Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants

BACKGROUND

In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA is well understood, gene body methylation is not associated with transcriptional repression, and its biological importance remains unclear.

RESULTS

We report a newly discovered type of GbM in plants, which is under constitutive addition and removal by dynamic methylation modifiers in all cells, including the germline. Methylation at Dynamic GbM genes is removed by the DRDD demethylation pathway and added by an unknown source of de novo methylation, most likely the maintenance methyltransferase MET1. We show that the Dynamic GbM state is present at homologous genes across divergent lineages spanning over 100 million years, indicating evolutionary conservation. We demonstrate that Dynamic GbM is tightly associated with the presence of a promoter or regulatory chromatin state within the gene body, in contrast to other gene body methylated genes. We find Dynamic GbM is associated with enhanced gene expression plasticity across development and diverse physiological conditions, whereas stably methylated GbM genes exhibit reduced plasticity. Dynamic GbM genes exhibit reduced dynamic range in drdd mutants, indicating a causal link between DNA demethylation and enhanced gene expression plasticity.

CONCLUSIONS

We propose a new model for GbM in regulating gene expression plasticity, including a novel type of GbM in which increased gene expression plasticity is associated with the activity of DNA methylation writers and erasers and the enrichment of a regulatory chromatin state.

Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time

Cytosine methylation is a reversible epigenetic modification of DNA. In plants, removal of cytosine methylation is accomplished by the four members of the DEMETER (DME) family of 5-methylcytosine DNA glycosylases, named DME, DEMETER-LIKE2 (DML2), DML3, and REPRESSOR OF SILENCING1 (ROS1) in Arabidopsis thaliana. Demethylation by DME is critical for seed development, preventing experiments to determine the function of the entire gene family in somatic tissues by mutant analysis. Here, we bypassed the reproductive defects of dme mutants to create somatic quadruple homozygous mutants of the entire DME family. dme; ros1; dml2; and dml3 (drdd) leaves exhibit hypermethylated regions compared with wild-type leaves and rdd triple mutants, indicating functional redundancy among all four demethylases. Targets of demethylation include regions co-targeted by RNA-directed DNA methylation and, surprisingly, CG gene body methylation, indicating dynamic methylation at these less-understood sites. Additionally, many tissue-specific methylation differences are absent in drdd, suggesting a role for active demethylation in generating divergent epigenetic states across wild-type tissues. Furthermore, drdd plants display an early flowering phenotype, which involves 5'-hypermethylation and transcriptional down-regulation of FLOWERING LOCUS C. Active DNA demethylation is therefore required for proper methylation across somatic tissues and defines the epigenetic landscape of intergenic and coding regions.

Transcriptional and imprinting complexity in Arabidopsis seeds at single-nucleus resolution

Seeds are a key life cycle stage for many plants. Seeds are also the basis of agriculture and the primary source of calories consumed by humans¹. Here, we employ single-nucleus RNA-sequencing to generate a transcriptional atlas of developing Arabidopsis thaliana seeds, with a focus on endosperm. Endosperm, the primary site of gene imprinting in flowering plants, mediates the relationship between the maternal parent and the embryo². We identify transcriptionally uncharacterized nuclei types in the chalazal endosperm, which interfaces with maternal tissue for nutrient unloading^3,4. We demonstrate that the extent of parental bias of maternally expressed imprinted genes varies with cell-cycle phase, and that imprinting of paternally expressed imprinted genes is strongest in chalazal endosperm. Thus, imprinting is spatially and temporally heterogeneous. Increased paternal expression in the chalazal region suggests that parental conflict, which is proposed to drive imprinting evolution, is fiercest at the boundary between filial and maternal tissues.

Principles of Epigenetic Homeostasis Shared Between Flowering Plants and Mammals

In diverse eukaryotes, epigenetic information such as DNA methylation is stably propagated over many cell divisions and generations, and can remain the same over thousands or millions of years. However, this stability is the product of dynamic processes that add and remove DNA methylation by specialized enzymatic pathways. The activities of these dynamic pathways must therefore be finely orchestrated in order to ensure that the DNA methylation landscape is maintained with high fidelity - a concept we term epigenetic homeostasis. In this review, we summarize recent insights into epigenetic homeostasis mechanisms in flowering plants and mammals, highlighting analogous mechanisms that have independently evolved to achieve the same goal of stabilizing the epigenetic landscape.

Ancient duons may underpin spatial patterning of gene expression in C4 leaves

If the highly efficient C4 photosynthesis pathway could be transferred to crops with the C3 pathway there could be yield gains of up to 50%. It has been proposed that the multiple metabolic and developmental modifications associated with C4 photosynthesis are underpinned by relatively few master regulators that have allowed the evolution of C4 photosynthesis more than 60 times in flowering plants. Here we identify a component of one such regulator that consists of a pair of cis-elements located in coding sequence of multiple genes that are preferentially expressed in bundle sheath cells of C4 leaves. These motifs represent duons as they play a dual role in coding for amino acids as well as controlling the spatial patterning of gene expression associated with the C4 leaf. They act to repress transcription of C4 photosynthesis genes in mesophyll cells. These duons are also present in the C3 model Arabidopsis thaliana, and, in fact, are conserved in all land plants and even some algae that use C3 photosynthesis. C4 photosynthesis therefore appears to have coopted an ancient regulatory code to generate the spatial patterning of gene expression that is a hallmark of C4 photosynthesis. This intragenic transcriptional regulatory sequence could be exploited in the engineering of efficient photosynthesis of crops.

Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit

Epigenetic states are stably propagated in eukaryotes. In plants, DNA methylation patterns are faithfully inherited over many generations but it is unknown how the dynamic activities of cytosine DNA methyltransferases and 5-methylcytosine DNA glycosylases interact to maintain epigenetic homeostasis. Here we show that a methylation-sensing gene regulatory circuit centered on a 5-methylcytosine DNA glycosylase gene is required for long-term epigenetic fidelity in Arabidopsis. Disrupting this circuit causes widespread methylation losses and abnormal phenotypes that progressively worsen over generations. In heterochromatin, these losses are counteracted such that methylation returns to a normal level over four generations. However, thousands of loci in euchromatin progressively lose DNA methylation between generations and remain unmethylated. We conclude that an actively maintained equilibrium between methylation and demethylation activities is required to ensure long-term stable inheritance of epigenetic information.

DNA methylation patterns are inherited over many generations in plants. Here, Williams and Gehring show that the 5-methylcytosine DNA glycosylase ROS1 functions as part of a methylation-sensitive circuit that ensures long-term epigenetic fidelity in Arabidopsis.

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention

Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species.

An Untranslated cis-Element Regulates the Accumulation of Multiple C4 Enzymes in Gynandropsis gynandra Mesophyll Cells

C4 photosynthesis is a complex phenotype that allows more efficient carbon capture than the ancestral C3 pathway. In leaves of C4 species, hundreds of transcripts increase in abundance compared with C3 relatives and become restricted to mesophyll (M) or bundle sheath (BS) cells. However, no mechanism has been reported that regulates the compartmentation of multiple enzymes in M or BS cells. We examined mechanisms regulating CARBONIC ANHYDRASE4 (CA4) in C4 Gynandropsis gynandra. Increased abundance is directed by both the promoter region and introns of the G. gynandra gene. A nine-nucleotide motif located in the 5' untranslated region (UTR) is required for preferential accumulation of GUS in M cells. This element is present and functional in three additional 5' UTRs and six 3' UTRs where it determines accumulation of two isoforms of CA and pyruvate,orthophosphate dikinase in M cells. Although the GgCA4 5' UTR is sufficient to direct GUS accumulation in M cells, transcripts encoding GUS are abundant in both M and BS. Mutating the GgCA4 5' UTR abolishes enrichment of protein in M cells without affecting transcript abundance. The work identifies a mechanism that directs cell-preferential accumulation of multiple enzymes required for C4 photosynthesis.

Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment

Gluconeogenesis is a fundamental metabolic process that allows organisms to make sugars from non-carbohydrate stores such as lipids and protein. In eukaryotes only one gluconeogenic route has been described from organic acid intermediates and this relies on the enzyme phosphoenolpyruvate carboxykinase (PCK). Here we show that two routes exist in Arabidopsis, and that the second uses pyruvate, orthophosphate dikinase (PPDK). Gluconeogenesis is critical to fuel the transition from seed to seedling. Arabidopsis pck1 and ppdk mutants are compromised in seed-storage reserve mobilization and seedling establishment. Radiolabelling studies show that PCK predominantly allows sugars to be made from dicarboxylic acids, which are products of lipid breakdown. However, PPDK also allows sugars to be made from pyruvate, which is a major product of protein breakdown. We propose that both routes have been evolutionarily conserved in plants because, while PCK expends less energy, PPDK is twice as efficient at recovering carbon from pyruvate.

During seed germination plants use gluconeogenesis to mobilize noncarbohydrate energy reserves. Here Eastmond et al. show that plants, unlike other eukaryotes, do not solely rely on a gluconeogenic pathway via the enzyme PCK but also use a second pathway relying on PPDK.

Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat

Genomes must balance active suppression of transposable elements (TEs) with the need to maintain gene expression. In Arabidopsis, euchromatic TEs are targeted by RNA-directed DNA methylation (RdDM). Conversely, active DNA demethylation prevents accumulation of methylation at genes proximal to these TEs. It is unknown how a cellular balance between methylation and demethylation activities is achieved. Here we show that both RdDM and DNA demethylation are highly active at a TE proximal to the major DNA demethylase gene ROS1. Unexpectedly, and in contrast to most other genomic targets, expression of ROS1 is promoted by DNA methylation and antagonized by DNA demethylation. We demonstrate that inducing methylation in the ROS1 proximal region is sufficient to restore ROS1 expression in an RdDM mutant. Additionally, methylation-sensitive expression of ROS1 is conserved in other species, suggesting it is adaptive. We propose that the ROS1 locus functions as an epigenetic rheostat, tuning the level of demethylase activity in response to methylation alterations, thus ensuring epigenomic stability.

Organisms must adapt to dynamic and variable internal and external environments. Maintaining homeostasis in core biological processes is crucial to minimizing the deleterious consequences of environmental fluctuations. Genomes are also dynamic and variable, and must be robust against stresses, including the invasion of genomic parasites, such as transposable elements (TEs). In this work we present the discovery of an epigenetic rheostat in plants that maintains homeostasis in levels of DNA methylation. DNA methylation typically silences transcription of TEs. Because there is positive feedback between existing and de novo DNA methylation, it is critical that methylation is not allowed to spread and potentially silence transcription of genes. To maintain homeostasis, methylation promotes the production of a demethylase enzyme that removes methylation from gene-proximal regions. The demethylation of genes is therefore always maintained in concert with the levels of methylation suppressing TEs. In addition, this DNA demethylating enzyme also represses its own production in a negative feedback loop. Together, these feedback mechanisms shed new light on how the conflict between gene expression and genome defense is maintained in homeostasis. The presence of this rheostat in multiple species suggests it is an evolutionary conserved adaptation.

Two-party secret key distribution via a modified quantum secret sharing protocol

We present and demonstrate a novel protocol for distributing secret keys between two and only two parties based on N-party single-qubit Quantum Secret Sharing (QSS). We demonstrate our new protocol with N = 3 parties using phase-encoded photons. We show that any two out of N parties can build a secret key based on partial information from each other and with collaboration from the remaining N - 2 parties. Our implementation allows for an accessible transition between N-party QSS and arbitrary two party QKD without modification of hardware. In addition, our approach significantly reduces the number of resources such as single photon detectors, lasers and dark fiber connections needed to implement QKD.

Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis

C4 photosynthesis has independently evolved from the ancestral C3 pathway in at least 60 plant lineages, but, as with other complex traits, how it evolved is unclear. Here we show that the polyphyletic appearance of C4 photosynthesis is associated with diverse and flexible evolutionary paths that group into four major trajectories. We conducted a meta-analysis of 18 lineages containing species that use C3, C4, or intermediate C3-C4 forms of photosynthesis to parameterise a 16-dimensional phenotypic landscape. We then developed and experimentally verified a novel Bayesian approach based on a hidden Markov model that predicts how the C4 phenotype evolved. The alternative evolutionary histories underlying the appearance of C4 photosynthesis were determined by ancestral lineage and initial phenotypic alterations unrelated to photosynthesis. We conclude that the order of C4 trait acquisition is flexible and driven by non-photosynthetic drivers. This flexibility will have facilitated the convergent evolution of this complex trait. DOI:http://dx.doi.org/10.7554/eLife.00961.001.

Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis

C4 photosynthesis has independently evolved from the ancestral C3 pathway in at least 60 plant lineages, but, as with other complex traits, how it evolved is unclear. Here we show that the polyphyletic appearance of C4 photosynthesis is associated with diverse and flexible evolutionary paths that group into four major trajectories. We conducted a meta-analysis of 18 lineages containing species that use C3, C4, or intermediate C3-C4 forms of photosynthesis to parameterise a 16-dimensional phenotypic landscape. We then developed and experimentally verified a novel Bayesian approach based on a hidden Markov model that predicts how the C4 phenotype evolved. The alternative evolutionary histories underlying the appearance of C4 photosynthesis were determined by ancestral lineage and initial phenotypic alterations unrelated to photosynthesis. We conclude that the order of C4 trait acquisition is flexible and driven by non-photosynthetic drivers. This flexibility will have facilitated the convergent evolution of this complex trait. DOI:http://dx.doi.org/10.7554/eLife.00961.001.

Molecular evolution of genes recruited into C₄ photosynthesis

The C₄ pathway is found in 62 lineages of land plants. We assess evidence for parallel versus convergent evolution of C₄ photosynthesis from three approaches: (i) studies of specific genes and cis-elements controlling their expression; (ii) phylogenetic analyses of mRNAs and inferred amino acid sequences; and (iii) analysis of C₃ and C₄ genomes and transcriptomes. Evidence suggests that although convergent evolution is common, parallel evolution can underlie both changes to gene expression and amino acid sequence. cis-elements that direct cell specificity in C₄ leaves are present in C₃ orthologues of genes recruited into C₄, probably facilitating this parallel evolution. From this, and genomic data, we propose that gene duplication followed by neofunctionalisation is not necessarily important in the evolution of C₄ biochemistry.

Multiple Arabidopsis genes primed for recruitment into C₄ photosynthesis

C(4) photosynthesis occurs in the most productive crops and vegetation on the planet, and has become widespread because it allows increased rates of photosynthesis compared with the ancestral C(3) pathway. Leaves of C(4) plants typically possess complicated alterations to photosynthesis, such that its reactions are compartmented between mesophyll and bundle sheath cells. Despite its complexity, the C(4) pathway has arisen independently in 62 separate lineages of land plants, and so represents one of the most striking examples of convergent evolution known. We demonstrate that elements in untranslated regions (UTRs) of multiple genes important for C(4) photosynthesis contribute to the metabolic compartmentalization characteristic of a C(4) leaf. Either the 5' or the 3' UTR is sufficient for cell specificity, indicating that functional redundancy underlies this key aspect of C(4) gene expression. Furthermore, we show that orthologous PPDK and CA genes from the C(3) plant Arabidopsis thaliana are primed for recruitment into the C(4) pathway. Elements sufficient for M-cell specificity in C(4) leaves are also present in both the 5' and 3' UTRs of these C(3) A. thaliana genes. These data indicate functional latency within the UTRs of genes from C(3) species that have been recruited into the C(4) pathway. The repeated recruitment of pre-existing cis-elements in C(3) genes may have facilitated the evolution of C(4) photosynthesis. These data also highlight the importance of alterations in trans in producing a functional C(4) leaf, and so provide insight into both the evolution and molecular basis of this important type of photosynthesis.

Association between neonatal temperament, SLC6A4, DRD4 and a functional polymorphism located in TFAP2B

Genetic studies on human personality have provided little satisfactory results to date mainly because of the complexity of this trait. Neonatal temperament using observational measures is an alternative phenotype to approach genetics to human behavior. An association study was conducted on 117 Caucasian newborns. Their temperament was evaluated using the Neonatal Behavior Assessment Scale 48 h after birth. Thirteen polymorphisms in the SLC6A4, DRD4 and TFAP2B genes were genotyped. Linear regression was performed to analyze data, and Bonferroni correction was applied. To check the functional effect of the TFAP2B Indel Intron 2 polymorphism, reporter gene luciferase assays using a mouse cortical neural progenitor cell line and quantitative polymerase chain reaction (qPCR) studies in human post-mortem brain samples were performed. A significant association was found between 5-HTTLPR, 5-HTTLPR + rs25531 and TFAP2B Indel Intron 2 with Range of State cluster as well as an interaction between rs25531 and TFAP2B Indel Intron 2 with Range of State. DRD4 variable number tandem repeat exon 3 was associated with orientation. A 30% increase in the luciferase levels of the TFAP2B 5-repeat alleles compared with the 6-repeat alleles (P-value = 0.03) was found using the pGL3 promoter vector. The qPCR experiments showed the same trend as the in vitro studies, although no significant results were obtained. This study supports a role of the SLC6A4, DRD4 and TFAP2B genes in the temperament, including a gene-gene interaction between SLC6A4 and TFAP2B. It also provides evidence about an effect of the TFAP2B polymorphism in TFAP2B gene transcription.

Field demonstration of simultaneous wind and temperature measurements from 5 to 50 km with a Na double-edge magneto-optic filter in a multi-frequency Doppler lidar

We report the first (to our knowledge) field demonstration of simultaneous wind and temperature measurements with a Na double-edge magneto-optic filter implemented in the receiver of a three-frequency Na Doppler lidar. Reliable winds and temperatures were obtained in the altitude range of 10-45 km with 1 km resolution and 60 min integration under the conditions of 0.4 W lidar power and 75 cm telescope aperture. This edge filter with a multi-frequency lidar concept can be applied to other direct-detection Doppler lidars for profiling both wind and temperature simultaneously from the lower to the upper atmosphere.

Continuous-wave sodium D2 resonance radiation generated in single-pass sum-frequency generation with periodically poled lithium niobate

With two cw single-mode Nd:YAG lasers at 1064 and 1319 nm and a periodically poled lithium niobate crystal, 11 mW of 2 kHz/100 ms bandwidth single-mode tunable 589 nm cw radiation has been detected using single-pass sum-frequency generation. The demonstrated conversion efficiency is approximately 3.2%[W(-1) cm(-1)]. This compact solid-state light source has been used in a solid-state-dye laser hybrid sodium fluorescence lidar transmitter to measure temperatures and winds in the upper atmosphere (80-105 km); it is being implemented into the transmitter of a mobile all-solid-state sodium temperature and wind lidar under construction.

Na double-edge magneto-optic filter for Na lidar profiling of wind and temperature in the lower atmosphere

A Na double-edge magneto-optic filter is proposed for incorporation into the receiver of a three-frequency Na Doppler lidar to extend its wind and temperature measurements into the lower atmosphere. Two prototypes based on cold- and hot-cell designs were constructed and tested with laser scanning and quantum mechanics modeling. The hot-cell filter exhibits superior performances over the cold-cell filter containing buffer gas. Lidar simulations, metrics, and error analyses show that simultaneous wind and temperature measurements are feasible in the altitude range of 20-50 km using the hot-cell filter and reasonable Na lidar parameters.

The generation of cellular diversity in the cerebral cortex

We have used retroviral vectors to study cell lineage in the embryonic rat cerebral cortex both in vivo and in dissociated cell culture. We provide evidence that during the late phase of corticogenesis, most precursor cells of the ventricular zone are specified for the production of a single cell type, either neurons or one of the glial cell types. Although specified, the precursor cells that generate neurons can apparently generate both pyramidal and non-pyramidal cells. Earlier stages of development are dominated by a different type of precursor cell with a number of properties that lead us to believe that it is the founding, multipotential precursor cell of the cerebral cortex. We discuss a possible model of cell lineage which unifies these various observations.

Neural stem cells

In recent papers on neural stem cells, two areas of progress stand out. First, there has been a substantial growth in the published examples of 'transdifferentiation'. Second, there has been progress, albeit more modest, in studies of repair by neural stem cells following transplantation into animal models of disease.

Water quality in cattle feedyard playas in winter and summer

OBJECTIVE

To determine the impact of feedyards on endotoxin concentration, fecal coliform count, and other water quality measurements during winter and summer in feedyard playas (shallow lakes).

SAMPLE POPULATION

Water samples obtained from 7 feedyard playas and 3 nonfeedyard control playas.

PROCEDURE

Surface water samples were collected from each playa and at various depths from 3 feedyard playas. Endotoxin concentrations, 22 water quality variables, and fecal coliform counts were determined in samples collected in summer and winter from various combinations of playas.

RESULTS

Cattle numbers per feedyard ranged from 40,000 to 175,000 head/y. Mean endotoxin concentrations were significantly lower in control playas than in feedyard playas in winter and summer. Endotoxin concentration appeared to be homogenous at various water depths. Values for 20 of 22 water quality variables were higher in the feedyard playas than in control playas in winter and summer. In winter only, mean total fecal coliform concentration in feedyard playas was significantly greater than in control playas.

CONCLUSIONS AND CLINICAL RELEVANCE

Results indicated that feedyards have the potential to impact water quality in playas, and cattle should not be allowed access to them. Feedyard playa water should not be used under high pressure to settle dust in pens with cattle or to cool cattle, because aerosols containing pathogens and high concentrations of endotoxin are a health hazard for humans and cattle?

Bipotent cortical progenitor cells process conflicting cues for neurons and glia in a hierarchical manner

Neurons and glia of the cerebral cortex are thought to arise from a common, multipotent progenitor cell that is instructed toward alternate fates by extracellular cues. How do these cells behave when confronted with conflicting cues? We show here that nestin-positive neuroepithelial (NE) cells from embryonic day 14 rat cortex coexpress surface receptor proteins for ciliary neurotrophic factor (CNTF) and platelet-derived growth factor (PDGF). Both sets of these receptor proteins are functional in NE cells, as shown by ligand-dependent activation of downstream signal-generating proteins. Transient (30') exposure to CNTF instructs NE cells toward an astrocyte fate. Brief exposure to PDGF initiates neuronal differentiation. However, when challenged with conflicting cues, PDGF is dominant to CNTF. Moreover, CNTF-treated NE cells can be "redirected" by a subsequent exposure to PDGF to form neurons instead of astrocytes, whereas the converse is not true. The asymmetric relationship between CNTF and PDGF indicates that these two growth factors act on a common progenitor cell that has, at a minimum, two fates available to it rather than separate populations of precommitted neuroblasts and astroblasts. This bipotent progenitor cell processes conflicting cues for neurons and glia in a hierarchical manner.

A PDGF-regulated immediate early gene response initiates neuronal differentiation in ventricular zone progenitor cells

When exposed to platelet-derived growth factor (PDGF), uncommitted neuroepithelial cells from the developing cortex of embryonic day 14 (E14) rats develop into neurons. Outward signs of the neuronal phenotype are not observed for 4 days following exposure to PDGF. However, only a brief (2-3 hr) period of PDGF receptor activation is required to initiate neuronal development. During the window of receptor activation, RNA synthesis is essential, but protein synthesis is not. These observations indicate that specification of neuronal fate is mediated by an immediate early gene response.

Magneto-optic Doppler analyzer: a new instrument to measure mesopause winds

The magneto-optic Doppler analyzer (MODA) is a new type of passive optical instrument that one can use to measure the Doppler shift of the sodium nightglow emitted at approximately 91 km near the mesopause. From this measurement, horizontal wind signatures are inferred. The MODA is based on a sodium vapor magneto-optic filter that provides inherent wavelength stability at a low cost. The instrument has been used to take nightly zonal and meridional wind measurements since October 1994 at Niwot Ridge, Colorado (40 °N, 105 °W). We obtained an internally consistent wind signal and measured the semidiurnal tide for several seasons.

Evidence for multiple precursor cell types in the embryonic rat cerebral cortex

Cell lineage studies of the rat cerebral cortex suggest that by midneurogenesis, most precursor cells of the ventricular zone are specified to produce a single cell type. Yet there is also evidence for multipotential precursor cells. We used a retroviral vector to follow the developmental potential of cortical precursor cells by labeling cortical cells in cultures from embryos between 12 and 18 days of gestation. We found specified precursor cells as early as embryonic day 12, in addition to bipotential cells that generate neurons and astrocytes. Most importantly, we discovered a type of neural precursor cell, a neuroepithelial cell, that predominates earlier in development, differs distinctly from the specified precursor cells, and as a population, appears to be multipotential. These data suggest that corticogenesis progresses from an early phase dominated by neuroepithelial cells to a later phase characterized by multiple populations of specified precursor cells.

Precursor cell types in the germinal zone of the cerebral cortex

Retroviral lineage tracing experiments suggest that the cortical ventricular zone is composed of a mixture of precursor cell types. The majority generate a single cell type (neurones, astrocytes or oligodendrocytes) and the remainder generate neurones and a single type of glial cell. Pluripotential precursor cells, that have the ability to generate all three cell types, are not observed. A recent paper, however, reports that when single ventricular zone cells are cultured in isolation, a small percentage of these cells are pluripotential. This review will discuss what this knowledge tells us about cortical development.

The specification of neuronal fate: a common precursor for neurotransmitter subtypes in the rat cerebral cortex in vitro

Neurotransmitter choice is a crucial step in neural development. In the cerebral cortex, pyramidal neurons use the excitatory neurotransmitter glutamate, whereas non-pyramidal cells use the inhibitory neurotransmitter GABA. We are interested in how these two neuronal types are generated. We labelled precursor cells from embryonic rat cerebral cortex with a retroviral vector in dissociated cell cultures, and examined the neurotransmitter phenotype of their progeny immunohistochemically after 2 weeks in vitro. We discovered, first, that precursor cells in culture generate glutamatergic and GABAergic neurons in proportions similar to those in vivo. Second, we found that neuronal precursor cells gave rise to both GABAergic and glutamatergic neurons. These results suggest that neuronal precursor cells in the cerebral cortex have the potential to generate both neuronal subtypes. Moreover, these data are consistent with a stochastic model of neurotransmitter specification.

Multiple restricted lineages in the embryonic rat cerebral cortex

We have labelled precursor cells in the embryonic rat cerebral cortex using BAG, a retroviral vector that expresses beta-galactosidase. We had previously reported that labelled precursor cells generate clusters of labelled cells that could be classified into four types by their morphological appearance and anatomical distribution (Price and Thurlow, 1988). In this study, we have used immunohistochemistry and intracellular dye labelling to identify the cell types that make up these clusters. We discovered that clusters are almost always composed of a single cell type. In addition to clusters composed entirely of neurones, we found four different types of glial cell clusters. In the grey matter, glial clusters are composed either of protoplasmic astrocytes, or of cells that have an astrocyte morphology, but no glial filaments. In the white matter, clusters are composed of either fibrous astrocytes or oligodendocytes. Our results indicate that each of these different cortical cell types is generated from a separate population of precursor cells.

What have tissue culture studies told us about the development of oligodendrocytes?

One major success of studying neural cell development in tissue culture has been the discovery of the O-2A cell. This bipotential cell generates oligodendrocytes or, under certain conditions, a type of astrocyte. This essay considers the evidence that the characteristic properties demonstrated by the O-2A cells in vitro are an accurate reflection of oligodendrocyte development in vivo.

The generation of neurons and oligodendrocytes from a common precursor cell

We have used a recombinant retrovirus carrying the lacZ gene to study the developmental potential of precursor cells from the embryonic rat cerebral cortex in dissociated cell culture. Virus was used to label a small number of cultured cells genetically so that their fate could be determined. Infected clones were detected with an anti-beta-galactosidase serum, and the labeled cells were identified using monoclonal antibodies. The results revealed that most precursor cells generated a single cell type, the majority being either neurons or oligodendrocytes. However, a proportion of the neuronal clones also included oligodendrocytes. This proportion increased until embryonic day 16 when 18% of the neuronal clones were of this type. This suggests that during neurogenesis in the cerebral cortex there exists a cell with the potential to generate these two quite different neural cell types.

Localization of the receptor gene for type D simian retroviruses on human chromosome 19

Simian retrovirus (SRV) serotypes 1 to 5 are exogenous type D viruses causing immune suppression in macaque monkeys. These viruses exhibit receptor interference with each other, with two endogenous type D viruses of the langur (PO-1-Lu) and squirrel monkey, and with two type C retroviruses, feline endogenous virus (RD114/CCC) and baboon endogenous virus (BaEV), indicating that each utilizes the same cell surface receptor (M. A. Sommerfelt and R. A. Weiss, Virology 176:58-69, 1990). Vesicular stomatitis virus pseudotype particles bearing envelope glycoproteins of RD114, BaEV, and the seven SRV strains were employed to detect receptors expressed in human-rodent somatic cell hybrids segregating human chromosomes. The only human chromosome common to all the susceptible hybrids was chromosome 19. By using hybrids retaining different fragments of chromosome 19, a provisional subchromosomal localization of the receptor gene was made to 19q13.1-13.2. Antibodies previously reported to be specific to a BaEV receptor (L. Thiry, J. Cogniaux-Leclerc, R. Olislager, S. Sprecher-Goldberger, and P. Burkens, J. Virol. 48:697-708, 1983) did not block BaEV, RD114, or SRV pseudotypes or syncytia. Antibodies to known surface markers determined by genes mapped to chromosome 19 did not block virus-receptor interaction. The identity of the receptor remains to be determined.

Chromosomal localization of zinc finger protein genes in man and mouse

We have determined the mouse and human chromosomal location of a gene (Zfp-3) that codes for a protein that contains potential DNA zinc-binding fingers. An analysis of the segregation of restriction fragment length polymorphisms in recombinant inbred strains and in an interspecific backcross demonstrated that Zfp-3 is located on mouse chromosome 11. Zfp-3 is very closely linked to the Trp53-1 locus but unlinked to another finger protein gene Zfp-4 located on mouse chromosome 8. In humans ZFP3 has been localized to chromosome 17p12-17pter and thus is part of the conserved linkage group between this chromosome and the distal half of mouse chromosome 11.

Human T cell leukemia viruses use a receptor determined by human chromosome 17

Human T cell leukemia viruses (HTLV-I and HTLV-II) can infect many cell types in vitro. HTLV-I and HTLV-II use the same cell surface receptor, as shown by interference with syncytium formation and with infection by vesicular stomatitis virus (VSV) pseudotypes bearing the HTLV envelope glycoproteins. Human-mouse somatic cell hybrids were used to determine which human chromosome was required to confer susceptibility to VSV(HTLV) infection. The only human chromosome common to all susceptible cell hybrids was chromosome 17, and the receptor gene was localized to 17cen-qter. Antibodies to surface antigens known to be determined by genes on 17q did not block the HTLV receptor.

A human sequence homologous to v-sea maps to chromosome 11, band q13

Human sequences homologous to the v-sea oncogene have been localised in the human genome to the region 11q13. This region of the genome has been implicated in chronic lymphocytic leukaemia and also encodes the INT-2 human oncogene.

Biochemical and genetic analysis of the OKa blood group antigen

The monoclonal antibody TRA-1-85 recognizes a cell surface antigen which is expressed by all human cell types tested, including red blood cells (RBCs), but not by mouse cells. All the human RBCs tested were TRA-1-85 positive except those with the rare phenotype Ok(a-). Oka is a blood group antigen of very high frequency and only three unrelated Ok(a-) people are known. The red cells of all three propositi were negative with the TRA-1-85 antibody. To confirm the relationship between the TRA-1-85 antibody and anti-Oka, the immune antibody found in the serum of Ok(a-) individuals, Western blot analysis was used: the TRA-1-85 antibody and anti-Oka gave identical but complex patterns of reactivity in Western blot analysis of human cell lysates or membranes. This suggests that the anti-Oka and TRA-1-85 antibodies recognize the same cell-surface determinant and implies that Oka is not restricted in its expression to the surface of RBCs but is expressed on white blood cells (WBCs) of Ok(a+) individuals and all human cell lines tested to date. WBCs from one of the Ok(a-) propositi were tested and found to be negative with the TRA-1-85 antibody. Finally, the species specificity of the TRA-1-85 antibody has been exploited by the use of somatic cell hybrids and DNA transfection techniques to examine the genetic control of the Oka antigen defined by the TRA-1-85 antibody. We report that the determinant is controlled by a single gene OK present on human chromosome 19.

Macroglial cell development in embryonic rat brain: studies using monoclonal antibodies, fluorescence activated cell sorting, and cell culture

Astrocytes, ependymal cells, and oligodendrocytes have been shown to develop on the same schedule in dissociated cell cultures of early embryonic rat brain as in vivo. Subsequent studies showed that there are two major types of astrocyte (type-1 and type-2), which, in cultures of perinatal optic nerve, develop as two distinct lineages. In such cultures, type-2 astrocytes and oligodendrocytes develop from the same, bipotential, (O-2A) progenitor cells, which differentiate into type-2 astrocytes in 10% fetal calf serum (FCS) and into oligodendrocytes in less than or equal to 0.5% FCS. In light of these findings, we now have extended our studies on macroglial cell development in rat brain and show the following: (i) The first astrocytes to develop have a type-1 phenotype, while astrocytes with a type-2 phenotype do not develop until almost 2 weeks later, just as in the optic nerve. (ii) Most importantly, type-2 astrocytes, like the other macroglial cells, develop on the same schedule in cultures of early embryonic (less than or equal to E15) brain as they do in vivo. (iii) By contrast, both oligodendrocytes and type-2 astrocytes develop prematurely in cultures of E17 brain, and FCS influences this development in the same way it does in perinatal optic nerve cultures. (iv) Type-2 astrocyte precursors are labeled by the A2B5 monoclonal antibody, as shown previously for oligodendrocyte precursors in brain and for O-2A progenitor cells in optic nerve. Taken together with our previous findings, these results suggest that oligodendrocytes and type-2 astrocytes in brain develop from bipotential O-2A progenitor cells, whose choice of developmental pathway and timing of differentiation depend on mechanisms that operate independently of brain morphogenesis.

The in vitro differentiation of a bipotential glial progenitor cell

We have studied the properties of a glial progenitor cell from 7-day-old rat optic nerve that differentiates in vitro into an oligodendrocyte if cultured in serum-free medium and into an astrocyte if cultured in foetal calf serum (FCS). Using galactocerebroside as a marker of oligodendrocyte differentiation and glial fibrillary acidic protein as a marker of astrocyte differentiation, we show that the acquisition of these marker molecules occurs rapidly in culture and requires both RNA and protein synthesis. We provide evidence that the effect of FCS on the development of the glial progenitor cell is not due to its influence on cell-substrate adherence or actin filament organization and is not mimicked by an increase in intracellular cyclic AMP, cyclic GMP or pH. The progenitor cell contains vimentin filaments and retains them on becoming an astrocyte but loses them on becoming an oligodendrocyte. Most importantly, we show that the choice of developmental pathway taken by the bipotential glial progenitor cells in culture is reversible for 1-2 days and then becomes fixed, at least under the conditions we studied.

A4: an antigenic marker of neural tube-derived cells

The A4 monoclonal antibody was originally found to bind to the surface of the majority of neurons in rat CNS cultures, but not to PNS neurons or non-neural cells. It was subsequently shown to bind to immature oligodendrocytes and their precursor cells but not to the most mature oligodendrocytes. In the present study, we have used immunofluorescence assays on cell suspensions and cultures and on semi-thin, frozen tissue sections to show that protoplasmic and fibrous astrocytes and most ependymal cells are also A4+. Taken together, these results suggest that in adult rats A4 is expressed exclusively by cells of the CNS and that all cell types derived from the neural tube are A4+, at least at some time in their development. While neurons, astrocytes and ependymal cells continue to express the antigen in adults, most oligodendrocytes appear to lose it as they mature. The finding that macrophages in CNS cell suspensions and cultures are A4- suggests that microglial cells are not derived from the neural tube.

Tracing the development of oligodendrocytes from precursor cells using monoclonal antibodies, fluorescence-activated cell sorting, and cell culture

We have used antibody and complement-mediated cell killing, fluorescence-activated cell sorting and tissue culture to study the development of rat oligodendrocytes. We show that (1) three ligands that bind to the majority of CNS neurons (the monoclonal antibodies A4 and A2B5 and tetanus toxin) also bind to immature oligodendrocytes and to precursor cells in 14-day embryonic rat brain that develop into oligodendrocytes in vitro; and (2) precursor cells in 17- to 18-day embryonic rat optic nerve can develop into oligodendrocytes in vitro in the absence of living neurons.