crystalline lens during childhood is thought to be important in the emmetropization of the maturing eye. However, in humans and model organisms, little is known about the factors that determine the dimensions of the crystalline lens and in particular whether these different parameters (axial thickness, surface curvatures, equatorial diameter, and volume) are under a common source of control or regulated independently of other aspects of eye size and shape. METHODS: Using chickens from a broiler-layer experimental cross as a model system, three-dimensional magnetic resonance imaging (MRI) scans were obtained at 115-microm isotropic resolution for one eye of 501 individuals aged 3-weeks old. After fixation with paraformaldehyde, the excised eyes were scanned overnight (16 h) in groups of 16 arranged in a 2x2x4 array. Lens dimensions were calculated from each image by fitting a three-dimensional mesh model to the lens, using the semi-automated analysis program mri3dX. The lens dimensions were compared to measures of eye and body size obtained in vivo using techniques that included keratometry and A-scan ultrasonography. RESULTS: A striking finding was that axial lens thickness measured using ex vivo MRI was only weakly correlated with lens thickness measured in vivo by ultrasonography (r=0.19, p<0.001). In addition, the MRI lens thickness estimates had a lower mean value and much higher variance. Indeed, about one-third of crystalline lenses showed a kidney-shaped appearance instead of the typical biconvex shape. Since repeat MRI scans of the same eye showed a high degree of reproducibility for the scanning and mri3dX analysis steps (the correlation in repeat lens thickness measurements was r=0.95, p<0.001) and a recent report has shown that paraformaldehyde fixation induces a loss of water from the human crystalline lens, it is likely that the tissue fixation step caused a variable degree of shrinkage and a change in shape to the lenses examined here. Despite this serious source of imprecision, we found significant correlations between lens volume and eye/body size (p<0.001) and between lens equatorial diameter and eye/body size (p<0.001) in these chickens. CONCLUSIONS: Our results suggest that certain aspects of lens size (specifically, lens volume and equatorial diameter) are controlled by factors that also regulate the size of the eye and body (presumably, predominantly genetic factors). However, since it has been shown previously that axial lens thickness is regulated almost independently of eye and body size, these results suggest that different systems might operate to control lens volume/diameter and lens thickness in normal chickens.