Genetic tuning of intrinsically photosensitive retinal ganglion cell subtype identity to drive visual behavior

The melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs) comprise a subset of the ∼40 retinal ganglion cell types in the mouse retina and drive a diverse array of light-evoked behaviors from circadian photoentrainment to pupil constriction to contrast sensitivity for visual perception. Central to the ability of ipRGCs to control this diverse array of behaviors is the distinct complement of morphophysiological features and gene expression patterns found in the M1-M6 ipRGC subtypes. However, the genetic regulatory programs that give rise to subtypes of ipRGCs are unknown. Here, we identify the transcription factor Brn3b (Pou4f2) as a key genetic regulator that shapes the unique functions of ipRGC subtypes and their diverse downstream visual behaviors.

Atypical retinal function in a mouse model of Fragile X syndrome

Altered function of peripheral sensory neurons is an emerging mechanism for symptoms of autism spectrum disorders. Visual sensitivities are common in autism, but whether differences in the retina might underlie these sensitivities is not well-understood. We explored retinal function in the Fmr1 knockout model of Fragile X syndrome, focusing on a specific type of retinal neuron, the "sustained On alpha" retinal ganglion cell. We found that these cells exhibit changes in dendritic structure and dampened responses to light in the Fmr1 knockout. We show that decreased light sensitivity is due to increased inhibitory input and reduced E-I balance. The change in E-I balance supports maintenance of circuit excitability similar to what has been observed in cortex. These results show that loss of Fmr1 in the mouse retina affects sensory function of one retinal neuron type. Our findings suggest that the retina may be relevant for understanding visual function in Fragile X syndrome.

An ethologically relevant paradigm to assess visual contrast sensitivity in rodents

In the animal kingdom, threat information is perceived mainly through vision. The subcortical visual pathway plays a critical role in the rapid processing of visual information-induced fear, and triggers a response. Looming-evoked behavior in rodents, mimicking response to aerial predators, allowed identify the neural circuitry underlying instinctive defensive behaviors; however, the influence of disk/background contrast on the looming-induced behavioral response has not been examined, either in rats or mice. We studied the influence of the dark disk/gray background contrast in the type of rat and mouse defensive behavior in the looming arena, and we showed that rat and mouse response as a function of disk/background contrast adjusted to a sigmoid-like relationship. Both sex and age biased the contrast-dependent response, which was dampened in rats submitted to retinal unilateral or bilateral ischemia. Moreover, using genetically manipulated mice, we showed that the three type of photoresponsive retinal cells (i.e., cones, rods, and intrinsically photoresponsive retinal ganglion cells (ipRGCs)), participate in the contrast-dependent response, following this hierarchy: cones ˃> rods ˃>>ipRGCs. The cone and rod involvement was confirmed using a mouse model of unilateral non-exudative age-related macular degeneration, which only damages canonical photoreceptors and significantly decreased the contrast sensitivity in the looming arena.

The cognitive impact of light: illuminating ipRGC circuit mechanisms

Ever-present in our environments, light entrains circadian rhythms over long timescales, influencing daily activity patterns, health and performance. Increasing evidence indicates that light also acts independently of the circadian system to directly impact physiology and behaviour, including cognition. Exposure to light stimulates brain areas involved in cognition and appears to improve a broad range of cognitive functions. However, the extent of these effects and their mechanisms are unknown. Intrinsically photosensitive retinal ganglion cells (ipRGCs) have emerged as the primary conduit through which light impacts non-image-forming behaviours and are a prime candidate for mediating the direct effects of light on cognition. Here, we review the current state of understanding of these effects in humans and mice, and the tools available to uncover circuit-level and photoreceptor-specific mechanisms. We also address current barriers to progress in this area. Current and future efforts to unravel the circuits through which light influences cognitive functions may inform the tailoring of lighting landscapes to optimize health and cognitive function.

Recommendations for measuring and standardizing light for laboratory mammals to improve welfare and reproducibility in animal research

Light enables vision and exerts widespread effects on physiology and behavior, including regulating circadian rhythms, sleep, hormone synthesis, affective state, and cognitive processes. Appropriate lighting in animal facilities may support welfare and ensure that animals enter experiments in an appropriate physiological and behavioral state. Furthermore, proper consideration of light during experimentation is important both when it is explicitly employed as an independent variable and as a general feature of the environment. This Consensus View discusses metrics to use for the quantification of light appropriate for nonhuman mammals and their application to improve animal welfare and the quality of animal research. It provides methods for measuring these metrics, practical guidance for their implementation in husbandry and experimentation, and quantitative guidance on appropriate light exposure for laboratory mammals. The guidance provided has the potential to improve data quality and contribute to reduction and refinement, helping to ensure more ethical animal use.

Melanopsin activates divergent phototransduction pathways in intrinsically photosensitive retinal ganglion cell subtypes

Melanopsin signaling within intrinsically photosensitive retinal ganglion cell (ipRGC) subtypes impacts a broad range of behaviors from circadian photoentrainment to conscious visual perception. Yet, how melanopsin phototransduction within M1-M6 ipRGC subtypes impacts cellular signaling to drive diverse behaviors is still largely unresolved. The identity of the phototransduction channels in each subtype is key to understanding this central question but has remained controversial. In this study, we resolve two opposing models of M4 phototransduction, demonstrating that hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are dispensable for this process and providing support for a pathway involving melanopsin-dependent potassium channel closure and canonical transient receptor potential (TRPC) channel opening. Surprisingly, we find that HCN channels are likewise dispensable for M2 phototransduction, contradicting the current model. We instead show that M2 phototransduction requires TRPC channels in conjunction with T-type voltage-gated calcium channels, identifying a novel melanopsin phototransduction target. Collectively, this work resolves key discrepancies in our understanding of ipRGC phototransduction pathways in multiple subtypes and adds to mounting evidence that ipRGC subtypes employ diverse phototransduction cascades to fine-tune cellular responses for downstream behaviors.

The Retinal Basis of Light Aversion in Neonatal Mice

Aversive responses to bright light (photoaversion) require signaling from the eye to the brain. Melanopsin-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs) encode absolute light intensity and are thought to provide the light signals for photoaversion. Consistent with this, neonatal mice exhibit photoaversion before the developmental onset of image vision, and melanopsin deletion abolishes photoaversion in neonates. It is not well understood how the population of ipRGCs, which constitutes multiple physiologically distinct types (denoted M1-M6 in mouse), encodes light stimuli to produce an aversive response. Here, we provide several lines of evidence that M1 ipRGCs that lack the Brn3b transcription factor drive photoaversion in neonatal mice. First, neonatal mice lacking TRPC6 and TRPC7 ion channels failed to turn away from bright light, while two photon Ca2+ imaging of their acutely isolated retinas revealed reduced photosensitivity in M1 ipRGCs, but not other ipRGC types. Second, mice in which all ipRGC types except for Brn3b-negative M1 ipRGCs are ablated exhibited normal photoaversion. Third, pharmacological blockade or genetic knockout of gap junction channels expressed by ipRGCs, which reduces the light sensitivity of M2-M6 ipRGCs in the neonatal retina, had small effects on photoaversion only at the brightest light intensities. Finally, M1s were not strongly depolarized by spontaneous retinal waves, a robust source of activity in the developing retina that depolarizes all other ipRGC types. M1s therefore constitute a separate information channel between the neonatal retina and brain that could ensure behavioral responses to light but not spontaneous retinal waves.SIGNIFICANCE STATEMENT At an early stage of development, before the maturation of photoreceptor input to the retina, neonatal mice exhibit photoaversion. On exposure to bright light, they turn away and emit ultrasonic vocalizations, a cue to their parents to return them to the nest. Neonatal photoaversion is mediated by intrinsically photosensitive retinal ganglion cells (ipRGCs), a small percentage of the retinal ganglion cell population that express the photopigment melanopsin and depolarize directly in response to light. This study shows that photoaversion is mediated by a subset of ipRGCs, called M1-ipRGCs. Moreover, M1-ipRGCs have reduced responses to retinal waves, providing a mechanism by which the mouse distinguishes light stimulation from developmental patterns of spontaneous activity.

Melanopsin phototransduction: beyond canonical cascades

Melanopsin is a visual pigment that is expressed in a small subset of intrinsically photosensitive retinal ganglion cells (ipRGCs). It is involved in regulating non-image forming visual behaviors, such as circadian photoentrainment and the pupillary light reflex, while also playing a role in many aspects of image-forming vision, such as contrast sensitivity. Melanopsin was initially discovered in the melanophores of the skin of the frog Xenopus, and subsequently found in a subset of ganglion cells in rat, mouse and primate retinas. ipRGCs were initially thought to be a single retinal ganglion cell population, and melanopsin was thought to activate a single, invertebrate-like Gq/transient receptor potential canonical (TRPC)-based phototransduction cascade within these cells. However, in the 20 years since the discovery of melanopsin, our knowledge of this visual pigment and ipRGCs has expanded dramatically. Six ipRGC subtypes have now been identified in the mouse, each with unique morphological, physiological and functional properties. Multiple subtypes have also been identified in other species, suggesting that this cell type diversity is a general feature of the ipRGC system. This diversity has led to a renewed interest in melanopsin phototransduction that may not follow the canonical Gq/TRPC cascade in the mouse or in the plethora of other organisms that express the melanopsin photopigment. In this Review, we discuss recent findings and discoveries that have challenged the prevailing view of melanopsin phototransduction as a single pathway that influences solely non-image forming functions.

M1 Intrinsically Photosensitive Retinal Ganglion Cells Integrate Rod and Melanopsin Inputs to Signal in Low Light

Light influences various behaviors and physiological processes that occur outside of our conscious perception, including circadian photoentrainment, sleep, and even learning and mood. The M1, melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs) relay a combination of rod/cone and melanopsin signals to drive these functions. However, little is known about how M1 ipRGCs integrate these signals in low light. We measure the dim light response of M1 ipRGCs and find that they exhibit a wide spectrum of responses to dim, scotopic light stimulation that are driven by a combination of rod pathway input and melanopsin phototransduction. The presence of rod input to M1 ipRGCs correlates with larger and more complex dendritic arbors. Collectively, these results show variability in the rod input to M1 ipRGCs and a surprising contribution of melanopsin to the light responses of M1 ipRGCs at very low light.

M1 intrinsically photosensitive retinal ganglion cells (ipRGCs) control an array of non-image-forming functions. Lee et al. report diverse light responses of M1 ipRGCs in scotopic light that are determined by the degree of rod and melanopsin inputs and find that degree of rod input correlates with dendritic complexity.

Diversity of intrinsically photosensitive retinal ganglion cells: circuits and functions

The melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs) are a relatively recently discovered class of atypical ganglion cell photoreceptor. These ipRGCs are a morphologically and physiologically heterogeneous population that project widely throughout the brain and mediate a wide array of visual functions ranging from photoentrainment of our circadian rhythms, to driving the pupillary light reflex to improve visual function, to modulating our mood, alertness, learning, sleep/wakefulness, regulation of body temperature, and even our visual perception. The presence of melanopsin as a unique molecular signature of ipRGCs has allowed for the development of a vast array of molecular and genetic tools to study ipRGC circuits. Given the emerging complexity of this system, this review will provide an overview of the genetic tools and methods used to study ipRGCs, how these tools have been used to dissect their role in a variety of visual circuits and behaviors in mice, and identify important directions for future study.

A noncanonical inhibitory circuit dampens behavioral sensitivity to light

Retinal ganglion cells (RGCs) drive diverse, light-evoked behaviors that range from conscious visual perception to subconscious, non-image-forming behaviors. It is thought that RGCs primarily drive these functions through the release of the excitatory neurotransmitter glutamate. We identified a subset of melanopsin-expressing intrinsically photosensitive RGCs (ipRGCs) in mice that release the inhibitory neurotransmitter γ-aminobutyric acid (GABA) at non-image-forming brain targets. GABA release from ipRGCs dampened the sensitivity of both the pupillary light reflex and circadian photoentrainment, thereby shifting the dynamic range of these behaviors to higher light levels. Our results identify an inhibitory RGC population in the retina and provide a circuit-level mechanism that contributes to the relative insensitivity of non-image-forming behaviors at low light levels.

Overlapping morphological and functional properties between M4 and M5 intrinsically photosensitive retinal ganglion cells

Multiple retinal ganglion cell (RGC) types in the mouse retina mediate pattern vision by responding to specific features of the visual scene. The M4 and M5 melanopsin-expressing, intrinsically photosensitive retinal ganglion cell (ipRGC) subtypes are two RGC types that are thought to play major roles in pattern vision. The M4 ipRGCs overlap in population with ON-alpha RGCs, while M5 ipRGCs were recently reported to exhibit opponent responses to different wavelengths of light (color opponency). Despite their seemingly distinct roles in visual processing, previous reports have suggested that these two populations may exhibit overlap in their morphological and functional properties, which calls into question whether these are in fact distinct RGC types. Here, we show that M4 and M5 ipRGCs are distinct morphological classes of ipRGCs, but they cannot be exclusively differentiated based on color opponency and dendritic morphology as previously reported. Instead, we find that M4 and M5 ipRGCs can only be distinguished based on soma size and the number of dendritic branch points in combination with SMI-32 immunoreactivity. These results have important implications for clearly defining RGC types and their roles in visual behavior.

Melanopsin Retinal Ganglion Cells Regulate Cone Photoreceptor Lamination in the Mouse Retina

Newborn neurons follow molecular cues to reach their final destination, but whether early life experience influences lamination remains largely unexplored. As light is among the first stimuli to reach the developing nervous system via intrinsically photosensitive retinal ganglion cells (ipRGCs), we asked whether ipRGCs could affect lamination in the developing mouse retina. We show here that ablation of ipRGCs causes cone photoreceptors to mislocalize at different apicobasal positions in the retina. This effect is partly mediated by light-evoked activity in ipRGCs, as dark rearing or silencing of ipRGCs leads a subset of cones to mislocalize. Furthermore, ablation of ipRGCs alters the cone transcriptome and decreases expression of the dopamine receptor D4, while injection of L-DOPA or D4 receptor agonist rescues the displaced cone phenotype observed in dark-reared animals. These results show that early light-mediated activity in ipRGCs influences neuronal lamination and identify ipRGC-elicited dopamine release as a mechanism influencing cone position.

Cellular properties of intrinsically photosensitive retinal ganglion cells during postnatal development

BACKGROUND

Melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs) respond directly to light and have been shown to mediate a broad variety of visual behaviors in adult animals. ipRGCs are also the first light sensitive cells in the developing retina, and have been implicated in a number of retinal developmental processes such as pruning of retinal vasculature and refinement of retinofugal projections. However, little is currently known about the properties of the six ipRGC subtypes during development, and how these cells act to influence retinal development. We therefore sought to characterize the structure, physiology, and birthdate of the most abundant ipRGC subtypes, M1, M2, and M4, at discrete postnatal developmental timepoints.

METHODS

We utilized whole cell patch clamp to measure the electrophysiological and morphological properties of ipRGC subtypes through postnatal development. We also used EdU labeling to determine the embryonic timepoints at which ipRGC subtypes terminally differentiate.

RESULTS

Our data show that ipRGC subtypes are distinguishable from each other early in postnatal development. Additionally, we find that while ipRGC subtypes terminally differentiate at similar embryonic stages, the subtypes reach adult-like morphology and physiology at different developmental timepoints.

CONCLUSIONS

This work provides a broad assessment of ipRGC morphological and physiological properties during the postnatal stages at which they are most influential in modulating retinal development, and lays the groundwork for further understanding of the specific role of each ipRGC subtype in influencing retinal and visual system development.

Distinct ipRGC subpopulations mediate light's acute and circadian effects on body temperature and sleep

The light environment greatly impacts human alertness, mood, and cognition by both acute regulation of physiology and indirect alignment of circadian rhythms. These processes require the melanopsin-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs), but the relevant downstream brain areas involved remain elusive. ipRGCs project widely in the brain, including to the central circadian pacemaker, the suprachiasmatic nucleus (SCN). Here we show that body temperature and sleep responses to acute light exposure are absent after genetic ablation of all ipRGCs except a subpopulation that projects to the SCN. Furthermore, by chemogenetic activation of the ipRGCs that avoid the SCN, we show that these cells are sufficient for acute changes in body temperature. Our results challenge the idea that the SCN is a major relay for the acute effects of light on non-image forming behaviors and identify the sensory cells that initiate light’s profound effects on body temperature and sleep.

Light, whether natural or artificial, affects our everyday lives in several ways. Exposure to light impacts on our health and well-being. It plays a crucial but indirect role in helping to align our internal body clock with the 24-hour cycle of day and night, and a burst of bright light in the middle of the night can wake us up from sleep.

Decades of research have revealed the circuitry that controls the indirect effects of light on the body's internal clock. A tiny set of cells in the base of the brain called the suprachiasmatic nucleus (SCN for short) generates the body’s daily or “circadian” rhythm. A small group of nerve cells in the retina of the eye called intrinsically photosensitive retinal ganglion cells (ipRGCs) connect with the SCN. These ipRGCs relay information about light to the SCN to ensure that daily rhythms happen at the appropriate times of day. But scientists do not yet know if the same brain circuits regulate the direct effects of light on alertness.

Mice are often used in studies of circadian rhythms but, unlike humans, mice are normally active at night and sleep throughout the day. This means that a burst of bright light in the middle of the night causes mice to become less alert.

Now, in experiments with mice, Rupp et al. show there are two separate circuits from the retina to the brain that influence wakefulness. In the experiments, some mice were genetically engineered to only have ipRGCs that connect with the SCN and to lack those that connect with other brain areas. These mice lived in cages with a normal day/night cycle and their body temperature and sleep-related brain activity were monitored as Rupp et al. sporadically exposed them to bright light at night. These mice continued their normal routines and were unaffected by the bursts of light. In a second set of experiments, ipRGCs that do not connect with the SCN were activated in other mice. This caused an immediate and sustained drop in the body temperature of the mice, which is linked to them becoming less alert.

The experiments suggest that the circuit that connects ipRGCs to the SCN to align the body’s circadian rhythm with light does not control the direct effect of light on wakefulness. Instead, a separate circuit that extends from ipRGCs to an unknown part of the brain area influences wakefulness. Better understanding this second circuit could allow scientists to develop ways to keep people like emergency personnel or overnight shift workers awake and alert at night while avoiding harmful disruptions to their circadian rhythms.

Thrombospondin-1 Mediates Axon Regeneration in Retinal Ganglion Cells

Neuronal subtypes show diverse injury responses, but the molecular underpinnings remain elusive. Using transgenic mice that allow reliable visualization of axonal fate, we demonstrate that intrinsically photosensitive retinal ganglion cells (ipRGCs) are both resilient to cell death and highly regenerative. Using RNA sequencing (RNA-seq), we show genes that are differentially expressed in ipRGCs and that associate with their survival and axon regeneration. Strikingly, thrombospondin-1 (Thbs1) ranked as the most differentially expressed gene, along with the well-documented injury-response genes Atf3 and Jun. THBS1 knockdown in RGCs eliminated axon regeneration. Conversely, RGC overexpression of THBS1 enhanced regeneration in both ipRGCs and non-ipRGCs, an effect that was dependent on syndecan-1, a known THBS1-binding protein. All structural domains of the THBS1 were not equally effective; the trimerization and C-terminal domains promoted regeneration, while the THBS type-1 repeats were dispensable. Our results identify cell-type-specific induction of Thbs1 as a novel gene conferring high regenerative capacity.

Light-dependent pathways for dopaminergic amacrine cell development and function

Retinal dopamine is a critical modulator of high acuity, light-adapted vision and photoreceptor coupling in the retina. Dopaminergic amacrine cells (DACs) serve as the sole source of retinal dopamine, and dopamine release in the retina follows a circadian rhythm and is modulated by light exposure. However, the retinal circuits through which light influences the development and function of DACs are still unknown. Intrinsically photosensitive retinal ganglion cells (ipRGCs) have emerged as a prime target for influencing retinal dopamine levels because they costratify with DACs in the inner plexiform layer and signal to them in a retrograde manner. Surprisingly, using genetic mouse models lacking specific phototransduction pathways, we find that while light influences the total number of DACs and retinal dopamine levels, this effect does not require ipRGCs. Instead, we find that the rod pathway is a critical modulator of both DAC number and retinal dopamine levels.

Divergent projection patterns of M1 ipRGC subtypes

In addition to its well-known role in pattern vision, light influences a wide range of non-image forming, subconscious visual behaviors including circadian photoentrainment, sleep, mood, learning, and the pupillary light reflex. Each of these behaviors is thought to require input from the M1 subtype of melanopsin-expressing, intrinsically photosensitive retinal ganglion cell (ipRGC). Recent work has demonstrated that the M1 subtype of ipRGC can be further subdivided based on expression of the transcription factor Brn3b. Brn3b-positive M1 ipRGCs project to the olivary pretectal nucleus and are necessary for the pupillary light reflex, while Brn3b-negative M1 ipRGCs project to the suprachiasmatic nucleus (SCN) and are sufficient for circadian photoentrainment. However, beyond the circadian and pupil systems, little is known about the projection patterns of M1 ipRGC subtypes. Here we show that Brn3b-positive M1 ipRGCs comprise the majority of sparse M1 ipRGC inputs to the thalamus, midbrain, and hypothalamus. Our data demonstrate that very few brain targets receive convergent input from both M1 ipRGC subpopulations, suggesting that each subpopulation drives a specific subset of light-driven behaviors.

Melanopsin Phototransduction Is Repurposed by ipRGC Subtypes to Shape the Function of Distinct Visual Circuits

Melanopsin is expressed in distinct types of intrinsically photosensitive retinal ganglion cells (ipRGCs), which drive behaviors from circadian photoentrainment to contrast detection. A major unanswered question is how the same photopigment, melanopsin, influences such vastly different functions. Here we show that melanopsin's role in contrast detection begins in the retina, via direct effects on M4 ipRGC (ON alpha RGC) signaling. This influence persists across an unexpectedly wide range of environmental light levels ranging from starlight to sunlight, which considerably expands the functional reach of melanopsin on visual processing. Moreover, melanopsin increases the excitability of M4 ipRGCs via closure of potassium leak channels, a previously unidentified target of the melanopsin phototransduction cascade. Strikingly, this mechanism is selective for image-forming circuits, as M1 ipRGCs (involved in non-image forming behaviors), exhibit a melanopsin-mediated decrease in excitability. Thus, melanopsin signaling is repurposed by ipRGC subtypes to shape distinct visual behaviors.

Morphological Identification of Melanopsin-Expressing Retinal Ganglion Cell Subtypes in Mice

Melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs) are a relatively recently discovered class of photoreceptor. ipRGCs can be subdivided into at least five subtypes (M1-M5), each of which has a distinct complement of morphological and physiological properties. ipRGC subtypes can be identified morphologically based on a combination of dendritic morphology and immunostaining for a cell-type specific marker. In this chapter, we describe methods for conclusively identifying each of the five ipRGC subtypes through a combination of patch clamp electrophysiology, Neurobiotin filling, visualization of ipRGC dendrites, and immunostaining for the marker SMI-32.

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells

The discovery of cell type-specific markers can provide insight into cellular function and the origins of cellular heterogeneity. With a recent push for the improved understanding of neuronal diversity, it is important to identify genes whose expression defines various subpopulations of cells. The retina serves as an excellent model for the study of central nervous system diversity, as it is composed of multiple major cell types. The study of each major class of cells has yielded genetic markers that facilitate the identification of these populations. However, multiple subtypes of cells exist within each of these major retinal cell classes, and few of these subtypes have known genetic markers, although many have been characterized by morphology or function. A knowledge of genetic markers for individual retinal subtypes would allow for the study and mapping of brain targets related to specific visual functions and may also lend insight into the gene networks that maintain cellular diversity. Current avenues used to identify the genetic markers of subtypes possess drawbacks, such as the classification of cell types following sequencing. This presents a challenge for data analysis and requires rigorous validation methods to ensure that clusters contain cells of the same function. We propose a technique for identifying the morphology and functionality of a cell prior to isolation and sequencing, which will allow for the easier identification of subtype-specific markers. This technique may be extended to non-neuronal cell types, as well as to rare populations of cells with minor variations. This protocol yields excellent-quality data, as many of the libraries have provided read depths greater than 20 million reads for single cells. This methodology overcomes many of the hurdles presented by Single-cell RNA-Seq and may be suitable for researchers aiming to profile cell types in a straightforward and highly efficient manner.

Topological phase transitions of (BixSb1-x)2Se3 alloys by density functional theory

We have performed an ab initio total energy investigation of the topological phase transition, and the electronic properties of topologically protected surface states of (BixSb1-x)2Se3 alloys. In order to provide an accurate alloy concentration for the phase transition, we have considered the special quasirandom structures to describe the alloy system. The trivial → topological transition concentration was obtained by (i) the calculation of the band gap closing as a function of Bi concentration (x), and (ii) the calculation of the Z2 topological invariant number. We show that there is a topological phase transition, for x around 0.4, verified for both procedures (i) and (ii). We also show that in the concentration range 0.4 < x < 0.7, the alloy does not present any other band at the Fermi level besides the Dirac cone, where the Dirac point is far from the bulk states. This indicates that a possible suppression of the scattering process due to bulk states will occur.

Loss of gq/11 genes does not abolish melanopsin phototransduction

In mammals, a subset of retinal ganglion cells (RGCs) expresses the photopigment melanopsin, which renders them intrinsically photosensitive (ipRGCs). These ipRGCs mediate various non-image-forming visual functions such as circadian photoentrainment and the pupillary light reflex (PLR). Melanopsin phototransduction begins with activation of a heterotrimeric G protein of unknown identity. Several studies of melanopsin phototransduction have implicated a G-protein of the G_q/11 family, which consists of Gna11, Gna14, Gnaq and Gna15, in melanopsin-evoked depolarization. However, the exact identity of the G_q/11 gene involved in this process has remained elusive. Additionally, whether G_q/11 G-proteins are necessary for melanopsin phototransduction in vivo has not yet been examined. We show here that the majority of ipRGCs express both Gna11 and Gna14, but neither Gnaq nor Gna15. Animals lacking the melanopsin protein have well-characterized deficits in the PLR and circadian behaviors, and we therefore examined these non-imaging forming visual functions in a variety of single and double mutants for G_q/11 family members. All G_q/11 mutant animals exhibited PLR and circadian behaviors indistinguishable from WT. In addition, we show persistence of ipRGC light-evoked responses in Gna11^−/−; Gna14^−/− retinas using multielectrode array recordings. These results demonstrate that G_q, G₁₁, G₁₄, or G₁₅ alone or in combination are not necessary for melanopsin-based phototransduction, and suggest that ipRGCs may be able to utilize a G_q/11-independent phototransduction cascade in vivo.

A role for melanopsin in alpha retinal ganglion cells and contrast detection

Distinct subclasses of retinal ganglion cells (RGCs) mediate vision and nonimage-forming functions such as circadian photoentrainment. This distinction stems from studies that ablated melanopsin-expressing intrinsically photosensitive RGCs (ipRGCs) and showed deficits in nonimage-forming behaviors, but not image vision. However, we show that the ON alpha RGC, a conventional RGC type, is intrinsically photosensitive in mammals. In addition to their classical response to fast changes in contrast through rod/cone signaling, melanopsin expression allows ON alpha RGCs to signal prior light exposure and environmental luminance over long periods of time. Consistent with the high contrast sensitivity of ON alpha RGCs, mice lacking either melanopsin or ON alpha RGCs have behavioral deficits in contrast sensitivity. These findings indicate a surprising role for melanopsin and ipRGCs in vision.

Diverse types of ganglion cell photoreceptors in the mammalian retina

Photoreceptors carry out the first step in vision by capturing light and transducing it into electrical signals. Rod and cone photoreceptors efficiently translate photon capture into electrical signals by light activation of opsin-type photopigments. Until recently, the central dogma was that, for mammals, all phototransduction occurred in rods and cones. However, the recent discovery of a novel photoreceptor type in the inner retina has fundamentally challenged this view. These retinal ganglion cells are intrinsically photosensitive and mediate a broad range of physiological responses such as photoentrainment of the circadian clock, light regulation of sleep, pupillary light reflex, and light suppression of melatonin secretion. Intrinsically photosensitive retinal ganglion cells express melanopsin, a novel opsin-based signaling mechanism reminiscent of that found in invertebrate rhabdomeric photoreceptors. Melanopsin-expressing retinal ganglion cells convey environmental irradiance information directly to brain centers such as the hypothalamus, preoptic nucleus, and lateral geniculate nucleus. Initial studies suggested that these melanopsin-expressing photoreceptors were an anatomically and functionally homogeneous population. However, over the past decade or so, it has become apparent that these photoreceptors are distinguishable as individual subtypes on the basis of their morphology, molecular markers, functional properties, and efferent projections. These results have provided a novel classification scheme with five melanopsin photoreceptor subtypes in the mammalian retina, each presumably with differential input and output properties. In this review, we summarize the evidence for the structural and functional diversity of melanopsin photoreceptor subtypes and current controversies in the field.

Intrinsically photosensitive retinal ganglion cells: many subtypes, diverse functions

For decades, rods and cones were thought to be the only photoreceptors in the mammalian retina. However, a population of atypical photoreceptive retinal ganglion cells (RGCs) expresses the photopigment melanopsin and is intrinsically photosensitive (ipRGCs). These ipRGCs are crucial for relaying light information from the retina to the brain to control circadian photoentrainment, pupillary light reflex, and sleep. ipRGCs were initially described as a uniform population involved solely in signaling irradiance for non-image forming functions. Recent work, however, has uncovered that ipRGCs are unexpectedly diverse at the molecular, cellular and functional levels, and could even be involved in image formation. This review summarizes our current understanding of the diversity of ipRGCs and their various roles in modulating behavior.

Structure and function of bistratified intrinsically photosensitive retinal ganglion cells in the mouse

A subpopulation of retinal ganglion cells (RGCs) expresses the photopigment melanopsin, rendering these cells intrinsically photosensitive (ipRGCs). These cells are critical for competent circadian entrainment, pupillary light reflex, and other non-imaging-forming photic responses. Research has now demonstrated the presence of multiple subpopulations of ipRGC based on the dendritic stratification in the inner plexiform layer (IPL), those monostratified in the Off sublamina (M1), those monostratified in the On sublamina (M2,4,5), and those bistratified in both the On and the Off sublaminae (M3). Despite evidence that M1 and M2 cells are distinct subpopulations of ipRGC based on distinct morphological and physiological properties, the inclusion of M3 cells as a distinct subtype has remained controversial. Aside from the identification of M3 cells as a morphological subpopulation of ipRGC, to date there have been no functional descriptions of M3 cell physiology or synaptic inputs. Our data provide the first in-depth description of M3 cell structural and functional properties. We report that M3 cells form a morphologically heterogeneous population but one that is physiologically homogeneous with properties similar to those of M2 cells.

Intrinsic phototransduction persists in melanopsin-expressing ganglion cells lacking diacylglycerol-sensitive TRPC subunits

In mammals, intrinsically photosensitive retinal ganglion cells (ipRGCs) mediate various non-image-forming photic responses, such as circadian photoentrainment, pupillary light reflex and pineal melatonin suppression. ipRGCs directly respond to environmental light by activation of the photopigment melanopsin followed by the opening of an unidentified cation-selective channel. Studies in heterologous expression systems and in the native retina have strongly implicated diacylglycerol-sensitive transient receptor potential channels containing TRPC3, TRPC6 and TRPC7 subunits in melanopsin-evoked depolarization. Here we show that melanopsin-evoked electrical responses largely persist in ipRGCs recorded from early postnatal (P6-P8) and adult (P22-P50) mice lacking expression of functional TRPC3, TRPC6 or TRPC7 subunits. Multielectrode array (MEA) recordings performed at P6-P8 stages under conditions that prevent influences from rod/cone photoreceptors show comparable light sensitivity for the melanopsin-evoked responses in these mutant mouse lines in comparison to wild-type (WT) mice. Patch-clamp recordings from adult mouse ipRGCs lacking TRPC3 or TRPC7 subunits show intrinsic light-evoked responses equivalent to those recorded in WT mice. Persistence of intrinsic light-evoked responses was also noted in ipRGCs lacking TRPC6 subunits, although with significantly smaller magnitudes. These results demonstrate that the melanopsin-evoked depolarization in ipRGCs is not mediated by either TRPC3, TRPC6 or TRPC7 channel subunits alone. They also suggest that the melanopsin signaling pathway includes TRPC6-containing heteromeric channels in mature retinas.

An isolated retinal preparation to record light response from genetically labeled retinal ganglion cells

The first steps in vertebrate vision take place when light stimulates the rod and cone photoreceptors of the retina. This information is then segregated into what are known as the ON and OFF pathways. The photoreceptors signal light information to the bipolar cells (BCs), which depolarize in response to increases (On BCs) or decreases (Off BCs) in light intensity. This segregation of light information is maintained at the level of the retinal ganglion cells (RGCs), which have dendrites stratifying in either the Off sublamina of the inner plexiform layer (IPL), where they receive direct excitatory input from Off BCs, or stratifying in the On sublamina of the IPL, where they receive direct excitatory input from On BCs. This segregation of information regarding increases or decreases in illumination (the On and Off pathways) is conserved and signaled to the brain in parallel. The RGCs are the output cells of the retina, and are thus an important cell to study in order to understand how light information is signaled to visual nuclei in the brain. Advances in mouse genetics over recent decades have resulted in a variety of fluorescent reporter mouse lines where specific RGC populations are labeled with a fluorescent protein to allow for identification of RGC subtypes and specific targeting for electrophysiological recording. Here, we present a method for recording light responses from fluorescently labeled ganglion cells in an intact, isolated retinal preparation. This isolated retinal preparation allows for recordings from RGCs where the dendritic arbor is intact and the inputs across the entire RGC dendritic arbor are preserved. This method is applicable across a variety of ganglion cell subtypes and is amenable to a wide variety of single-cell physiological techniques.

Inwardly rectifying potassium channel Kir4.1 is responsible for the native inward potassium conductance of satellite glial cells in sensory ganglia

Satellite glial cells (SGCs) surround primary afferent neurons in sensory ganglia, and increasing evidence has implicated the K(+) channels of SGCs in affecting or regulating sensory ganglion excitability. The inwardly rectifying K(+) (Kir) channel Kir4.1 is highly expressed in several types of glial cells in the central nervous system (CNS) where it has been implicated in extracellular K(+) concentration buffering. Upon neuronal activity, the extracellular K(+) concentration increases, and if not corrected, causes neuronal depolarization and uncontrolled changes in neuronal excitability. Recently, it has been demonstrated that knockdown of Kir4.1 expression in trigeminal ganglia leads to neuronal hyperexcitability in this ganglia and heightened nociception. Thus, we investigated the contribution of Kir4.1 to the membrane K(+) conductance of SGCs in neonatal and adult mouse trigeminal and dorsal root ganglia. Whole cell patch clamp recordings were performed in conjunction with immunocytochemistry and quantitative transcript analysis in various mouse lines. We found that in wild-type mice, the inward K(+) conductance of SGCs is blocked almost completely with extracellular barium, cesium and desipramine, consistent with a conductance mediated by Kir channels. We then utilized mouse lines in which genetic ablation led to partial or complete loss of Kir4.1 expression to assess the role of this channel subunit in SGCs. The inward K(+) currents of SGCs in Kir4.1+/- mice were decreased by about half while these currents were almost completely absent in Kir4.1-/- mice. These findings in combination with previous reports support the notion that Kir4.1 is the principal Kir channel type in SGCs. Therefore Kir4.1 emerges as a key regulator of SGC function and possibly neuronal excitability in sensory ganglia.

An ab initio study of energetic stability and electronic confinement for different structural phases of ZnO nanowires

We performed an ab initio total energy investigation of hexagonal (wurtzite and graphitic) and zinc blende ZnO nanowires (NWs) aligned along the [0001] and [111] directions, respectively, as a function of the NW diameter. We have considered unpassivated and (hydrogen) passivated NW surfaces. For the unpassivated system, we find that the wurtzite phase represents the energetically most favorable configuration. The width of the energy bandgap of wurtzite ZnO NWs increases by reducing the NW diameter, which is in accordance with the one-dimensional confinement effect. In contrast, this property fails in the zinc blende and graphitic NWs. In the former it is due to the high density of surface states within the fundamental bandgap, while in the latter system the energy bandgap becomes indirect and increases slowly by reducing the NW diameter. Our total energy results indicate that the hydrogen-passivated ZnO NWs are more stable than the unpassivated ones. For thin hydrogen-passivated NWs, we find that the graphitic phase becomes more stable than the wurtzite. For NW diameters around 2 nm, the graphitic and wurtzite phases present similar formation energies, while for larger diameters the wurtzite NWs become energetically more favorable. Finally, comparing the behavior and the positions of the valence and conduction band edges for the unpassivated ZnO NWs, we proposed the formation of type II band alignment for a hypothetical wurtzite/graphitic NW heterojunction.

Differential Investment Behavior between Grandparents and Grandchildren: The Role of Paternity Uncertainty

Kin selection theory predicts that grandparents will differentially invest in their grandchildren as a function of paternity certainty. This study explored the hypothesis of “discriminative grandparental solicitude” ( Euler and Weitzel, 1996 ; Smith, 1988 ) in a sample of college students. Students with four living grandparents were asked to indicate the frequency of various behaviors received from or directed to each grandparent. A significant linear trend on a majority of the measures supported this hypothesis. Reported contact and closeness were highest with the maternal grandmother (most genetically certain) and lowest with the paternal grandfather (least genetically certain); maternal grandfathers and paternal grandmothers were intermediate. The “preferential investment hypothesis” ( Laham, Gonsalkorale, and von Hippel, 2005 ) predicts that the investment behavior of the maternal grandfather and the paternal grandmother should differ only when there are cousins through the father's sisters. Contrary to the predictions of this hypothesis, grandchildren did not rate the maternal grandfather consistently higher on any of the indices when more certain investment outlets were available to the paternal grandmother.

Novel insights into non-image forming visual processing in the retina

A small subset of retinal ganglion cells projecting to the suprachiasmatic nucleus and other brain areas, is implicated in non-image forming visual responses to environmental light such as the pupillary light reflex, seasonal adaptations in physiology, photic inhibition of nocturnal melatonin release, and modulation of sleep, alertness and activity. These cells are intrinsically photosensitive (ipRGCs) and express an opsin-like photopigment called melanopsin. Two recent studies utilizing selective genetic ablation of ipRGCs demonstrate the key role of these inner retinal cells in conveying luminance signals to the brain for non-image forming visual processing. These findings advance our understanding of functional organization of a novel photosensory system in the mammalian retina, demonstrating well-defined roles for ipRGCs in circadian timing and other homeostatic functions related to ambient illumination.

Intrinsic and extrinsic light responses in melanopsin-expressing ganglion cells during mouse development

Melanopsin (Opn4) is a photopigment found in a subset of retinal ganglion cells (RGCs) that project to various brain areas. These neurons are intrinsically photosensitive (ipRGCs) and are implicated in nonimage-forming responses to environmental light such as the pupillary light reflex and circadian entrainment. Recent evidence indicates that ipRGCs respond to light at birth, but questions remain as to whether and when they undergo significant functional changes. We used bacterial artificial chromosome transgenesis to engineer a mouse line in which enhanced green fluorescent protein (EGFP) is expressed under the control of the melanopsin promoter. Double immunolabeling for EGFP and melanopsin demonstrates their colocalization in ganglion cells of mutant mouse retinas. Electrophysiological recordings of ipRGCs in neonatal mice (postnatal day 0 [P0] to P7) demonstrated that these cells responded to light with small and sluggish depolarization. However, starting at P11 we observed ipRGCs that responded to light with a larger and faster onset (<1 s) and offset (<1 s) depolarization. These faster, larger depolarizations were observed in most ipRGCs by early adult ages. However, on application of a cocktail of synaptic blockers, we found that all cells responded to light with slow onset (>2.5 s) and offset (>10 s) depolarization, revealing the intrinsic, melanopsin-mediated light responses. The extrinsic, cone/rod influence on ipRGCs correlates with their extensive dendritic stratification in the inner plexiform layer. Collectively, these results demonstrate that ipRGCs make use of melanopsin for phototransduction before eye opening and that these cells further integrate signals derived from the outer retina as the retina matures.

The effects of oxygen on the surface passivation of InP nanowires

The effects of surface passivation on the electronic and structural properties of InP nanowires have been investigated by first-principles calculations. We compare the properties of nanowires whose surfaces have been passivated in several ways, always by H atoms and OH radicals. Taking as the initial reference nanowires that are fully passivated by H atoms, we find that the exchange of these atoms at the surface by OH radicals is always energetically favorable. A nanowire fully passivated by OH radicals is about 2.5 eV per passivated dangling bond more stable than a nanowire fully passivated by H atoms. However, the energetically most stable passivated surface is predicted to have all In atoms bonded to OH radicals and all P atoms bonded to H atoms. This mixed passivation is 2.66 eV per passivated dangling bond more stable than a nanowire fully passivated by H atoms. Our results show that, in comparison with the fully H-saturated nanowire, the fully OH-saturated nanowire has a smaller energy band gap and localized states near the energy band edges. Also, more interestingly, concerning optical applications, the most stable H+OH passivated nanowire has a well-defined energy band gap, only 10% smaller than the H-saturated nanowire energy gap, and few localized states always close to the valence band maximum.

Changes in Synechococcus population size and cellular ribosomal RNA content in response to predation and nutrient limitation

A mathematical model of predator-prey interactions was used to predict the relationship between population size and cellular growth rate in a two-tiered trophic system consisting of Synechococcus PCC 6301 and Tetrahymena pyriformis. As predicted, axenic chemostat cultures of Synechococcus responded to increased nutrient availability by expanding the equilibrium population size without a concurrent change in growth rate. Likewise, the addition of the predator Tetrahymena pyriformis decreased the Synechococcus population size by 85% and increased the Synechococcus growth rate. Synechococcus populations in the surface waters of the Gulf of Mexico were sampled to ascertain whether the relationship between population size and cellular 16S rRNA concentration conformed to that predicted by the model. Direct counts of autofluorescent cells in size-fractionated seawater samples provided an estimate of Synechococcus population size. The growth rate of in situ populations was estimated by measuring the extent of hybridization of an oligonucleotide probes complementary to Synechococcus 16S rRNA, based on evidence that ribosomal RNA content increases concurrently with growth rate. The comparison of in situ population sizes and specific growth rates revealed that relatively large Synechococcus populations were growing slowly, indicative of nutrient limitation, and that quickly growing populations were relatively small, as predicted for predator-limited populations.

Archaeal nucleic acids in picoplankton from great lakes on three continents

Phylogenetic analysis of PCR-amplified 16S rRNA genes revealed the presence of archaea in picoplankton collected from the Laurentian Great Lakes in North America, Africa's Lake Victoria, and Lakes Ladoga and Onega in northeastern Eurasia. From 1 to 10% of the rRNA extracted from size-fractionated picoplankton (>0.2 microm but <1.2 microm) collected in the epilimnion and hypolimnion of these lakes was specific to the Archaea, whereas the majority of rRNA was derived from Bacteria. Analysis of the 16S rRNA genes cloned from these samples indicated they were closely related to crenarchaeal sequences that have been widely characterized from marine environments. The presence of nearly identical 16S rDNA clones in several of these geographically disparate lakes suggests a cosmopolitan distribution of specific subgroups of these Archaea in freshwater environments. Despite their abundance in the water column of freshwater lakes, we have no representatives of these crenarchaea in pure culture, and so their physiological characteristics and ecological role remain unknown.

The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta release of 9.0 debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences. New analysis services include a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). A new interactive tutorial guides users through the basics of rRNA sequence analysis. Other services include probe checking, phylogenetic placement of user sequences, screening of users' sequences for chimeric rRNA sequences, automated alignment, production of similarity matrices, and services to plan and analyze terminal restriction fragment polymorphism (T-RFLP) experiments. The RDP-II email address for questions or comments is rdpstaff@msu.edu.

Effects of trifluoperazine on the contraction kinetics of the isolated intact tracheal and pulmonary artery smooth muscle

BACKGROUND

We studied the effect of the calmodulin antagonist trifluoperazine (TFP) on isolated intact rat tracheal and pulmonary artery smooth muscle contractile behaviour.

METHODS

Experimental series: 1) TFP-dose-response curves for TFP's effect on force generation were constructed using rat tracheal smooth muscles and rat pulmonary artery preparations (n = 8). A concentration of 1 micromol/l TFP was chosen for the subsequent experimental series. 2) Tracheas and pulmonary arteries (n = 14) were dissected in three segments. One of them was used immediately for experiments ("native"), the other two were treated for 12 h in 4 degrees C Tyrode solution without ("12 h cold storage") or with 1 micromol/l TFP ("12 h cold storage + TFP"). These preparations contracted after supramaximal effective electrical field stimulation. The force-clamping technique was used to analyse kinetic and mechanical parameters of smooth-muscle contraction in both types of preparation (measurement conditions: resting tension 2 mN, 37 degrees C, modified Krebs-Henseleit solution).

RESULTS

1) TFP decreased developed force dose-dependently in pulmonary artery and tracheal smooth muscle. 2) During sustained tonic activation, the contraction kinetics become slower both with and without TFP treatment (p < 0.0001). 3) TFP caused a dramatic retardation of the velocity of force generation in both types of preparation for any given time interval during the course of a tonic activation (p < 0.0005). 4) The dramatic effects of TFP on the contraction kinetics were not associated with effects on the extent of force generation.

CONCLUSIONS

These results support the assumption that tracheal and pulmonary artery smooth muscle cross-bridge rates are controlled by a calcium-calmodulin-dependent myosin light chain kinase. This finding suggests the involvement of a calmodulin-independent regulator process responsible for the changes observed in the cross-bridge cycling rates during sustained tonic activation. A direct intervention on the contractile apparatus level is a measure for reduction of smooth-muscle tone without negative inotropic side effects.

Taxonomic characterization of Ketogulonigenium vulgare gen. nov., sp. nov. and Ketogulonigenium robustum sp. nov., which oxidize L-sorbose to 2-keto-L-gulonic acid

Four bacterial strains that oxidize L-sorbose to 2-keto-L-gulonic acid, a key intermediate in the synthesis of vitamin C, were isolated from soils of geographically distinct locations. All were Gram-negative, facultatively anaerobic, chemoheterotrophic rods. Comparative analysis revealed nearly identical 16S rDNA sequences amongst them (99.7-100% identical) and identified them as members of the alpha-subclass of the Proteobacteria. Phylogenetic analysis identified the closest taxonomically defined genus as Roseobacter (92.1-92.8% identical). On the basis of phylogenetic, phenotypic and genotypic analyses, a new genus is proposed, Ketogulonigenium gen. nov. Based upon these analyses, we also propose the reclassification of strain DSM 4025TP, originally identified as Gluconobacter oxydans, to the genus Ketogulonigenium. Two species are proposed: the type species Ketogulonigenium vulgare gen. nov., sp. nov., consisting of strains 62A-12APP, 266-13BPP and the type strain K. vulgare DSM 4025TP, and Ketogulonigenium robustum gen. nov., sp. nov., consisting of the type strain K. robustum X6LTP (= NRRL B-21627 = KCTC 0858BP). The species affiliation of the fifth strain (291-19PP) remains unresolved.

The RDP-II (Ribosomal Database Project)

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173-174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and approximately 75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.h tml). RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment polymorphism experiments. The RDP-II email address for questions and comments has been changed from curator@cme.msu.edu to rdpstaff@msu.edu.

rrndb: the Ribosomal RNA Operon Copy Number Database

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme. msu.edu.

rRNA operon copy number reflects ecological strategies of bacteria

Although natural selection appears to favor the elimination of gene redundancy in prokaryotes, multiple copies of each rRNA-encoding gene are common on bacterial chromosomes. Despite this conspicuous deviation from single-copy genes, no phenotype has been consistently associated with rRNA gene copy number. We found that the number of rRNA genes correlates with the rate at which phylogenetically diverse bacteria respond to resource availability. Soil bacteria that formed colonies rapidly upon exposure to a nutritionally complex medium contained an average of 5.5 copies of the small subunit rRNA gene, whereas bacteria that responded slowly contained an average of 1.4 copies. In soil microcosms pulsed with the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), indigenous populations of 2,4-D-degrading bacteria with multiple rRNA genes ( = 5.4) became dominant, whereas populations with fewer rRNA genes ( = 2.7) were favored in unamended controls. These findings demonstrate phenotypic effects associated with rRNA gene copy number that are indicative of ecological strategies influencing the structure of natural microbial communities.

The RDP (Ribosomal Database Project) continues

The Ribosomal Database Project (RDP-II), previously described by Maidak et al., continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 7.1 (September 17, 1999) included more than 10 700 small subunit rRNA sequences. More than 850 type strain sequences were identified and added to the prokaryotic alignment, bringing the total number of type sequences to 3324 representing 2460 different species. Availability of an RDP-II mirror site in Japan is also near completion. RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/ ). Analysis services include rRNA probe checking, approx-i-mate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment length polymorphism (T-RFLP) experiments.

Application of Traditional and Phylogenetically Based Comparative Methods to Test for a Trade-off in Bacterial Growth Rate at Low versus High Substrate Concentration

Abstract It is often hypothesized that those organisms that are superior competitors for sparse resources fare poorly in competition for abundant resources, and vice versa. If there is indeed such a systematic trade-off, then this has important implications for the choice of bacterial strains in bioremediation and other applications. We studied seven bacterial strains that can grow on either 2,4-dichlorophenoxyacetate (2,4-D) or succinate as a sole source of carbon. Growth rates were measured on each substrate at both low (5 µg/ml) and high (500 µg/ml) concentrations. We used two different methods to test the significance of correlations among growth rates, a traditional method that treats each strain as an independent observation and a newer method that takes into account phylogenetic relationships between strains, thereby avoiding spurious correlations caused by a lack of statistical independence of strains. In both 2,4-D and succinate, we observed significant positive correlations between growth rates measured at high and low substrate concentrations by the traditional comparative method. No significant correlations were detected after adjusting for the phylogenetic relationships among the strains. In neither case did we observe the negative correlation expected from a trade-off between growth rates at high and low substrate levels.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p191.html</hea