Identification of Neural Crest and Neural Crest-Derived Cancer Cell Invasion and Migration Genes Using High-throughput Screening and Deep Attention Networks

Background

Cell migration and invasion are well-coordinated processes in development and disease but remain poorly understood. We previously showed that highly migratory neural crest (NC) cells share a 45-gene panel with other cell invasion phenomena, including cancer. To identify critical genes of the 45-gene panel, we performed a high-throughput siRNA screen and used statistical and deep learning methods to compare NC- versus non-NC-derived human cell lines.

Results

We find 14 out of 45 genes significantly reduces c8161 melanoma cell migration; only 4 are shared with HT1080 fibrosarcoma cells (BMP4, ITGB1, KCNE3, RASGRP1). Deep learning attention network analysis identified distinct cell-cell interaction patterns and significant alterations after BMP4 or RASGRP1 knockdown in c8161 cells. Addition of recombinant proteins to the culture media identified 5 out of the 10 known secreted molecules stimulate c8161 cell migration, including BMP4. BMP4 siRNA knockdown inhibited c8161 cell invasion in vivo and in vitro ; however, its addition to the culture media rescued c8161 cell invasion.

Conclusion

A high-throughput screen and deep learning rapidly distilled a 45-gene panel to a small subset of genes that appear critical to melanoma cell invasion and warrant deeper in vivo functional analysis for their role in driving the neural crest.

A one-dimensional individual-based mechanical model of cell movement in heterogeneous tissues and its coarse-grained approximation

Mechanical heterogeneity in biological tissues, in particular stiffness, can be used to distinguish between healthy and diseased states. However, it is often difficult to explore relationships between cellular-level properties and tissue-level outcomes when biological experiments are performed at a single scale only. To overcome this difficulty, we develop a multi-scale mathematical model which provides a clear framework to explore these connections across biological scales. Starting with an individual-based mechanical model of cell movement, we subsequently derive a novel coarse-grained system of partial differential equations governing the evolution of the cell density due to heterogeneous cellular properties. We demonstrate that solutions of the individual-based model converge to numerical solutions of the coarse-grained model, for both slowly-varying-in-space and rapidly-varying-in-space cellular properties. We discuss applications of the model, such as determining relative cellular-level properties and an interpretation of data from a breast cancer detection experiment.

Variable species densities are induced by volume exclusion interactions upon domain growth

In this work we study the effect of domain growth on spatial correlations in agent populations containing multiple species. This is important as heterogenous cell populations are ubiquitous during the embryonic development of many species. We have previously shown that the long-term behavior of an agent population depends on the way in which domain growth is implemented. We extend this work to show that, depending on the way in which domain growth is implemented, different species dominate in multispecies simulations. Continuum approximations of the lattice-based model that ignore spatial correlations cannot capture this behavior, while those that explicitly account for spatial correlations can. The results presented here show that the precise mechanism of domain growth can determine the long-term behavior of multispecies populations and, in certain circumstances, establish spatially varying species densities.

Coupling volume-excluding compartment-based models of diffusion at different scales: Voronoi and pseudo-compartment approaches

Numerous processes across both the physical and biological sciences are driven by diffusion. Partial differential equations are a popular tool for modelling such phenomena deterministically, but it is often necessary to use stochastic models to accurately capture the behaviour of a system, especially when the number of diffusing particles is low. The stochastic models we consider in this paper are 'compartment-based': the domain is discretized into compartments, and particles can jump between these compartments. Volume-excluding effects (crowding) can be incorporated by blocking movement with some probability. Recent work has established the connection between fine- and coarse-grained models incorporating volume exclusion, but only for uniform lattices. In this paper, we consider non-uniform, hybrid lattices that incorporate both fine- and coarse-grained regions, and present two different approaches to describe the interface of the regions. We test both techniques in a range of scenarios to establish their accuracy, benchmarking against fine-grained models, and show that the hybrid models developed in this paper can be significantly faster to simulate than the fine-grained models in certain situations and are at least as fast otherwise.

How domain growth is implemented determines the long-term behavior of a cell population through its effect on spatial correlations

Domain growth plays an important role in many biological systems, and so the inclusion of domain growth in models of these biological systems is important to understanding how these systems function. In this work we present methods to include the effects of domain growth on the evolution of spatial correlations in a continuum approximation of a lattice-based model of cell motility and proliferation. We show that, depending on the way in which domain growth is implemented, different steady-state densities are predicted for an agent population. Furthermore, we demonstrate that the way in which domain growth is implemented can result in the evolution of the agent density depending on the size of the domain. Continuum approximations that ignore spatial correlations cannot capture these behaviors, while those that account for spatial correlations do. These results will be of interest to researchers in developmental biology, as they suggest that the nature of domain growth can determine the characteristics of cell populations.

Reconciling transport models across scales: The role of volume exclusion

Diffusive transport is a universal phenomenon, throughout both biological and physical sciences, and models of diffusion are routinely used to interrogate diffusion-driven processes. However, most models neglect to take into account the role of volume exclusion, which can significantly alter diffusive transport, particularly within biological systems where the diffusing particles might occupy a significant fraction of the available space. In this work we use a random walk approach to provide a means to reconcile models that incorporate crowding effects on different spatial scales. Our work demonstrates that coarse-grained models incorporating simplified descriptions of excluded volume can be used in many circumstances, but that care must be taken in pushing the coarse-graining process too far.

An adaptive multi-level simulation algorithm for stochastic biological systems

Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, "Multi-level Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics," SIAM Multiscale Model. Simul. 10(1), 146-179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency of our method using a number of examples.

Deriving appropriate boundary conditions, and accelerating position-jump simulations, of diffusion using non-local jumping

In this paper we explore lattice-based position-jump models of diffusion, and the implications of introducing non-local jumping; particles can jump to a range of nearby boxes rather than only to their nearest neighbours. We begin by deriving conditions for equivalence with traditional local jumping models in the continuum limit. We then generalize a previously postulated implementation of the Robin boundary condition for a non-local process of arbitrary maximum jump length, and present a novel implementation of flux boundary conditions, again generalized for a non-local process of arbitrary maximum jump length. In both these cases we validate our results using stochastic simulation. We then proceed to consider two variations on the basic diffusion model: a hybrid local/non-local scheme suitable for models involving sharp concentration gradients, and the implementation of biased jumping. In all cases we show that non-local jumping can deliver substantial time savings for stochastic simulations.

The effect of sampling rate on observed statistics in a correlated random walk

Tracking the movement of individual cells or animals can provide important information about their motile behaviour, with key examples including migrating birds, foraging mammals and bacterial chemotaxis. In many experimental protocols, observations are recorded with a fixed sampling interval and the continuous underlying motion is approximated as a series of discrete steps. The size of the sampling interval significantly affects the tracking measurements, the statistics computed from observed trajectories, and the inferences drawn. Despite the widespread use of tracking data to investigate motile behaviour, many open questions remain about these effects. We use a correlated random walk model to study the variation with sampling interval of two key quantities of interest: apparent speed and angle change. Two variants of the model are considered, in which reorientations occur instantaneously and with a stationary pause, respectively. We employ stochastic simulations to study the effect of sampling on the distributions of apparent speeds and angle changes, and present novel mathematical analysis in the case of rapid sampling. Our investigation elucidates the complex nature of sampling effects for sampling intervals ranging over many orders of magnitude. Results show that inclusion of a stationary phase significantly alters the observed distributions of both quantities.

Modelling Aedes aegypti mosquito control via transgenic and sterile insect techniques: endemics and emerging outbreaks

The invasion of pest insects often changes or destroys a native ecosystem, and can result in food shortages and disease endemics. Issues such as the environmental effects of chemical control methods, the economic burden of maintaining control strategies and the risk of pest resistance still remain, and mosquito-borne diseases such as malaria and dengue fever prevail in many countries, infecting over 100 million worldwide in 2010. One environmentally friendly method for mosquito control is the Sterile Insect Technique (SIT). This species-specific method of insect control relies on the mass rearing, sterilization and release of large numbers of sterile insects. An alternative transgenic method is the Release of Insects carrying a Dominant Lethal (RIDL). Our objective is to consider contrasting control strategies for two invasive scenarios via SIT and RIDL: an endemic case and an emerging outbreak. We investigate how the release rate and size of release region influence both the potential for control success and the resources needed to achieve it, under a range of conditions and control strategies, and we discuss advantageous strategies with respect to reducing the release resources and strategy costs (in terms of control mosquito numbers) required to achieve complete eradication of wild-type mosquitoes.

Nonlinear effects on Turing patterns: time oscillations and chaos

We show that a model reaction-diffusion system with two species in a monostable regime and over a large region of parameter space produces Turing patterns coexisting with a limit cycle which cannot be discerned from the linear analysis. As a consequence, the patterns oscillate in time. When varying a single parameter, a series of bifurcations leads to period doubling, quasiperiodic, and chaotic oscillations without modifying the underlying Turing pattern. A Ruelle-Takens-Newhouse route to chaos is identified. We also examine the Turing conditions for obtaining a diffusion-driven instability and show that the patterns obtained are not necessarily stationary for certain values of the diffusion coefficients. These results demonstrate the limitations of the linear analysis for reaction-diffusion systems.

The dynamics of Turing patterns for morphogen-regulated growing domains with cellular response delays

Since its conception in 1952, the Turing paradigm for pattern formation has been the subject of numerous theoretical investigations. Experimentally, this mechanism was first demonstrated in chemical reactions over 20 years ago and, more recently, several examples of biological self-organisation have also been implicated as Turing systems. One criticism of the Turing model is its lack of robustness, not only with respect to fluctuations in the initial conditions, but also with respect to the inclusion of delays in critical feedback processes such as gene expression. In this work we investigate the possibilities for Turing patterns on growing domains where the morphogens additionally regulate domain growth, incorporating delays in the feedback between signalling and domain growth, as well as gene expression. We present results for the proto-typical Schnakenberg and Gierer-Meinhardt systems: exploring the dynamics of these systems suggests a reconsideration of the basic Turing mechanism for pattern formation on morphogen-regulated growing domains as well as highlighting when feedback delays on domain growth are important for pattern formation.

Travelling gradients in interacting morphogen systems

Morphogen gradients are well known to play several important roles in development; however the mechanisms underlying the formation and maintenance of these gradients are often not well understood. In this work, we investigate whether the presence of a secondary morphogen can increase the robustness of the primary morphogen gradient to perturbation, thereby providing a more stable mechanism for development. We base our model around the interactions of Fibroblast Growth Factor 8 and retinoic acid, which have been shown to act as morphogens in many developmental systems. In particular, we investigate the formation of opposing gradients of these morphogens along the antero-posterior axis of vertebrate embryos, thereby controlling temporal and spatial aspects of axis segmentation and neuronal differentiation.

Dispersion relation in oscillatory reaction-diffusion systems with self-consistent flow in true slime mold

In the large amoeboid organism Physarum, biochemical oscillators are spatially distributed throughout the organism and their collective motion exhibits phase waves, which carry physiological signals. The basic nature of this wave behaviour is not well-understood because, to date, an important effect has been neglected, namely, the shuttle streaming of protoplasm which accompanies the biochemical rhythms. Here we study the effects of self-consistent flow on the wave behaviour of oscillatory reaction-diffusion models proposed for the Physarum plasmodium, by means of numerical simulation for the dispersion relation and weakly nonlinear analysis for derivation of the phase equation. We conclude that the flow term is able to increase the speed of phase waves (similar to elongation of wave length). We compare the theoretical consequences with real waves observed in the organism and also point out the physiological roles of these effects on control mechanisms of intracellular communication.

A Study of the Temperature Dependence of Bienzyme Systems and Enzymatic Chains

It is known that most enzyme-facilitated reactions are highly temperature dependent processes. In general, the temperature coefficient,Q10, of a simple reaction reaches 2.0–3.0. Nevertheless, some enzyme-controlled processes have much lowerQ10(about 1.0), which implies that the process is almost temperature independent, even if individual reactions involved in the process are themselves highly temperature dependent. In this work, we investigate a possible mechanism for this apparent temperature compensation: simple mathematical models are used to study how varying types of enzyme reactions are affected by temperature. We show that some bienzyme-controlled processes may be almost temperature independent if the modules involved in the reaction have similar temperature dependencies, even if individually, these modules are strongly temperature dependent. Further, we show that in non-reversible enzyme chains the stationary concentrations of metabolites are dependent only on the relationship between the temperature dependencies of the first and last modules, whilst in reversible reactions, there is a dependence on every module. Our findings suggest a mechanism by which the metabolic processes taking place within living organisms may be regulated, despite strong variation in temperature.

A mechanism for morphogen-controlled domain growth

Many developmental systems are organised via the action of graded distributions of morphogens. In the Drosophila wing disc, for example, recent experimental evidence has shown that graded expression of the morphogen Dpp controls cell proliferation and hence disc growth. Our goal is to explore a simple model for regulation of wing growth via the Dpp gradient: we use a system of reaction-diffusion equations to model the dynamics of Dpp and its receptor Tkv, with advection arising as a result of the flow generated by cell proliferation. We analyse the model both numerically and analytically, showing that uniform domain growth across the disc produces an exponentially growing wing disc.

A clock and wavefront mechanism for somite formation

Somitogenesis, the sequential formation of a periodic pattern along the antero-posterior axis of vertebrate embryos, is one of the most obvious examples of the segmental patterning processes that take place during embryogenesis and also one of the major unresolved events in developmental biology. In this article, we develop a mathematical formulation of a new version of the Clock and Wavefront model proposed by Pourquié and co-workers (Dubrulle, J., McGrew, M.J., Pourquié, O., 2001. FGF signalling controls somite boundary position and regulates segmentation clock control of spatiotemporal Hox gene activation. Cell 106, 219-232). Dynamic expression of FGF8 in the presomitic mesoderm constitutes the wavefront of determination which sweeps along the body axis interacting as it moves with the segmentation clock to gate cells into somites. We also show that the model can mimic the anomalies formed when progression of the wavefront is disturbed and make some experimental predictions that can be used to test the hypotheses underlying the model.

A mathematical investigation of a Clock and Wavefront model for somitogenesis

Somites are transient blocks of cells that form sequentially along the antero-posterior axis of vertebrate embryos. They give rise to the vertebrae, ribs and other associated features of the trunk. In this work we develop and analyse a mathematical formulation of a version of the Clock and Wavefront model for somite formation, where the clock controls when the boundaries of the somites form and the wavefront determines where they form. Our analysis indicates that this interaction between a segmentation clock and a wavefront can explain the periodic pattern of somites observed in normal embryos. We can also show that a simplification of the model provides a mechanism for predicting the anomalies resulting from perturbation of the wavefront.

CO2 emission benefit of diesel (versus gasoline) powered vehicles

Concerns regarding global warming have increased the pressure on automobile manufacturers to decrease emissions of CO2 from vehicles. Diesel vehicles have higher fuel economy and lower CO2 emissions than their gasoline counterparts. Increased penetration of diesel powered vehicles into the market is a possible transition strategy toward a more sustainable transportation system. To facilitate discussions regarding the relative merits of diesel vehicles it is important to have a clear understanding of their CO2 emission benefits. Based on European diesel and gasoline certification data, this report quantifies such CO2 reduction opportunities for cars and light duty trucks in today's vehicles and those in the year 2015. Overall, on a well-to-wheels per vehicle per mile basis, the CO2 reduction opportunity for today's vehicles is approximately 24-33%. We anticipate that the gap between diesel and gasoline well-to-wheel vehicle CO2 emissions will decrease to approximately 14-27% by the year 2015.

A mathematical formulation for the cell-cycle model in somitogenesis: analysis, parameter constraints and numerical solutions

In this work we present an analysis, supported by numerical simulations, of the formulation of the cell-cycle model for somitogenesis proposed in Collier et al. (J. Theor Biol. 207 (2000), 305-316). The analysis indicates that by introducing appropriate parameter constraints on model parameters the cell-cycle mechanism can indeed give rise to the periodic pattern of somites observed in normal embryos. The analysis also provides a greater understanding of the signalling process controlling somite formation and allows us to understand which parameters influence somite length.

GABAA receptor maturation in relation to eye opening in the rat visual cortex

Changes in subunit composition of N-methyl-D-aspartate (NMDA) receptors have been reported to be affected by visual experience and may therefore form a major aspect of neuronal plasticity in the CNS during development. In contrast, putative alterations in the expression and functioning of the inhibitory GABAA receptor around eye opening have not been well defined yet. Here we describe the timing of changes in GABAA receptor subunit expression and the related synaptic functioning in the neonatal rat visual cortex and the influence of visual experience on this process. Quantitative analysis of all GABAA receptor subunit transcripts revealed a marked alpha3 to alpha1 subunit switch, in addition to a change in alpha4 and alpha5 expression. The changes were correlated with an acceleration of the decay of spontaneous inhibitory postsynaptic currents (sIPSCs). Both changes in receptor expression and synaptic functioning were initiated well before eye opening. Moreover, dark rearing could not prevent the robust upregulation of alpha1 or the change in sIPSC kinetics, indicating that this is not dependent of sensory (visual) input. Upon eye opening a positive correlation was observed between a faster decay of the sIPSCs and an increase in sIPSC frequency, which was absent in dark-reared animals. Thus, lack of extrinsic input to the cortex does not affect overall developmental regulation of synaptic functioning of GABAA receptors. However, we cannot exclude the possibility that visual experience is involved in proper shaping of the inhibitory network of the primary visual cortex.

Impaired dendritic spine maturation in GABAA receptor α1 subunit knock out mice

In this study we investigated the functional implications of GABAA receptor alpha1 subunit deletion on dendritic arborization and spine maturation in the visual cortex. This subunit is normally strongly upregulated during early postnatal development. Our main finding is that mice lacking the GABAA receptor alpha1 subunit displayed an increased density of dendritic filopodia during the second and third postnatal weeks. However, there was a concomitant decreased density of mature mushroom-shaped spines, which became more pronounced in adults. In contrast, dendritic arborization was not altered in these mice. We propose that an increased efficacy of the inhibitory synaptic transmission in the alpha1 knock out mice may lead to an enhancement of the outgrowth of filopodia around eye opening, but to a failure in spine maturation at later stages.

Post-mortem brain tissue cultures from elderly control subjects and patients with a neurodegenerative disease

Aging may be viewed as a progressive loss of normal biological function. Due to complex genetic and environmental interactions, the sequence of functional impairment shows a high degree of individual variability. In humans life style and health care have an additional influence on the aging process. To study aging and age-related disorders of the human nervous system, brain tissue that has undergone aging and pathological alterations can provide valuable study material. Recently, we have shown that adult human postmortem brain tissue can be cultured and experimentally manipulated. This approach permits the study of cellular aspects of human neuronal aging and neurodegenerative processes and complements those existing research methods such as in vivo imaging (MRI, PET, etc.) and fixed or frozen postmortem brain tissue examination.

Physiological effects of sustained blockade of excitatory synaptic transmission on spontaneously active developing neuronal networks--an inquiry into the reciprocal linkage between intrinsic biorhythms and neuroplasticity in early ontogeny

Spontaneous bioelectric activity (SBA) taking the form of extracellularly recorded spike trains (SBA) has been quantitatively analyzed in organotypic neonatal rat visual cortex explants at different ages in vitro, and the effects investigated of both short- and long-term pharmacological suppression of glutamatergic synaptic transmission. In the presence of APV, a selective NMDA receptor blocker, 1-2- (but not 3-)week-old cultures recovered their previous SBA levels in a matter of hours, although in imitation of the acute effect of the GABAergic inhibitor picrotoxin (PTX), bursts of action potentials were abnormally short and intense. Cultures treated either overnight or chronically for 1-3 weeks with APV, the AMPA/kainate receptor blocker DNQX, or a combination of the two were found to display very different abnormalities in their firing patterns. NMDA receptor blockade for 3 weeks produced the most severe deviations from control SBA, consisting of greatly prolonged and intensified burst firing with a strong tendency to be broken up into trains of shorter spike clusters. This pattern was most closely approximated by acute GABAergic disinhibition in cultures of the same age, but this latter treatment also differed in several respects from the chronic-APV effect. In 2-week-old explants, in contrast, it was the APV+DNQX treated group which showed the most exaggerated spike bursts. Functional maturation of neocortical networks, therefore, may specifically require NMDA receptor activation (not merely a high level of neuronal firing) which initially is driven by endogenous rather than afferent evoked bioelectric activity. Putative cellular mechanisms are discussed in the context of a thorough review of the extensive but scattered literature relating activity-dependent brain development to spontaneous neuronal firing patterns.

Function of the ski4p (Csl4p) and Ski7p proteins in 3'-to-5' degradation of mRNA

One of two general pathways of mRNA decay in the yeast Saccharomyces cerevisiae occurs by deadenylation followed by 3'-to-5' degradation of the mRNA body. Previous results have shown that this degradation requires components of the exosome and the Ski2p, Ski3p, and Ski8p proteins, which were originally identified due to their superkiller phenotype. In this work, we demonstrate that deletion of the SKI7 gene, which encodes a putative GTPase, also causes a defect in 3'-to-5' degradation of mRNA. Deletion of SKI7, like deletion of SKI2, SKI3, or SKI8, does not affect various RNA-processing reactions of the exosome. In addition, we show that a mutation in the SKI4 gene also causes a defect in 3'-to-5' mRNA degradation. We show that the SKI4 gene is identical to the CSL4 gene, which encodes a core component of the exosome. Interestingly, the ski4-1 allele contains a point mutation resulting in a mutation in the putative RNA binding domain of the Csl4p protein. This point mutation strongly affects mRNA degradation without affecting exosome function in rRNA or snRNA processing, 5' externally transcribed spacer (ETS) degradation, or viability. In contrast, the csl4-1 allele of the same gene affects rRNA processing but not 3'-to-5' mRNA degradation. We identify csl4-1 as resulting from a partial-loss-of-function mutation in the promoter of the CSL4 gene. These data indicate that the distinct functions of the exosome can be separated genetically and suggest that the RNA binding domain of Csl4p may have a specific function in mRNA degradation.

The N terminus of the centromere H3-like protein Cse4p performs an essential function distinct from that of the histone fold domain

Cse4p is an evolutionarily conserved histone H3-like protein that is thought to replace H3 in a specialized nucleosome at the yeast (Saccharomyces cerevisiae) centromere. All known yeast, worm, fly, and human centromere H3-like proteins have highly conserved C-terminal histone fold domains (HFD) but very different N termini. We have carried out a comprehensive and systematic mutagenesis of the Cse4p N terminus to analyze its function. Surprisingly, only a 33-amino-acid domain within the 130-amino-acid-long N terminus is required for Cse4p N-terminal function. The spacing of the essential N-terminal domain (END) relative to the HFD can be changed significantly without an apparent effect on Cse4p function. The END appears to be important for interactions between Cse4p and known kinetochore components, including the Ctf19p/Mcm21p/Okp1p complex. Genetic and biochemical evidence shows that Cse4p proteins interact with each other in vivo and that nonfunctional cse4 END and HFD mutant proteins can form functional mixed complexes. These results support different roles for the Cse4p N terminus and the HFD in centromere function and are consistent with the proposed Cse4p nucleosome model. The structure-function characteristics of the Cse4p N terminus are relevant to understanding how other H3-like proteins, such as the human homolog CENP-A, function in kinetochore assembly and chromosome segregation.

Ectopic adenoviral vector-directed expression of Sema3A in organotypic spinal cord explants inhibits growth of primary sensory afferents

Sema3A (Sema III, SemD, collapsin-1) can induce neuronal growth cone collapse and axon repulsion of distinct neuronal populations. To study Sema3A function in patterning afferent projections into the developing spinal cord, we employed the recombinant adenoviral vector technique in embryonic rat spinal cord slices. Virus solution was injected in the dorsal aspect of organotypic spinal cord cultures with segmentally attached dorsal root ganglia (sc-DRG). In cultures grown in the presence of nerve growth factor (NGF), injected either with the control virus AdCMVLacZ or with vehicle only, afferent innervation patterns were similar to those of control. However, unilateral injection of AdCMVSema3A/AdCMVLacZ in sc-DRG slices revealed a strong inhibitory effect on NGF-dependent sensory afferent growth. Ectopic Sema3A in the dorsal spinal cord, the target area of NGF-responsive DRG fibers in vivo, created an exclusion zone for these fibers and as a result they failed to reach and innervate their appropriate target zones. Taken together, gain of Sema3A function in the dorsal aspect of sc-DRG cultures revealed a dominant inhibitory effect on NGF-dependent, nociceptive sensory DRG afferents, an observation in line with the model proposed by E. K. Messersmith et al. (1995, Neuron 14, 949-959), suggesting that Sema3A secreted by spinal cord cells can act to repel central sensory fibers during the formation of lamina-specific connections in the spinal cord.

Analysis of primary structural determinants that distinguish the centromere-specific function of histone variant Cse4p from histone H3

Cse4p is a variant of histone H3 that has an essential role in chromosome segregation and centromere chromatin structure in budding yeast. Cse4p has a unique 135-amino-acid N terminus and a C-terminal histone-fold domain that is more than 60% identical to histone H3 and the mammalian centromere protein CENP-A. Cse4p and CENP-A have biochemical properties similar to H3 and probably replace H3 in centromere-specific nucleosomes in yeasts and mammals, respectively. In order to identify regions of Cse4p that distinguish it from H3 and confer centromere function, a systematic site-directed mutational analysis was performed. Nested deletions of the Cse4p N terminus showed that this region of the protein contains at least one essential domain. The C-terminal histone-fold domain of Cse4p was analyzed by changing Cse4p amino acids that differ between Cse4p and H3 to the analogous H3 residues. Extensive substitution of contiguous Cse4p residues with H3 counterparts resulted in cell lethality. However, all large lethal substitution alleles could be subdivided into smaller viable alleles, many of which caused elevated rates of mitotic chromosome loss. The results indicate that residues critical for wild-type Cse4p function and high-fidelity chromosome transmission are distributed across the entire histone-fold domain. Our findings are discussed in the context of the known structure of H3 within the nucleosome and compared with previous results reported for CENP-A.

Selective inhibition of the Na+/H+ exchanger type 3 activates CO2/H+-sensitive medullary neurones

Hypercapnia as well as lowered intracellular pH (pHi) increase the bioelectric activity of CO2/H+-sensitive neurones (VLNcs) of the ventrolateral medulla oblongata. Here we describe that immunoreactive Na+/H+ exchanger (NHE3) is present in ventrolateral neurones from medullary organotypic cultures (obex level). To test whether VLNcs can be acidified and thereby activated by inhibition of NHE3, we used the novel high-affinity NHE3-inhibitors S1611 and S3226. Both drugs raised the firing rates of VLNcs to at least 150% of the control values, and depolarized membrane potential by up to 15 mV at concentrations (0.5-1 micromol/l) suitable for selective inhibition of NHE3. The changes in bioelectric activity strongly resembled the responses to hypercapnia (PCO2: 60-100 mmHg). In BCECF-AM-loaded cultures a subfraction of ventrolateral VLNcs was found to be intracellularly acidified by 0.05-0.1 pH units following treatment with S1611; the time course of this acidification was similar to that evoked by hypercapnia. All drug effects were sustained and readily reversible upon washing. Non-CO2/H+-responsive medullary neurones as well as hippocampal CA3 neurones were unaffected by up to 20 micromol/l S1611. It is concluded that the selective inhibition of NHE3 acidifies and activates CO2/H+-sensitive neurones within the ventrolateral medulla oblongata.

Magnetic resonance imaging of regenerating and dystrophic mouse muscle

Magnetic resonance imaging allows serial visualization of living muscle. Clinically magnetic resonance imaging would be the first step in selecting a region of interest for assessment of muscle disease state and treatment effects by magnetic resonance spectroscopy. In this study, magnetic resonance imaging was used to follow dystrophy and regeneration in the mdx mouse, a genetic homologue to human Duchenne muscular dystrophy. It was hypothesized that images would distinguish normal control from mdx muscle and that regenerating areas (spontaneous and after an imposed injury) would be evident and evolve over time. T2-weighted images of hind-limb muscles were obtained on anaesthetized mice in a horizontal bore 7.1-T experimental magnet. Magnetic resonance images of mdx muscle appeared heterogeneous in comparison to homogeneous images of control muscle. Foci of high intensity in mdx images corresponded to dystrophic lesions observed in the histologic sections of the same muscles. In addition, it was possible to follow chronologically the extent of injury and repair after an imposed crush injury to mdx muscle. These results should make it possible to obtain meaningful magnetic resonance spectra from particular regions of interest in muscle as viewed in magnetic resonance images (i.e., regenerating, degenerating, normal muscle) acquired during neuromuscular diseases and treatment regimens.

Mutations synthetically lethal with cep1 target S. cerevisiae kinetochore components

CP1 (encoded by CEP1) is a Saccharomyces cerevisiae chromatin protein that binds a DNA element conserved in centromeres and in the 5'-flanking DNA of methionine biosynthetic (MET) genes. Strains lacking CP1 are defective in chromosome segregation and MET gene transcription, leading to the hypothesis that CP1 plays a general role in assembling higher order chromatin structures at genomic sites where it is bound. A screen for mutations synthetically lethal with a cep1 null allele yielded five recessive csl (cep1 synthetic lethal) mutations, each defining a unique complementation group. Four of the five mutations synergistically increased the loss rate of marker chromosomes carrying a centromere lacking the CP1 binding site, suggesting that the cep1 synthetic lethality was due to chromosome segregation defects. Three of these four CSL genes were subsequently found to be known or imputed kinetochore genes: CEP3, NDC10, and CSE4. The fourth, CSL4, corresponded to ORF YNL232w on chromosome XIV, and was found to be essential. A human cDNA was identified that encoded a protein homologous to Csl4 and that complemented the csl4-1 mutation. The results are consistent with the view that the major cellular role of CP1 is to safeguard the biochemical integrity of the kinetochore.

Growth of pyramidal, but not non-pyramidal, dendrites in long-term organotypic explants of neonatal rat neocortex chronically exposed to neurotrophin-3

The present study was undertaken to determine the effects of neurotrophin-3 (NT3) and spontaneous bioelectric activity (SBA) on dendritic elongation and branching in long-term isolated organotypic explants of rat neocortex. Viral vector-directed expression of NT3 was used as an effective means to ensure a continuous, local production of the neurotrophic factor. Quantitative light microscopic measurement of dendritic branching patterns was carried out on Golgi-stained materials. Explants were exposed to an adenoviral vector encoding the genetic sequence for neurotrophin-3 (Ad-NT3), or to exogenous additions of the neuropeptide NT3. In order to test for activity-dependent growth effects under control and experimental conditions, explants were exposed to glutamatergic blockade using a cocktail of APV and DNQX. Both Ad-NT3 and NT3 peptide potently promoted apical and basal dendritic growth (elongation and branching) in pyramidal neurons. This growth was observed to be significant in layers II-IV and V. These growth effects were also not activity dependent, inasmuch as they were elicited from explants in which spontaneous bioelectric activity had been suppressed. Non-pyramidal neurons, throughout the neocortical slice, showed no significant dendritic responses to the prolonged presence of NT3. These findings show that pyramidal dendritic growth in long-term neocortical explants responds to at least one neurotrophic growth factor, NT3, and is independent of intrinsic bioelectric activity. The use of viral vectors in delivering a continuous high level of neurotrophic factor within developing neural tissues demonstrates its potential application to in vivo tissues during development, or in the stimulation of neuritogenesis and neuroregeneration following injuries.

CO2-sensitive medullary neurons: activation by intracellular acidification

Bioelectric activity of CO2-sensitive, ventrolateral medullary neurons (VLN(CS)) in organotypic cultures from the obex level of newborn rats was tested during changes of the intracellular pH (pHi) measured in BCECF-AM loaded cultures. Hypercapnia (pCO2 80-100 mmHg) reduced pHi by 0.15 +/- 0.06 units and stimulated neuronal discharges. Replacement of CO2/HCO3- in the bath by HEPES (26 mM, pH 7.4) for 10 min acidified pHi (0.07 +/- 0.03 units) and also excited VLN(CS). Ammonium chloride (10 mM, 1 min) initially alkalized (0.1 +/- 0.04) and thereafter acidified pHi (0.06 +/- 0.03), while the extracellular pH was first acidified and then alkalized. This resulted in neuronal discharge which were first suppressed and then accelerated. The findings strongly suggest that intracellular rather than extracellular acidification activates CO2-sensitive neurons.

Chronic blockade of glutamate-mediated bioelectric activity in long-term organotypic neocortical explants differentially effects pyramidal/non-pyramidal dendritic morphology

Dendritic/axonal growth has been examined in long-term organotypic neocortical explants taken from neonatal rat pups and grown either as isolated slices or as co-cultures. The quantitative light microscopic measurement of dendritic and axonal branching patterns within both types of explants was carried out on Golgi-stained materials. Spontaneous bioelectric activity (SBA) was blocked within both types of explants using a combination of APV and DNQX, NMDA and non-NMDA receptor antagonists, respectively. No extracellularly measurable SBA was observed to occur in the silenced explants in the presence of both antagonists but reappeared following wash-out with control medium. In both control and silenced explants, the overall cellular organization of the slice was maintained throughout the culturing period, with distinguishable pyramidal and non-pyramidal neurons located within the same layers and with the same orientations as observed in situ. The major findings of the present study show the following. (i) Pyramidal neurones chronically exposed to APV/DNQX exhibited no basal dendritic growth in co-cultured explants, while growth of apical dendritic lengths was similar to control values in the absence of SBA. (ii) Pyramidal neurones, nonetheless, exhibited significant terminal segment growth under SBA blockade which was correlated with a concomitant decrease in number of basal dendrites. (iii) Axonal growth in co-cultures was not sustained in silenced pyramidal neurones. (iv) Non-pyramidal neurones showed significant total dendritic and axonal growth in co-cultures following APV/DNQX treatment. (v) Non-pyramidal cells in co-cultures experienced an increase in terminal segment length at 2 weeks which declined in the third week. This increase-decrease was correlated with a decrease-increase in the total number of dendritic segments during the second and third weeks, respectively. (vi) In isolated explants the only departure from control growth curves was a significant increase in terminal segment length which was offset by a similar decrease in number of dendritic segments under APV/DNQX growth conditions. Thus the chronic loss of glutamate-mediated SBA differentially effected pyramidal and non-pyramidal neurones in isolated and co-cultured explants, with pyramidal neurones experiencing the more pronounced effects. We conclude that SBA effects the dynamics of neuritic elongation and branching and that these changes are most dramatically seen in co-cultures which cross-innervate one another, presumably via pyramidal axons. We hypothesize that the activity-dependent changes associated with reduction in pyramidal dendritic and axonal growth may be associated with neurotrophin receptor production/maturation.

Plasticity in fast synaptic inhibition of adult oxytocin neurons caused by switch in GABA(A) receptor subunit expression

We found that magnocellular oxytocin neurons in adult female rats exhibit an endogenous GABA(A) receptor subunit switch around parturition: a decrease in alpha1:alpha2 subunit mRNA ratio correlated with a decrease in allopregnanolone potentiation and increase in decay time constant of the GABA(A) receptor-mediated IPSCs in these cells. The causal relationship between changes in alpha1:alpha2 mRNA ratio and the ion channel kinetics was confirmed using in vitro antisense deletion. Further, GABA(A) receptors exhibited a tonic inhibitory influence upon oxytocin release in vivo, and allopregnanolone helped to restrain oxytocin neuron in vitro firing only before parturition, when the alpha1:alpha2 subunit mRNA ratio was still high. Such observations provide evidence for the physiological significance of GABA(A) receptor subunit heterogeneity and plasticity in the adult brain.

Glutamate dependent dendritic outgrowth in developing neuronal networks of rat hippocampal cells in vitro

The present study was undertaken to determine whether release of glutamate is capable of influencing dendritic morphology in a developing network of rat hippocampal neurons in vitro. Control cultures developed a dense network of fibers and evinced spontaneous electrical activity from the third day in vitro. Dendrites were examined in cultures maintained for 2 weeks in vitro: the experimental group grown in medium containing the glutamate receptor antagonists AP-5 and DNQX. Dendritic extensions were analyzed as a function of time (days in vitro) using a number of morphometric parameters, vis. the number of processes, the number and length of intermediate and terminal segments, as well as the total length of all segments. We found that the effect of age and treatment was most prominently reflected in the length of the terminal segments. Chronic addition of ionotropic glutamate receptor antagonists from day 2 in culture arrested all dendrite parameters at the prefunctional level. The results suggest that glutamate release is crucial for the onset of dendritic morphological development in hippocampal neurons.

Cocultured, but not isolated, cortical explants display normal dendritic development: a long-term quantitative study

Dendritic growth has been studied in long-term organotypic neonatal rat occipital neocortex grown either apart as isolated explants or in tandem as cocultures. Quantitative light microscopic measurement of dendritic and axonal branching patterns within the cortical slice was accomplished using rapid Golgi stained materials. In both isolates and cocultures the overall cellular organization of the slice was maintained over 4 weeks in vitro with morphologically distinguishable pyramidal and nonpyramidal neurons located within the same layers and with the same orientations as observed in situ. Long-term increases in the total length of basal dendrites, apical dendrite and axons were observed only in cocultures and were similar to growth patterns reported for in situ materials. Dendritic growth was mainly due to elongation of terminal dendritic segments. Surprisingly, isolated explants showed no long-term increases in total (basal) dendrites, apical dendrites or axons with time in vitro. A transient decrease in the number of basal dendritic segments and increase in terminal segment lengths at the end of the first week in vitro, however, was observed in nonpyramidal neurons. It is hypothesized that (i) afferent inputs and/or efferent targets develop only in cocultures and provide a crucial conditions for the continued growth of dendritic/axonal arborization for neocortical neurons in vitro, (ii) intrinsic interconnectivity within isolated explants is not sufficient to maintain long-term growth of neuritic arbors, and (iii) remodelling of dendritic arbors within isolated explants occurs at the same time as these explants are showing noticeable increases in the level of spontaneous bioelectric activity, which suggests that dendritic growth and network formation may be function dependent.

Rhythm generation in organotypic medullary cultures of newborn rats

Organotypic transverse medullary slices (obex level) from six-day-old rats, cultured for two to four weeks in chemically defined medium contained rhythmically discharging neurones which were activated by CO2 and H+. The mechanisms underlying this rhythmicity and the spread of excitation and synaptic transmission within this organotypic tissue were examined by modifying the composition of the external solution. Our findings showed that (1) Exposure to tetrodotoxin (0.2 microM) or to high magnesium (6 mM) and low calcium (0.2 mM) concentrations abolished periodic activity. (2) Neither the blockade of GABAergic potentials with bicuculline methiodide (200 microM) and/or hydroxysaclofen (200 microM) nor the blockade of glycinergic potentials with strychnine hydrochloride (100 microM) abolished rhythmicity. (3) While atropine sulphate (5 microM) was ineffective in modulating periodic discharges nicotine (100 microM) - like CO2-shortened the intervals between the periodic events; hexamethonium (50-100 microM) reduced both periodic and aperiodic activity. (4) Exposure to the NMDA antagonist 2-aminophosphonovaleric acid (50 microM) suppressed periodic events only transiently. In the presence of 2-aminophosphonovaleric acid rhythmicity recovered. However, the AMPA-antagonist 6-cyano-7-nitroquinoxaline-2,3-dione (10-50 microM), abolished periodic activity reversibly within less than 5 min. When 6-cyano-7-nitroquinoxaline-2,3-dione and nicotine were administered simultaneously periodic events persisted for up to 10 min. These findings indicate that synaptic excitatory drive is a prerequisite for the generation of rhythmic discharges of medullary neurones in this preparation. This drive may activate voltage-dependent channels or it may facilitate endogenous cellular mechanisms which initiate oscillations of intracellular calcium concentration. To test the latter possibility (5) calcium antagonists were added to the bath saline. The organic calcium antagonists verapamil and flunarizine (50-100 microM each) and the inorganic calcium antagonists cobalt (2 mM) and magnesium (6 mM) suppressed periodic activity and abolished or weakened the chemosensitivity towards CO2/acidosis. (6) Dantrolene (10 microM). an inhibitor of intracellular calcium release decreased the periodicity, while thapsigargin (2 microM) which blocks endoplasmic Ca(2+)-ATPase, transiently accelerated the occurrence of periodic events. (7) Oscillations of intracellular free calcium concentrations in Fura-2 AM-loaded cells were weakened or abolished by cobalt (2 mM). The results of (5)-(7) indicate that transmembrane calcium fluxes as well as intracellular Ca(2+)-release and -clearance mechanisms are a prerequisite for intracellular free calcium oscillations which may be important in the generation of rhythmic discharges in medullary neurones.

Suppression of rhythmic discharges of medullary neurones in organotypic cultures of new-born rats by calcium antagonists

The contribution of transmembrane calcium flux to the generation of periodic bioelectric activity in cultured organotypic medullary tissue of 6 day old rats was determined by adding calcium antagonists (CA) to the recording saline and by lowering the calcium concentration of this saline. Organic CA flunarizine and verapamil (50-100 mumol/l) reversibly suppressed rhythmic discharge and diminished the CO2 response of medullary neurones within 30-60 min. Inorganic CA cobalt and magnesium exerted the same effects within a few minutes. After lowering the calcium concentration rhythmic activity became unstable, but recovered on exposure to increased CO2 concentration, the excitatory effect of which was strongly reduced. These findings point to a significant role for transmembrane calcium flux and intracellular calcium concentration in sustaining both periodic activity and the CO2 response of medullary neurones.

Antisense oligonucleotide-induced block of individual GABAA receptor alpha subunits in cultured visual cortex slices reduces amplitude of evoked inhibitory postsynaptic currents

Whole cell patch clamp recordings were made in layer II-IV from organotypic slices of rat primary visual cortex, explanted at postnatal day 6 and maintained in a serum-free medium. Neurons evinced current clamp characteristics typical for stellate cells. Between 7 and 21 days in culture, both glutamate- and GABA-mediated postsynaptic currents were observed. Long-term culturing in the presence of a degenerate 15-mer antisense oligonucleotide directed against the transcripts of all alpha subunits genes of the GABAA receptor resulted in a dose dependent reduction of evoked GABA synaptic currents. This reduction was maximal (80%) at 20 microM. A randomized control oligo had no effect. Evoked glutamatergic excitatory postsynaptic currents were unaffected following oligo treatment. A 15-mer antisense oligo directed against the alpha 1 subunit gave variable effects: in some cells the amplitude of evoked GABAergic inhibitory postsynaptic currents (IPSCs) was reduced by 50-75%, while in other cells recorded from the same slices, there was little or no effect. An antisense oligo, directed against the alpha 2 subunit, however, gave a consistent and robust 80% reduction of the amplitude of evoked IPSCs. A 15-mer 3-base mismatch oligo against alpha 2 had no effect. We conclude that the alpha 2 subunit functions in postsynaptic GABAA receptors located on or close to the cell bodies of stellate cells. The role of the alpha 1 subunit is less clear, but this subunit seems spatially differentiated. The in situ antisense oligo technique should provide further insight into the biophysical and pharmacological consequences of the subunit composition of ligand gated channels at functional synapses.

Development and isoproterenol-induced regulation of adrenoceptor binding in cultured rat neocortical explants is seen only with the beta-1, not with the beta-2 subtype

The presence and time-course of beta-adrenoceptor density in cultured explants of neocortex obtained from 6-day-old rat pups were investigated using a [125I]ICYP binding assay. A delayed, but more pronounced, increase in the receptor expression was observed as compared to the situation previously described in vivo. These changes only occurred for the beta 1-subtype of the receptor, whereas the beta 2-subtype binding remained constant up to 3 weeks in vitro. The delay of beta 1-adrenoceptor expression may be due to the incomplete presence of the proper maturational input, and the late enhancement of receptor expression to upregulation related to the absence in vitro of noradrenergic input. Decreased beta-adrenoceptor levels could be induced by chronic treatment of the beta-agonist isoproterenol (1 microM) introduced either for 3 or 13 days. Again, changes in density were found only for the beta 1-adrenoceptor binding sites. There is no reduction of receptor density following return to control conditions for 10 days after a 3-day treatment with isoproterenol, demonstrating the ability of this model to attain its final receptor density notwithstanding the developmental insult.

Role of the Saccharomyces cerevisiae general regulatory factor CP1 in methionine biosynthetic gene transcription

Saccharomyces cerevisiae general regulatory factor CP1 (encoded by the gene CEP1) is required for optimal chromosome segregation and methionine prototrophy. MET16-CYC1-lacZ reporter constructs were used to show that MET16 5'-flanking DNA contains a CP1-dependent upstream activation sequence (UAS). Activity of the UAS required an intact CP1-binding site, and the effects of cis-acting mutations on CP1 binding and UAS activity correlated. In most respects, MET16-CYC1-lacZ reporter gene expression mirrored that of chromosomal MET16; however, the endogenous gene was found to be activated in response to amino acid starvation (general control). The latter mechanism was both GCN4 and CP1 dependent. MET25 was also found to be activated by GCN4, albeit weakly. More importantly, MET25 transcription was strongly CP1 dependent in gcn4 backgrounds. The modulation of MET gene expression by GCN4 can explain discrepancies in the literature regarding CP1 dependence of MET gene transcription. Lastly, micrococcal nuclease digestion and indirect end labeling were used to analyze the chromatin structure of the MET16 locus in wild-type and cep1 cells. The results indicated that CP1 plays no major role in configuring chromatin structure in this region, although localized CP1-specific differences in nuclease sensitivity were detected.

Total contact casting

The treatment of diabetic foot ulcerations has been a difficult task for podiatrists. Numerous methods and materials have been used in an attempt to alleviate this frustrating and complex treatment dilemma. However, there is one treatment method that has been used successfully for decades on plantar ulcerations of the neuropathic foot. Total contact casting has been an easily applicable and effective treatment modality for neuropathic ulcerations of the diabetic foot.

In vivo and in vitro characterization of Allpyral grass pollen extracts

The Food and Drug Administration, Center for Biologics Evaluation and Research (CBER) has developed methodology to standardize both aqueous and freeze-dried (lyophilized) extracts. Thus far, it has not been determined whether or not this methodology can be used to standardize alum-adsorbed extracts. This study was designed to examine the in vivo and in vitro potency of selected Allpyral grass pollen extracts, including timothy, orchard grass, perennial ryegrass, sweet vernalgrass, and meadow fescue. Puncture testing was performed on highly grass-sensitive subjects with the concentrate of each of the five Allpyral grass extracts. Additionally, puncture testing was done on 22 subjects to compare Allpyral timothy grass with a lyophilized, standardized timothy grass extract. The ID50EAL (Intradermal Dilution for 50 mm sum of Erythema determines the Allergy Unit) skin test method was used to determine allergy units of the Allpyral extracts. Relative potency of the Allpyral timothy extracts to a timothy laboratory standard was determined using an ELISA-inhibition assay. Intradermal tests were also performed to examine the potency of the supernatant obtained after centrifugation of the whole Allpyral timothy extract. The puncture test responses to the Allpyral timothy extracts were less than those to the lyophilized extract. Those 10,000 PNU/mL Allpyral grass pollen extracts tested were determined to contain a calculated 10,000 BAU/mL. By ELISA inhibition, the Allpyral timothy extracts were determined to be approximately 1,000-fold less potent than the laboratory standard. The estimated concentration of the supernatant preparation to elicit a target response was notably (mean = 1,175 times) greater than that of the whole Allpyral timothy extract needed to elicit the same erythema response.(ABSTRACT TRUNCATED AT 250 WORDS)

Structural maturation, cell proliferation and bioelectric activity in long-term slice-cultures of immature rat hippocampus

Explants of transverse slices of the 6-day-old rat hippocampus were grown in a serum-free medium for 2-14 days. Histology performed after various culturing periods demonstrated that these slices maintain a high degree of 3-dimensional organotypy, while undergoing growth and differentiation of the main cellular elements similar to that seen in vivo. Histological indications of continuing cell proliferation were verified by autoradiography showing a labelling of neuroblasts in the dentate gyrus and of glioblasts at the sites of gliogenesis observed in vivo. Spontaneous bioelectric activity and evoked potentials were recorded, both indicating the development of impulse generation and neuronal connectivity within the explant. Silver impregnation and electron microscopic studies lent further support for the presence of neuronal networks intrinsic to the hippocampus. These findings suggest that within the period studied the hippocampal slice cultures mature in a fashion similar to that seen in situ.

Mutational analysis of the Saccharomyces cerevisiae general regulatory factor CP1

The Saccharomyces cerevisiae general regulatory factor CP1, a helix-loop-helix protein that binds the centromere DNA element I (CDEI) of yeast centromeres, is required in yeast for optimal centromere function and for methionine prototrophy. Mutant alleles of CEP1, the gene encoding CP1, were generated by linker insertion, 5'- and 3'-deletion, and random mutagenesis and assayed for DNA binding activity and their ability to confer CP1 function when expressed in yeast. A heterologous CDEI-binding protein, TFEB, was also tested for CP1 function. The results suggested that DNA binding is required for both biological functions of CP1 but is not sufficient. A direct and quantitative correlation was observed between the chromosome loss and nutritional (i.e., Met) phenotypes of strains carrying loss of function alleles, but qualitatively the chromosome loss phenotype was more sensitive to decreased CP1 expression. The data are consistent with a model in which CP1 performs the same general chromatin-related function at centromeres and MET gene promoters and is normally present in functional excess.